From which ancestor species did humans inherit orgasm?

From what ancestors did humans inherit orgasm?

Do fish experience orgasm?

Are the male and female orgasm the homologues that can be traced to the time when there was no difference in sex between individuals (as in fish) or developed independently?

Let's assume that pleasure from sexual intercourse might be indicative of some sort of orgasm. Then this would suggest that any evidence of autoerotic behaviour would point to the existence of orgasm, or certanly physical pleasure.

I found this quotation on the Wikipedia page for Animal sexual behavior, amongst a lot of information about mammals :

Many birds masturbate by mounting and copulating with tufts of grass, leaves or mounds of earth…

apparently from Bruce Bagemihl: Biological Exuberance: Animal Homosexuality and Natural Diversity. St. Martin's Press, 1999. ISBN 0-312-19239-8

If this is taken to imply that the last common ancestor of birds and mammals experienced this pleasure then we have got fairly deep into evolutionary history, although not as far as fish.

Timeline of human evolution

The timeline of human evolution outlines the major events in the evolutionary lineage of the modern human species, Homo sapiens, throughout the history of life, beginning some 4.2 billion years ago down to recent evolution within H. sapiens during and since the Last Glacial Period.

It includes brief explanations of the various taxonomic ranks in the human lineage. The timeline reflects the mainstream views in modern taxonomy, based on the principle of phylogenetic nomenclature in cases of open questions with no clear consensus, the main competing possibilities are briefly outlined.

The Evolutionary Reason Why Women Orgasm

Why do women have orgasms? The question has long confused scientists after all, orgasm isn’t necessary for conception, and women can orgasm even when they’re not having reproductive sex. Now, a new study brings an interesting new theory into the mix: Women’s orgasms could be a vestige left over by evolution itself.

In a literature review recently published in the Journal of Evolutionary Zoology, a pair of developmental evolutionary specialists posit that as the female reproductive system evolved, so did the role of the orgasm. Once necessary for conception, female orgasms now appear to be a bonus for human intercourse. But similar to vestigial organs like tonsils or appendix, the orgasm remained. 

The secret lies in ovulation, the mechanism that causes ovaries to discharge eggs for reproduction. In some species, like cats and rabbits, physical stimulation is needed to prompt the egg to be released—a phenomenon called induced ovulation. But in humans, ovulation happens spontaneously (without stimulation), often on a regular schedule. And not only can human females come to orgasm without penetration, but a recent survey of more than 1,000 women suggests that many—only 61.6 percent of heterosexual women—do not orgasm during intercourse at all. Nor is female orgasm associated with a higher number of offspring in humans.

This has long confused scientists, who in the past came up with two hypotheses. Some think that women do need orgasms to reproduce, but researchers have not yet figured out why. Others consider orgasms to be happy accidents associated with the clitoris, the organ responsible for sexual stimulation that is sometimes thought of as the female version of the male penis.

The authors of the new study, however, don't think the human female orgasm is accidental or related to male evolution. Rather, they trace it to ovulation. “By just reading the literature, we found that there is an endocrine surge just following the female orgasm in humans,” the study’s author, Mihaela Pavličev of Cincinnati Children’s Hospital Medical Center, told

This surge of hormones, including prolactin and oxytocin, is similar to other surges observed in animals like rats, who need these natural chemicals to tell their body to ovulate. The surge can also help eggs implant in species like rodents. Some studies even suggest that humans have similar connections between egg implantation with post-orgasmic hormone shifts.

That hormone-orgasm connection in both humans and induced ovulators led Pavličev to believe that they were once connected long before humans became a species. She speculates that spontaneous ovulation likely evolved in the last common ancestor of primates and rodents. Eventually, however, they must have evolved into so-called spontaneous ovulators, but the hormonal reactions associated with orgasms remained.

This concept is supported by a fascinating finding: the development of spontaneous ovulation parallels a shift in clitoris position. Based on the evolutionary ties between a range of animals, the researches found that later-evolving creatures, humans included, ovulated spontaneously. And this change coincided with the clitoris shifting northward, further away from the vagina. 

“At that point,” says Pavličev, “the clitoris lost its function for reproduction.”

Pavličev’s work raises other, even more fascinating questions. Why did humans start ovulating spontaneously in the first place? Which came first: spontaneous ovulation or induced ovulation? And what evolutionary pressures sparked these changes in women?

Pavličev is particularly interested in the connection between female orgasms and their apparent association with egg implantation. If there really is an evolutionary case for that adaptation, she says—or if humans simply haven’t evolved past the orgasm-implantation connection yet—further research could one day lead to changes in recommendations for women trying to get pregnant through in vitro fertilization.

Perhaps the most intriguing aspect of Pavličev’s study is the implication that there is an evolutionary reason women don’t always orgasm. “It’s not that there’s anything wrong,” she says. “It’s just how our anatomy is.” Translation: Women who don’t achieve orgasm during sexual intercourse are not defective—just highly evolved.

Editor's Note, August 1, 2016: This article has been changed to clarify that spontaneous ovulation likely evolved in mammals long before humans split off as a species.

Misconceptions and how to correctly read a phylogenetic tree

Trees can be confusing to read. A common mistake is to read the tips of the trees and think their order has meaning. In the tree in Figure 1 above, the closest relative to species C is not species B. Both A and B are equally distant from, or related to, species C. In fact, switching the labels of species A and B would result in a topologically equivalent tree. It is the order of branching along the time axis that matters. The illustration below shows that rotating the branches around the nodes, much like a hanging mobile, does not affect the structure of the tree:

Hanging bird mobile by Charlie Harper

It can also be difficult to recognize how the trees model evolutionary relationships. One thing to remember is that any tree represents a minuscule subset of species from the full tree of life.

A tree of 5 species (A, Q, D, X, S) with evolutionary time shown in millions of years ago (Mya). The purple dotted line represents an evolutionary lineage of a currently living species not represented in the 5-species tree. The fine dotted lines indicate a few evolutionary lineages that have gone extinct note that they do not extend vertically to the present day. Image credit: Diagram is original work of Jung Choi.

Given just the 5-species tree (ignoring the dotted branches), it is tempting to think that taxon S is the most “primitive,” or most like the common ancestor represented by the root node, because there are no additional nodes between S and the root. However, there were undoubtedly many branches off that lineage during the course of evolution, most leading to extinct species (99% of all species are thought to have gone extinct), and many to living species (like the purple dotted line) that are just not shown in the tree. What matters, then, is the total distance along the time axis (vertical axis, in this tree). The time axis indicates that species S evolved for 5 million years, the same length of time as any of the other 4 species. As the tree is drawn, with the time axis vertical, the horizontal axis has no meaning, and serves only to separate the species and their lineages for the viewer’s benefit. So, none of the currently living species are any more “primitive” nor any more “advanced” than any of the others they have all evolved for the same length of time from their most recent common ancestor.

The time axis also allows us to measure evolutionary distances quantitatively. The distance between A and Q is 4 million years (A evolved for 2 million years since they split, and Q also evolved independently of A for 2 million years after the split). The distance between A and D is 6 million years, and they split from their common ancestor 3 million years ago.

