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Domestic breeding of animals (and plants) by humans seems to match some of the definitions of evolution I have been able to find:
- "a process that results in heritable changes in a population spread over many generations." (the TalkOrigins website)
- "cumulative inherited change in a population of organisms through time leading to the appearance of new forms" (Merriam-Webster)
- "Changes in the heritable attributes of populations of organisms over time" (this SE's 'evolution' tag info)
But other definitions seem to be less of a fit:
- "the way in which living things change and develop over millions of years" (Cambridge)
(domestic breeding does not take millions of years)
- "The process by which different kinds of living organism are believed to have developed from earlier forms during the history of the earth" (Oxford)
(Does breeding lead to different 'kinds' or organisms?)
- "The gradual development of more complex organisms from simpler ones" (Chambers)
(Breeding may not result in more complex organisms)
I've seen people argue that domestic breeding can not be considered evolution, because domestic breeding:
- does not involve natural selection
- doesn't direct towards 'fitness'
- does not lead to new species
- decreases, rather than increases, the size of the gene pool (is this actually true?)
- does not (or may not) lead to more complex organisms
I was not able to find whether or not there is a general consensus among experts from relevant fields on whether domestic breeding can be considered evolution. Is there?
EDIT: I've made the list of arguments I've heard against calling it evolution a bit clearer, and also added an extra one.
EDIT 2: Added why the second set of definitions seem to exclude domestic breeding as evolution
Yes, selective breeding results in evolution.
Definitions of evolution
I don't understand why you say that for 3 of the definitions you found, selective breeding would not be considered as evolution. To me, all of these definitions match with the idea that selective breeding results in evolution. If you think otherwise, can you please explain why?
There are a number of related definition out there, some of them being more clear and straight forward than others. The simplest definition is probably the classical population genetics definition which says
Evolution is a change in allele frequency over time.
See wikipedia > allele. You might want to have a look at How to define evolution? too.
Under this definition, any event of death or birth in a population is evolution as it affects allele frequency. In the human species for example, that means an evolution happens about 254 times per second (computed from these numbers from ecology.com)!
All these statements are stupid and none-sense! The easiest is probably for you to just have a look at an intro course to evolutionary biology (such as Understanding Evolution by UC Berkeley for example) and you will be able to refute those statements yourself.
Let's go through these statements…
- There is no natural selection
First, evolution is much more than just natural selection. There is genetic drift, mutations, gene flow and plenty of interacting processes.
Second, it is silly to separate natural selection from artificial selection (aka. selective breeding). The only difference between these two is that in artificial selection someone is willingly affecting the environment of the individual to affect selection pressures. This is really it.
Note, btw, you never totally get rid of natural selection. Under selective breeding you may affect the environment but some things will remain the same. For example, a mutation causing the cell membranes to be extremely unstable will not be selected for whether under an artificial setting or a natural one.
- It doesn't direct towards 'fitness'
The claim is unclear. What is "it" and assuming it refers to a population, then what does it mean a population is directing toward "fitness"?
Fitness is a function of survival and fecundity. Each genotype is associated to a particular fitness in a specific environment. Ignoring stochastic processes such as genetic drift, the mean fitness of a population is increasing from one generation to the other by the amount of the additive genetic variance. This is true for (artificial or natural) selection.
The only thing to consider is that the environments under which this happen is different. Under selective breeding, the population evolves to a higher fitness for the specific environmental conditions set by the farmer (or who ever who selectively breed). It is possible (and quite common in fact) that genotypes associated with a high fitness under one environment has a low fitness under another environment.
- It does not lead to new species
In short, 1) it does lead to new species 2) the concept of species is often meaningless as poorly defined 3) evolution > speciation. In more details, below…
It does lead to new species. Different lineages of cabbage are considered different species. Cows and ox are different species. Pigs and boars are often considered different species. While wolves and dogs are considered same species, some lineages within this species (such as a Chihuahua and a Great Dane) are, I think, reproductively isolated. You might also want to have a look at the post Have we ever observed two drosophila lineages that evolved reproductive isolation in labs?
The question of whether selective breeding lead to speciation or not does not matter much on the question of whether it leads to evolution. Speciation is one outcome of evolution but is definitely not the same as evolution. Evolution does not need to lead to speciation. For example, evolution of the lactase gene in humans (see this post) did not lead to any speciation. It is still an evolutionary process.
The concept of species is mainly arbitrary. If you want to understand the concept of species, have a look at the post How could humans have interbred with Neanderthals if we're a different species?.
- It decreases, rather than increases, the size of the gene pool (is this actually true?)
The term "size of the gene pool" is very undefined. I suppose, it just means genetic diversity, aka. expected heterozygosity.
All act of selection, whether artificial or natural, decreases genetic diversity. This is correct. Mutations is the fundamental process increasing this genetic diversity and selection selects the variants associate with the highest fitness.
Because, the selection pressures imposed under selective breeding are often extreme, the decrease of genetic diversity via selection is often faster in selective breeding than in nature.
Note however, that if we split a lineage in two and select the two populations under different optimas, then the total genetic diversity will increased (the within-population genetic diversity will still decrease). As such, via selective breeding we created a gigantic diversity of dogs and a fantastic diversity of cabbage but each cabbage lineage (e.g. brussel sprouts) and each dog lineage (cocker spaniel) have very low genetic diversity.
What the claim is suggesting is that because selection is often stronger (and therefore change in allele frequencies is faster) under selective breeding than in natural environments, we should not consider artificial selection as resulting in evolution? How silly is that!
The answer is "yes". Evolution is defined as a change in heritable characteristics of a population over generations, and to me, there is no reason not to define domestic animals as populations.
The statements you list can all be refuted:
Part of the selection human-driven, part "natural". You cannot control all genes.
The concept of fitness talks about offspring and contribution to the gene pool. Humans enhancing the fitness of desired individuals should also count as fitness. It is just the "human selection" that partly drives the evolution (i.e. human selection works as an environment).
Dog, chicken, cow are all species created by domestic breeding. They are all considered species by some biologists.
Strong selection pressure sometimes decreases the size of the gene pool, but again if you take dogs as an example: they are likely genetically more diverse than wolves. There are so many factors involved in domestic breeding that you cannot say that it decreases the size of the gene pool. It can go both ways.
But again, evolution is a human-created concept to understand our surroundings. If somebody wants to think that humans should not be a driving factor in evolution, that is fine for me.
Next logical question would be whether gene-manipulation is evolution. I will leave that for someone :)
There is not consensus among scientists, that human sciences of should be equaled to natural sciences.
Scientists don't agree if pets and farm stock are new species, and we all agree, domestic animals are in a different, recent, group to all other and selection processes. It's Yes and No andwer. It shares and conflicts with evolution and seems to deserves a human sciences category of it's own.
"Evolution of the chihuaha specif traits from the wolf", wouldn't qualify for a science journal.
Survival of the funny looking animal, for a dominant species, that has a large brain, that devises breeding methods. Contrary to survival of the fittest. It's a form of evolution that was seen only 50k years from 4 billion, that's 0.00125% of evolutionary history. You can compare it to evolution of captive algea used by coral, and ant-aphid relationships.
Darwin studied the topic for decades, and in the actual title of his book he wrote "Natural" selection, so he clearly made a mental difference between human and wild, natural processes.
The difference of the concepts is similar to human geography and physical geography. They are described by different books.
To make a language's semantics clear, it's best not to group different groups of processes with the same word, when new semantics be invented where a discussion is required to differentiate the two.
It's the only form of evolution that uses artificial foods, artificial walls and fences, artificial mating, to make funny looking animals for amusement, and social animals companionship and work.
The result is generally low fitness, stamina, immune system, fainting goats, deaf dogs, dogs that can't breathe well due to snout length, dogs which are tremendously unfit. and animals that are fit for human amusement.
How does selective breeding support evolution?
I assume you are asking about the Darwinian idea of evolution and if this is the case you will find a very thorough and interesting answer to this question in Chapter 1 of The Origin of Species the famous work of Charles Darwin. I can however give you a more brief, although significantly less eloquent, answer.
Selective breeding is the process used by domestic breeders to improve the characteristics of their population. Darwin uses the example of breeding pigeons. A good breeder will only allow specimens with the most desirable outward characteristics to reproduce. In this way the favourable characteristics are preserved and the less favourable characteristics become less prominent in the population. This process provides evidence that their is a degree of inheritance between parent and offspring. When we contemplate this process over a period of what is known as deep time (long time periods) we can appreciate that, by breeding out undesirable characteristics, it is possible to change the animal entirely.
At the time of publication Darwin's ideas were considered to be fairly controversial. Many believed that God had created and breathed life into every immutable variety of creature in its unchanging and perfect state. Darwin discusses selective breeding because it demonstrates in a familiar context that change through inheritance is possible and this is fundamental to the principle of natural selection or evolution.
The limitation of this model is that selective breeding can only be carried out to preserve the outwardly visible characteristics which are considered desirable by the beholder. Evolution or natural selection goes further than this. Natural selection recognises that any variation however slight, irrelevant of its outward visibility, which gives an animal an advantage over others of its kind will make that animal more likely to survive and therefore more likely to procreate.
Selective breeding supports the idea of inheritance and the struggle for survival suggests that only the fittest animals will survive and breed. Combining these ideas gives weight to the theory that only characteristics favourable to the species will be preserved, thus the species will evolve. In its extreme this supports the idea that no species is immutable. A species without desirable characteristics for survival in any particular environment will become extinct.
Darwin only identified this process of evolution he could not explain inheritance. It was the work on DNA carried out by Crick and Watson which completed Darwin's explanation.
We’ve sped up dog evolution – but not enough
Charles Darwin pointed out that humans have accelerated the process of selection by choosing particular individuals for breeding, based on certain desired characteristics – what we call artificial selection. Natural selection generally requires much more time, because it acts on novel variants introduced into the gene pool through the slow process of chance DNA mutation. Nevertheless, the power of artificial selection in generating extreme phenotypes does not change the fundamental fact that dog breeds have been separated for only a short evolutionary time.
Great Dane, meet Chihuahua. You have lots in common. Ellen Levy Finch, CC BY-SA
This means that dog breeds differ drastically in their appearance and other characteristics, while most of their genomes are still very much alike. Comparing different breeds, most of their genomes indeed show only little differentiation. In other words, Chihuahuas and Great Danes are overall very similar to one another. The vast physical differences are largely driven by relatively few loci (regions) in the genome. These loci have a large phenotypic effect, leading to strong differentiation among breeds.
This is particularly interesting for evolutionary biologists, and pinpointing such regions in the genome has for example recovered the genetic basis of size variation among dog breeds. We now also have an understanding of the mutations that control traits such as coat characteristics and ear floppiness.
Darwin’s Three Kinds of Selection
In The Variation of Animals and Plants Under Domestication, Darwin (1868) considered two types of artificial selection in addition to natural selection Footnote 1 : methodical selection and unconscious selection. As he explained (Darwin 1868, p. 153),
Methodical selection is that which guides a man who systematically endeavours to modify a breed according to some predetermined standard. Unconscious selection is that which follows from men naturally preserving the most valued and destroying the less valued individuals, without any thought of altering the breed.
Darwin’s three types of selection—methodical, unconscious, and natural—are united by a fundamental mechanistic similarity, namely that they involve a non-random difference in reproductive success among individuals on the basis of heritable traits. What differs among these processes is simply the reason why some individuals will reproduce while others become genetic dead ends. For obvious reasons, the form of artificial selection that Darwin dubbed methodical selection has also been called “deliberate” or “conscious” or “intentional” selection (e.g., Harlan et al 1973 Heiser 1988 Zohary 2004 Emshwiller 2006). It is sometimes argued that the current use of this concept differs from that initially proposed by Darwin (see Heiser 1988 Zohary 2004), but fundamentally this involves a process whereby humans actively choose individuals from among an available sample in order to preserve, and ultimately enhance, traits of interest. Unconscious selection, by contrast, is a much more passive form of artificial selection and may involve no specific intent whatsoever. Humans still determine which individuals will contribute most to the next generation, but in this case they may do so without the knowledge that this can have a long-term effect. Natural selection resides at the far end of this continuum, whereby the reproductive success of individuals is not determined by selective breeding or cultivation Footnote 2 .
The Uses and Usefulness of Darwin’s Analogy
According to Evans (1984), “Darwin’s recognition of the power of selection in changing organisms was almost entirely due to what he learned of plant and animal breeding.” Certainly, Darwin himself wished to convey that his discovery of natural selection grew from his studies of artificial selection. He indicated in his private autobiography that his recognition of artificial selection as the key process in domestication primed him to conceive of natural selection when he read the essay by Malthus on human populations (Darwin 1958 written in 1876 and first published in 1887). A similar sequence of events was presented by Darwin in letters written to friends before the publication of the Origin Footnote 3 . Nonetheless, citing additional evidence such as Darwin’s notebooks and his use of other published works, historians and philosophers have continued to debate both the role that artificial selection played (or did not play) in Darwin’s development and justification of the concept of natural selection and the nature of the analogy that he intended to draw between artificial and natural selection (e.g., Vorzimmer 1969b Herbert 1971 Ruse 1973, 1975 Schweber 1977 Kohn 1980 Cornell 1984 Evans 1984 Rheinberger and McLaughlin 1984 Waters 1986 Bartley 1992 Richards 1997 Sterrett 2002 Gildenhuys 2004).
