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What are some examples of interbreeding between species that are separated by 5 million years or more?

What are some examples of interbreeding between species that are separated by 5 million years or more?



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Interbreeding is constrained with that the offspring shares the gene pool of the parents. What are some examples of interbreeding that has occurred, where the two species were separated by 5 million years or more?


I depends a little bit about what you mean by interbreeding. In any case, my answer won't be fully satisfactory.

Horizontal gene transfer

If you are referring to any exchange of genetic materials than, you can have a look at Salzberg et al. (2001) who report 40 genes that were horizontally transferred from bacteria.

Elysia chlorotica is sea slug which is able of photosynthesis thanks to a horizontal gene transfer (Schwartz et al., 2014)

Typical interbreeding

If you are thinking about some kind of more common type of inbreeding, then you might want to consider

mule who is the hybrid between a male donkey and a female horse. Donkey and horse share a common ancestor that is about 4.5 millions years old (according to Live Science). Mules are often sterile but some of them have been fertile (Rong et al. 1988; see also this article from the Denver post; thanks @iayork)

Platanus × acerifolia is a hybrid between Platanus orientalis and Platanus occidentalis. Platanus are a rather old genera with fossils of 115 millions years old found (from wiki). However, I don't know how old is the common ancestor between P. orientalis and P. occidentalis

There are plenty of other examples in wikipedia > hybrid but I failed to find good estimate of common ancestry for those who may have had a common ancestor older than 5 millions years but it probably exist given that the mule example is already 4.5 millions years old.


Here's some research about a fern hybrid converging after 60 million years:

http://www.iflscience.com/plants-and-animals/distant-species-produce-hybrid-60-million-years-after-their-split/

Some yeasts in a brewery apparently after 10-20 million years: http://www.iflscience.com/plants-and-animals/distant-species-produce-hybrid-60-million-years-after-their-split/

a Goat Sheep Geep after 7 million years: https://whyevolutionistrue.wordpress.com/2014/08/03/a-new-geep-a-sheepgoat-hybrid/

for timing evolution http://www.timetree.org/


Chimps interbred with bonobos, surprising study reveals

Just like early humans interbred with Neanderthals, it seems that our closest relatives also had some fun times with each other. According to a new genetic analysis, one percent of the chimpanzee genome comes from bonobos.

Chimps and bonobos are the only two species in the genus Pan and they represent our closest genetic relatives. Both species inhabit the Congo jungle in sub-Saharan Africa, and in some areas their habitats are really close to each other – though separated by the Congo river. Despite being intelligent and exhibiting several human traits, they are endangered and often hunted or kept as captives. This is the main reason why the study was carried out – not to identify connections between the two species, but to help preserve the chimpanzees.

“This is the largest analysis of chimpanzee genomes to date and shows that genetics can be used to locate quite precisely where in the wild a chimpanzee comes from,” said Dr Chris Tyler Smith, from the Wellcome Trust Sanger Institute.

“This can aid the release of illegally captured chimpanzees back into the right place in the wild and provide key evidence for action against the captors.”

Still, the research did yield some interesting biological info. Researchers found that the two species diverged from a common ancestor between 1.5 and 2 million years ago. But some chimp populations had a surprise: bonobo DNA embedded in their own genes.

“We found that central and eastern chimpanzees share significantly more genetic material with bonobos than the other chimpanzee subspecies. These chimpanzees have at least 1% of their genomes derived from bonobos. This shows that there wasn’t a clean separation, but that the initial divergence was followed by occasional episodes of mixing between the species.

Many biologists didn’t even consider interbreeding between the two species so this came as quite a surprise, but the results are pretty clear. There is a clear resemblance between what study on our own species have found — early humans and Neanderthals diverged from the same ancestor, but they also interbred for a long time. Non-African humans carry within them a significant part of Neanderthal DNA. Dr Tomàs Marquès-Bonet, leader of the study from the Institute of Biological Evolution (University Pompeu Fabra and CSIC), Barcelona, said:

“This is the first study to reveal that ancient gene flow events happened amongst the living species closest to humans — the bonobos and chimpanzees. It implies that successful breeding between close species might have been actually widespread in the ancestors of humans and living apes.”


Earliest interbreeding event between ancient human populations discovered

IMAGE: An evolutionary tree including four proposed episodes of gene flow. The previously unknown event 744,372 years ago (orange) suggests interbreeding occurred between super-archaics and Neanderthal-Denisovan ancestors in Eurasia. view more

Credit: Adapted from Alan Rogers

For three years, anthropologist Alan Rogers has attempted to solve an evolutionary puzzle. His research untangles millions of years of human evolution by analyzing DNA strands from ancient human species known as hominins. Like many evolutionary geneticists, Rogers compares hominin genomes looking for genetic patterns such as mutations and shared genes. He develops statistical methods that infer the history of ancient human populations.

In 2017, Rogers led a study which found that two lineages of ancient humans, Neanderthals and Denisovans, separated much earlier than previously thought and proposed a bottleneck population size. It caused some controversy--anthropologists Mafessoni and Prüfer argued that their method for analyzing the DNA produced different results. Rogers agreed, but realized that neither method explained the genetic data very well.

"Both of our methods under discussion were missing something, but what?" asked Rogers, professor of anthropology at the University of Utah.

The new study has solved that puzzle and in doing so, it has documented the earliest known interbreeding event between ancient human populations--a group known as the "super-archaics" in Eurasia interbred with a Neanderthal-Denisovan ancestor about 700,000 years ago. The event was between two populations that were more distantly related than any other recorded. The authors also proposed a revised timeline for human migration out of Africa and into Eurasia. The method for analyzing ancient DNA provides a new way to look farther back into the human lineage than ever before.

"We've never known about this episode of interbreeding and we've never been able to estimate the size of the super-archaic population," said Rogers, lead author of the study. "We're just shedding light on an interval on human evolutionary history that was previously completely dark."

The paper was published on Feb. 20, 2020, in the journal Science Advances.

Out of Africa and interbreeding

Rogers studied the ways in which mutations are shared among modern Africans and Europeans, and ancient Neanderthals and Denisovans. The pattern of sharing implied five episodes of interbreeding, including one that was previously unknown. The newly discovered episode involves interbreeding over 700,000 years ago between a distantly related "super-archaic" population which separated from all other humans around two million years ago, and the ancestors of Neanderthals and Denisovans.

The super-archaic and Neanderthal-Denisovan ancestor populations were more distantly related than any other pair of human populations previously known to interbreed. For example, modern humans and Neanderthals had been separated for about 750,000 years when they interbred. The super-archaics and Neanderthal-Denisovan ancestors were separated for well over a million years.

"These findings about the timing at which interbreeding happened in the human lineage is telling something about how long it takes for reproductive isolation to evolve," said Rogers.

The authors used other clues in the genomes to estimate when the ancient human populations separated and their effective population size. They estimated the super-archaic separated into its own species about two million years ago. This agrees with human fossil evidence in Eurasia that is 1.85 million years old.