Phylogenetic trees can have different forms—they may be oriented sideways, inverted (most recent at bottom), or the branches may be curved, or the tree may be radial (oldest at the center). Regardless of how the tree is drawn, the branching patterns all convey the same information: evolutionary ancestry and patterns of divergence.

This video does a great job of explaining how to interpret species relatedness using trees, including describing some of the common incorrect ways to read trees:

Did Stoeckel and Thaler conclude that “90% of animal species appeared at same time as humans”?

The answer is No. Here is the relevant quote from the published paper:

the extant population, no matter what its current size or similarity to fossils of any age, has expanded from mitochondrial uniformity within the past 200,000 years.

In other words, the genetic diversity observed in mitochondrial genomes of most species alive today can be attributed to the accumulation of mutations from an ancestral genome within the past 200,000 years.

Their conclusions are interesting (and to some extent unexpected) but they are not shocking, nor do they defy evolutionary theory. To see why, let’s unpack what the authors have claimed. First, it is important to note that the authors never claim that most “species” came into existence within the past 200,000 years. Rather, what has come into existence within that time frame is the genetic variation observed in one gene in the mitochondrial genome. By tracing the mutations in that one gene, we can trace the origin of the gene back to the last common female ancestor of all living members of a certain species (the so-called “mitochondrial Eve”). But this discovery, at best, tells us the minimum age of the species. It tells us little to nothing about the maximum age of a species.

To understand the difference between “minimum” and “maximum” age for a species, consider the cheetah (Acinonyx jubatu). The cheetah has remarkably little genetic variation in both its nuclear and mitochondrial genome. Using the same methods employed by Stoeckle and Thaler, this species appears to be no more than 12,000 years old (unlike 90% of other mammal species, which are hundreds of thousands of years old). However, the fossil record of the cheetah species extends back several hundred thousand years. These two observations are not contradictory. The species is very old, but its mitochondrial DNA appears quite young. 12,000 years ago, at the end of the last Ice Age, cheetahs were migrating—presumably as a result of large climatic changes—from their native Asian point of origin to their present home in Africa. It appears this move resulted in a significant population bottleneck, wherein only a small number of cheetahs made it to Africa the ancestors of the present population. All other cheetahs in Asia—along with their genetic diversity—went extinct. The mitochondrial genetic “clock” was reset by the genetic bottleneck. Examining mitochondrial DNA variation alone, we can only predict when the most recent bottleneck occurred for the mtDNA lineages found in cheetahs. We cannot predict the age of the cheetahs as a species.

The scenario above can be played out for most species. An examination of the mitochondrial genome of any species will only tell us when the common ancestor of all modern members of this species existed, which will almost invariably occur after the evolutionary origin of the species. What Stoeckle and Thaler have potentially discovered, by examining the variation of a single gene in the mtDNA, is that most species experienced a mitochondrial genetic “bottleneck” between 100 and 200 thousand years ago.

How might this bottleneck have occured? Stoeckle and others have provided several hypotheses. One scenario invokes the effects of significant ice ages during this time period. Such dramatic climate change has the effect of causing mass migrations, leading to rapid contractions and expansions of populations. In such times, variation in mitochondrial lineages is squeezed out of many species, even as they may retain a considerable amount of variation in their main (nuclear) genomes. In this respect, the results reported in this paper are not particularly surprising, because they fit well with what we already know about this phase of natural history.

In summary: Do Stoeckle and Thaler’s findings undermine evolutionary theory and prove that most animals were created recently? Definitely not

Testing Common Ancestry: It’s All About the Mutations

One question that comes up frequently about evolutionary biology is whether it really boils down to speculation and assumption. Most of evolution happened in the distant past, after all. We claim that humans and chimpanzees descended from a single ancestral species over millions of years, for example, but none of us was there to observe that process. To a scientist, though, the right question is not, “Were you there?” but rather “What if?” What if we do share a common ancestor–what should we see? How can we test a hypothesis about the ancient past?

One way we can test for shared ancestry with chimpanzees is to look at the genetic differences between the two species. If shared ancestry is true, these differences result from lots of mutations that have accumulated in the two lineages over millions of years. That means they should look like mutations. On the other hand, if humans and chimpanzees appeared by special creation, we would not expect their genetic differences to bear the distinctive signature of descent from a common ancestor.

What do mutations look like, then? DNA consists of a long string of four chemical bases, which we usually call A, C, G and T (for adenine, cytosine, guanine, and thymine). A mutation is any change to that string. In the simplest mutations, one base replaces another when DNA is incorrectly copied or repaired, e.g., a C at a particular site in a chromosome is replaced by a T, which is then passed onto offspring. These substitutions do not all happen at the same rate some occur more often than others. For example, C and T are chemically similar to one another, as are A and G, and chemically similar bases are more likely to be mistaken for one another when DNA is being copied. Thus, we find an A becoming a G more often than a T.

This means that as they accumulate, mutations create a characteristic pattern of more and less common changes. It is that pattern that we can look for to see if genetic differences were caused by mutations. To determine exactly what the pattern is, we can just look at genetic differences between individual humans, because these represent mutations that occurred since those two people last shared a common ancestor. 1 Twelve possible substitutions can occur (A→C, A→G, A→T, C→G, C→T, C→A, etc.), but if we are only looking at differences between two copies of DNA, we cannot distinguish some of the substitutions. For example, if I have an A and you have a C at a specific location, unless we have our ancestors’ DNA to look at, we cannot tell whether it was originally an A that mutated into a C in your DNA, or whether it was originally a C that mutated into an A in my DNA. Thus we have to lump the two possibilities together and just count the number of places one of us has an A and the other a C. An additional complication: our DNA has two complementary strands, and we do not know which strand a mutation occurred on. Perhaps it was not actually our ancestor’s A that turned into your C. On the other strand of his DNA, the A was matched by a T (the complementary base to A) perhaps that was the base that actually mutated. The bottom line is that there turn out to be four distinguishable classes of substitution: (1) What we call “transitions” occur between the chemically similar bases A and G, or C and T these changes happen more often than the others. (2) A difference between A and T (which I will label A↔T). (3) A difference between G and C (G↔C). (4) A difference between either A and C or G and T (A↔C /G↔T).

Now we are in a position to test whether genetic differences between humans and chimps look like mutations. To determine the pattern for mutations, I calculated the rates for the four classes using human diversity data (which is available online). Then I calculated the pattern seen when comparing human and chimpanzee DNA, also using public data. The first graph is the distribution for humans. As expected, transitions are the most common. That pattern is our signature–the sign that mutation has been at work.

The second graph is the same distribution for differences between human and chimpanzee DNA. The overall rates are different–there are 12 times as many differences between human and chimpanzee DNA as there are between DNA from two humans (note the different scale on the y-axis of the graphs)–but the pattern is almost identical.

Remember my opening question: if humans and chimpanzees shared a common ancestor, what should we see? What we should see is what we do see: genetic differences between the species that look exactly like they were produced by mutations. In scientific terms, I had a hypothesis about the distant past, I tested the hypothesis with data, and it passed the test.