Whether or not Darwin discovered natural selection via the route of artificial selection, he made heavy use of it in arguing for the historical reality of common descent and the efficacy of natural selection. It should be no surprise, then, that the analogy became a target for critics of Darwin’s theory following the publication of the Origin (Hull 1973 Evans 1984). More interestingly and as several authors have noted (e.g., Evans 1984 Rheinberger and McLaughlin 1984 Richards 1997 Ross-Ibarra et al. 2007), it was not only Darwin’s opponents but also some of his most ardent supporters who questioned the validity of comparing artificial selection with processes occurring in the wild. The example cited most often is that of Alfred Russel Wallace, whose independent discovery of natural selection prompted Darwin to publish the Origin. In his paper presented jointly with Darwin’s to the Linnean Society of London in 1858, Wallace went so far as to argue,
We see, then, that no inferences as to varieties in a state of nature can be deduced from the observation of those occurring among domestic animals. The two are so much opposed to each other in every circumstance of their existence, that what applies to the one is almost sure not to apply to the other. Domestic animals are abnormal, irregular, artificial they are subject to varieties which never occur and never can occur in a state of nature their very existence depends altogether on human care so far are many of them removed from that just proportion of faculties, that true balance of organization, by means of which alone an animal left to its own resources can preserve its existence and continue its race.
It bears noting, however, that Wallace’s position on this matter appears to have softened over the ensuing decades. In his book Darwinism, published several years after Darwin’s death, Wallace (1889, p. vi) indicated his continued preference for data drawn from natural species when he noted that “it has always been considered a weakness in Darwin’s work that he based his theory, primarily, on the evidence of variation in domesticated animals and cultivated plants”. Yet, he also dedicated a chapter to the topic of domestication, making it clear that he had come to consider the topic a useful one in explaining the operation and importance of selection in nature. His primary focus in this case was on the extensive variation observed among individual plants and animals under domestication, which paralleled that witnessed in nature. He further noted, in the introduction to the following chapter on natural selection (p. 102–103),
we have seen how similar variations, occurring in cultivated plants and domestic animals, are capable of being perpetuated and accumulated by artificial selection, till they have resulted in all the wonderful varieties of our fruits, flowers, and vegetables, our domestic animals and household pets, many of which differ from each other far more in external characters, habits, and instincts than do species in a state of nature. We have now to inquire whether there is any analogous process in nature, by which wild animals and plants can be permanently modified and new races or new species produced.
Regardless of how the debate surrounding Darwin’s use of it is ultimately settled, and despite significant early criticism of its validity, it is evident that the analogy between artificial selection and natural selection continues to be considered useful among modern biologists. In fact, recent discoveries in a range of disciplines from archeology to molecular biology have made Darwin’s analogy more relevant than ever. Indeed, the evolution of plants and animals in response to artificial selection is increasingly seen as a very productive model for studying general questions about adaptive evolution (e.g., Gepts 2004 Ross-Ibarra et al. 2007). Artificial selection also remains a useful tool for illustrating key principles in evolutionary biology, especially since most people are familiar with many of the species that have been domesticated and with the general concept of selective breeding.
In this regard, Darwin’s use of the analogy in discovering natural selection or his intent in invoking it becomes of secondary importance to the role that the analogy can play in modern evolutionary research and education. Thus, one may still ask, as Darwin did: What is known about artificial selection and domestication, and what can be learned from this about evolution in nature?
In order to highlight the enduring utility of Darwin’s emphasis on artificial selection, the remainder of the article presents ten lessons that can be learned from a study of artificial selection and illustrates them with examples drawn from recent studies of well-known species.
Lesson 1: Selection Can Result in Profound Changes
Though they have since been the focus of much research and are recognized as a classic case of evolution in action (Grant and Grant 2008), Darwin’s finches of the Galapagos Islands are not mentioned specifically in the Origin. By contrast, Darwin dedicated several pages to a discussion of domesticated pigeons in the Origin in 1859 and expanded this to a treatment spanning two entire chapters in Variation in 1868. In Darwin’s day, pigeon breeding was a common pastime, with fanciers seeking to produce new and dramatic varieties through diligently imposed artificial selection. Darwin was a member of pigeon fancier societies and even experimented with pigeon breeding himself, keeping up to 90 pigeons at a time at his home (Secord 1981). He marveled at the extraordinary variety of form produced by the methodical selection applied by skilled breeders (Fig. 1). In fact, artificial selection by pigeon fanciers had been so effective that Darwin (1859) noted,
“when I first kept pigeons and watched the several kinds, knowing well how true they bred, I felt truly as much difficulty in believing that they could ever have descended from a common parent, as any naturalist could in coming to a similar conclusion in regard to the many species of finches, or other large groups of birds, in nature.”
Today, a (literally) more familiar example is provided by dogs (Canis lupus familiaris), several hundred distinct breeds of which have been generated. Domestic dogs display more morphological diversity than any other species of mammal, but most of these breeds have been produced within a few hundred years and all are derived from an early domesticated descendant of the gray wolf (Canis lupus lupus Vilà et al. 1997 Savolainen et al. 2002).
Drawings of four of the six pigeon breeds presented by Darwin (1868), as drawn by Luke Wells. a English pouter, b short-faced English tumbler, c English carrier, d English fantail. As extraordinary as the differences among them appear in these drawings, Darwin (1868) noted that “the characters of the six breeds which have been figured are not in the least exaggerated.” Darwin himself became an active breeder of pigeons and attempted not only to demonstrate that all of the fancy breeds produced by artificial selection descended from a single wild species (the rock pigeon, Columba livia) but to reconstruct their historical relationships (Fig. 4)
Plants, too, have undergone substantial changes under the influence of prolonged artificial selection. As Doebley et al. (2006) noted, “most members of our modern industrial societies have never seen and would not recognize the unpromising wild plants that are the progenitors of our remarkably productive crops.” Beginning with the agricultural revolution around 10,000 years ago, hundreds of plants were domesticated on several continents (Fig. 2). However, nearly 70% of the calories consumed by humans derive from 15 species of plants—the top four of these being rice, wheat, maize (corn), and sugarcane (Ross-Ibarra et al. 2007). Many people are surprised to learn that these species, along with oats, barley, and sorghum, are all grasses in the family Poaceae. Of these, maize and rice have been particularly well studied in recent years, and a great deal of light has been shed on their evolution from wild grasses through artificial selection.
Numerous sites of domestication have been identified based on archeological evidence for both a plants and b animals. a From Doebley et al. (2006) and b from Mignon-Grasteau et al. (2005), reproduced by permission of Elsevier and Dr. John Doebley
For example, it is now most commonly accepted that maize (Zea mays ssp. mays) is descended from the wild Mexican grass teosinte (Zea mays ssp. parviglumis) Footnote 4 . However, the morphological differences between maize and teosinte are so large that the hypothesis of their close affinity was rejected by many authors for decades after it was proposed (Wilkes 2004 Buckler and Stevens 2006 Fig. 3). Moreover, some authors argued that the differences between these plants were too drastic, and therefore the genetic underpinnings too complex, to have evolved in a straightforward way under domestication (see Wang et al. 2005). Indeed, teosinte was originally classified in the genus Euchlaena rather than with maize in the genus Zea (Buckler and Stevens 2006 Emshwiller 2006).
A plant of the maize progenitor, teosinte (left), with multiple stalks and long branches, is shown next to a plant of cultivated maize (right) with its single stalk. A maize ear (inset) bears its grain naked on the surface of the ear, whereas a teosinte ear (inset) has its grain (not visible) enclosed in the triangular casing that comprises the ear. From Doebley et al. (2006), reproduced by permission of Elsevier and Dr. John Doebley
Maize, rice, wheat, and many other domesticated seed plants exhibit a common suite of features collectively known as the “domestication syndrome” (Harlan et al. 1973 Heiser 1988 Doebley et al. 2006 Zeder et al. 2006a Ross-Ibarra et al. 2007). Depending on the species, this typically includes:
Simultaneous ripening of seeds on the plant
Loss of natural seed dispersal (no “shattering”)
Compaction of seeds into highly visible “packages”
Reduced seed coat thickness
Simultaneous and rapid germination
Loss of toxic or unpleasant compounds (e.g., reduced bitterness) or other means of defense against herbivores
These novel characteristics greatly alter the means by which plants grow and reproduce. Yet, despite these major differences, most domesticated crops remain capable of intercrossing with their wild progenitors and at most represent distinct subspecies. In this regard, it could be argued (as it was by Wallace in 1858) that artificial selection differs fundamentally from natural selection. However, this is not always the case. Notably, modern bread wheat, Triticum aestivum, represents a separate hybrid species whose cells contain the genomes of three other species, some wild and some independently domesticated (Salamini et al. 2002 Motley 2006).
Lesson 2: Unique Evolutionary Events Can Be Reconstructed Using Several Types of Data
There is no scientific debate as to whether domesticated animals and plants are descended from wild ancestors—i.e., this is accepted as historical fact (Gregory 2008a). The specific mechanism(s) involved in this transformation—most notably artificial selection—represents the theory proposed to explain the fact and also is generally agreed upon. Where there is often significant disagreement is in regard to the path of evolution under domestication: When did domestication take place? Where? From which ancestor? Once or multiple times for a particular species? Involving what historical sequence of changes? Under what cultural or environmental circumstances?
Such questions can almost never be answered with certainty because, a few examples notwithstanding (e.g., strawberries, pecans, sugar beets, rubber), most plants and animals were first domesticated long before the beginning of recorded history (Diamond 2002 Wilkes 2004). Obviously, no eyewitness testimony exists to detail the transformation of wild animals or plants into domesticates, and in any case the process has almost always been too gradual to have been noticeable on the timescale of an observer’s lifetime (see below). Nor is every intermediate stage preserved such that a step-by-step transition can be determined Footnote 5 , and in many cases the wild progenitor is extinct. In this sense, the challenge of reconstructing the history of domestication is similar to that of studying natural evolutionary change over deep time. Darwin (1837–1838, Notebook B, p.217) used this fact to expose the absurdity of demands for a complete series of fossil intermediates before common descent is acknowledged: “Opponent will say: show them [to] me. I will answer yes, if you will show me every step between bull dog and greyhound.”
Whether in reference to domestication or evolution at large, the challenge of reconstructing the past can be met by drawing careful inferences from diverse lines of evidence (Wilkes 2004 Zeder et al. 2006a, b Burger et al. 2008). The primary lines of evidence used in the study of evolution by artificial selection are outlined below, and all have parallels with the approaches used in evolutionary biology generally.
One of the simplest means of investigating the historical relationships among living species is through a comparison of their physical characteristics. As a notable early example, Darwin (1868) compared the features of various breeds of pigeons and used this information to construct a diagram of their hypothetical relationships (Fig. 4). This represents one of the first attempts to reconstruct an evolutionary tree, or phylogeny, through a comparison of living organisms (see Gregory 2008b). Similar analyses are often conducted in studies of domesticated animals and plants in order to indicate plausible ancestors and to suggest probable changes that were experienced during their evolution under artificial selection. However, as noted, the differences between domesticates and their ancestors can be profound, thereby confounding analyses based solely on morphological features.
Geographical distribution and diversity
Darwin’s (1868) attempt to classify the various breeds of pigeons (Fig. 1) according to their physical characteristics and inferred historical relationships following their common descent from the wild rock pigeon (Columba livia)
In cases where a wild progenitor species is reasonably well established, one may use the approach pioneered by de Candolle and Vavilov of identifying the geographical region in which the progenitor is most common and in which its populations are the most diverse (see Wilkes 2004). This is often taken as an indication of the center of origin for domesticated species, though other types of data sometimes reveal the history of particular domesticates to be more complex than this method alone would imply (Wilkes 2004). Based on these and other data, it is now recognized that domestication has occurred independently and repeatedly in various parts of the world (Fig. 2).
The discovery of preserved prehistoric remains is important in the study of domestication (archeology), just as the fossil record is in the study of large-scale evolution (paleontology) (see Smith 2006). In some cases, intact remains of plants or animals can provide a clear indication not only of where early domestication took place but, thanks to radiometric dating and other techniques, also when. As an example, Piperno and Flannery (2001) reported the discovery of ancient maize cobs from Guilá Naquitz Cave (near Mitla, Oaxaca, Mexico) which dated to about 6,250 years ago (see also Benz 2001). A remarkable series of maize remains of increasingly recent ages reveals several of the transitions thought to have taken place between wild teosinte and the domesticated crop (Wilkes 2004).