The researchers also proposed there were three waves of human migration into Eurasia. The first was two million years ago when the super-archaics migrated into Eurasia and expanded into a large population. Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the super-archaics. Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

"I've been working for the last couple of years on this different way of analyzing genetic data to find out about history," said Rogers. "It's just gratifying that you come up with a different way of looking at the data and you end up discovering things that people haven't been able to see with other methods."

Nathan S. Harris and Alan A. Achenbach from the Department of Anthropology at the University of Utah also contributed to the study.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.


Ancestors of Neanderthals and Denisovans Interbred with ‘Superarchaic’ Hominin

A new study by researchers from the Department of Anthropology at the University of Utah shows that over 700,000 years ago, the ancestors of Neanderthals and Denisovans interbred with their Eurasian predecessors — members of a ‘superarchaic’ population that separated from other humans about 2 million years ago.

Early Neanderthals that lived at Sima de los Huesos, a cave site in Atapuerca Mountains, Spain. Image credit: © Kennis & Kennis / Madrid Scientific Films.

“We’ve never known about this episode of interbreeding and we’ve never been able to estimate the size of the superarchaic population,” said University of Utah’s Professor Alan Rogers, the lead author of the study.

“We’re just shedding light on an interval on human evolutionary history that was previously completely dark.”

Professor Rogers and colleagues studied the ways in which mutations are shared among modern Africans and Europeans, and ancient Neanderthals and Denisovans.

The pattern of sharing implied five episodes of interbreeding, including one that was previously unknown.

The newly discovered episode involves interbreeding over 700,000 years ago between a distantly related ‘superarchaic’ population which separated from all other humans around 2 million years ago, and the ancestors of Neanderthals and Denisovans.

The superarchaic and Neanderthal-Denisovan ancestor populations were more distantly related than any other pair of human populations previously known to interbreed. For example, modern humans and Neanderthals had been separated for about 750,000 years when they interbred.

The superarchaics and Neanderthal-Denisovan ancestors were separated for well over a million years.

“These findings about the timing at which interbreeding happened in the human lineage is telling something about how long it takes for reproductive isolation to evolve,” Professor Rogers said.

The researchers used other clues in the genomes to estimate when the ancient human populations separated and their effective population size.

They estimated the superarchaics separated into its own species about 2 million years ago. This agrees with human fossil evidence in Eurasia that is 1.85 million years old.

An evolutionary tree including four proposed episodes of gene flow the previously unknown event 744,372 years ago (orange) suggests interbreeding occurred between superarchaics and Neanderthal-Denisovan ancestors in Eurasia. Image credit: Rogers et al, doi: 10.1126/sciadv.aay5483.

The scientists also proposed there were three waves of human migration into Eurasia.

The first was 2 million years ago when the superarchaics migrated into Eurasia and expanded into a large population.

Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the superarchaics.

Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

“I’ve been working for the last couple of years on this different way of analyzing genetic data to find out about history,” Professor Rogers said.

“It’s just gratifying that you come up with a different way of looking at the data and you end up discovering things that people haven’t been able to see with other methods.”


Could Interbreeding Between Humans and Neanderthals Have Led to an Enhanced Human Brain?

A new study suggests that human evolution was not just a matter of spontaneous advantageous mutations arising within the human lineage.

Might mating between an ancient human and a Neanderthal - perhaps occurring in only a single instance - have introduced a gene variant into the human population that enhanced human brain function? That question is at the heart of a new study by researchers at the Howard Hughes Medical Institute and the University of Chicago.

The new research, which was published online during the week of November 6, 2006, in the early edition of the Proceedings of the National Academy of Sciences (PNAS), suggests that human evolution was not just a matter of spontaneous advantageous mutations arising within the human lineage. Human evolution may also have been influenced by interbreeding with other Homo species, which introduced gene variants, known as alleles, that are beneficial to human reproductive fitness, said the study's senior author Bruce T. Lahn, a Howard Hughes Medical Institute researcher at the University of Chicago.

By no means do these findings constitute definitive proof that a Neanderthal was the source of the original copy of the D allele. However, our evidence shows that it is one of the best candidates.

The scientists said they have developed the most robust genetic evidence to date that suggests humans and Neanderthals interbred when they existed together thousands of years ago. The interbreeding hypothesis contrasts with at least one prominent theory that posits that no interbreeding occurred when the two species encountered one another.

Lahn collaborated on the studies with Patrick D. Evans, Nitzan Mekel-Bobrov, Eric J. Vallender and Richard R. Hudson, all of the University of Chicago.

In their studies, Lahn and his colleagues performed a detailed statistical analysis of the DNA sequence structure of the gene microcephalin, which is known to play a role in regulating brain size in humans. Mutations in the human gene cause development of a much smaller brain, a condition called microcephaly.

Earlier studies by Lahn's group yielded evidence that the microcephalin gene has two distinct classes of alleles. One class, called the D alleles, is comprised of a group of alleles with rather similar DNA sequences. The other class is called the non-D alleles. Lahn and colleagues previously showed that all modern copies of the D alleles arose from a single progenitor copy about 37,000 years ago, which then increased in frequency rapidly and are now present in about 70 percent of the world's population. This rapid rise in frequency indicates that the D alleles underwent positive selection in the recent history of humans. This means that these alleles conferred a fitness advantage on those who possessed one of them such that these people had slightly higher reproductive success than people who didn't possess the alleles, said Lahn.

The estimate that all modern copies of the D alleles descended from a single progenitor copy about 37,000 years ago is based on the measurement of sequence difference between different copies of the D alleles. As a copy of a gene is passed from one generation to the next, mutations are introduced at a steady rate, such that a certain number of generations later, the descendent copies of the gene would on average vary from one another in DNA sequence by a certain amount. The greater the number of the generations, the more DNA sequence difference there would be between two descendent copies, said Lahn. The amount of sequence difference between different copies of a gene can therefore be used to estimate the amount of evolutionary time that has elapsed since the two copies descended from their common progenitor.

In the new studies reported in PNAS, the researchers performed detailed sequence comparisons between the D alleles and the non-D alleles of microcephalin. The scientists determined that these two classes of alleles have likely evolved in two separate lineages for about 1.1 million years -- with the non-D alleles having evolved in the Homo sapiens lineage and the D alleles having evolved in an archaic, and now extinct, Homo lineage. Then, about 37,000 years ago, a copy of the D allele crossed from the archaic Homo lineage into humans, possibly by interbreeding between members of the two populations. This copy subsequently spread in humans from a single copy when it first crossed into humans to an allele that is now present in an estimated 70 percent of the population worldwide today.

The estimate of 1.1 million years that separates the two lineages is based on the amount of sequence difference between the D and the non-D alleles. Although the identity of this archaic Homo lineage is yet to be determined, the researchers argue that a likely candidate is the Neanderthals. The 1.1 million year separation between humans and this archaic Homo species is roughly consistent with previous estimates of the amount of evolutionary time separating the Homo sapiens lineage and the Neanderthal lineage, said Lahn. Furthermore, the time of introgression of the D allele into humans -- about 37,000 years ago -- is when humans and Neanderthals coexisted in many parts of the world.