Now, when scientists point to similarities between human and chimpanzee DNA, critics sometimes object that similarities don’t really prove anything, since they could be explained equally well by a common design plan: the creator might well use similar stretches of DNA to carry out similar tasks in separately created species. That objection does not apply here, though, because we are looking at the differences between species. I cannot think of any reason why a designer should choose to make the differences look exactly like they were the result of lots of mutations. The obvious conclusion is that things are what they seem: humans and chimpanzees differ genetically in just this pattern because they have diverged from a single common ancestor.

We can make the same comparison for other pairs of species, all of which are thought to have common ancestry. Here is the breakdown for the differences between humans and some other primates, including apes and Old World monkeys, and some nonhuman comparisons as well. (In order to display the results on a single chart, I have rescaled the other distributions to have the same total rate as the human-human comparison.)

Everywhere we look, the pattern is the same. That’s true even though the overall rate of genetic difference ranges from less than 1% (human vs chimpanzee) to more than 5% (humans vs baboons). The genetic differences between species always look like mutations.

I also took a look at some species that are less similar to humans—mostly out of curiosity, since I was not sure exactly what to expect. Mutation patterns vary subtly even between human populations, probably because of small differences in some of the hundreds of proteins responsible for DNA replication and repair such variations are likely to become more pronounced as we look at more distantly related species. One thing I did expect, though, was still to see more transitions than other substitutions since that difference is rooted in the basic chemical similarity of some bases. The set shown here includes cats compared to dogs, cows compared to dolphins, a comparison between a couple of species of finch, and even two species of pufferfish.

There is one additional test we can make. When I made the plots above, I excluded a small part (approximately 1%) fraction of DNA because it is known to mutate much faster than the rest. The higher mutation rate occurs when a C is immediately followed by a G in the DNA sequence, a pairing known as a “CpG” (“p” stands for the phosphate group that links adjacent DNA bases). A wide range of animal species chemically modify the C when it occurs in a CpG. This has an interesting effect: modified C can spontaneously turn into a T. As a result, mutation is much more common at CpGs than for other DNA, especially for C mutating into T.

We can therefore define a more comprehensive signature of mutation by measuring the rates for the same categories as before, but now at CpG sites. (This adds three new categories rather than four, since A↔T cannot occur at a CpG site.) This signature is shown in the first plot, which once again comes from human diversity data. The second figure shows the same categories for human compared to chimpanzee DNA. Once again, the two line up almost perfectly. Even at these special sites, differences between species look exactly like they were caused by mutations.

This kind of thing is the reason that most geneticists have no doubt about common descent: it makes sense of everything we see. Even better, it makes predictions. When I started to put together this post, the only data I had seen was for humans and chimpanzees, but I still had a very good idea what I would see when I looked at other primates.

Of course, none of this says anything at all about God’s role in human origins, nor does it rule out miraculous intervention. But it does provide strong evidence that we share ancestry with other species.

Notes & References

1. Since we are comparing common descent with the special creation of a single ancestral couple, we also have to consider the possibility that some of the genetic variation that we inherit was already present in Adam and Eve and not the result of subsequent mutation. To avoid this possibility, I looked only at genetic variants that were seen in roughly 1% of the modern population any variant we inherit from Adam and Eve would be shared by a larger fraction of the population.

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Ancient human relative could walk on two feet, use tools and swing in trees

An extinct human relative found in a dark, cramped cave in South Africa was adept at both swinging in the trees and walking on two feet, making it unique among our known ancient forerunners, scientists say.

A fresh analysis of hand and foot bones of Homo naledi, the latest addition to the human genus, shows that while the creature’s foot resembles that of modern humans, its fingers are curved, in an unmistakable sign of arboreal living.

Researchers unveiled Homo naledi last month after discovering the remains of 15 individuals in the Rising star cave near Johannesburg. The bones have yet to be dated, making it impossible for scientists to work out where the species fits in the story of human evolution.

Homo naledi was small and slender with a tiny brain compared with modern humans. The adult males stood about 5ft, with the females a little shorter. From the first excavations, the hand and feet bones looked unusual, bearing the hallmarks of a creature that made and used tools, was an accomplished climber, but spent most of its time walking upright.

Scientists have now performed more detailed studies on a near complete right hand and more than a hundred pieces of foot bone and, in two papers published in the journal Nature Communications, reveal how extraordinary the remains are.

The wrist and thumb show that Homo naledi had a powerful grasp and was well-equipped for making and using stone tools. But these more modern features sit alongside highly curved fingers, a signature of early human ancestors that lived in the trees.

“That combination was really quite surprising,” said Tracy Kivell, who studied the bones at the University of Kent. “It shows you can have a hand that is quite specialised for manipulation and tool use in a species that is still using its hands for climbing, and moving around in the trees or on rocks.”

The team has yet to recover any stone implements near the remains of Homo naledi, but if the species did smash rocks together to make cutting and scraping tools, it did so without much in the way of brain power.

Homo naledi, discovered in South Africa, could combine land walking and tree swinging. Photograph: Mark Thiessen/National Geographi/PA

“It shows we have a much greater diversity in the fossils of human ancestors than we thought possible,” said Kivell.

Another team led by William Harcourt-Smith at the City University of New York analysed 107 pieces of Homo naledi foot bone. Writing in the journal, they describe how the foot is similar to those of Neanderthals and modern humans, but with a number of subtle differences. The toe bones are slightly curved, which may have helped Homo naledi a little when it took to the trees. The arch of the foot is low, or absent entirely, making Homo naledi flat-footed.

“It was unequivocally spending more time walking upright than not,” said Harcourt-Smith. “But you can imagine it spending time in the trees to gather fruit, or perhaps nesting in trees, or going there when there are predators around.” The curved toe bones are thought to be skeletal adaptations that Homo naledi inherited from its more arboreal ancestors and had not lost.

Until the bones can be dated, one of the major questions surrounding Homo naledi will remain: did the species emerge millions of years ago and live in successful isolation, perhaps even overlapping with modern humans? That is one possibility. Another is that Homo naledi is an evolutionary side-branch, a sister species of a known human ancestor, such as Homo erectus.

“You can imagine this lineage emerging early on, close to the origins of the Homo genus, and hanging on for a long period of time,” said Harcourt-Smith. “But that’s speculation. Evolution is messy. There is lots of experimentation going on, and lots of dead ends.”

Parallel evolution

Given a particular trait that occurs in each of two lineages descended from a specified ancestor, it is possible in theory to define parallel and convergent evolutionary trends strictly, and distinguish them clearly from one another. [2] However the criteria for defining convergent as opposed to parallel evolution often are unclear in practice, so that arbitrary diagnosis is common in some cases.