As with the fossil record, intact specimens are less common than fragments or other sources of indirect information. In this case, archeologists may discover small remnants of plants that provide information about the time of origin of particular features. For example, wheat spikelets, which in living plants provide the points of attachment of stalk to seed-bearing ear, may be smooth at the site of detachment, meaning that they broke off easily as in wild plants (dehiscent), or may be jagged, indicating that threshing was required to remove the seeds, as with domesticated wheat (indehiscent) (Tanno and Willcox 2006 Balter 2007 Fig. 5). By examining the proportions of dehiscent to indehiscent spikelets from archeological samples, Tanno and Willcox (2006) were able to reconstruct the timing of the transition between wild and domesticated wheat.
A summary of some of the major differences between a wild and b domesticated wheat, most notably the loss of shattering and larger seeds in the latter wheat. In wild wheat, shattering leaves behind a smooth scar at the point of attachment, whereas domesticated wheat requires threshing to remove seeds (making them easier to harvest), leaving behind a rough scar. From Salamini et al. (2002), reproduced by permission of Nature Publishing Group and Dr. Francesco Salamini, with inset photos of detachment scars from Tanno and Willcox (2006), reproduced by permission of the American Association for the Advancement of Science and Dr. George Willcox
In some cases, only microscopic remains are available, as with starch grains or phytoliths (“plant stones” tiny silica particles formed in living cells of plants as protection from predators, reservoirs of carbon dioxide, and structural support). Both starch grains and phytoliths can be used to distinguish plant species and in some cases can indicate domesticated versus wild subspecies (Piperno et al. 2004 Smith 2006). Phytoliths, in particular, are inorganic and do not readily decay, and their use in identifying the plant that produced them has been recognized since Darwin’s time (e.g., Darwin 1846). In cases where starch grains or phytoliths do not by themselves provide positive identification of particular domesticated crops, the presence of samples from multiple cultivated plants in the same location can provide indirect evidence (Smith 2006 Thompson 2006). Finally, the presence of artifacts such as farm implements, grinding wheels, or cooking vessels used in association with domesticated plants can provide further means of identifying when and where early cultivation occurred.
Some of the earliest genetic data used to assess relationships among crop plants and wild relatives involved analyses of chromosome number and morphology. For example, work in the 1930s made use of chromosome number information to support the proposed affinity between maize and wild teosinte. Beginning in the 1940s, chromosome comparisons revealed that specific characteristics such as the lengths of chromosome arms, the positions of centromeres, and the sizes and positions of unique features such as dense heterochromatic knobs are very similar in maize and Mexican teosintes but different from other proposed progenitor species (see Doebley 2004). Chromosome data continue to be of interest, especially in studies of hybrids in which multiple genomes are combined or genomes are duplicated. Today, this may involve sophisticated approaches for “painting” chromosomes with fluorescent probes to identify similar regions among species (e.g., Zhang et al. 2002).
Protein-coding nuclear genes
The study of domestication, like that of evolution generally, has been revolutionized by the advent of molecular genetics. Some of the first means of assessing genetic variation within species of interest involved comparisons of enzyme variants (allozymes or isozymes) that differ slightly in physical properties and therefore can be separated using an electric current run through a gel (see Jones and Brown 2000 Emshwiller 2006). In addition, comparisons of sequences of the amino acids that make up proteins provided important insights into relationships among species. These techniques are still in use, but even more detailed information is now available through the analysis of DNA sequences. Not only can more general differences at the DNA level provide convincing evidence of historical links between domesticates and their wild relatives (e.g., Bruford et al. 2003) but, as described in more detail below, it is even becoming possible to identify the specific genes involved in the evolution of domesticated animals and plants.
In most animals and plants, protein-coding genes make up only a small minority of the genome. Most DNA in these organisms takes the form of non-coding DNA of several types (Gregory 2005). Sequences such as microsatellites, which are highly repeated segments of DNA that are present in varying amounts among species and/or populations, can provide a sensitive marker for studying relationships among plants and animals (e.g., Bruford et al. 2003 Emshwiller 2006). Moreover, because non-coding sequences usually are not constrained in the same manner as functional protein-coding genes, they are often thought to evolve largely at random and can be used (with caution) as “molecular clocks” to infer the timing of divergences among lineages (Bromham and Penny 2003 Ho and Larson 2006).
Transposable elements, which are sequences capable of inserting copies of themselves in various locations in the genome, are particularly useful for inferring historical events (e.g., Kumar and Bennetzen 1999 Kumar and Hirochika 2001 Schulman et al. 2004a, b Panaud 2008). These elements are often described as parasites of the genome because they reproduce themselves independently. Retrotransposons, in particular, are very abundant in animal and plant genomes and, like retroviruses, spread by being transcribed into RNA and then reinserting back into the DNA of the “host” chromosomes. These new copies remain incorporated in the host genome and are passed on to offspring, such that insertions can accumulate over time in lineages of plants and animals. By comparing the locations of transposable element insertions, it is possible to reconstruct the historical order in which species branched from common ancestors: species sharing many common insertions are more closely related and diverged more recently than those with only a few such shared insertions (see Shedlock and Okada 2000 Shedlock et al. 2004 Mansour 2008). This type of analysis has been used in reconstructing relationships among domesticated rice and its relatives, for example (Cheng et al. 2002 Xu et al. 2007). The same approach has been used to illustrate the close evolutionary ties between whales and even-toed ungulates (e.g., Nikaido et al. 1999, 2006) and to elucidate relationships among primates (e.g., Salem et al. 2003 Xing et al. 2005 Herke et al. 2007).
As the bodies of animals and plants function through the action of specialized organs, so the survival of individual animal and plants cells depends on the presence of subcellular organelles. Prominent among these are mitochondria, which are essential for cellular respiration in both animals and plants, and chloroplasts, which carry out photosynthesis in plants. Both mitochondria and chloroplasts are descendents of formerly free-living microorganisms (α-proteobacteria and cyanobacteria, respectively) that have become incorporated into host cells but continue to reproduce independently inside them. Though many of their genes have been lost or have migrated to the nucleus, these organelles retain their own genomes which evolve largely independently of the nuclear genome. Analyses of mitochondrial genes, in particular (and often in concert with microsatellite data), have proved very useful in disentangling the complex history of domestication of various animals (e.g., Savolainen et al. 2002 Bruford et al. 2003 Driscoll et al. 2007). Similarly, chloroplast DNA has long been used in the study of domesticated plants (e.g., Palmer 1985 Matsuoka et al. 2002 Wills and Burke 2006 Kawakami et al. 2007). Because they evolve largely independently of the nuclear genome, organelle genomes provide yet another source of genetic data for testing evolutionary hypotheses.
Analyses of particular segments of DNA have only been used in force for studies of domestication since the early 1990s. The field advances so rapidly, however, that this already has expanded to include methods that focus on entire genomes. The technique known as amplified fragment length polymorphism analysis, for example, has undergone considerable advances since its emergence in the mid-1990s and is now often used in studies of domesticated species (Salamini et al. 2002 Meudt and Clarke 2007). This approach involves using enzymes to digest total genomic DNA, followed by selective amplification of fragments of mostly non-coding DNA from regions distributed throughout the genome (see Meudt and Clarke 2007).
The most recent addition to the arsenal of evolutionary science is the ability to read the letter-by-letter sequence of entire genomes. A draft of the human genome sequence was published in 2001, and since then the field of comparative genomics has exploded to include dozens of animals, plants, and fungi (and hundreds of bacteria). Most of the eukaryote species sequenced to date have been chosen because of their importance as disease organisms or vectors (e.g., malaria, mosquitoes) or medical/biological research models (e.g., nematode worm, vinegar fly, mouse, rat, rhesus macaque). Domesticated species have been high-priority targets for genome sequencing as well. At the time of this writing, genome sequences are either published or under way for cat, dog, chicken, turkey, pig, cow, rabbit, horse, alpaca, honeybee, silkworm moth, rice, maize, wheat, barley, sorghum, oat, rye, soybean, tomato, potato, alfalfa, cauliflower, grape, orange, coffee, cocoa, cotton, banana, kidney bean, and manioc (Liolios et al. 2008 http://www.genomesonline.org). There is little doubt that the availability of complete genome sequence information from these and related species will provide unprecedented insights into the process of domestication through artificial selection.
Studies of genes from modern populations of domesticated animals and plants can reveal the genetic underpinnings of traits that were selected by early farmers (see below). These may also make it possible to evaluate some historical patterns of genetic change, but this cannot extend beyond statistical inference. Fortunately, direct insights about the genetics of ancestral animal and plant populations are becoming possible through the recovery of DNA from archeological material (see Brown 1999 Jones and Brown 2000 Bruford et al. 2003 Zeder et al. 2006a, b). In one recent example, Jaenicke-Després et al. (2003) retrieved ancient DNA from archeological maize cobs from Mexico and the southwestern United States ranging in age from 4,400 to 660 years ago. This allowed them to trace the increase in frequency of three gene variants (alleles) encoding features that were under selection during early maize domestication. Ancient DNA analyses have also been used in studies investigating the domestication history of animals, as for example in the recent work by Leonard et al. (2002) on dogs and of Larson et al. (2007) on pigs. Ancient DNA is coming to play a significant role in broader evolutionary studies as well. In some extraordinary cases, this involves not only the recovery of particular gene sequences but of entire genomes. Remarkable examples include the ongoing project to sequence the Neanderthal genome (Noonan et al. 2006) and the recent publication of the genome sequence of the extinct woolly mammoth (Miller et al. 2008).
Data from other disciplines
Evolutionary research is, by its nature, strongly interdisciplinary. This is no less true when the evolution under study is the result of artificial selection. Thus, the study of domestication has benefited from information derived from geology, paleoclimatology, physical and cultural anthropology, and even linguistics in order to identify the environmental and cultural contexts in which these transitions took place (e.g., Diamond 1997, 2002 Bellwood 2005).
The Power of Consilience
It is a simple truism that unique, irreproducible, prehistoric events cannot be known with absolute certainty. However, it is far from true that these cannot be inferred with great confidence. As the study of domesticated animals and plants shows, a wide range of independent lines of evidence can be brought to bear on such questions, made all the more powerful by their common convergence on similar answers. Domestication has been investigated using comparative morphology, biogeography, archeology, and numerous independent sources of genetic data ranging from chromosome number to gene sequences to complete genomes to ancient DNA. The rise of each new approach allows previous hypotheses to be tested and, where necessary, new ones to be postulated. For this reason, claims regarding evolutionary relationships between domesticates and wild species can be, and regularly are, tested empirically. No reliable observation has yet been made to refute the notion that livestock, pets, and crops evolved from wild predecessors. On the contrary, the details of when, where, and how this occurred are becoming increasingly clear. Where there is disagreement, it relates not to the fact of evolutionary descent but to specific points about the mechanisms, locations, or timing of change. All of these considerations apply in the study of evolution by natural selection as well.
Lesson 3: Selection Requires Heritable Variation, Which Arises by Chance
The Hand of Nature
There can be no selection, artificial or otherwise, if all individuals are the same or if the differences among individuals are not heritable. It is clear that Darwin recognized this fact, even though the mechanisms of inheritance were unknown to him. In the introduction to The Variation of Animals and Plants Under Domestication, Darwin (1868, p. 2) noted that, regardless of the intensity of artificial selection, “if organic beings had not possessed an inherent tendency to vary, man could have done nothing.” In addition, Darwin understood well that selection itself does not cause variation and therefore that no severity of need or strength of preference can make beneficial traits appear. As he wrote (Darwin 1868, p. 3), “although man does not cause variability and cannot even prevent it, he can select, preserve, and accumulate the variations given to him by the hand of nature in any way which he chooses.” Thus, the traits that come to be selected either already exist in a minority of individuals, arise by chance, or are introduced from outside through crossbreeding. Even methodical selection, Darwin realized, is dependent on variants that arise without regard to human desire. In this case, most changes that happen to occur will be considered neither positive nor negative and will simply be ignored. Of those changes that are visible, most are likely to be less desirable than the current standard—but on rare occasions, differences of interest will become available.
Detecting Domestication in the DNA
Domesticated animals and plants have played an important role throughout the history of genetics. Indeed, the term “gene” itself is derived indirectly from Darwin’s (incorrect) theory of blending inheritance known as “pangenesis,” which was presented in volume II of The Variation of Animals and Plants Under Domestication. A correct particulate theory of heredity likewise was developed using domesticated species, most notably in the famous crosses of pea plants performed by Gregor Mendel.
For more than 50 years, it has been known that genetic mutations—undirected errors at the DNA level—are responsible for generating the heritable variation among individuals upon which all other evolutionary processes rely. Nevertheless, and notwithstanding the strong historical link between genetics and domestication, the question of the specific genetic changes that have undergirded the domestication of animals and plants has only been the subject of intensive study since the early 1990s (Doebley 1992 Emshwiller 2006). Progress in elucidating the genetics of evolution under artificial selection has been remarkably swift, especially with regard to crops (e.g., Gepts 2004 Doebley et al. 2006 Ross-Ibarra et al. 2007 Burger et al. 2008). As Burger et al. (2008) noted recently with regard to crops,
These advances not only allow for an investigation of the overall genetic architecture of the wild-crop transition, but also make possible the identification of genomic regions and genes that were subjected to selection during the evolution of various crops. In some cases, researchers have been able to pinpoint the exact nucleotide changes responsible for the production of key crop-related traits.