Lahn said the group's data suggest that the interbreeding was unlikely to be a thorough genetic mixing, but rather a rare - and perhaps even a single -- event that introduced the ancestral D allele previously present in this other Homo species into the human line.

“By no means do these findings constitute definitive proof that a Neanderthal was the source of the original copy of the D allele,” said Lahn. “However, our evidence shows that it is one of the best candidates. The timeline - including the introgression of the allele into humans 37,000 years ago and its origin in a lineage that separated with the human line 1.1 million years ago -- agrees with the contact between, and the evolutionary history of, Neanderthals and humans.

“And a third line of evidence, albeit weaker, is that the D alleles are much more prevalent in Eurasia and lower in sub-Saharan Africa, which is consistent with an origin in the former area. And we know that Neanderthals evolved outside of Africa,” said Lahn.

Lahn also said that although the disruption of the microcephalin gene in humans leads to smaller brains, the role of the D alleles in brain evolution remains unknown. “The D alleles may not even change brain size they may only make the brain a bit more efficient if it indeed affects brain function,” he said. “For example, someone inheriting the D allele may have only a slightly more efficient brain on average. While that enhancement might confer only a subtle evolutionary advantage on that person, when that effect is propagated over a thousand generations of natural selection, the result will be to drive the D alleles to a very high prevalence.”

Lahn and his colleagues believe that other genes might well show similar telltale signs of an origin in archaic Homo lineages such as Neanderthals. They are currently using their analytical tool to search for evidence of that origin for other genes in the human genome.

Such findings may have broader implications for understanding human evolution than just revealing the possibility of human-Neanderthal interbreeding, he said. “In addition to being perhaps the most robust genetic evidence for introgression of genes from archaic Homo species into humans, I think this finding demonstrates that the evolution of our species has been profoundly impacted by gene flow from our relative species,” said Lahn.

“Finding evidence of mixing is not all that surprising. But our study demonstrates the possibility that interbreeding contributed advantageous variants into the human gene pool that subsequently spread. This implies that the evolution of human biology has been affected by the contribution of advantageous genetic variants from archaic relatives that we have replaced or even killed off,” he said.

Until now, said Lahn, the scientific debate over genetic exchange between humans and other Homo species has led to two prominent competing theories. One holds that anatomically modern humans replaced archaic species, with no interbreeding. And the other states that extensive interbreeding did take place and that modern humans evolved from that interbreeding in many regions of the world.

Genetic and fossil evidence for the latter “multiregional” theory has been inconclusive, said Lahn, so that theory has been largely discredited. However, he said, the newer evidence of gene exchange -- as well as other genetic evidence that might follow -- could give rise to a more moderate version holding that some genetic exchange did take place. Furthermore, it will become increasingly appreciated that such genetic exchange might have made our species much more fit.


Contents

Genetics Edit

Proportion of admixture Edit

On 7 May 2010, following the genome sequencing of three Vindija Neanderthals, a draft sequence of the Neanderthal genome was published and revealed that Neanderthals shared more alleles with Eurasian populations (e.g. French, Han Chinese, and Papua New Guinean) than with sub-Saharan African populations (e.g. Yoruba and San). [8] According to Green et al. (2010), the authors, the observed excess of genetic similarity is best explained by recent gene flow from Neanderthals to modern humans after the migration out of Africa. [8] They estimated the proportion of Neanderthal-derived ancestry to be 1–4% of the Eurasian genome. [8] Prüfer et al. (2013) estimated the proportion to be 1.5–2.1% for non-Africans, [9] Lohse and Frantz (2014) infer a higher rate of 3.4–7.3% in Eurasia. [10] In 2017, Prüfer et al. revised their estimate to 1.8–2.6% for non-Africans outside Oceania. [11]

According to a later study by Chen et al. (2020), Africans (specifically, the 1000 Genomes African populations) also have Neanderthal admixture, [12] with this Neanderthal admixture in African individuals accounting for 17 megabases, [12] which is 0.3% of their genome. [3] According to the authors, Africans gained their Neanderthal admixture predominantly from a back-migration by peoples (modern humans carrying Neanderthal admixture) that had diverged from ancestral Europeans (postdating the split between East Asians and Europeans). [12] This back-migration is proposed to have happened about 20,000 years ago. [3] However, some scientists, such as geneticist David Reich, dispute the study's conclusions suggesting Neanderthal admixture in sub-Saharan Africans. [13]

Introgressed genome Edit

About 20% of the Neanderthal genome has been found introgressed or assimilated in the modern human population (by analyzing East Asians and Europeans), [14] but the figure has also been estimated at about a third. [15]

Subpopulation admixture rate Edit

A higher Neanderthal admixture was found in East Asians than in Europeans, [14] [16] [17] [18] [19] which is estimated to be about 20% more introgression into East Asians. [14] [16] [19] This could possibly be explained by the occurrence of further admixture events in the early ancestors of East Asians after the separation of Europeans and East Asians, [4] [14] [16] [17] [19] dilution of Neanderthal ancestry in Europeans by populations with low Neanderthal ancestry from later migrations, [4] [16] [19] or natural selection that may have been relatively lower in East Asians than in Europeans. [4] [18] [19] Studies simulating admixture models indicate that a reduced efficacy of purifying selection against Neanderthal alleles in East Asians could not account for the greater proportion of Neanderthal ancestry of East Asians, thus favoring more-complex models involving additional pulses of Neanderthal introgression into East Asians. [20] [21] Such models show a pulse to ancestral Eurasians, followed by separation and an additional pulse to ancestral East Asians. [4] It is observed that there is a small but significant variation of Neanderthal admixture rates within European populations, but no significant variation within East Asian populations. [14] Prüfer et al. (2017) remarked that East Asians carry more Neanderthal DNA (2.3–2.6%) than Western Eurasians (1.8–2.4%). [11]

It was later determined by Chen et al. (2020) that East Asians have 8% more Neanderthal ancestry, revised from the previous reports of 20% more Neanderthal ancestry, compared to Europeans. [12] This stems from the fact that Neanderthal ancestry shared with Africans had been masked, because Africans were thought to have no Neanderthal admixture and were therefore used as reference samples. [12] Thus, any overlap in Neanderthal admixture with Africans resulted in an underestimation of Neanderthal admixture in non-Africans and especially in Europeans. [12] The authors give a single pulse of Neanderthal admixture after the out-of-Africa dispersal as the most parsimonious explanation for the enrichment in East Asians, but they add that variation in Neanderthal ancestry may also be attributed to dilution to account for the now-more-modest differences found. [12] As a proportion of the total amount of Neanderthal sequence for each population, 7.2% of the sequence in Europeans is shared exclusively with Africans, while 2% of the sequence in East Asians is shared exclusively with Africans. [12]