When two species are similar in a particular character, evolution is defined as parallel if the ancestors shared that similarity if they did not, the evolution of that character in those species is defined as convergent. However, this distinction is not clear-cut. For one thing, the stated conditions are partly a matter of degree all organisms share more or less recent common ancestors. In evolutionary biology the question of how far back to look for similar ancestors, and how similar those ancestors need to be for one to consider parallel evolution to have taken place, cannot always be resolved. Some scientists accordingly have argued that parallel evolution and convergent evolution are more or less indistinguishable. [3] Others insist that in practice we should not shy away from the gray area because many important distinctions between parallel and convergent evolution remain. [4]

When the ancestral forms are unspecified or unknown, or the range of traits considered is not clearly specified, the distinction between parallel and convergent evolution becomes more subjective. For instance, Richard Dawkins in The Blind Watchmaker describes the striking similarity between placental and marsupial forms as the outcome of convergent evolution, because mammals on their respective ancestral continents had a long evolutionary history before the extinction of the dinosaurs. That period of separation would have permitted the accumulation of many relevant differences. Stephen Jay Gould differed he described some of the same examples as having started from the common ancestor of all marsupials and placentals, and hence amounting to parallel evolution. And certainly, whenever similarities can be described in concept as having evolved from a common attribute deriving from a single remote ancestral line, that legitimately may be regarded as parallel evolution.

In contrast, where quite different structures clearly have been co-opted to a similar form and function, one must necessarily regard the evolution as convergent. For example, consider Mixotricha paradoxa, a eukaryotic microbe which has assembled a system of rows of apparent cilia and basal bodies closely resembling the system in ciliates. However, on inspection it turns out that in Mixotricha paradoxa, what appear to be cilia actually are smaller symbiont microorganisms there is no question of parallel evolution in such a case. Again, the differently oriented tails of fish and whales derived at vastly different times from radically different ancestors and any similarity in the resultant descendants must therefore have evolved convergently any case in which lineages do not evolve together at the same time in the same ecospace might be described as convergent evolution at some point in time.

The definition of a trait is crucial in deciding whether a change is seen as divergent, or as parallel or convergent. For example, the evolution of the sesamoid "thumb" of the giant panda certainly is not parallel to that of the thumbs of primates, particularly hominins, and it also differs morphologically from primate thumbs, but from some points of view it might be regarded as convergent in function and appearance.

Again, in the image above, note that since serine and threonine possess similar structures with an alcohol side chain, the example marked "divergent" would be termed "parallel" if the amino acids were grouped by similarity instead of being considered individually. As another example, if genes in two species independently become restricted to the same region of the animals through regulation by a certain transcription factor, this may be described as a case of parallel evolution - but examination of the actual DNA sequence will probably show only divergent changes in individual basepair positions, since a new transcription factor binding site can be added in a wide range of places within the gene with similar effect.

A similar situation occurs considering the homology of morphological structures. For example, many insects possess two pairs of flying wings. In beetles, the first pair of wings is hardened into elytra, wing covers with little role in flight, while in flies the second pair of wings is condensed into small halteres used for balance. If the two pairs of wings are considered as interchangeable, homologous structures, this may be described as a parallel reduction in the number of wings, but otherwise the two changes are each divergent changes in one pair of wings.

Similar to convergent evolution, evolutionary relay describes how independent species acquire similar characteristics through their evolution in similar ecosystems, but not at the same time, such as the dorsal fins of sharks, cetaceans and ichthyosaurs.

Examples Edit

  • Colouration that serves as a warning to predators and for mating displays has evolved in many different species.
  • In the plant kingdom, the most familiar examples of parallel evolution are the forms of leaves, where very similar patterns have appeared again and again in separate genera and families.
  • In Arabidopsis thaliana it has been suggested that populations adapt to local climate through parallel evolution [5]
  • In butterflies, many close similarities are found in the patterns of wing colouration, both within and among families. and New Worldporcupines shared a common ancestor, both evolved strikingly similar quill structures this is also an example of convergent evolution as similar structures evolved in hedgehogs, echidnas and tenrecs.
  • Some extinct archosaurs evolved an upright posture and likely were warm-blooded. These two characteristics are also found in most mammals. Modern crocodiles have a four chambered heart and a crurotarsal, the latter being also a characteristic of therian mammals.
  • The extinct pterosaurs and the birds both evolved wings as well as a distinct beak, but not from a recent common ancestor. has evolved independently in sharks, some amphibians and amniotes.
  • The patagium is a fleshy membrane that is found in gliding mammals such as flying lemurs, flying squirrels, sugar gliders and the extinct Volaticotherium. These mammals all acquired the patagium independently. evolved a body plan similar to proboscideans.
  • The extinct South American litoptern ungulate Thoatherium had legs that are difficult to distinguish from those of horses.
  • The eye of the octopus has the same complicated structure as the human eye. As a result, it is often substituted in studies of the eye when using a human eye would be inappropriate. As the two species diverged at the time animals evolved into vertebrates and invertebrates this is extraordinary.
  • Certain arboreal frog species, 'flying' frogs, in both Old World families and New World families have developed the ability of gliding flight. They have "enlarged hands and feet, full webbing between all fingers and toes, lateral skin flaps on the arms and legs, and reduced weight per snout-vent length". [6]
  • The treeplant habit has evolved separately in unrelated classes of plants.

Parallel evolution between marsupials and placentals Edit

A number of examples of parallel evolution are provided by the two main branches of the mammals, the placentals and marsupials, which have followed independent evolutionary pathways following the break-up of land-masses such as Gondwanaland roughly 100 million years ago. In South America, marsupials and placentals shared the ecosystem (before the Great American Interchange) in Australia, marsupials prevailed and in the Old World and North America the placentals won out. However, in all these localities mammals were small and filled only limited places in the ecosystem until the mass extinction of dinosaurs sixty-five million years ago. At this time, mammals on all three landmasses began to take on a much wider variety of forms and roles. While some forms were unique to each environment, surprisingly similar animals have often emerged in two or three of the separated continents. Examples of these include the placental sabre-toothed cats (Machairodontinae) and the South American marsupial sabre-tooth (Thylacosmilus) the Tasmanian wolf and the European wolf likewise marsupial and placental moles, flying squirrels, and (arguably) mice.


Vestigial features may take various forms for example, they may be patterns of behavior, anatomical structures, or biochemical processes. Like most other physical features, however functional, vestigial features in a given species may successively appear, develop, and persist or disappear at various stages within the life cycle of the organism, ranging from early embryonic development to late adulthood.

Vestigiality, biologically speaking, refers to organisms retaining organs that have seemingly lost their original function. The issue is controversial and not without dispute nonetheless, vestigial organs are common evolutionary knowledge. [2] In addition, the term vestigiality is useful in referring to many genetically determined features, either morphological, behavioral, or physiological in any such context, however, it need not follow that a vestigial feature must be completely useless. A classic example at the level of gross anatomy is the human vermiform appendix—though vestigial in the sense of retaining no significant digestive function, the appendix still has immunological roles and is useful in maintaining gut flora.

Similar concepts apply at the molecular level—some nucleic acid sequences in eukaryotic genomes have no known biological function some of them may be "junk DNA", but it is a difficult matter to demonstrate that a particular sequence in a particular region of a given genome is truly nonfunctional. The simple fact that it is noncoding DNA does not establish that it is functionless. Furthermore, even if an extant DNA sequence is functionless, it does not follow that it has descended from an ancestral sequence of functional DNA. Logically such DNA would not be vestigial in the sense of being the vestige of a functional structure. In contrast pseudogenes have lost their protein-coding ability or are otherwise no longer expressed in the cell. Whether they have any extant function or not, they have lost their former function and in that sense, they do fit the definition of vestigiality.