Two major approaches have been taken to discovering genes involved in generating the domestication syndrome in crops, which Ross-Ibarra et al. (2007) categorize as either “top-down” or “bottom-up.” The top-down approach involves observing phenotypic differences between crops and their wild progenitors and then performing tests to identify regions of the genome involved in producing them. Traditionally, this has included carrying out numerous crosses (either of inbred strains or of closely related species) and examining the patterns by which traits of interest segregate. By using molecular markers, specific features of known genomic location, it is possible to map the location of regions linked to the appearance of particular phenotypic traits. These are known as quantitative trait loci (QTLs) and may be genes, regulatory regions, or other elements linked to genes involved in producing particular characteristics (see Collard et al. 2005). Methods developed in mammalian genetics, such as linkage disequilibrium mapping, also have been applied recently in the detection of relevant genes among crops (Mackay and Powell 2006 Ross-Ibarra et al. 2007). Once identified, genetic loci associated with particular traits can then be further analyzed by DNA sequencing and compared with other known genes to determine their precise roles.
The bottom-up approach, by contrast, begins with analyses aimed at detecting regions in the genome that have been under selection and then seeks to determine the phenotype with which they may be associated. This can be accomplished by examining a large sample of plants and assessing the amount of diversity among them at particular genetic loci. Because selection involves allowing only a subset of each population to reproduce, it has the effect of reducing total genetic variation—sometimes severely (e.g., Haudry et al. 2007). However, the “bottleneck” effect of selection is not exerted uniformly in the genome: regions associated with traits under selection will be particularly strongly affected and therefore will exhibit especially low diversity in modern populations compared to “neutral” genes not under selection (Ross-Ibarra et al. 2007 Fig. 6). Another approach involves scanning the genome for sequences that show signs of having been under selection (see Wright and Gaut 2005 Nielsen et al. 2005). Once such regions have been identified, the next step is to investigate their phenotypic impacts, for example by experimentally disrupting their function and observing the consequences (Vollbrecht and Sigmon 2005 Doebley et al. 2006).
Domestication results in a genetic bottleneck for genes under selection (right) as well as neutral genes that are not under selection (left). In this figure, the different shades of balls represent genetic diversity, with more significant loss of diversity occurring in genes under selection. This can be used to detect genes that have been involved in domestication, although it should be borne in mind that severe bottlenecks may greatly reduce variation in neutral genes as well and thereby make it difficult to determine which genes have been under selection. From Doebley et al. (2006), reproduced by permission of Elsevier and Dr. John Doebley
Recent Discoveries in Cereal Crops
Using the approaches outlined above, biologists have made a number of recent discoveries that highlight the ways in which random mutation and artificial selection have generated profound changes in domesticated animals and plants. Some notable recent examples from cereal crops are outlined in the following sections.
Maize: turning teosinte inside out
Maize is unique among crops in the dramatic physical differences that separate it from its wild ancestor, in particular with regard to the structure of the ear (i.e., the seed-bearing female inflorescence). In teosinte, the ears are composed of multiple stalks, each of which includes five to 12 kernels. Teosinte kernels fall separately to the ground when mature and are enclosed within a hard stony fruit case made up of a cupule in which the kernel sits and a glume that covers the cupule opening. These fruit cases are sufficiently strong to survive passage through the digestive system of an animal. Maize ears, in stark contrast, are single-stalked and may possess 500 or more kernels arranged into 20 or more rows. More significantly, the kernels of maize are naked (i.e., lack a hard case) and remain firmly attached to a central cob when mature (Doebley 2004 Buckler and Stevens 2006 Fig. 3). In light of such major differences, it was argued that too many genetic changes would be required to convert teosinte into maize in less than 10,000 years (see Doebley 2004 Wang et al. 2005). Yet, it was soon shown that maize remains genetically similar enough to its wild relatives that the two subspecies may readily be crossed (Doebley 2004). Therefore, reconciling the extreme morphological disparity but close genetic similarity between maize and teosinte became an important objective for understanding maize evolution.
The first major insight along these lines came in the early 1970s when George Beadle crossed maize and teosinte and categorized 50,000 descendant plants as having ears identical to teosinte, identical to maize, or intermediate between them. He found that the frequencies of teosinte and maize ears both were roughly one in 500, from which it was concluded that around five genes of large effect could have underlain the evolution of primitive maize, with various additional genes later providing more modest input (see Doebley 2004 Buckler and Stevens 2006). These data arrived several decades after the teosinte hypothesis was proposed, and it took another 20 years before specific candidate genes were identified. Thanks to modern molecular analyses, insights have begun to accumulate rapidly (e.g., see reviews by Doebley 2004 Pozzi et al. 2004 Buckler and Stevens 2006 Doebley et al. 2006).
The kernels of maize are not enclosed within a stony fruit case, but cupules and glumes are still present: they form the central cob to which the kernels are attached. As Wang et al. (2005) put it, “In a sense, maize domestication involved turning the teosinte ear inside out.” A QTL known as teosinte glume architecture 1 (tga1) has been identified as playing an important role in this transition (Doebley 2004). Tga1 may represent one gene or several linked genes. However, it has been established that the difference between teosinte and maize alleles involves as few as 7-bp substitutions which result in a single amino acid change that may impact regulatory function (Wang et al. 2005). Though minor at the genetic level, these changes result in a substantial morphological effect, namely the loss of fruit cases around grains (Fig. 3).
Another QTL of major effect known as teosinte branched 1 (tb1) has been found to result in maize with one stalk rather than the more highly branched form found in teosinte. This gene(s) is part of a family of regulatory genes known as TCP transcriptional regulators which influence the expression of other genes involved in regulating the cell cycle. It is thought that tb1 represses cell division and prevents the outgrowth of additional branches, leading to single stalks tipped by ears (Doebley 2004 Doebley et al. 2006). Once again, this may represent a relatively minor genetic alteration, but one that exerts substantial impacts through its role in regulating plant development.
Many other genes of smaller effect are expected to have influenced features such as the size of the ear, growth conditions, and the nutrient content of kernels. More specifically, a scan of portions of the maize genome provided an estimate that 2–4% of genes have experienced artificial selection (Wright et al. 2005). Several candidate genes have already been identified (Wright et al. 2005), with some especially notable examples relating to kernel nutrient content. For example, a gene encoding prolamin box binding factor (pbf) regulates the storage of proteins in maize while a gene known as sugary1 (su1) encodes enzymes involved in the storage of starch (Whitt et al. 2002 Jaenicke-Després et al. 2003). Sweet corn results from naturally occurring recessive mutations that may include the sugary (su), sugar enhanced (se), or shrunken (sh2) genes which control the conversion of starch into sugar in the endosperm of kernels. Another kernel nutrient gene, yellow 1 (y1), encodes an enzyme that produces yellow kernels with high-level carotenoids, a precursor for vitamin A synthesis (Palaisa et al. 2003). In this case, the difference relates to a change in a promoter sequence such that this gene is expressed in kernels and not just in leaves where it usually is activated. This gene is of interest because it has been under intense recent selection: when it was discovered in the 1930s that yellow corn is more nutritious for farm animals, almost all corn production in the US switched from white varieties to yellow (Doebley et al. 2006).
The grasses Oryza rufipogon and Oryza sativa are morphologically similar, closely related genetically, and capable of interbreeding—in fact, O. sativa is thought to be descended from O. rufipogon (or the annual form thereof, sometimes known as Oryza nivara Sweeney and McCouch 2007). However, there is a major distinction between them: O. rufipogon is listed as a noxious weed in the United States whereas O. sativa (domesticated rice) is the primary source of nourishment for one third of the world’s population. Interestingly, this extreme disparity in impact between the domesticated crop and its wild progenitor is derived from differences in some relatively simple features. Most notably, O. rufipogon produces seeds that fall from the plant (or “shatter”), which contributes to its weedy ability to disperse widely and makes it difficult to harvest Footnote 6 . Farmed rice, by contrast, exhibits the characteristics typical of the domestication syndrome, including a loss of shattering such that its mature seeds remain attached and are readily harvested. Indeed, shattering remains a major source of crop loss when it occurs and is a feature still under selection in modern breeding programs (Lin et al. 2007).
As with several features central to the domestication of maize, the loss of shattering in rice appears to be controlled by a small number of genes. In 2006, two independent research groups reported the existence of genes involved in this critical transition. First, Li et al. (2006) identified a QTL dubbed shattering4 (sh4) that exists in a dominant form in the wild species and controls the majority of the variance in shattering in crosses of wild and cultivated rice. The QTL maps to a region about 1,700 bp in length and, in the domesticated form, involves a single amino acid change that reduces but does not eliminate shattering. This makes it possible to harvest the grains but not impossible to remove them from the stalk (Doebley 2006 Doebley et al. 2006). Second, Konishi et al. (2006) identified another genomic region in crosses of the two subspecies of domesticated rice (japonica and indica) named QTL of seed shattering in chromosome 1 (qSH1) which involves a single base pair change (G to T) in a regulatory region that prevents expression of the gene at the site where seeds break free (the abscission layer) but which does not render it non-functional in other tissues. More recently, Lin et al. (2007) discovered another gene on chromosome 4, shattering 1 (sha1), which also plays a role in eliminating shattering in domesticated rice and, as with qSH1, involves a single nucleotide substitution (also G to T) in a regulatory region.
Overall, at least five genetic loci are involved in the loss of shattering, while another six have been implicated in the loss of seed dormancy, another factor critical in the initial domestication of rice (Kovach et al. 2007). Dozens of additional genes of smaller effect recently have been recognized to influence features such as grain size, shape, number, color, and nutrient content, as well as other traits relating to growth and reproductive mode in rice (Kovach et al. 2007). Examples include: grain size3 (GS3), which influences grain length and weight (Fan et al. 2006) grain incomplete filling1 (gif1), which affects grain weight (Wang et al. 2008) grain number1 (Gn1a), which contributes to higher yield (Ashikari et al. 2005) red pericarp (rc), which determines seed color (Sweeney et al. 2006) waxy, which specifies amylose content and is important in sticky rice (Olsen et al. 2006) prostrate growth 1 (prog1), which reduces the number of extra stems or “tillers” (Jin et al. 2008) and two genes (including fgr) that relate to fragrance (Bradbury et al. 2005 Fitzgerald et al. 2008).
The list of genes recognized to have played a role in early domestication and subsequent improvement of crops is growing rapidly. While it is too early to draw detailed conclusions, some general patterns are emerging. First, it can be seen that many of the major early transitions involved a small number of minor genetic changes with large phenotypic effects, for example mutations in regulatory elements and developmental control genes. Second, many of the subsequent improvements or variety-level differences that have evolved relate to larger numbers of small-scale mutations. Third, whereas many of the features that distinguish varieties are based on loss-of-function mutations, this clearly is not always the case. In fact, as far as is known, the genes of major effect at the heart of domestication in many species are functional (Doebley 2006 Doebley et al. 2006 Burger et al. 2008).
Lesson 4: Selection Is a Population-Level Process that Occurs over Many Generations
Identifying mutations that have played a key role in domestication is an important step in understanding how such remarkable transformations have taken place. It also raises an important question regarding the source of variation upon which early artificial selection depended: were these fortuitous new mutations that arose shortly before and/or sequentially during domestication, or were they already present in wild populations? In some cases, wild progenitor populations appear to be devoid of the alleles that determine the features of crops, as is the case with loss of shattering in rice or loss of the seed casing in maize (Doebley et al. 2006). In other cases, mutant genes important in domestication can still be found at low frequencies in wild populations, as has been reported for alleles affecting fruit size in tomato and plant structure in maize (Doebley et al. 2006). Some authors have suggested that it was not new mutations per se that resulted in the unique phenotype of maize but selection on standing variation and the bringing together of several rare variants for the first time (e.g., Vollbrecht and Sigmon 2005 Doebley et al. 2006). In any case, it is well recognized that populations of some wild progenitors, such as teosinte, exhibit remarkable levels of standing genetic variation, supplying ample raw material for the operation of artificial selection (e.g., Doebley 2004 Buckler and Stevens 2006).
Whether they were based on a series of new mutations or combinations of preexisting alleles, it is very likely that the key traits favored by early farmers initially would have been present in very low numbers within wild populations. This is especially probable given that many of the gene variants important in early domestication (e.g., reduced shattering, loss of seed cases) make their possessors less able to propagate on their own. Artificial selection explains how these rare variants became ubiquitous (“fixed”) within modern domesticated populations. Unfortunately, the mechanism of selection is often misunderstood, and clarifying this process with the familiar example of domestication can provide useful means of improving the understanding of larger-scale evolution through natural selection. In this regard, some important points about the operation of artificial selection are outlined in the following sections.