Genomic analysis suggests that there is a global division in Neanderthal introgression between sub-Saharan African populations and other modern human groups (including North Africans) rather than between African and non-African populations. [22] North African groups share a similar excess of derived alleles with Neanderthals as do non-African populations, whereas sub-Saharan African groups are the only modern human populations that generally did not experience Neanderthal admixture. [23] The Neanderthal genetic signal among North African populations was found to vary depending on the relative quantity of autochthonous North African, European, Near Eastern and sub-Saharan ancestry. Using f4 ancestry ratio statistical analysis, the Neanderthal inferred admixture was observed to be: highest among the North African populations with maximal autochthonous North African ancestry such as Tunisian Berbers, where it was at the same level or even higher than that of Eurasian populations (100–138%) high among North African populations carrying greater European or Near Eastern admixture, such as groups in North Morocco and Egypt (∼60–70%) and lowest among North African populations with greater Sub-Saharan admixture, such as in South Morocco (20%). [24] Quinto et al. (2012) therefore postulate that the presence of this Neanderthal genetic signal in Africa is not due to recent gene flow from Near Eastern or European populations since it is higher among populations bearing indigenous pre-Neolithic North African ancestry. [25] Low but significant rates of Neanderthal admixture has also been observed for the Maasai of East Africa. [26] After identifying African and non-African ancestry among the Maasai, it can be concluded that recent non-African modern human (post-Neanderthal) gene flow was the source of the contribution since around an estimated 30% of the Maasai genome can be traced to non-African introgression from about 100 generations ago. [17]

Distance to lineages Edit

Presenting a high-quality genome sequence of a female Altai Neanderthal, it has been found that the Neanderthal component in non-African modern humans is more related to the Mezmaiskaya Neanderthal (Caucasus) than to the Altai Neanderthal (Siberia) or the Vindija Neanderthals (Croatia). [9] By high-coverage sequencing the genome of a 50,000-year-old female Vindija Neanderthal fragment, it was later found that the Vindija and Mezmaiskaya Neanderthals did not seem to differ in the extent of their allele-sharing with modern humans. [11] In this case, it was also found that the Neanderthal component in non-African modern humans is more closely related to the Vindija and Mezmaiskaya Neanderthals than to the Altai Neanderthal. [11] These results suggest that a majority of the admixture into modern humans came from Neanderthal populations that had diverged (about 80–100kya) from the Vindija and Mezmaiskaya Neanderthal lineages before the latter two diverged from each other. [11]

Analyzing chromosome 21 of the Altai (Siberia), El Sidrón (Spain), and Vindija (Croatia) Neanderthals, it is determined that—of these three lineages—only the El Sidrón and Vindija Neanderthals display significant rates of gene flow (0.3–2.6%) into modern humans, suggesting that the El Sidrón and Vindija Neanderthals are more closely related than the Altai Neanderthal to the Neanderthals that interbred with modern humans about 47,000–65,000 years ago. [28] Conversely, it is also determined that significant rates of modern human gene flow into Neanderthals occurred—of the three examined lineages—for only the Altai Neanderthal (0.1–2.1%), suggesting that modern human gene flow into Neanderthals mainly took place after the separation of the Altai Neanderthals from the El Sidrón and Vindija Neanderthals that occurred roughly 110,000 years ago. [28] The findings show that the source of modern human gene flow into Neanderthals originated from a population of early modern humans from about 100,000 years ago, predating the out-of-Africa migration of the modern human ancestors of present-day non-Africans. [28]

Mitochondrial DNA and Y chromosome Edit

No evidence of Neanderthal mitochondrial DNA has been found in modern humans. [29] [30] [31] This suggests that successful Neanderthal admixture happened in pairings with Neanderthal males and modern human females. [32] [33] Possible hypotheses are that Neanderthal mitochondrial DNA had detrimental mutations that led to the extinction of carriers, that the hybrid offspring of Neanderthal mothers were raised in Neanderthal groups and became extinct with them, or that female Neanderthals and male Sapiens did not produce fertile offspring. [32] However this is contested by recent findings that suggest that the Neanderthal's Y chromosome was replaced by Sapiens' Y chromosomes after the human Y chromosome entered the Neanderthal gene pool, meaning that male Sapiens must have mated with female Neanderthals at some point. [2]

As shown in an interbreeding model produced by Neves and Serva (2012), the Neanderthal admixture in modern humans may have been caused by a very low rate of interbreeding between modern humans and Neanderthals, with the exchange of one pair of individuals between the two populations in about every 77 generations. [34] This low rate of interbreeding would account for the absence of Neanderthal mitochondrial DNA from the modern human gene pool as found in earlier studies, as the model estimates a probability of only 7% for a Neanderthal origin of both mitochondrial DNA and Y chromosome in modern humans. [34]

Reduced contribution Edit

There is a presence of large genomic regions with strongly reduced Neanderthal contribution in modern humans due to negative selection, [14] [18] partly caused by hybrid male infertility. [18] These large regions of low Neanderthal contribution were most-pronounced on the X chromosome—with fivefold lower Neanderthal ancestry compared to autosomes. [4] [18] They also contained relatively high numbers of genes specific to testes. [18] This means that modern humans have relatively few Neanderthal genes that are located on the X chromosome or expressed in the testes, suggesting male infertility as a probable cause. [18] It may be partly affected by hemizygosity of X chromosome genes in males. [4]

Deserts of Neanderthal sequences may also be caused by genetic drift involving intense bottlenecks in the modern human population and background selection as a result of strong selection against deleterious Neanderthal alleles. [4] The overlap of many deserts of Neanderthal and Denisovan sequences suggests that repeated loss of archaic DNA occur at specific loci. [4]

It has also been shown that Neanderthal ancestry has been selected against in conserved biological pathways, such as RNA processing. [18]

Consistent with the hypothesis that purifying selection has reduced Neanderthal contribution in present-day modern human genomes, Upper Paleolithic Eurasian modern humans (such as the Tianyuan modern human) carry more Neanderthal DNA (about 4–5%) than present-day Eurasian modern humans (about 1–2%). [35]

Rates of selection against Neanderthal sequences varied for European and Asian populations. [4]

Changes in modern humans Edit

In Eurasia, modern humans inherited adaptive introgression from archaic humans, which provided a source of advantageous genetic variants that are adapted to local environments and a reservoir for additional genetic variation. [4] Adaptive introgression from Neanderthals has targeted genes involved with keratin filaments, sugar metabolism, muscle contraction, body fat distribution, enamel thickness, and oocyte meiosis, as well as brain size and functioning. [36] There are signals of positive selection, as the result of adaptation to diverse habitats, in genes involved with variation in skin pigmentation and hair morphology. [36] In the immune system, introgressed variants have heavily contributed to the diversity of immune genes, of which there's an enrichment of introgressed alleles that suggest a strong positive selection. [36]

Genes affecting keratin were found to have been introgressed from Neanderthals into modern humans (shown in East Asians and Europeans), suggesting that these genes gave a morphological adaptation in skin and hair to modern humans to cope with non-African environments. [14] [18] This is likewise for several genes involved in medical-relevant phenotypes, such as those affecting systemic lupus erythematosus, primary biliary cirrhosis, Crohn's disease, optic disk size, smoking behavior, interleukin 18 levels, and diabetes mellitus type 2. [18]