Vestigial structures are often called vestigial organs, although many of them are not actually organs. Such vestigial structures typically are degenerate, atrophied, or rudimentary, [3] and tend to be much more variable than homologous non-vestigial parts. Although structures commonly regarded "vestigial" may have lost some or all of the functional roles that they had played in ancestral organisms, such structures may retain lesser functions or may have become adapted to new roles in extant populations. [4]

It is important to avoid confusion of the concept of vestigiality with that of exaptation. Both may occur together in the same example, depending on the relevant point of view. In exaptation, a structure originally used for one purpose is modified for a new one. For example, the wings of penguins would be exaptational in the sense of serving a substantial new purpose (underwater locomotion), but might still be regarded as vestigial in the sense of having lost the function of flight. In contrast Darwin argued that the wings of emus would be definitely vestigial, as they appear to have no major extant function however, function is a matter of degree, so judgments on what is a "major" function are arbitrary the emu does seem to use its wings as organs of balance in running. Similarly, the ostrich uses its wings in displays and temperature control, though they are undoubtedly vestigial as structures for flight.

Vestigial characters range from detrimental through neutral to favorable in terms of selection. Some may be of some limited utility to an organism but still degenerate over time if they do not confer a significant enough advantage in terms of fitness to avoid the effects of genetic drift or competing selective pressures. Vestigiality in its various forms presents many examples of evidence for biological evolution. [5]

Vestigial structures have been noticed since ancient times, and the reason for their existence was long speculated upon before Darwinian evolution provided a widely accepted explanation. In the 4th century BC, Aristotle was one of the earliest writers to comment, in his History of Animals, on the vestigial eyes of moles, calling them "stunted in development" due to the fact that moles can scarcely see. [6] However, only in recent centuries have anatomical vestiges become a subject of serious study. In 1798, Étienne Geoffroy Saint-Hilaire noted on vestigial structures:

Whereas useless in this circumstance, these rudiments. have not been eliminated, because Nature never works by rapid jumps, and She always leaves vestiges of an organ, even though it is completely superfluous, if that organ plays an important role in the other species of the same family. [7]

His colleague, Jean-Baptiste Lamarck, named a number of vestigial structures in his 1809 book Philosophie Zoologique. Lamarck noted "Olivier's Spalax, which lives underground like the mole, and is apparently exposed to daylight even less than the mole, has altogether lost the use of sight: so that it shows nothing more than vestiges of this organ." [8]

Charles Darwin was familiar with the concept of vestigial structures, though the term for them did not yet exist. He listed a number of them in The Descent of Man, including the muscles of the ear, wisdom teeth, the appendix, the tail bone, body hair, and the semilunar fold in the corner of the eye. Darwin also noted, in On the Origin of Species, that a vestigial structure could be useless for its primary function, but still retain secondary anatomical roles: "An organ serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other. [A]n organ may become rudimentary for its proper purpose, and be used for a distinct object." [9]

In the first edition of On the Origin of Species, Darwin briefly mentioned inheritance of acquired characters under the heading "Effects of Use and Disuse", expressing little doubt that use "strengthens and enlarges certain parts, and disuse diminishes them and that such modifications are inherited". [10] In later editions he expanded his thoughts on this, [11] and in the final chapter of the 6th edition concluded that species have been modified "chiefly through the natural selection of numerous successive, slight, favorable variations aided in an important manner by the inherited effects of the use and disuse of parts". [12]

In 1893, Robert Wiedersheim published The Structure of Man, a book on human anatomy and its relevance to man's evolutionary history. The Structure of Man contained a list of 86 human organs that Wiedersheim described as, "Organs having become wholly or in part functionless, some appearing in the Embryo alone, others present during Life constantly or inconstantly. For the greater part Organs which may be rightly termed Vestigial." [13] Since his time, the function of some of these structures have been discovered, while other anatomical vestiges have been unearthed, making the list primarily of interest as a record of the knowledge of human anatomy at the time. Later versions of Wiedersheim's list were expanded to as many as 180 human "vestigial organs". This is why the zoologist Horatio Newman said in a written statement read into evidence in the Scopes Trial that "There are, according to Wiedersheim, no less than 180 vestigial structures in the human body, sufficient to make of a man a veritable walking museum of antiquities." [14]

Vestigial structures are often homologous to structures that are functioning normally in other species. Therefore, vestigial structures can be considered evidence for evolution, the process by which beneficial heritable traits arise in populations over an extended period of time. The existence of vestigial traits can be attributed to changes in the environment and behavior patterns of the organism in question. Through an examination of these various traits, it is clear that evolution had a hard role in the development of organisms. Every anatomical structure or behavior response has origins in which they were, at one time, useful. As time progressed, the ancient common ancestor organisms did as well. Evolving with time, natural selection played a huge role. More advantageous structures were selected, while others were not. With this expansion, some traits were left to the wayside. As the function of the trait is no longer beneficial for survival, the likelihood that future offspring will inherit the "normal" form of it decreases. In some cases, the structure becomes detrimental to the organism (for example the eyes of a mole can become infected [9] ). In many cases the structure is of no direct harm, yet all structures require extra energy in terms of development, maintenance, and weight, and are also a risk in terms of disease (e.g., infection, cancer), providing some selective pressure for the removal of parts that do not contribute to an organism's fitness. A structure that is not harmful will take longer to be 'phased out' than one that is. However, some vestigial structures may persist due to limitations in development, such that complete loss of the structure could not occur without major alterations of the organism's developmental pattern, and such alterations would likely produce numerous negative side-effects. The toes of many animals such as horses, which stand on a single toe, are still evident in a vestigial form and may become evident, although rarely, from time to time in individuals.

The vestigial versions of the structure can be compared to the original version of the structure in other species in order to determine the homology of a vestigial structure. Homologous structures indicate common ancestry with those organisms that have a functional version of the structure. [15] Douglas Futuyma has stated that vestigial structures make no sense without evolution, just as spelling and usage of many modern English words can only be explained by their Latin or Old Norse antecedents. [16]

Vestigial traits can still be considered adaptations. This is because an adaptation is often defined as a trait that has been favored by natural selection. Adaptations, therefore, need not be adaptive, as long as they were at some point. [17]

Non-human animals Edit

Vestigial characters are present throughout the animal kingdom, and an almost endless list could be given. Darwin said that "it would be impossible to name one of the higher animals in which some part or other is not in a rudimentary condition." [9]

The wings of ostriches, emus, and other flightless birds are vestigial they are remnants of their flying ancestors' wings. The eyes of certain cavefish and salamanders are vestigial, as they no longer allow the organism to see, and are remnants of their ancestors' functional eyes. Animals that reproduce without sex (via asexual reproduction) generally lose their sexual traits, such as the ability to locate/recognize the opposite sex and copulation behavior. [18]