Domestication occurs over many generations
The notion of an “agricultural revolution” may sometimes be taken to imply a rapid switch from hunter–gatherer lifestyles to one based on crop production. And indeed, within the span of human history, this was a comparatively brisk transition. However, on the scale of individual human lifetimes, it may have been so gradual as to be nearly imperceptible. As Kovach et al. (2007) put it, “domestication is not a single ‘event’ but rather a dynamic evolutionary process that occurs over time and, in some species, continues to this day.” It is quite possible that a predomestication period of harvesting extended back 20,000 years for some species (Allaby et al. 2008). This is supported by evidence from microfossils and starch grains embedded in stones which indicates that cereals were being used millennia before evidence of major morphological changes arose (Zeder et al. 2006b).
There is increasing evidence that the process of domestication itself occurred over the span of a great many generations of plants (and farmers). Even transitions considered “fast” would involve 100–200 generations of plants (Gepts 2004), and there are growing indications that most processes have been nowhere near this rapid. For example, archeological evidence shows that corn cob form was under selection for thousands of years, and ancient DNA evidence indicates that even genes of large effect were present in maize at least 4,400 years ago but still were not fixed by 2,000 years ago (Jaenicke-Després et al. 2003). Similarly, archeological collections of wheat spikelets show that early populations contained both wild and non-shattering forms. Despite the substantial benefit provided by non-shattering ears, the process of fixation of this trait was drawn out over a millennium (Tanno and Willcox 2006 Balter 2007). Such a protracted rate of change under artificial selection appears to be typical among cereal crops, with changes in grain size taking 500–1,000 years and alleles for loss of shattering becoming fixed after another 1,000–2,000 years (Fuller 2007).
It has been suggested that this surprisingly slow pace of change could have resulted because selection by humans was relatively weak (Fuller 2007) or because early farmers supplemented their seed stocks with wild varieties during lean years (Tanno and Willcox 2006). However, even under intense and uninterrupted selection, the process of changing allele frequencies in entire populations takes time. As an interesting illustration of this, crop domestication researcher John Doebley has initiated an experiment he dubs the “Redomestication Project” (http://teosinte.wisc.edu/redomestication.html):
How long did it take ancient peoples to domesticate maize from teosinte? We don’t know the answer to this question and will likely never have a very precise answer, but there are ways we can make an educated guess to this and related questions. With this thought in mind, I began a “long term” selection study with teosinte (Zea mays ssp. parviglumis) to see if I can change the population to be more maize-like, i.e. to “redomesticate” maize. This study involves growing a large number of teosinte plants each year and harvesting seed from the most maize-like individuals for the next generation. I hope to continue this process for 30 generations.
Even with selection carried out in a controlled manner by an expert researcher, the prospects for change during the span of a human lifetime are modest. As Doebley writes on the project website (accessed Dec. 2008),
Over the next 28 years (the funding gods agreeable), I will grow out about 3000 seed of the selected progeny from the preceding generation and select the short-branch plants.
I don’t anticipate that this selection experiment will actually produce a maize replica. The plants should become more maize-like for branch length (and perhaps seed size and tillering), but for most other traits they should remain true to the teosinte condition. There is a chance that some other correlated traits such as the number of fruitcases per ear may change.
Doebley’s experiment is also important in demonstrating the fact that traits may be selected individually (though often with correlated implications) and that selection is simply a matter of preserving and propagating variants with a slightly more favorable trait from one generation to the next, not of finding a fully domesticated plant hidden within a field of wild relatives. It also demonstrates that selection is not a process that occurred only in the distant past but also can be observed in the present.
Individual organisms do not evolve
In order to understand the process of artificial selection (and by extension, both domestication and natural selection), it is critical to bear two additional points in mind. First, features acquired by an individual organism during its lifetime are not passed on to offspring. The source of new variation in the next generation is mutation occurring in the germ of parents. Second, the undirected generation of heritable variation by mutation and the subsequent non-random sorting of variants by selection are two independent processes. This means that no matter how intense the selection pressure imposed by breeders may be, it will not cause specific favorable mutations to occur. Therefore, evolution is not a process in which individual organisms change in response to pressures from the environment (which may include choosy farmers). Rather, selection involves change in the average properties of the entire population as a non-random subset of each generation producing the next generation. In other words, individuals do not evolve, populations do.
Selection is most effective in large populations
As Darwin (1859) and Wallace (1889) both recognized, artificial selection is likely to be most effective in large populations. This is true for three major reasons. First, favorable mutations are rare, and having more animals or plants reproducing in the population provides more opportunities for them to occur. Darwin described this explicitly in the Origin (Darwin 1859, p.40–41):
A high degree of variability is obviously favourable, as freely giving the materials for selection to work on not that mere individual differences are not amply sufficient, with extreme care, to allow of the accumulation of a large amount of modification in almost any desired direction. But as variations manifestly useful or pleasing to man appear only occasionally, the chance of their appearance will be much increased by a large number of individuals being kept and hence this comes to be of the highest importance to success.
Second, the chance of losing a favorable mutation due to chance by the process known as genetic drift is much higher when the population is small. Third, larger populations tend to be more variable and to be less affected by the loss of genetic diversity through domestication bottlenecks (Eyre-Walker et al. 1998 Doebley et al. 2006).
Using genetic data, it is possible to infer some information regarding the sizes of ancestral populations for domesticated animals and plants. In maize, for example, conservative estimates suggest an initial teosinte population size of 500 to 4,000 individual plants. Biologically speaking, this is a small population, but it is very different from simply picking between a few different plants. As cultivation increased, so too did the population sizes of the plants. Today, the number of maize plants cultivated is enormous given the ubiquity of this crop in processed food, livestock production, and a range of other industries (see Jahren and Kraft 2008). Wilkes (2004) suggested that “it takes 25 corn plants per person per day to support the American way of life.” In another assessment, Buckler and Stevens (2006) pointed out that “if 10 people derive 10% of their calories from maize, it is estimated that roughly 250,000–350,000 plants would have to be grown annually.”
Lesson 5: Adaptation Builds on What Is Already Present
With the advent of genetic engineering, it has now become possible to add specific characteristics to crops and livestock at will, including by transplanting genes for desirable traits from other species. Traditional approaches based on selective cultivation or breeding, on the other hand, are more indirect and typically involve modifications of genes and physical features that are already present rather than the addition of fundamentally new characteristics. This process of altering existing features rather than redesigning from scratch—commonly called “tinkering”—is a hallmark of evolutionary adaptation (for review, see Gregory 2008c). In maize, for example, the cob is formed from modifications of the cupule and glume, which in wild teosinte form the seed case (Wang et al. 2005). In other cases, different parts of the plant may be modified in very different ways. Notably, selective breeding in the wild cabbage species Brassica oleracea has produced a wide variety of distinct cultivars, each representing a modification of a particular part of the plant (Purugganan et al. 2000 Fig. 7). As Doebley (2006) aptly remarked, “Tinkering. is the order of the day in domestication as in natural selection and Darwin’s use of domestication as a proxy for evolution under natural selection was, not surprisingly, right on the mark.”
An example of the modification of existing structures through artificial selection. (a) Wild Brassica oleracea, from which various domesticated cultivars have been produced based on changes to specific plant parts: (b) broccoli (and cauliflower flower clusters), (c) cabbage (leaves), (d) kale (leaves), (e) Brussels sprouts (leaf buds), and (f) kohlrabi (stems). All images from Wikipedia
Lesson 6: What Matters Is Reproductive Success, Not Survival Per se
Domesticated animals and plants depend on humans in order to survive and/or reproduce. As a result, they are ill-suited to life in the wild and would be at a severe disadvantage if forced to compete with wild relatives. However, under the conditions that they actually face—namely those created by humans—it is the domesticated forms that have been the most successful, by definition. In this sense, artificial selection provides an excellent illustration of a crucial point: selection is not about survival per se but about reproductive success. Thus, the phrase “survival of the fittest,” which was coined by Herbert Spencer (a contemporary of Darwin’s), is misleading if it implies physical fitness or other measures of survival ability. “Fitness” in the evolutionary sense is usually defined specifically in terms of reproductive success (e.g., Futuyma 2005), and survival is only relevant insofar as it contributes to enhanced reproduction. Put another way, regardless of how well an individual survives in its environment, it will not be evolutionarily fit unless its traits are actually passed on to the next generation.
If an individual possesses a heritable trait that, for whatever reason, results in its leaving more offspring than individuals lacking the trait, then that trait will become proportionately more common in the next generation. In terms of artificial selection, the traits that lead to greater relative reproductive success may be physiological, developmental, biochemical, or behavioral and may in fact be based on little more than human whim. But if the result is that individuals bearing them are statistically more successful in passing on their traits, then these will increase in frequency under artificial selection. Whether adapting to the new human-imposed environment made the plants dependent on farmers is irrelevant to considerations of what constitutes “fit”—dependency can also evolve under natural selection, for example among parasites or endosymbionts and their hosts. Therefore, criticisms of Darwin’s analogy based on the fact that domesticated species are “less fit” in the wild (e.g., Richards 1997) are misplaced.
Lesson 7: What Is Fit Today May Not Be Fit Tomorrow
For most of their history, the species from which domesticated forms are derived evolved under pressures related to survival and reproduction in the wild. This includes requirements for obtaining nutrients, avoiding being eaten, and reproducing successfully by dispersing seeds or acquiring mates. Through the non-random survival and reproduction of individuals from one generation to the next (i.e., natural selection), these plants and animals have become adapted to their particular environments. When early farmers began cultivating or raising these plants and animals, the traits that equated with higher fitness changed dramatically. Individual plants that were less able to disperse their seeds, that were less well protected against herbivory, and that invested more energy in features of interest to farmers (e.g., more sugar and starch in seeds) were the ones whose traits were passed on more frequently. Similarly, animals that were less aggressive and easier to manage were those that ultimately passed on their genes at the highest rate.
Changes in selective pressures, which sometimes may be dramatic, have played an important role in the evolution of life at large and help to explain its enormous diversity. From the perspective of the animals and plants under artificial selection, the arrival of humans and the imposition of their preferences in determining reproductive success are just another example of this.
Lesson 8: Selection Can Lead to Either Divergence or Stability
Though domestication is often described as a transformation of wild species into forms that are suitable for, and dependent on, human cultivation, it is generally not the case that the entire progenitor has been transformed. Rather, domestication involves changing a subset of the original species in several species, domesticated populations and wild populations both continue to exist (Doebley et al. 2006 Tanno and Willcox 2006 Vaughan et al. 2008) (In this case, it must be noted that both domesticated and modern wild populations are descendants of an ancestral wild population such that this represents a case of divergence of one form into two (Emshwiller 2006) Footnote 7 . For this reason, it is no less misguided to ask “why are there still populations of teosinte now that domesticated maize has evolved?” than “why are there still apes now that humans have evolved?” Gregory 2008b). The primary cause of this divergence has been the existence of differing selective pressures: in undomesticated forms, these remain pressures related to survival and reproduction in the wild, whereas in cultivated forms the pressures are imposed by farmers. Similarly, differing selective pressures applied to domesticated animals and plants can lead to divergence in the form of cultivars or breeds.
Darwin recognized the role that differing selective pressures would play in creating biological diversity by identifying the “principle of divergence.” The principle of divergence clearly applies in the case of methodical selection (Sterrett 2002), in which breeders develop very different forms according to their particular preferences (Fig. 1). However, once a specific breed has been established, the process of selective breeding becomes one of choosing individuals that conform most closely to recognized standards. In this case, mutations that cause deviation away from the current form are selected against, with the net effect of preventing further change. Both “directional selection” (pressure favoring one extreme and leading to change) and “stabilizing selection” or “purifying selection” (pressure preventing change away from the current state) are common in nature, and so once again artificial selection provides a clear example of an important general principle.
Lesson 9: Selection Is Neither an Unlimited nor an Exclusive Mechanism
In light of the extensive change that has been brought about in many domesticated species, it may be tempting to assume that all features of domesticates are the product of artificial selection and that the potential influence of this process is effectively limitless. There are several reasons why neither supposition would be correct.
The Power of Selection Is Not Unlimited
As Darwin (1868) recognized, without heritable variation with which to work, even the choosiest breeder or most diligent farmer would be powerless to effect change. Thus, one of the most obvious limitations of the power of selection is the dependence of the process on mutations that arise by chance. If relevant mutations simply never occur, then particular avenues of adaptive change will remain inaccessible.
The availability of mutations is just one of many factors, some internal and some external, that can determine—or block—the path to domestication in different species. Indeed, it is clear that certain groups of animals and plants are far less amenable to domestication than others (Diamond 1997, 2002 Gepts 2004 Zeder et al. 2006b). Intrinsic factors such as the amount of crossbreeding (i.e., transfer of genes among populations or “gene flow”), reproductive mode (e.g., propensity for self-fertilization in plants), generation time, tolerance of new environments, and genetic characteristics may all make it more or less likely that particular species will respond to artificial selection. External factors such as climate, soil conditions, water availability, and other features may similarly dictate which regions are likely to serve as cradles of domestication (Balter 2007 Allaby et al. 2008). Even among those species that are domesticated, these intrinsic and extrinsic factors may affect how rapidly (or how many times) the process occurs.