Researchers found Neanderthal introgression of 18 genes—several of which are related to UV-light adaptation—within the chromosome 3p21.31 region (HYAL region) of East Asians. [37] The introgressive haplotypes were positively selected in only East Asian populations, rising steadily from 45,000 years BP until a sudden increase of growth rate around 5,000 to 3,500 years BP. [37] They occur at very high frequencies among East Asian populations in contrast to other Eurasian populations (e.g. European and South Asian populations). [37] The findings also suggests that this Neanderthal introgression occurred within the ancestral population shared by East Asians and Native Americans. [37]

Evans et al. (2006) had previously suggested that a group of alleles collectively known as haplogroup D of microcephalin, a critical regulatory gene for brain volume, originated from an archaic human population. [38] The results show that haplogroup D introgressed 37,000 years ago (based on the coalescence age of derived D alleles) into modern humans from an archaic human population that separated 1.1 million years ago (based on the separation time between D and non-D alleles), consistent with the period when Neanderthals and modern humans co-existed and diverged respectively. [38] The high frequency of the D haplogroup (70%) suggest that it was positively selected for in modern humans. [38] The distribution of the D allele of microcephalin is high outside Africa but low in sub-Saharan Africa, which further suggest that the admixture event happened in archaic Eurasian populations. [38] This distribution difference between Africa and Eurasia suggests that the D allele originated from Neanderthals according to Lari et al. (2010), but they found that a Neanderthal individual from the Mezzena Rockshelter (Monti Lessini, Italy) was homozygous for an ancestral allele of microcephalin, thus providing no support that Neanderthals contributed the D allele to modern humans and also not excluding the possibility of a Neanderthal origin of the D allele. [39] Green et al. (2010), having analyzed the Vindija Neanderthals, also could not confirm a Neanderthal origin of haplogroup D of the microcephalin gene. [8]

It has been found that HLA-A*02, A*26/*66, B*07, B*51, C*07:02, and C*16:02 of the immune system were contributed from Neanderthals to modern humans. [40] After migrating out of Africa, modern humans encountered and interbred with archaic humans, which was advantageous for modern humans in rapidly restoring HLA diversity and acquiring new HLA variants that are better adapted to local pathogens. [40]

It is found that introgressed Neanderthal genes exhibit cis-regulatory effects in modern humans, contributing to the genomic complexity and phenotype variation of modern humans. [41] Looking at heterozygous individuals (carrying both Neanderthal and modern human versions of a gene), the allele-specific expression of introgressed Neanderthal alleles was found to be significantly lower in the brain and testes relative to other tissues. [4] [41] In the brain, this was most pronounced at the cerebellum and basal ganglia. [41] This downregulation suggests that modern humans and Neanderthals possibly experienced a relative higher rate of divergence in these specific tissues. [41]

Furthermore, correlating the genotypes of introgressed Neanderthal alleles with the expression of nearby genes, it is found that archaic alleles contribute proportionally more to variation in expression than nonarchaic alleles. [4] Neanderthal alleles affect expression of the immunologically genes OAS1/2/3 and TLR1/6/10, which can be specific to cell-type and is influenced by environmental stimuli. [4]

Studying the high-coverage female Vindija Neanderthal genome, Prüfer et al. (2017) identified several Neanderthal-derived gene variants, including those that affect levels of LDL cholesterol and vitamin D, and has influence on eating disorders, visceral fat accumulation, rheumatoid arthritis, schizophrenia, as well as the response to antipsychotic drugs. [11]

Examining European modern humans in regards to the Altai Neanderthal genome in high-coverage, results show that Neanderthal admixture is associated with several changes in cranium and underlying brain morphology, suggesting changes in neurological function through Neanderthal-derived genetic variation. [42] Neanderthal admixture is associated with an expansion of the posterolateral area of the modern human skull, extending from the occipital and inferior parietal bones to bilateral temporal locales. [42] In regards to modern human brain morphology, Neanderthal admixture is positively correlated with an increase in sulcal depth for the right intraparietal sulcus and an increase in cortical complexity for the early visual cortex of the left hemisphere. [42] Neanderthal admixture is also positively correlated with an increase in white and gray matter volume localized to the right parietal region adjacent to the right intraparietal sulcus. [42] In the area overlapping the primary visual cortex gyrification in the left hemisphere, Neanderthal admixture is positively correlated with gray matter volume. [42] The results also show evidence for a negative correlation between Neanderthal admixture and white matter volume in the orbitofrontal cortex. [42]

In Papuans, assimilated Neanderthal inheritance is found in highest frequency in genes expressed in the brain, whereas Denisovan DNA has the highest frequency in genes expressed in bones and other tissues. [43]

Population substructure theory Edit

Although less parsimonious than recent gene flow, the observation may have been due to ancient population sub-structure in Africa, causing incomplete genetic homogenization within modern humans when Neanderthals diverged while early ancestors of Eurasians were still more closely related to Neanderthals than those of Africans to Neanderthals. [8] On the basis of allele frequency spectrum, it was shown that the recent admixture model had the best fit to the results while the ancient population sub-structure model had no fit–demonstrating that the best model was a recent admixture event that was preceded by a bottleneck event among modern humans—thus confirming recent admixture as the most parsimonious and plausible explanation for the observed excess of genetic similarities between modern non-African humans and Neanderthals. [44] On the basis of linkage disequilibrium patterns, a recent admixture event is likewise confirmed by the data. [45] From the extent of linkage disequilibrium, it was estimated that the last Neanderthal gene flow into early ancestors of Europeans occurred 47,000–65,000 years BP. [45] In conjunction with archaeological and fossil evidence, the gene flow is thought likely to have occurred somewhere in Western Eurasia, possibly the Middle East. [45] Through another approach—using one genome each of a Neanderthal, Eurasian, African, and chimpanzee (outgroup), and dividing it into non-recombining short sequence blocks—to estimate genome-wide maximum-likelihood under different models, an ancient population sub-structure in Africa was ruled out and a Neanderthal admixture event was confirmed. [10]

Morphology Edit

The early Upper Paleolithic burial remains of a modern human child from Abrigo do Lagar Velho (Portugal) features traits that indicate Neanderthal interbreeding with modern humans dispersing into Iberia. [46] Considering the dating of the burial remains (24,500 years BP) and the persistence of Neanderthal traits long after the transitional period from a Neanderthal to a modern human population in Iberia (28,000–30,000 years BP), the child may have been a descendant of an already heavily admixed population. [46]

The remains of an early Upper Paleolithic modern human from Peștera Muierilor (Romania) of 35,000 years BP shows a morphological pattern of European early modern humans, but possesses archaic or Neanderthal features, suggesting European early modern humans interbreeding with Neanderthals. [47] These features include a large interorbital breadth, a relatively flat superciliary arches, a prominent occipital bun, an asymmetrical and shallow mandibular notch shape, a high mandibular coronoid processus, the relative perpendicular mandibular condyle to notch crest position, and a narrow scapular glenoid fossa. [47]