Boas and pythons have vestigial pelvis remnants, which are externally visible as two small pelvic spurs on each side of the cloaca. These spurs are sometimes used in copulation, but are not essential, as no colubrid snake (the vast majority of species) possesses these remnants. Furthermore, in most snakes, the left lung is greatly reduced or absent. Amphisbaenians, which independently evolved limblessness, also retain vestiges of the pelvis as well as the pectoral girdle, and have lost their right lung. [ citation needed ]

A case of vestigial organs was described in polyopisthocotylean Monogeneans (parasitic flatworms). These parasites usually have a posterior attachment organ with several clamps, which are sclerotised organs attaching the worm to the gill of the host fish. These clamps are extremely important for the survival of the parasite. In the family Protomicrocotylidae, species have either normal clamps, simplified clamps, or no clamps at all (in the genus Lethacotyle). After a comparative study of the relative surface of clamps in more than 100 Monogeneans, this has been interpreted as an evolutionary sequence leading to the loss of clamps. Coincidentally, other attachment structures (lateral flaps, transverse striations) have evolved in protomicrocotylids. Therefore, clamps in protomicrocotylids were considered vestigial organs. [19]

In the foregoing examples the vestigiality is generally the (sometimes incidental) result of adaptive evolution. However, there are many examples of vestigiality as the product of drastic mutation, and such vestigiality is usually harmful or counter-adaptive. One of the earliest documented examples was that of vestigial wings in Drosophila. [20] Many examples in many other contexts have emerged since. [21]

Humans Edit

Human vestigiality is related to human evolution, and includes a variety of characters occurring in the human species. Many examples of these are vestigial in other primates and related animals, whereas other examples are still highly developed. The human caecum is vestigial, as often is the case in omnivores, being reduced to a single chamber receiving the content of the ileum into the colon. The ancestral caecum would have been a large, blind diverticulum in which resistant plant material such as cellulose would have been fermented in preparation for absorption in the colon. [22] [23] [24] Analogous organs in other animals similar to humans continue to perform similar functions. The coccyx, [25] or tailbone, though a vestige of the tail of some primate ancestors, is functional as an anchor for certain pelvic muscles including: the levator ani muscle and the largest gluteal muscle, the gluteus maximus. [26]

Other structures that are vestigial include the plica semilunaris on the inside corner of the eye (a remnant of the nictitating membrane) [27] and, as pictured, muscles in the ear [28] and other parts of the body. Other organic structures (such as the occipitofrontalis muscle) have lost their original functions (keep the head from falling) but are still useful for other purposes (facial expression). [29]

Humans also bear some vestigial behaviors and reflexes. The formation of goose bumps in humans under stress is a vestigial reflex [30] its function in human ancestors was to raise the body's hair, making the ancestor appear larger and scaring off predators. The arrector pili muscle, which is a band of smooth muscle that connects the hair follicle to connective tissue, contracts and creates the goosebumps on skin. [31]

There are also vestigial molecular structures in humans, which are no longer in use but may indicate common ancestry with other species. One example of this is a gene that is functional in most other mammals and which produces L-gulonolactone oxidase, an enzyme that can make vitamin C. A documented mutation deactivated the gene in an ancestor of the modern infraorder of monkeys, and apes, and it now remains in their genomes, including the human genome, as a vestigial sequence called a pseudogene. [32]

The shift in human diet towards soft and processed food over time caused a reduction in the number of powerful grinding teeth, especially the third molars or wisdom teeth, which were highly prone to impaction. [33]

Plants and fungi Edit

Plants also have vestigial parts, including functionless stipules and carpels, leaf reduction of Equisetum, paraphyses of Fungi. [34] Well known examples are the reductions in floral display, leading to smaller and/or paler flowers, in plants that reproduce without outcrossing, for example via selfing or obligate clonal reproduction. [35] [36]

Biologists classify humans, along with only a few other species, as great apes (species in the family Hominidae). The living Hominidae include two distinct species of chimpanzee (the bonobo, Pan paniscus, and the common chimpanzee, Pan troglodytes), two species of gorilla (the western gorilla, Gorilla gorilla, and the eastern gorilla, Gorilla graueri), and two species of orangutan (the Bornean orangutan, Pongo pygmaeus, and the Sumatran orangutan, Pongo abelii). The great apes with the family Hylobatidae of gibbons form the superfamily Hominoidea of apes.

Apes, in turn, belong to the primate order (>400 species), along with the Old World monkeys, the New World monkeys, and others. Data from both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) indicate that primates belong to the group of Euarchontoglires, together with Rodentia, Lagomorpha, Dermoptera, and Scandentia. [1] This is further supported by Alu-like short interspersed nuclear elements (SINEs) which have been found only in members of the Euarchontoglires. [2]

A phylogenetic tree is usually derived from DNA or protein sequences from populations. Often, mitochondrial DNA or Y chromosome sequences are used to study ancient human demographics. These single-locus sources of DNA do not recombine and are almost always inherited from a single parent, with only one known exception in mtDNA. [3] Individuals from closer geographic regions generally tend to be more similar than individuals from regions farther away. Distance on a phylogenetic tree can be used approximately to indicate:

  1. Genetic distance. The genetic difference between humans and chimpanzees is less than 2%, [4] or three times larger than the variation among modern humans (estimated at 0.6%). [5]
  2. Temporal remoteness of the most recent common ancestor. The mitochondrial most recent common ancestor of modern humans is estimated to have lived roughly 160,000 years ago, [6] the latest common ancestors of humans and chimpanzees roughly 5 to 6 million years ago. [7]

The separation of humans from their closest relatives, the non-human apes (chimpanzees and gorillas), has been studied extensively for more than a century. Five major questions have been addressed:

  • Which apes are our closest ancestors?
  • When did the separations occur?
  • What was the effective population size of the common ancestor before the split?
  • Are there traces of population structure (subpopulations) preceding the speciation or partial admixture succeeding it?
  • What were the specific events (including fusion of chromosomes 2a and 2b) prior to and subsequent to the separation?

General observations Edit

As discussed before, different parts of the genome show different sequence divergence between different hominoids. It has also been shown that the sequence divergence between DNA from humans and chimpanzees varies greatly. For example, the sequence divergence varies between 0% to 2.66% between non-coding, non-repetitive genomic regions of humans and chimpanzees. [8] The percentage of nucleotides in the human genome (hg38) that had one-to-one exact matches in the chimpanzee genome (pantro6) was 84.38%. Additionally gene trees, generated by comparative analysis of DNA segments, do not always fit the species tree. Summing up:

  • The sequence divergence varies significantly between humans, chimpanzees and gorillas.
  • For most DNA sequences, humans and chimpanzees appear to be most closely related, but some point to a human-gorilla or chimpanzee-gorilla clade.
  • The human genome has been sequenced, as well as the chimpanzee genome. Humans have 23 pairs of chromosomes, while chimpanzees, gorillas and orangutans have 24. Human chromosome 2 is a fusion of two chromosomes 2a and 2b that remained separate in the other primates. [9]

Divergence times Edit

The divergence time of humans from other apes is of great interest. One of the first molecular studies, published in 1967 measured immunological distances (IDs) between different primates. [10] Basically the study measured the strength of immunological response that an antigen from one species (human albumin) induces in the immune system of another species (human, chimpanzee, gorilla and Old World monkeys). Closely related species should have similar antigens and therefore weaker immunological response to each other's antigens. The immunological response of a species to its own antigens (e.g. human to human) was set to be 1.