Sometimes, the prospects for domestication can depend on the probability of major genetic changes (such as genome duplications and/or hybridizations, as in polyploid wheat), but it also may be as simple as the nature of the genetic system underlying specific features. As an interesting example of this, Diamond (2002) considers why almonds were domesticated but other trees such as oak were not. Both almonds and acorns are bitter and toxic in the wild, but domesticated almonds have been selected for a loss of toxicity. Acorns have traditionally been an important wild food source for foragers, and occasional non-toxic trees do arise and are preferred. However, whereas almond toxicity is controlled by one gene such that mutant plants provide offspring that are also non-toxic, toxicity in oak is determined by multiple genes, meaning that offspring of non-poisonous oaks are rarely non-poisonous themselves. This difference in genetic system, and its associated consequences for the reliability of breeding outcomes, may explain why almonds and not acorns are widely cultivated.
Adaptation Comes with Tradeoffs
While it is possible to select among individuals on the basis of particular traits, it is nonetheless the case that organisms are integrated entities whose parts are functionally interconnected. In addition, a finite number of resources is available for the construction of an adult animal or plant, meaning that not all parts can be accentuated indefinitely without compromising the function of other parts. The consequences of these facts are known as “tradeoffs.”
Tradeoffs have played an important role in domestication, just as they do in other examples of adaptation. As a notable example, selection for higher yield often comes at a cost of lower protein content per seed among cereal crops: domestic grains may exhibit only 50% of the protein content of those of their wild relatives (Doebley et al. 2006). Moreover, the production of plants with larger, more flavorful grains may require more water or nutrients to produce, may grow more slowly, and may become host to new insect pests, thereby necessitating a significant investment of human labor for their cultivation. Similarly, selection for more rapid growth has had the consequence of drawing resources away from features such as brain size and acuity of sense organs in domesticated animals (Diamond 2002).
Tradeoffs may also occur between the organism level and population level during domestication (or under natural selection). The non-random subsampling of genetic diversity that underlies selection results in a reduction in genetic variation across generations. This lack of variability can make populations of plants or animals less able to adapt to novel challenges such as emerging pests and pathogens or climate change and may affect long-term viability. It is also recognized that artificial selection can cause deleterious mutations to accumulate in domesticated populations for various reasons, including inbreeding and the hitchhiking of deleterious genes along with those under intense artificial selection (e.g., Lu et al. 2006 Cruz et al. 2008). In short, artificial selection for specific features brings with it consequences both for other components of organisms and for the populations of which organisms are a part.
Selection Is Not the only Mechanism of Evolution
The generation of new heritable variation is not an outcome of selection, rather this occurs by mutation and recombination. Selection is a process by which the frequencies of existing variants changes from one generation to the next, and it is not the only one. The movement of genes from one population to another (gene flow) provides an additional mechanism, and the chance sorting of variants (genetic drift) is yet another. Chance processes are particularly relevant in smaller populations because of the increased probability of drawing an unrepresentative sample of existing diversity. Because it is independent of fitness, genetic drift can cause fit, unfit, or neutral alleles to become fixed. This may be particularly relevant in domestication because of the major bottleneck that this entails.
In some cases, features commonly associated with domestication have not been selected directly but rather represent side effects of the relaxation of selection (e.g., Dobney and Larson 2006). For example, the domestication of animals relaxes the selective pressure on males to compete for mates. This means that genes involved in producing traits relevant to this endeavor (e.g., large horns in male goats) are no longer under selection and become effectively neutral or even detrimental as they involve diversions of resources away from traits such as rapid growth that are under selection. The horns of domesticated livestock can therefore be lost not because humans select directly for their reduction but because a lack of sexual selection allows alleles specifying smaller horns to increase in frequency indirectly or by chance (Mignon-Grasteau et al. 2005 Zeder et al. 2006a). This example is very instructive, as it cautions against interpreting every feature of an organism (domestic or wild) as an adaptation brought about directly through selection.
Lesson 10: Conscious Thought and Long-term Goals Are Not Required for Selection to Operate
Among the most difficult concepts for students to grasp are that natural selection does not actively “select” in any conscious sense, that evolution has no long-term goals, and that individual organisms under selection do not attempt to improve in the face of environmental challenges. On the face of it, artificial selection—which does involve the input of conscious selecting agents—may seem to be a very poor model for use in correcting these misconceptions. This superficial interpretation is misleading, however. In fact, an understanding of domestication and artificial selection provides significant clarification on these points.
Crops and Domestic Animals Do Not Consciously Adapt
The process of artificial selection, whether methodical or unconscious, involves the non-random propagation of randomly varying individuals within an available population. The individual plants and animals under artificial selection do not make any conscious effort to meet the expectations of farmers. They have no understanding of genetics or selection and hold no long-term goal to become domesticated—they simply happen to possess traits of interest or they do not. The selective pressures in the wild are different, but there is no more conscious effort by animals and plants to adapt under natural selection than with artificial selection. Evolution in either case is a process in which gene variants change in proportion from one generation to the next. Conscious effort to pass on one’s genes is not necessary to drive this mechanism.
Early Domestication Probably Occurred Through Unconscious Selection
Whereas methodical selection involves intentional breeding to achieve a predefined ideal form, unconscious selection is not based on striving toward any long-term goal. It is therefore important that, in most cases, early domestication is thought to have occurred through unconscious selection rather than methodical selection (e.g., Darlington 1969 Heiser 1988 Zohary et al. 1998 Doebley et al. 2006 Zeder et al. 2006b Ross-Ibarra et al. 2007) Footnote 8 . As Diamond (2002) explained,
Food production could not possibly have arisen through a conscious decision, because the world’s first farmers had around them no model of farming to observe, hence they could not have known that there was a goal of domestication to strive for, and could not have guessed the consequences that domestication would bring for them.
Instead, domestication in seed crops probably began with a very simple input (see Doebley et al. 2006). For example, the first step may simply have involved burning inedible vegetation to encourage the growth of edible grasses. Being weedy, grasses would have been among the first to occupy these disturbed environments. (Alternatively, the early relationship between edible grasses and humans may have been one in which weeds that easily invaded disturbed areas appeared regularly near seasonal campgrounds used by migrating hunter–gatherers.) From this point, it would have been a small step to not only clearing existing vegetation but also to actively sowing seeds from plants gathered elsewhere and thence to sowing seeds from plants in the same area from season to season. Later, traits that made it easier for seeds to be collected, such as loss of shattering, would have been selected—again, largely unconsciously because those that shatter simply would have been more difficult to collect. Methodical selection for flavor, color, or other specific features would have occurred only later.
A similar situation probably applies to domesticated animals. In both dogs and livestock, it is thought that the early stages of domestication involved unconscious selection for behavioral traits (e.g., for tameness and reduced aggression e.g., Jensen 2006 Zeder et al. 2006a, b). In turn, this had significant consequences for physical and developmental features that may have been selected only indirectly. The plausibility of this hypothesis is strengthened by the example of “domesticated” silver foxes, which have been the subject of a decades-long breeding experiment. Specifically, individual foxes have been selected purely on the basis of tameness, but major changes in behavior, development, and appearance have arisen as a result (see Trut 1999). In this case, selection has been intentional, but this mimics a probable unconscious process that occurred early in dog domestication when wolves and humans began coming into close contact.
In some cases, human farming practices may not only be unconscious but may engender unintended and undesirable consequences. For example, by clearing vegetation and tilling fields, humans have established new environments that favor increasingly weedy traits among plants other than the desired crops (Harlan et al. 1973). By definition, unconscious selection involves no goal-directed choices. Rather, it is a process that occurs naturally within the unnatural environment created by human agriculturists. In this regard, many authors have pointed out that there is no fundamental difference between unconscious selection and natural selection (e.g., Darlington 1969 Heiser 1988 Ross-Ibarra et al. 2007).
Domestication Has Caused Humans to Evolve as well
It is important to note that, as significant as the effects of artificial selection have been on domesticated plants and animals, this has not been a one-way interaction. Domestication is, in fact, a coevolutionary process in which both domesticates and human populations experience selection (e.g., Zeder et al. 2006b). In fact, the rise of agriculture is thought to have been a cause of extensive evolution in humans (e.g., Diamond 2002 Hawks et al. 2007). A shift to agriculture from hunting and gathering created a new environment for humans just as it did for plants and livestock. This included a change from high-protein to high-carbohydrate diets and increased disease due to higher population densities and the zoonotic transfer of pathogens from livestock to people (Diamond 1997, 2002). Recent analyses of human genomic data suggest that many genes have been under positive selection in recent history (e.g., Nielsen et al. 2005 Voight et al. 2006 Williamson et al. 2007 Sabeti et al. 2007), including some involved in taste and smell, lactose and sucrose digestion, and disease resistance. The increase in human population size is likely to have been particularly relevant in this regard, given that the total occurrence of new mutations is higher when there are more individuals and because selection is more effective in larger populations (Hawks et al. 2007). Artificial selection has reflected back on the species that imposed it and has been a significant factor in recent evolutionary change among humans.
Technology advances: deep sequencing + dense bones = paleogenomics
It has long been realized that performing archaeogenetics research correctly is extremely difficult [38, 45, 46, 48,49,50]. However, by the same token, during the last three decades the challenging nature of aDNA research has spurred significant technical innovation and rapid deployment of state-of-the-art genomics and ancillary technologies [46, 50, 88,89,90,91,92,93]. Undoubtedly, the most important scientific advance was the introduction of high-throughput sequencing (HTS) to archaeogenetics [94,95,96,97]. High-throughput sequencing technologies have been commercially available since 2005  and between 2007 and 2019 there has been an almost 100,000-fold reduction in the raw, per-megabase (Mb) cost of DNA sequencing . Currently, the dominant commercial HTS technology is based on massively parallel sequencing-by-synthesis of relatively short DNA segments [100, 101], which is ideally suited to fragmented aDNA molecules extracted from archaeological and museum specimens. In addition, the vast quantities of sequence data generated—literally hundreds of gigabases (Gb) from a single instrument run—can facilitate cost-effective analyses of archaeological specimens containing relatively modest amounts of endogenous aDNA (for technical reviews see [89,90,91,92,93, 102]).
The introduction of HTS and ancillary specialized methods for sample treatment, aDNA extraction, purification and library preparation have represented a genuinely transformative paradigm shift in archaeogenetics. It has ushered in the era of paleogenomics and the capacity to robustly genotype, analyze and integrate SNP data from thousands of genomic locations in purified aDNA from human and animal subfossils [103,104,105,106,107,108,109,110,111,112,113]. In a comparable fashion to human archaeogenetics , the first HTS paleogenomics studies of domestic animals or related species were focused on a single or a small number of “golden samples” [10, 69, 109, 114, 115].
One of the first HTS studies directly relevant to domestic animals was a technical tour de force which pushed the time frame for retrieval of aDNA and reconstruction of paleogenomes beyond 500 kya to the early stages of the Middle Pleistocene . In this study, Ludovic Orlando and colleagues were able to generate a 1.12× coverage genome from a horse bone excavated from permafrost at the Thistle Creek site in north-western Canada and dated to approximately 560–780 kya. Using this Middle Pleistocene horse genome in conjunction with another ancient genome from a 43 kya Late Pleistocene horse, and genome sequence data from Przewalski’s horse (Equus ferus przewalskii), the donkey (Equus asinus) and a range of modern horses, these authors showed that all extant equids shared a common ancestor at least four million years ago (mya), which is twice the previously accepted age for the Equus genus. They also showed that the demographic history of the horse has been profoundly impacted by climate history, particularly during warmer periods such as the interval after the LGM (Fig. 1), when population numbers retracted dramatically in the 15 millennia prior to domestication 5.5 kya. Finally, by focusing on genomic regions exhibiting unusual patterns of derived mutations in domestic horses, it was possible to tentatively identify genes that may have been subject to human-mediated selection during and after domestication .
The origins of the domestic dog (C. familiaris) and the dispersal of dogs across the globe during the Late Pleistocene and Holocene periods have been extremely contentious, particularly as population genetic, archaeogenetic and paleogenomic data sets have accumulated during the last two decades [8, 116, 117]. Again, like the Thistle Creek horse bone, a small number of key subfossil specimens have provided critical paleogenomic evidence concerning the evolutionary origins of domestic dogs and their genetic relationships with Late Pleistocene Eurasian wolf populations [10, 11, 115]. Pontus Skoglund and colleagues were able to generate a low coverage (
1×) nuclear genome from a 35 kya wolf (C. lupis) from the Taimyr Peninsula in northern Siberia . Analysis of this Taimyr specimen with WGS data from modern canids showed that this ancient wolf belonged to a population that was genetically close to the ancestor of modern gray wolves and dogs. The results supported a scenario whereby the ancestors of domestic dogs diverged from wolves by 27 kya, with domestication happening at some point subsequent to that event. In addition, this study provided compelling evidence that high-latitude dog breeds such as the Siberian Husky trace some of their ancestry back to the extinct wolf population represented by the Taimyr animal .