The early modern human Oase 1 mandible from Peștera cu Oase (Romania) of 34,000–36,000 14 C years BP presents a mosaic of modern, archaic, and possible Neanderthal features. [49] It displays a lingual bridging of the mandibular foramen, not present in earlier humans except Neanderthals of the late Middle and Late Pleistocene, thus suggesting affinity with Neanderthals. [49] Concluding from the Oase 1 mandible, there was apparently a significant craniofacial change of early modern humans from at least Europe, possibly due to some degree of admixture with Neanderthals. [49]

The earliest (before about 33 ka BP) European modern humans and the subsequent (Middle Upper Paleolithic) Gravettians, falling anatomically largely inline with the earliest (Middle Paleolithic) African modern humans, also show traits that are distinctively Neanderthal, suggesting that a solely Middle Paleolithic modern human ancestry was unlikely for European early modern humans. [50]

A late-Neanderthal jaw (more specifically, a corpus mandibulae remnant) from the Mezzena rockshelter (Monti Lessini, Italy) shows indications of a possible interbreeding in late Italian Neanderthals. [51] The jaw falls within the morphological range of modern humans, but also displayed strong similarities with some of the other Neanderthal specimens, indicating a change in late Neanderthal morphology due to possible interbreeding with modern humans. [51] However, a more recent aDNA analysis of this jaw has shown that it does not belong to a Neanderthal, but to a fully modern human of the Holocene. Previous reports of a Mezzena "Neanderthal hybrid" were based on a faulty DNA analysis. [52]

Manot 1, a partial calvarium of a modern human that was recently discovered at the Manot Cave (Western Galilee, Israel) and dated to 54.7±5.5 kyr BP, represents the first fossil evidence from the period when modern humans successfully migrated out of Africa and colonized Eurasia. [53] It also provides the first fossil evidence that modern humans inhabited the southern Levant during the Middle to Upper Palaeolithic interface, contemporaneously with the Neanderthals and close to the probable interbreeding event. [53] The morphological features suggest that the Manot population may be closely related to or given rise to the first modern humans who later successfully colonized Europe to establish early Upper Palaeolithic populations. [53]

History Edit

The interbreeding has been discussed ever since the discovery of Neanderthal remains in the 19th century, though earlier writers believed that Neanderthals were a direct ancestor of modern humans. Thomas Huxley suggested that many Europeans bore traces of Neanderthal ancestry, but associated Neanderthal characteristics with primitivism, writing that since they "belong to a stage in the development of the human species, antecedent to the differentiation of any of the existing races, we may expect to find them in the lowest of these races, all over the world, and in the early stages of all races". [54]

Until the early 1950s, most scholars thought Neanderthals were not in the ancestry of living humans. [55] : 232–34 [56] Nevertheless, Hans Peder Steensby proposed interbreeding in 1907 in the article Race studies in Denmark. He strongly emphasised that all living humans are of mixed origins. [57] He held that this would best fit observations, and challenged the widespread idea that Neanderthals were ape-like or inferior. Basing his argument primarily on cranial data, he noted that the Danes, like the Frisians and the Dutch, exhibit some Neanderthaloid characteristics, and felt it was reasonable to "assume something was inherited" and that Neanderthals "are among our ancestors."

Carleton Stevens Coon in 1962 found it likely, based upon evidence from cranial data and material culture, that Neanderthal and Upper Paleolithic peoples either interbred or that the newcomers reworked Neanderthal implements "into their own kind of tools." [58]

By the early 2000s, the majority of scholars supported the Out of Africa hypothesis, [59] [60] according to which anatomically modern humans left Africa about 50,000 years ago and replaced Neanderthals with little or no interbreeding. Yet some scholars still argued for hybridisation with Neanderthals. The most vocal proponent of the hybridisation hypothesis was Erik Trinkaus of Washington University. [61] Trinkaus claimed various fossils as products of hybridised populations, including the skeleton of a child found at Lagar Velho in Portugal [62] [63] [64] and the Peștera Muierii skeletons from Romania. [47]

Genetics Edit

Proportion of admixture Edit

It has been shown that Melanesians (e.g. Papua New Guinean and Bougainville Islander) share relatively more alleles with Denisovans when compared to other Eurasians and Africans. [65] It is estimated that 4% to 6% of the genome in Melanesians derives from Denisovans, while no other Eurasians or Africans displayed contributions of the Denisovan genes. [65] It has been observed that Denisovans contributed genes to Melanesians but not to East Asians, indicating that there was interaction between the early ancestors of Melanesians with Denisovans but that this interaction did not take place in the regions near southern Siberia, where as-of-yet the only Denisovan remains have been found. [65] In addition, Aboriginal Australians also show a relative increased allele sharing with Denisovans, compared to other Eurasians and African populations, consistent with the hypothesis of increased admixture between Denisovans and Melanesians. [66]

Reich et al. (2011) produced evidence that the highest presence of Denisovan admixture is in Oceanian populations, followed by many Southeast Asian populations, and none in East Asian populations. [67] There is significant Denisovan genetic material in eastern Southeast Asian and Oceanian populations (e.g. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, eastern Indonesians, Philippine Mamanwa and Manobo), but not in certain western and continental Southeast Asian populations (e.g. western Indonesians, Malaysian Jehai, Andaman Onge, and mainland Asians), indicating that the Denisovan admixture event happened in Southeast Asia itself rather than mainland Eurasia. [67] The observation of high Denisovan admixture in Oceania and the lack thereof in mainland Asia suggests that early modern humans and Denisovans had interbred east of the Wallace Line that divides Southeast Asia according to Cooper and Stringer (2013). [68]

Skoglund and Jakobsson (2011) observed that particularly Oceanians, followed by Southeast Asians populations, have a high Denisovans admixture relative to other populations. [69] Furthermore, they found possible low traces of Denisovan admixture in East Asians and no Denisovan admixture in Native Americans. [69] In contrast, Prüfer et al. (2013) found that mainland Asian and Native American populations may have a 0.2% Denisovan contribution, which is about twenty-five times lower than Oceanian populations. [9] The manner of gene flow to these populations remains unknown. [9] However, Wall et al. (2013) stated that they found no evidence for Denisovan admixture in East Asians. [17]

Findings indicate that the Denisovan gene flow event happened to the common ancestors of Aboriginal Filipinos, Aboriginal Australians, and New Guineans. [67] [70] New Guineans and Australians have similar rates of Denisovan admixture, indicating that interbreeding took place prior to their common ancestors' entry into Sahul (Pleistocene New Guinea and Australia), at least 44,000 years ago. [67] It has also been observed that the fraction of Near Oceanian ancestry in Southeast Asians is proportional to the Denisovan admixture, except in the Philippines where there is a higher proportional Denisovan admixture to Near Oceanian ancestry. [67] Reich et al. (2011) suggested a possible model of an early eastward migration wave of modern humans, some who were Philippine/New Guinean/Australian common ancestors that interbred with Denisovans, respectively followed by divergence of the Philippine early ancestors, interbreeding between the New Guinean and Australian early ancestors with a part of the same early-migration population that did not experience Denisovan gene flow, and interbreeding between the Philippine early ancestors with a part of the population from a much-later eastward migration wave (the other part of the migrating population would become East Asians). [67]