The ID between humans and gorillas was determined to be 1.09, that between humans and chimpanzees was determined as 1.14. However the distance to six different Old World monkeys was on average 2.46, indicating that the African apes are more closely related to humans than to monkeys. The authors consider the divergence time between Old World monkeys and hominoids to be 30 million years ago (MYA), based on fossil data, and the immunological distance was considered to grow at a constant rate. They concluded that divergence time of humans and the African apes to be roughly

5 MYA. That was a surprising result. Most scientists at that time thought that humans and great apes diverged much earlier (>15 MYA).

The gorilla was, in ID terms, closer to human than to chimpanzees however, the difference was so slight that the trichotomy could not be resolved with certainty. Later studies based on molecular genetics were able to resolve the trichotomy: chimpanzees are phylogenetically closer to humans than to gorillas. However, some divergence times estimated later (using much more sophisticated methods in molecular genetics) do not substantially differ from the very first estimate in 1967, but a recent paper [11] puts it at 11–14 MYA.

Divergence times and ancestral effective population size Edit

Current methods to determine divergence times use DNA sequence alignments and molecular clocks. Usually the molecular clock is calibrated assuming that the orangutan split from the African apes (including humans) 12-16 MYA. Some studies also include some old world monkeys and set the divergence time of them from hominoids to 25-30 MYA. Both calibration points are based on very little fossil data and have been criticized. [12]

If these dates are revised, the divergence times estimated from molecular data will change as well. However, the relative divergence times are unlikely to change. Even if we can't tell absolute divergence times exactly, we can be pretty sure that the divergence time between chimpanzees and humans is about sixfold shorter than between chimpanzees (or humans) and monkeys.

One study (Takahata et al., 1995) used 15 DNA sequences from different regions of the genome from human and chimpanzee and 7 DNA sequences from human, chimpanzee and gorilla. [13] They determined that chimpanzees are more closely related to humans than gorillas. Using various statistical methods, they estimated the divergence time human-chimp to be 4.7 MYA and the divergence time between gorillas and humans (and chimps) to be 7.2 MYA.

Additionally they estimated the effective population size of the common ancestor of humans and chimpanzees to be

100,000. This was somewhat surprising since the present day effective population size of humans is estimated to be only

10,000. If true that means that the human lineage would have experienced an immense decrease of its effective population size (and thus genetic diversity) in its evolution. (see Toba catastrophe theory)

Another study (Chen & Li, 2001) sequenced 53 non-repetitive, intergenic DNA segments from human, chimpanzee, gorilla and orangutan. [8] When the DNA sequences were concatenated to a single long sequence, the generated neighbor-joining tree supported the Homo-Pan clade with 100% bootstrap (that is that humans and chimpanzees are the closest related species of the four). When three species are fairly closely related to each other (like human, chimpanzee and gorilla), the trees obtained from DNA sequence data may not be congruent with the tree that represents the speciation (species tree).

The shorter internodal time span (TIN) the more common are incongruent gene trees. The effective population size (Ne) of the internodal population determines how long genetic lineages are preserved in the population. A higher effective population size causes more incongruent gene trees. Therefore, if the internodal time span is known, the ancestral effective population size of the common ancestor of humans and chimpanzees can be calculated.

When each segment was analyzed individually, 31 supported the Homo-Pan clade, 10 supported the Homo-Gorilla clade, and 12 supported the Pan-Gorilla clade. Using the molecular clock the authors estimated that gorillas split up first 6.2-8.4 MYA and chimpanzees and humans split up 1.6-2.2 million years later (internodal time span) 4.6-6.2 MYA. The internodal time span is useful to estimate the ancestral effective population size of the common ancestor of humans and chimpanzees.

A parsimonious analysis revealed that 24 loci supported the Homo-Pan clade, 7 supported the Homo-Gorilla clade, 2 supported the Pan-Gorilla clade and 20 gave no resolution. Additionally they took 35 protein coding loci from databases. Of these 12 supported the Homo-Pan clade, 3 the Homo-Gorilla clade, 4 the Pan-Gorilla clade and 16 gave no resolution. Therefore, only

70% of the 52 loci that gave a resolution (33 intergenic, 19 protein coding) support the 'correct' species tree. From the fraction of loci which did not support the species tree and the internodal time span they estimated previously, the effective population of the common ancestor of humans and chimpanzees was estimated to be

52 000 to 96 000. This value is not as high as that from the first study (Takahata), but still much higher than present day effective population size of humans.

A third study (Yang, 2002) used the same dataset that Chen and Li used but estimated the ancestral effective population of 'only'

12,000 to 21,000, using a different statistical method. [14]

The alignable sequences within genomes of humans and chimpanzees differ by about 35 million single-nucleotide substitutions. Additionally about 3% of the complete genomes differ by deletions, insertions and duplications. [15]

Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage. Only a very tiny fraction of those fixed differences gave rise to the different phenotypes of humans and chimpanzees and finding those is a great challenge. The vast majority of the differences are neutral and do not affect the phenotype. [ citation needed ]

Molecular evolution may act in different ways, through protein evolution, gene loss, differential gene regulation and RNA evolution. All are thought to have played some part in human evolution.

Gene loss Edit

Many different mutations can inactivate a gene, but few will change its function in a specific way. Inactivation mutations will therefore be readily available for selection to act on. Gene loss could thus be a common mechanism of evolutionary adaptation (the "less-is-more" hypothesis). [16]

80 genes were lost in the human lineage after separation from the last common ancestor with the chimpanzee. 36 of those were for olfactory receptors. Genes involved in chemoreception and immune response are overrepresented. [17] Another study estimated that 86 genes had been lost. [18]

Hair keratin gene KRTHAP1 Edit

A gene for type I hair keratin was lost in the human lineage. Keratins are a major component of hairs. Humans still have nine functional type I hair keratin genes, but the loss of that particular gene may have caused the thinning of human body hair. Based on the assumption of a constant molecular clock, the study predicts the gene loss occurred relatively recently in human evolution—less than 240 000 years ago, but both the Vindija Neandertal and the high-coverage Denisovan sequence contain the same premature stop codons as modern humans and hence dating should be greater than 750 000 years ago. [19]

Myosin gene MYH16 Edit

Stedman et al. (2004) stated that the loss of the sarcomeric myosin gene MYH16 in the human lineage led to smaller masticatory muscles. They estimated that the mutation that led to the inactivation (a two base pair deletion) occurred 2.4 million years ago, predating the appearance of Homo ergaster/erectus in Africa. The period that followed was marked by a strong increase in cranial capacity, promoting speculation that the loss of the gene may have removed an evolutionary constraint on brain size in the genus Homo. [20]

Another estimate for the loss of the MYH16 gene is 5.3 million years ago, long before Homo appeared. [21]

Other Edit

    , a cysteinyl aspartate proteinase. The loss of this gene is speculated to have reduced the lethality of bacterial infection in humans. [17]

Gene addition Edit

Segmental duplications (SDs or LCRs) have had roles in creating new primate genes and shaping human genetic variation.