Another important paleogenome study, published one year after the Taimyr wolf paper, described a high coverage (
28×) nuclear genome from a late Neolithic (4.8 kya) domestic dog specimen from Newgrange, a monumental passage grave tomb in eastern Ireland . Analyses of the ancient Newgrange dog genome, additional mtDNA genomes from ancient European dogs and modern wolf and dog genome-wide SNP data suggested that dogs were domesticated independently in the Late Pleistocene from distinct East and West Eurasian wolf populations and that East Eurasian dogs, migrating alongside humans at some time between 6.4 and 14 kya, partially replaced indigenous European dogs . In 2017, following publication of the Newgrange dog genome, Laura Botigué and colleagues generated two
9× coverage domestic dog nuclear genomes from Early (Herxheim,
7 kya) and Late (Cherry Tree Cave,
4.7 kya) Neolithic sites in present-day Germany . Comparison of these two ancient dog genomes with almost 100 modern canid whole genomes and a large genome-wide SNP data set of modern dogs and wolves did not support the dual domestication hypothesis proposed by Frantz et al. one year earlier , or the suggested East Eurasian partial replacement of Late Paleolithic or Early Neolithic European dogs.
The origins and fate of the domestic dog populations of the Americas prior to contact with European and African peoples has been the subject of a recent paleogenomics study involving comparisons of ancient and modern dogs. Máire Ní Leathlobhair and colleagues sequenced 71 mitochondrial and seven nuclear genomes from ancient North American and Siberian dogs . Comparative population genomics analyses of these data demonstrated that the first American domestic dogs did not trace their ancestry to American wolves. Instead, however, these pre-contact American dogs (PCDs) represent a distinct lineage that migrated from northeast Asia across the Beringian Steppe with humans more than 10 kya . These analyses also demonstrated that PCD populations were almost completely replaced by European dogs due to large-scale colonization of North and South America within the last 500 years. In a similar fashion to the post-contact human demographic transition in the Americas [119, 120], the authors hypothesize that infectious disease likely played a major role in the replacement of PCDs by European dogs. Finally, they also show that the genome of the canine transmissible venereal tumor (CTVT) cancer lineage, which has evolved to become an obligate conspecific asexual parasite , is the closest genomic relative of the first American dogs.
As has been previously noted, understanding the origins and early domestic history of dogs has been complicated by population bottlenecks, expansions, local extinctions and replacements and geographically localized gene flow among wolves and dogs and genetically distinct dog populations . It will, therefore, require systematic large-scale retrieval and analysis of ancient wolf and dog genomes across space and time to accurately reconstruct the evolutionary history of the first animal domesticate . However, this and similar undertakings for other domestic species will be greatly facilitated by another recent technical breakthrough that is described below.
In 2014, a team of Irish geneticists and archaeologists showed that the petrous portion of the temporal bone—the densest bone in the mammalian skeleton—produced the highest yields of endogenous DNA in some cases, up to 183-fold higher than other skeletal elements . The impact of this discovery has been such that the ancient DNA community now dub the period prior to 2014 “BP” (“before petrous”) . During the last 5 years, DNA extraction from petrous bones, coupled with constantly improving HTS and ancillary technologies, has led to a dramatic scale-up of human archaeogenetics, the cutting edge of which is now the statistically rigorous field of high-resolution population paleogenomics [82, 125,126,127,128,129]. Another notable outcome has been a substantial increase in the proportion of the Earth’s surface area where archaeological excavation can uncover suitable material for successful aDNA extraction and paleogenomics analysis. Previously, for the most part, aDNA research has been confined to regions of the globe where climate and topography were conducive to taphonomic preservation of skeletal DNA (Fig. 3) [90, 130]. However, in recent years human paleogenomics studies have been successfully conducted using samples from arid, subtropical and even tropical zones [131,132,133,134,135,136,137,138,139,140,141,142].
Geography of archaeological DNA survival prior to the discovery of high endogenous DNA content in the mammalian petrous bone. a Expected DNA survival after 10,000 years for 25-bp fragments and 150-bp fragments close to the ground surface (modified with permission from ). b Illustration of a sheep (Ovis aries) petrous bone retrieved from a Middle Neolithic site at Le Peuilh, France (modified with permission from )
Examples of Gene Flow
There are dogs of every shape and size in the world. The largest domestic dogs can dwarf a wild wolf. The smallest domestic dog, even as an adult, could easily be mistaken for a newborn wolf. From wolves, dogs have changed almost every aspect of their appearance in one population or another. Dogs are one of the best known examples of artificial selection, a process through which traits are established through selective breeding.
Around 15,000 years ago, all dogs were essentially wolves. However, some of these pre-dogs were much more likely to scavenge from the new human settlements springing up everywhere. The wolves moved further away from civilization, while the pre-dogs moved closer to the humans. Eventually a “social contract” of sorts was worked out between the humans and the dogs. In this contract, dogs provided a service such as waste removal, vermin control, or a hunting guide. Humans would then provide shelter and food. However, the many different human populations had different uses for their dogs.
Birds on an Island
Unlike the case of dogs, most cases of gene flow involve natural selection. Imagine a large population of birds on a mainland. When a big storm brews up, it forces some of the birds high into the air to avoid the storm. When the small flock comes down, they find themselves over the ocean. The wind carries them to a small island, where they set up a new home. The two populations are now sufficiently separated that they cannot regularly interbreed.
Over time, the environmental factors affecting the two different populations will differ. The island birds may have to learn to eat a new food, and may be subject to completely different weather patterns. Over time, this may even change the alleles present in the populations. However, there are always more storms. In another storm, some birds may get transferred back to the mainland. Here, they can once again interbreed with the main population, and gene flow occurs as the new alleles from the island are introduced into the population.
Likewise, if any birds go from the main population to the island population, they will bring with them the alleles selected for on the mainland. This gene flow will help add diversity to the island population. Because of the founder effect, the birds on the island may not have all the alleles on the mainland, and may benefit from gene flow from the mainland. The mainland birds can also benefit from the novel alleles developed on the island.
Bacteria are very interesting when it comes to gene flow. Unlike the rest of the organisms discussed in this article, bacteria are asexual. Without sexual reproduction, how do bacteria exchange genetic variation?
Bacteria, and other asexual organisms, sometimes transfer genetic variation through alternative processes. These processes, like horizontal gene transfer, allow DNA to pass between organisms without the need for sexual reproduction. In fact, much of the diversity present in life today was caused by these gene transfers millions of years ago. The chart below shows gene flow between the different domains of life.
A horizontal line shows any place which gene flow allowed genetic variation to pass between the various populations of organisms. It is through this horizontal gene flow that eukaryotes gained the pathways for both mitochondria and plastids such as chloroplasts.
1. Which of the following is NOT gene flow?
A. A bird flies to an island, and breeds with the birds there. He introduces new alleles.
B. Several hippos escape from the zoo and start a new population in New York City.
C. A tiger raised in captivity is released to the wild, where he reproduces with a wild tiger.
2. What is the difference between gene flow and migration?
A. Migration and gene flow describe the same process
B. Migration can occur without gene flow
C. Gene flow can occur without migration
3. Which of the following represents a BENEFIT of gene flow to a population?
A. Increased genetic diversity
B. Increased genetic load
C. Decreased adaptability
Study reveals domestic horse breed has third-lowest genetic diversity
Credit: CC0 Public Domain
A new study by Dr. Gus Cothran, professor emeritus at the Texas A&M School of Veterinary Medicine & Biomedical Sciences (CVM), has found that the Cleveland Bay (CB) horse breed has the third-lowest genetic variation level of domestic horses, ranking above only the notoriously inbred Friesian and Clydesdale breeds. This lack of genetic diversity puts the breed at risk for a variety of health conditions.
Genetic variation refers to the differences between different individuals' DNA codes. Populations where there is high genetic diversity will have a wider range of different traits and will be more stable, in part because disease traits will be more diluted. In populations with low genetic variation, many individuals will have the same traits and will be more vulnerable to disease.
The CB is the United Kingdom's oldest established horse breed and the only native warm-blood horse in the region. Used for recreational riding, driving, and equestrian competition, the CB is considered a critically endangered breed by the Livestock Conservancy.
Because maintaining genetic diversity within the breed is important to securing the horses' future, Cothran and his team worked to gain comprehensive genetic information about the breed to develop more effective conservation and breeding strategies.
In this study, published in Diversity, researchers genotyped hair from 90 different CB horses and analyzed their data for certain genetic markers. These samples were then compared to each other, as well as to samples from other horse breeds to establish the genetic diversity within the breed and between other breeds.
Both the heterozygosity and mean allele number for the breed were below average, indicating lower than average genetic diversity within the breed. This low genetic diversity should be seen as a red flag for possible health conditions.
"Low diversity is a marker for inbreeding, which can cause low fertility or any number of hereditary diseases or deformities," Cothran said. "With overall population numbers for the breed being so small, such problems could rapidly lead to the extinction of the breed."
The Cleveland Bay Horse Society of North America estimates that only around 900 CB purebreds exist globally. Such low population numbers mean the breed is considered to be critically rare.
This study also evaluated the diversity between the CB and other breeds using a majority-rule consensus tree, a type of analysis that shows an estimate of how different clades, or groups of organisms sharing a common ancestor, might fit together on their ancestral tree.
Cothran and his team's analysis found that the CB did not show a strong relationship with any other breeds, including other breeds within the same clade. Though this could be a result of the low genetic diversity within the breed, these data suggest that the CB is genetically unique from other breeds. These findings place emphasis on the importance of CB horses as a genetic resource.
"The CB is an unusual horse in that it is a fairly large sized horse but it is built like a riding horse rather than a draft horse," Cothran said, noting the uniqueness of the breed. "It frequently is bred to other breeds such as the Thoroughbred to create eventing or jumping horses, although this is a potential threat to maintaining diversity in the CB."
Cothran hopes his research will help to inform conservation efforts supporting the longevity of the CB breed, as well as inform breeders on how they can more responsibly further their horses' genetic lines.
"If any evidence of inbreeding is observed, breeders should report it to scientists for further analysis," Cothran said. "Efforts should be made to keep the numbers of CB horses as high as possible and to monitor breeding practices to minimize inbreeding and loss of variability."
"Domestic animals, including horses, are also at risk of declining populations, just like endangered species, but research can help determine which populations (breeds) are at risk and provide possible directions to help reduce risks or consequences," he said.
Though CB horses are currently at risk, Cothran remains optimistic that careful monitoring and management of the breed can preserve them as a cultural and genetic resource for years to come.
Drawing of the Tomarctus (credits: unknown)
On Earth for around 6.83 millions of years, Tomarctus inhabited most of the North American continent. Tomarctus had long tails for balance, sharp claws to catch preys while hunting and an appearance resembling our dogs of today.
As the giant mustelids and bear dogs started to disappear, Tomarctus further radiated to initiate a line of dogs which filled the hyena-like fruit eating and bone-crushing niches. We’ve been able to find specimens in California and up to the Montana/Canada line. We also found fossils as low as Panama. More information about the fossils discovered here.
Tomarctus had an incredibly strong bite force that exceeded what was required to kill a wild animal, the conclusion that streams is that Tomarctus’ diet was probably composed of a lot of scavenging. Carcasses and bones must have been a primary source of alimentation for Tomarctus as bone marrow by itself is one of the most nutritious food in the natural wild world. Plus, when kept in the bone under the right conditions, it can last for years after the death of the animal.
Since the Neolithic, humans have domesticated a large number of different plant species to create a reliable source of nutrition for themselves and their domestic animals. Crop plants comprise a large variety of species from diverse taxa that differ in habitat, growth habit, and life cycle, such as annual grasses, perennial trees, and medicinal herbs (Table 1, Fig. 1). However, world-wide crop production is dominated by a few major crops, such as wheat, rice, maize, potato, sugar cane, and soybean , that serve globally as staples for human and animal nutrition. By contrast, minor crops can be broadly defined as a non-homogeneous group comprising staple crops traditionally only of regional importance, such as quinoa, teff, and African rice or crops of world-wide importance but comparatively little contribution to human food consumption such as nuts or small fruits. Active research and breeding communities exist for almost every crop plant however, research into the molecular genetics of domestication has focused mainly on the major crops .
Time of domestication and genome size of domesticated plants.
Crop domestication has been studied for more than a century and benefited recently from technological innovations in genomics. Comparative analysis of population genomic data of large samples of current and past varieties of crops together with their wild progenitors provides insight into the domestication history of species [3, 4], for example, (i) when and where domestication occurred, (ii) how the domesticates spread to new habitats and which genetic changes accompanied this transition, and (iii) whether gene flow has occurred between the crops and wild relatives. A synthesis of archaeological and population genetic data evidence indicated that the initial stages of domestication in Southwest Asia should be considered a protracted process [5, 6] rather than a rapid evolution of cultivated plants as presumed previously [7,8,9]. The “democratization” of genomics [10, 11] has now opened new avenues for understanding the genetic consequences of domestication in a much wider range of species from different centers of origin such as Mesoamerica and Africa.