Finding components of Denisovan introgression with differing relatedness to the sequenced Denisovan, Browning et al. (2018) suggested that at least two separate episodes of Denisovan admixture has occurred. [71] Specifically, introgression from two distinct Denisovan populations is observed in East Asians (e.g. Japanese and Han Chinese), whereas South Asians (e.g. Telugu and Punjabi) and Oceanians (e.g. Papuans) display introgression from one Denisovan population. [71]

Exploring derived alleles from Denisovans, Sankararaman et al. (2016) estimated that the date of Denisovan admixture was 44,000–54,000 years ago. [5] They also determined that the Denisovan admixture was the greatest in Oceanian populations compared to other populations with observed Denisovan ancestry (i.e. America, Central Asia, East Asia, and South Asia). [5] The researchers also made the surprising finding that South Asian populations display an elevated Denisovan admixture (when compared to other non-Oceanian populations with Denisovan ancestry), albeit the highest estimate (which are found in Sherpas) is still ten times lower than in Papuans. [5] They suggest two possible explanations: There was a single Denisovan introgression event that was followed by dilution to different extents or at least three distinct pulses of Denisovan introgressions must have occurred. [5]

It has been shown that Eurasians have some but significantly lesser archaic-derived genetic material that overlaps with Denisovans, stemming from the fact that Denisovans are related to Neanderthals—who contributed to the Eurasian gene pool—rather than from interbreeding of Denisovans with the early ancestors of those Eurasians. [16] [65]

The skeletal remains of an early modern human from the Tianyuan cave (near Zhoukoudian, China) of 40,000 years BP showed a Neanderthal contribution within the range of today's Eurasian modern humans, but it had no discernible Denisovan contribution. [72] It is a distant relative to the ancestors of many Asian and Native American populations, but post-dated the divergence between Asians and Europeans. [72] The lack of a Denisovan component in the Tianyuan individual suggests that the genetic contribution had been always scarce in the mainland. [9]

Reduced contribution Edit

There are large genomic regions devoid of Denisovan-derived ancestry, partly explained by infertility of male hybrids, as suggested by the lower proportion of Denisovan-derived ancestry on X chromosomes and in genes that are expressed in the testes of modern humans. [5]

Changes in modern humans Edit

Exploring the immune system's HLA alleles, it has been suggested that HLA-B*73 introgressed from Denisovans into modern humans in western Asia due to the distribution pattern and divergence of HLA-B*73 from other HLA alleles. [40] Even though HLA-B*73 is not present in the sequenced Denisovan genome, HLA-B*73 was shown to be closely associated to the Denisovan-derived HLA-C*15:05 from the linkage disequilibrium. [40] From phylogenetic analysis, however, it has been concluded that it is highly likely that HLA-B*73 was ancestral. [36]

The Denisovan's two HLA-A (A*02 and A*11) and two HLA-C (C*15 and C*12:02) allotypes correspond to common alleles in modern humans, whereas one of the Denisovan's HLA-B allotype corresponds to a rare recombinant allele and the other is absent in modern humans. [40] It is thought that these must have been contributed from Denisovans to modern humans, because it is unlikely to have been preserved independently in both for so long due to HLA alleles' high mutation rate. [40]

Tibetan people received an advantageous EGLN1 and EPAS1 gene variant, associated with hemoglobin concentration and response to hypoxia, for life at high altitudes from the Denisovans. [36] The ancestral variant of EPAS1 upregulates hemoglobin levels to compensate for low oxygen levels—such as at high altitudes—but this also has the maladaption of increasing blood viscosity. [73] The Denisovan-derived variant on the other hand limits this increase of hemoglobin levels, thus resulting in a better altitude adaption. [73] The Denisovan-derived EPAS1 gene variant is common in Tibetans and was positively selected in their ancestors after they colonized the Tibetan plateau. [73]

Rapid decay of fossils in Sub-Saharan African environments makes it currently unfeasible to compare modern human admixture with reference samples of archaic Sub-Saharan African hominins. [4] [74]

From three candidate regions with introgression found by searching for unusual patterns of variations (showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size) in 61 non-coding regions from two hunter-gatherer groups (Biaka Pygmies and San who have significant admixture) and one West African agricultural group (Mandinka, who don't have significant admixture), it is concluded that roughly 2% of the genetic material found in the Biaka Pygmies and San was inserted into the human genome approximately 35,000 years ago from archaic hominins that separated from the ancestors of the modern human lineage around 700,000 years ago. [75] A survey for the introgressive haplotypes across many Sub-Saharan populations suggest that this admixture event happened with archaic hominins who once inhabited Central Africa. [75]

Researching high-coverage whole-genome sequences of fifteen Sub-Saharan hunter-gatherer males from three groups—five Pygmies (three Baka, a Bedzan, and a Bakola) from Cameroon, five Hadza from Tanzania, and five Sandawe from Tanzania—there are signs that the ancestors of the hunter-gatherers interbred with one or more archaic human populations, [74] probably over 40,000 years ago. [76] Analysis of putative introgressive haplotypes in the fifteen hunter-gatherer samples suggests that the archaic African population and modern humans diverged around 1.2 to 1.3 million years ago. [74]

According to a study published in 2020, there are indications that 2% to 19% (or about ≃6.6 and ≃7.0%) of the DNA of four West African populations may have come from an unknown archaic hominin which split from the ancestor of humans and Neanderthals between 360 kya to 1.02 mya. However, the study also finds that at least part of this proposed archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans). [77] [78] [79] Another recent study, which discovered substantial amounts of previously undescribed human genetic variation, also found ancestral genetic variation in Africans that predates modern humans and was lost in most non-Africans. [80]

In 2019, scientists discovered evidence, based on genetics studies using artificial intelligence (AI), that suggests the existence of an unknown human ancestor species, not Neanderthal or Denisovan, in the genome of modern humans. [81] [82]


Ancient mixers

The new research illustrates the complexity of humanity's deep history. Evidence has long been accumulating that humans and Neanderthals mated while their populations overlapped in Europe, before Neanderthals went extinct around 30,000 years ago. In 2010, researchers reported that between 1% and 4% of modern human genes in people in Asia, Europe and Oceania came from Neanderthal ancestors. When you add up all the snippets of Neanderthal DNA present in all modern humans today, some 20% of the Neanderthal genome may be preserved, according to 2014 research.

As scientists have been able to sequence more fragile fragments of DNA from fossils of ancient human ancestors, they've discovered a complex web of interbreeding stretching back millennia. Some Pacific Islanders, for example, carry pieces of the DNA of a mysterious ancient species of humans known as Denisovans.

The researchers of the new study used a computational method of comparing the genomes of two Neanderthals, a Denisovan and two modern African individuals. (Africans were chosen because modern people in Africa don't carry Neanderthal genes from the well-known human-Neanderthal interbreeding that occurred in Europe starting 50,000 years ago.) This method allowed the researchers to capture recombination events, in which segments of chromosomes — which are made up of DNA — from one individual get incorporated into the chromosomes of another.