Human-specific DNA insertions Edit

When the human genome was compared to the genomes of five comparison primate species, including the chimpanzee, gorilla, orangutan, gibbon, and macaque, it was found that there are approximately 20,000 human-specific insertions believed to be regulatory. While most insertions appear to be fitness neutral, a small amount have been identified in positively selected genes showing associations to neural phenotypes and some relating to dental and sensory perception-related phenotypes. These findings hint at the seemingly important role of human-specific insertions in the recent evolution of humans. [22]

Selection pressures Edit

Human accelerated regions are areas of the genome that differ between humans and chimpanzees to a greater extent than can be explained by genetic drift over the time since the two species shared a common ancestor. These regions show signs of being subject to natural selection, leading to the evolution of distinctly human traits. Two examples are HAR1F, which is believed to be related to brain development and HAR2 (a.k.a. HACNS1) that may have played a role in the development of the opposable thumb.

It has also been hypothesized that much of the difference between humans and chimpanzees is attributable to the regulation of gene expression rather than differences in the genes themselves. Analyses of conserved non-coding sequences, which often contain functional and thus positively selected regulatory regions, address this possibility. [23]

Sequence divergence between humans and apes Edit

When the draft sequence of the common chimpanzee (Pan troglodytes) genome was published in the summer 2005, 2400 million bases (of

3160 million bases) were sequenced and assembled well enough to be compared to the human genome. [15] 1.23% of this sequenced differed by single-base substitutions. Of this, 1.06% or less was thought to represent fixed differences between the species, with the rest being variant sites in humans or chimpanzees. Another type of difference, called indels (insertions/deletions) accounted for many fewer differences (15% as many), but contributed

1.5% of unique sequence to each genome, since each insertion or deletion can involve anywhere from one base to millions of bases. [15]

A companion paper examined segmental duplications in the two genomes, [24] whose insertion and deletion into the genome account for much of the indel sequence. They found that a total of 2.7% of euchromatic sequence had been differentially duplicated in one or the other lineage.

Percentage sequence divergence between humans and other hominids [8]
Locus Human-Chimp Human-Gorilla Human-Orangutan
Alu elements 2 - -
Non-coding (Chr. Y) 1.68 ± 0.19 2.33 ± 0.2 5.63 ± 0.35
Pseudogenes (autosomal) 1.64 ± 0.10 1.87 ± 0.11 -
Pseudogenes (Chr. X) 1.47 ± 0.17 - -
Noncoding (autosomal) 1.24 ± 0.07 1.62 ± 0.08 3.08 ± 0.11
Genes (Ks) 1.11 1.48 2.98
Introns 0.93 ± 0.08 1.23 ± 0.09 -
Xq13.3 0.92 ± 0.10 1.42 ± 0.12 3.00 ± 0.18
Subtotal for X chromosome 1.16 ± 0.07 1.47 ± 0.08 -
Genes (Ka) 0.8 0.93 1.96

The sequence divergence has generally the following pattern: Human-Chimp < Human-Gorilla << Human-Orangutan, highlighting the close kinship between humans and the African apes. Alu elements diverge quickly due to their high frequency of CpG dinucleotides which mutate roughly 10 times more often than the average nucleotide in the genome. The mutation rate is higher in the male germ line, therefore the divergence in the Y chromosome—which is inherited solely from the father—is higher than in autosomes. The X chromosome is inherited twice as often through the female germ line as through the male germ line and therefore shows slightly lower sequence divergence. The sequence divergence of the Xq13.3 region is surprisingly low between humans and chimpanzees. [25]

Mutations altering the amino acid sequence of proteins (Ka) are the least common. In fact

29% of all orthologous proteins are identical between human and chimpanzee. The typical protein differs by only two amino acids. [15] The measures of sequence divergence shown in the table only take the substitutional differences, for example from an A (adenine) to a G (guanine), into account. DNA sequences may however also differ by insertions and deletions (indels) of bases. These are usually stripped from the alignments before the calculation of sequence divergence is performed.

An international group of scientists completed a draft sequence of the Neanderthal genome in May 2010. The results indicate some breeding between modern humans (Homo sapiens) and Neanderthals (Homo neanderthalensis), as the genomes of non-African humans have 1–4% more in common with Neanderthals than do the genomes of subsaharan Africans. Neanderthals and most modern humans share a lactose-intolerant variant of the lactase gene that encodes an enzyme that is unable to break down lactose in milk after weaning. Modern humans and Neanderthals also share the FOXP2 gene variant associated with brain development and with speech in modern humans, indicating that Neanderthals may have been able to speak. Chimps have two amino acid differences in FOXP2 compared with human and Neanderthal FOXP2. [26] [27] [28]

H. sapiens is thought to have emerged about 300,000 years ago. It dispersed throughout Africa, and after 70,000 years ago throughout Eurasia and Oceania. A 2009 study identified 14 "ancestral population clusters", the most remote being the San people of Southern Africa. [29] [30]

With their rapid expansion throughout different climate zones, and especially with the availability of new food sources with the domestication of cattle and the development of agriculture, human populations have been exposed to significant selective pressures since their dispersal. For example, East Asians have been found to be separated from Europids by a number of concentrated alleles suggestive of selection pressures, including variants of the EDAR, ADH1B, ABCC1, and ALDH2genes. The East Asian types of ADH1B in particular are associated with rice domestication and would thus have arisen after the development of rice cultivation roughly 10,000 years ago. [31] Several phenotypical traits of characteristic of East Asians are due to a single mutation of the EDAR gene, dated to c. 35,000 years ago. [32]

As of 2017 [update] , the Single Nucleotide Polymorphism Database (dbSNP), which lists SNP and other variants, listed a total of 324 million variants found in sequenced human genomes. [33] Nucleotide diversity, the average proportion of nucleotides that differ between two individuals, is estimated at between 0.1% and 0.4% for contemporary humans (compared to 2% between humans and chimpanzees). [34] [35] This corresponds to genome differences at a few million sites the 1000 Genomes Project similarly found that "a typical [individual] genome differs from the reference human genome at 4.1 million to 5.0 million sites … affecting 20 million bases of sequence." [36]

In February 2019, scientists discovered evidence, based on genetics studies using artificial intelligence (AI), that suggest the existence of an unknown human ancestor species, not Neanderthal, Denisovan or human hybrid (like Denny (hybrid hominin)), in the genome of modern humans. [37] [38]

In March 2019, Chinese scientists reported inserting the human brain-related MCPH1 gene into laboratory rhesus monkeys, resulting in the transgenic monkeys performing better and answering faster on "short-term memory tests involving matching colors and shapes", compared to control non-transgenic monkeys, according to the researchers. [39] [40]