Much has been written on plant domestication. Recent review articles have focused on convergent phenotypic evolution , causative mutations affecting phenotypic variation [13, 14], the effect of gene functions on crop adaptation and selection mechanisms , the reduction of genetic diversity and the influence of epigenetic modifications , the impact of genomic methods in future crop improvement , the value of crop wild relatives , sequencing ancient plant DNA [19, 20], and general concepts in plant domestication research [21,22,23]. Here, we focus on the assembly of reference genome sequences for domesticated plants and their wild relatives surveying sequence diversity in large diversity panels and the application of novel approaches such as epigenomics, archaeogenetics, and genome editing to plant domestication research.
Species or Kinds?
Sometimes a creationist will say “there are no transitional species” or “animals do change, but one species never changes into another.” While I appreciate the sentiment, these claims are not true. In reality, new species do arise over time – a phenomenon we call speciation. Secularists sometimes claim that speciation is proof of Darwinian evolution, but this too is an error. All of these mistakes can be eliminated when we distinguish between species and kinds. Furthermore, when we study what the Bible says about kinds, and when we explore the scientific evidence pertaining to speciation, we see that the science confirms biblical creation and is inconsistent with evolution.
It is always important to define key terms in rational discussions. So, what exactly is a ‘species’ and how does the term differ from a ‘kind’? The biological definition of ‘species’ is a category of classification of biological organisms ranking below genus, that involves organisms that can generally interbreed and produce fertile offspring. So if we find that two animals can normally breed and produce offspring that are not sterile, then those two animals are classified as the same species.
Consider the various breeds of domestic dogs. These all belong to the same species because they can interbreed and produce fertile offspring. This does not necessarily mean that a male of any given breed can directly mate with a female of any other. Sometimes size differences would make this problematic. But through one or more intermediate breeds, the two are compatible. In other words, if dog A can breed with dog B, who can breed with C, who can breed with D (with each union producing fertile offspring), then D and A are the same species even if D and A cannot directly mate.
The offspring must also be able to reproduce if the parents are to be considered the same species. A female horse and male donkey can interbreed. But the resulting animal – the mule – is normally sterile. Therefore, the horse and donkey are classified as different species. Furthermore, such interbreeding must be typical. When held in captivity, coyotes and wolves can interbreed and produce fertile offspring. However, they are classified as different species because they do not generally interbreed in the wild.
Note that there is some ambiguity in the classification of species. Species are defined as organisms that generally interbreed and produce fertile offspring. But there is no precise quantitative guideline for what ‘generally’ means. Domestic dogs and wolves do sometimes interbreed – but do they generally interbreed? It depends on who you ask. Therefore, some biologists classify domestic dogs as a different species from wolves, whereas others classify them as the same species.
The word ‘kind’ can be used in all sorts of ways depending on context. However, when creation biologists use the word in the context of organisms, they have a very specific definition in mind. A kind is a group of organisms that are biologically related to each other – all organisms that share a common ancestor or can interbreed. All humans belong to the same kind because we are all related we are all descendants of Adam and Eve. Conversely, we are not the same kind as gorillas, because we do not share a common ancestor. Kinds are therefore distinguished by their different ancestors which the Lord originally created. We use this definition of ‘kind’ because we believe it to be consistent with the way the Bible uses the word as we will explore below.
In Genesis 1, we find that God created organisms “after their kind” or “after its kind.” This phrase (the exact wording of which will depend on the English translation) occurs ten times in the first chapter of Genesis. It is obviously very significant. It implies that organisms (specifically plants and animals) can be grouped into categories based on certain similar properties. The Lord’s choice to create organisms according to kinds is what makes our modern taxonomic system possible.
The kind is apparently the reproductive limit of an organism. In other words, a descendant will always be the same kind as its ancestor. We infer this from Genesis 6-8 in which God brought two of each kind of air-breathing land animal aboard the ark to preserve life (Genesis 6:19 Genesis 7:2-3). The Bible specifically tells us that the purpose of taking two of each kind is so that they can produce offspring (Genesis 7:3). (Conversely, if the kind were not the reproductive limit, then it would not be necessary to take two of each kind aboard the ark.)
Genesis 1 lists a few kinds of organisms specifically. Birds are a different kind from fish which are different from cattle. These groups of organisms are biologically unrelated they were originally supernaturally created by God, and their modern descendants do not share a common ancestor with other groups and cannot interbreed. Likewise, Adam was a special creation of God. All people today are descended from him. Humans are therefore not the same kind as any animal.
But Genesis doesn’t list, specifically, all the separate created kinds. This prompts us to ask questions like, “do lions, tigers, and domestic cats belong to the same kind, or are they descended from separate, supernaturally created ancestors?” The study of the original created kinds is called baraminology – a word derived from the Hebrew words for “created” (bara) and “kind” (min). Studies in this field have shown that lions, tigers, and house cats do in fact belong to the same kind. They are all descended from just two cats that were aboard Noah’s ark. But how do we know this?
It follows logically that two organisms can interbreed only if they are the same kind. Consider the parent organisms: A and B. They produce offspring C. Since organisms reproduce after their kind, C must be the same kind as A, and C must be the same kind as B. Therefore, A and B must be the same kind (by the transitive property). This gives us a test by which we can experimentally demonstrate whether two organisms belong to the same kind. Interbreeding studies are crucial to the field of baraminology. By such tests, we know that horses, donkeys, and mules are all part of the same kind, even though they are classified as separated species.
So, if two organisms can interbreed and produce offspring (regardless of whether the offspring are fertile), then the two organisms are the same kind. Some persons might be tempted to think that this implies that animals that cannot interbreed must be different kinds. But that is an error in reasoning. Sometimes, two organisms can be the same kind and yet are not able to interbreed for one of several reasons. After all, some husbands and wives are unable to have children, but this doesn’t mean that they are not the same kind!
While we can prove that two organisms are the same kind (if they interbreed), we cannot definitively prove that two organisms are different kinds merely on the basis that they fail to interbreed. To demonstrate that two organisms are separate kinds, we need other information. We need evidence that their ancestors are not biologically related. Studies in genetics can be very helpful in such determinations. Fossil evidence can also shed light on the issue. The field of baraminology is an exciting and rapidly developing field in creation science.
In general, a ‘species’ is not the same thing as a ‘kind.’ We have already seen some examples of this. A horse and donkey are the same kind because they can interbreed. But they are classified as different species. Studies in baraminology have demonstrated that domestic cats and tigers belong to the same kind. Yet, they are classified as different species. The biblical teaching is that organisms reproduce organisms of the same kind but not necessarily the same species. We would expect on the basis of Scripture that all organisms today are the same kinds as their original, supernaturally-created ancestors.
We would expect, therefore, that we will not find transitional forms between the major categories of organisms – those that belong to separate kinds. Science confirms this. Cats give rise to cats and nothing else. Dogs beget dogs and nothing else. We do observe a great deal of variation within the dog kind. Many breeds exist today that did not exist when God first created dogs. But we never observe a dog reproduce anything other than a dog.
Paleontology confirms that this has always been the case. We find fossil evidence of variation within kinds of organisms as creation-based models predict. But we do not find compelling evidence of transitions between the major categories of organisms (as evolutionary models would predict) – such as a sequence of gradual transitions from invertebrates to vertebrates. Considering that the hypothetical transformation from invertebrate to vertebrate would involve a complete and revolutionary inversion of structure, presumably such a process would be lengthy and would leave behind billions of transitions. Where are they? This is indeed the case with all major categories of organisms.
Of course, there are occasional claims of a transition between some major categories. But these are nearly always disputed even by the evolutionists themselves. In most cases, additional information reveals that such disputed specimens are fully within a given kind. We have seen so many examples of this, such as archaeopteryx, Nebraska man, Coelacanth, and so on. Clearly, the fossil evidence is consistent with the creation worldview, and challenges Darwinian evolution.
Most of the “evidence” that evolutionists like to present in defense of their position involves observations of changes within a kind. You will find textbook examples of proof of evolution that involves a horse giving rise to… a horse, or a camel giving rise to a new variety of camel. But they remain the same kind. Variation within a kind is biblical.
In some cases, variations within a kind of organism lead to groups that are not able to interbreed with each other, and are therefore classified as different species. However, this is perfectly compatible with biblical creation. The evolutionist, perhaps inadvertently, mischaracterizes the creationist’s claim. “Creationists say that organisms always remain the same species, but we have observed the contrary.” No, creationists embrace speciation. But the organisms always remain the same kind.
The Taxonomic Tree
The creation scientist Carolus Linnaeus is considered the father of modern taxonomy. He recognized that God is a God of order and has created a wide variety of organisms with both similarities and differences such that they can be arranged into a logical hierarchy. With slight modification, we still use the Linnaean system today. Organisms are classified from the broadest categories down to the most specific using the following hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
We have already seen that the biblical kind is not necessarily the same as a species. This may prompt us to ask, “what taxonomic level represents the biblical kind?” Creation biologists have found that the family level is most often aligned with the biblical kind. However, there is no reason to expect a one-to-one correspondence between the modern taxonomic system and the biblical definition of kinds since they use different criteria for classification. So, while the family level typically corresponds to the biblical kind, in some organisms, the kind is at the species or genus level. In some other cases, it may be at the order level. But the family level is typical.
One way in which critics sometimes mischaracterize the biblical position concerns the number of animals aboard Noah’s ark. The critic may claim that Noah’s ark is a silly myth because it could not possibly hold two of each species of animal. But the Bible doesn’t claim that two of each species were aboard the ark: only two of each kind of air-breathing land animal, which is a much smaller number. Since the family level more typically corresponds to the biblical kind, this is the more relevant taxonomic level by which to estimate the number of animals. Some apologists even use the genus level in order to give a generous upper limit in their estimates. One such estimate indicates a maximum of 16,000 animals aboard Noah’s ark (with the true number likely being considerably smaller). Since the ark had a volume of over 1.5 million cubic feet, space would not have been a problem.
Since there were only two of each kind of animal on board Noah’s ark (with seven of the “clean” kinds of which there are relatively few), and since today there are often multiple species within a given kind, it follows that new species have formed since the global flood. As one example, consider the horse kind. As already discussed, horses, donkeys, and mules are all part of the horse kind, even though they are separate species. Zebras also belong to the horse kind since they can interbreed with horses. All of these animals belong to the taxonomic family Equidae. Yet, there were only two Equids aboard Noah’s ark. Modern horses, donkeys, and zebras are all descended from those two horse-kind ancestors. How then did separate species come about after the flood?
God placed a remarkable amount of potential for variety in the DNA of each kind of animal. Such variations are possible because each animal has two sets of DNA, and it is the combination of instructions on the two sets that determine an organism’s traits. Thus, animals can contain information for traits that they do not express because they do not have the right combination but their offspring might. Placed in the DNA of the two Equids aboard Noah’s ark was the information necessary to produce zebras, donkeys, mules, and all the varieties of modern horse. These ancestral Equids probably did not look exactly like any modern equid, but had characteristics common to many of them.
As the animals departed Noah’s ark and multiplied, each descendent received only half of the genetic information from each parent, which leads to the possibility of new combinations, and hence traits that were encoded but not expressed in their parents. Under the right conditions, some of these genetic combinations can become fixed in a population such that all the population has a certain trait in common – like zebras having stripes. A different group of organisms of the same kind may inherent different genes, and the two populations begin to appear noticeably different in a process called genetic drift. In some cases, the drift can lead to reproductive incompatibility between the groups, in which case biologists will classify them as distinct species. For additional details on how this occurs, see Dr. Nathaniel Jeanson’s writings on this topic, including a helpful introductory article here, and a more detailed paper here.
The point here is that speciation has absolutely nothing to do with evolution in the Darwinian sense because the animals always remain exactly the same kind. No new information has been added to the DNA, and therefore such a process could never turn one kind of organism into another kind, since different kinds have different genetic information. Yes, we have seen the formation of new breeds of dogs – but they are still dogs. And they will never be anything but dogs. Yes, modern tigers and house cats are both descended from the same two cats aboard Noah’s ark. But they remain cats. They could never become anything else because they lack the genetic information to do so.
Scientifically, the speciation we observe in organisms is consistent with the predictions of biblical creation and not with Darwinian evolution. Speciation, genetic drift, natural selection, and mutations are all real phenomena. And they are all examples of variation within a kind. None of these processes has even been observed to produce a new kind of organism – something that is fundamentally different from its ancestor. Nor could these processes ever do such a thing even in principle. This is because none of these processes can add brand new information to the genome of any organism. But the addition of new genetic information would be essential in order for Darwinian evolution to be possible – even in principle. As always, science confirms creation.
 This definition pertains only to sexually reproducing organisms. Classification of asexual organisms like bacteria, though interesting, is beyond the scope of this article.
 In some cases, a female mule can produce offspring when mated with a horse or donkey. However, they cannot produce offspring from a male mule.
 It is the fallacy of the commutation of conditionals. Namely, the statement “If p then q” does not imply “if q then p.”