"We are trying to build a complete model for the evolutionary history of every segment of the genome, jointly across all of the analyzed individuals," Siepel said. "The ancestral recombination graph, as it is known, includes a tree that captures the relationships among all individuals at every position along the genome, and the recombination events that cause those trees to change from one position to the next."

One advantage of the method, Siepel said, is that it allows researchers to find recombination events inside of recombination events. For example, if a bit of ancient hominin DNA from an unknown ancestor were incorporated in the Neanderthal genome, and then a later mating event between Neanderthals and humans inserted that mystery DNA into the human genome, the method allows for the identification of this "nested" DNA.


Splitting apart

This kind of speciation, known as sympatry, was once thought to be extremely unlikely, says Chris Bird of Texas A&M University Corpus Christi, who studies how organisms are evolving by analysing their genomes. The conventional view is that speciation almost always requires two populations to be physically separated to prevent interbreeding, for example, living on different sides of a mountain, or on different islands in an archipelago.

This is because when animals mate, a process called recombination mixes up gene variants, meaning the genes of a mother and a father will be shuffled together in future generations. As long as interbreeding continues, it’s unlikely that two groups with distinctly different genetic traits will arise.

But Marques’ team found that the genetic differences between the two fish types are concentrated on the parts of chromosomes that are less likely to undergo recombination. As a result, the sets of gene variants that give the two types their distinct characteristics are less likely to get split up.


Genetic exchange

Professor Michael Kohn from Rice University in Houston, Texas, led the team of researchers who carried out the work.

"Our study is so special because it involves hybridisation between two species of mouse that are 1.5-3 million years removed from each other.

"Most of the offspring. do not reproduce, they are sterile - but there is a small window, which remains open for genes to be moved from one species to the other, and that's through a few fertile females - so there is a chance to leak genes from one species to another."

Thanks to these few fertile females, the vast majority of mice in Spain and a growing number in Germany have acquired resistance over a very short period of time, although scientists aren't exactly sure when the first genetic exchanges took place.

And while they may not look any different from normal household mice, in their genetic code they now have the ability to survive the strongest chemicals in the pest control armoury.

"There are a lot of genetic barriers between these species of mice, to see them hybridise and transfer genetic material is quite spectacular, to be frank," said Professor Kohn.

The researchers say that increased human travel and population growth are responsible for bringing these mice species together and putting them under evolutionary stress by trying to poison them.

They are concerned that similar human pressures could afford rats both the necessity and the opportunity to breed across species, resulting in rodents that are almost impossible to control.


Adaptive Radiation

The processes described in this page can occur over and over. In the case of Darwin's finches, they must have been repeated a number of times forming new species that gradually divided the available habitats between them. From the first arrival have come a variety of ground-feeding and tree-feeding finches as well as the warblerlike finch and the tool-using woodpeckerlike finch. The formation of a number of diverse species from a single ancestral one is called an adaptive radiation.

Speciateion in theHouse mice on the island of Madeira

A report in the 13 January 2000 issue of Nature describes a study of house mouse populations on the island of Madeira off the Northwest coast of Africa. These workers (Janice Britton-Davidian et al) examined the karyotypes of 143 house mice (Mus musculus domesticus) from various locations along the coast of this mountainous island.

  • There are 6 distinct populations (shown by different colors)
  • Each of these has a distinct karyotype, with a diploid number less than the "normal" (2n = 40).
  • The reduction in chromosome number has occurred through Robertsonian fusions. Mouse chromosomes tend to be acrocentric that is, the centromere connects one long and one very short arm. Acrocentric chromosomes are at risk of translocations that fuse the long arms of two different chromosomes with the loss of the short arms.
  • The different populations are allopatric isolated in different valleys leading down to the sea.
  • The distinct and uniform karyotype found in each population probably arose from genetic drift rather than natural selection.
  • The 6 different populations are technically described as races because there is no opportunity for them to attempt interbreeding.
  • However, they surely meet the definition of true species. While hybrids would form easily (no prezygotic isolating mechanisms), these would probably be infertile as proper synapsis and segregation of such different chromosomes would be difficult when the hybrids attempted to form gametes by meiosis.

Pizzly Bears

Scientists confirmed last week that a bear shot by an Inuvialuit hunter in the Northwest Territories is a second-generation grizzly-polar bear hybrid—a “pizzly” or “grolar” bear. Why can some interbreeding species produce fertile offspring, while others—like horses and donkeys—cannot?

Because they have more recent common ancestry. When geographical barriers—such as rising sea levels or retracting ice floes—separate populations, they may develop genetic, physiological, or behavioral differences changes in chromosome structure or number differently shaped genitalia or incompatible mating times and rituals—any of which can prevent successful reproduction. Take horses and donkeys, which probably diverged about 2.4 million years ago. Horses have 64 chromosomes, while donkeys have 62, and when they mate, their chromosomes don’t pair up properly, inhibiting meiosis in their offspring. As a result, mules are sterile. Brown bears and polar bears, by contrast, evolved from the same ancestor only about 150,000 years ago—a relatively brief period—and have not developed significant genetic differences.

The prevailing theory holds that polar bears diverged from brown bears at the end of the last ice age (the Pleistocene), when a population followed retreating ice northward. As they adapted to their new arctic home, the separated population lost the brown bear’s hump and developed the polar bear’s characteristic hair (which is actually clear), narrower shoulders, longer neck, smaller head, and partially webbed toes. Despite appearances, polar bears and grizzlies are still genetically quite similar. In fact, there are multiple instances of the two species successfully interbreeding in zoos.

The reason grizzlies and polar bears rarely interbreed in the wild is that, generally speaking, they don’t cross paths during mating season. Barren-ground grizzlies live primarily on land, where they feast on caribou and berries, and mate from May to July meanwhile, polar bears mate from April to June while hunting for seals along the sea ice. But four years ago, a sports hunter shot a male grizzly-polar bear hybrid near Banks Island (just west of Victoria Island), proving that at least a couple of wild bears bridged their differences. The hybrid shot last month was the offspring of a female hybrid and male grizzly, bringing the total known wild hybrid count to three (counting the two dead bears and hybrid mother). It’s possible there could be more out there. Some scientists are re-evaluating past sightings of bears that they assumed, at the time, were blonde grizzlies.

Some scientists believe that global warming could cause the hybridization of many arctic animals, particularly marine mammals. The thinking goes that as Arctic sea ice melts, closely related species in the North Pacific and North Atlantic will come into contact and interbreed. In the case of polar bears, loss of habitat could drive them to land, where they may come into contact with grizzlies. Other scientists, however, aren’t convinced that climate change is the trigger for the hybrid bears. Changes in sea ice have been less drastic in the Beaufort Sea than in other parts of the arctic, and it seems quite possible that the pizzlies resulted from breeding pairs that met on ice, rather than on land.

Got a question about today’s news? Ask the Explainer.

Explainer thanks Brendan P. Kelly of the International Arctic Research Center, Karyn D. Rode of U.S. Fish and Wildlife Service, Lily Peacock of the USGS Alaska Science Center, Sandra Talbot of the USGS Alaska Science Center, and Marsha Branigan of the Department of Environment and Natural Resources in the Northwest Territories.

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