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How much difference in genome is enough to prevent interbreeding?

How much difference in genome is enough to prevent interbreeding?


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I am not a biologist. I am a software developer interested in genetic algorithms therefore i am probably talking to biologists who also have a knowledge of genetic algorithms. I need to "breed" different solutions to a problem while allowing the number of genes in my solution to vary because i don't know in advance how many genes i need. This is why i need to be able to cross solutions with N genes with solutions with M genes and this is a serious problem. If N and M are very different the problem would be even more serious. I want to know what happens in the biological world. I am trying to understand how much difference in genome is "enough" to prevent interbreeding between different organisms. Would it be possible to say that if less than (approximately) X% of the genes of two organisms are different then they can probably mate and have offspring? Thank you

Wentu


Scientists Identify Neanderthal Genes in Modern Human DNA

In two new studies, genetic researchers have shown that about 20 percent of the Neanderthal genome survives in modern humans of non-African ancestry and identified exactly which areas of the human genome retain segments of Neanderthal DNA.

Neanderthal. Image credit: Trustees of the Natural History Museum, London.

About 30,000 years ago, Homo sapiens migrating out of Africa began encountering Neanderthals, a lineage that had diverged from modern humans hundreds of thousands of years before. Despite their differences, Homo sapiens and Neanderthals mingled, and over time, produced children with genes from both lineages.

Today, the biological remnants of that collision between two distinct populations remain alive in the genomes of Europeans and East Asians.

The first study, reported in the journal Nature, examines how Neanderthals influence the genetic composition of modern humans.

Study’s senior author Dr David Reich of Harvard Medical School said: “the goal was to understand the biological impact of the gene flow between Neanderthals and modern humans.”

“We reasoned that when these two groups met and mixed, some new traits would have been selected for and remained in the human genome, while some incompatibilities would have been selected against and removed.”

“As methods to analyze ancient DNA continue to improve, we are able to get at answers to ever more fine-grained questions about our evolutionary history,” added Dr Elizabeth Tran of the National Science Foundation, who was not involved in the studies.

Dr Reich and his colleagues analyzed genetic variants in 846 people of non-African heritage, 176 people from sub-Saharan Africa, and a 50,000-year-old Neanderthal.

They showed that nine previously identified human genetic variants known to be associated with specific traits likely came from Neanderthals. These variants affect lupus, biliary cirrhosis, Crohn’s disease, optic-disk size and type 2 diabetes and also some behaviors, such as the ability to stop smoking. The team expects that more variants will be found to have Neanderthal origins.

The team also measured how Neanderthal DNA present in human genomes today affects keratin production and disease risk.

“Neanderthal ancestry is increased in genes affecting keratin filaments. This fibrous protein lends toughness to skin, hair and nails and can be beneficial in colder environments by providing thicker insulation. It’s tempting to think that Neanderthals were already adapted to the non-African environment and provided this genetic benefit to humans,” Dr Reich said.

The scientists also found that some areas of the modern non-African human genome were rich in Neanderthal DNA, which may have been helpful for human survival, while other areas were more like ‘deserts’ with far less Neanderthal ancestry than average.

“The barren areas were the most exciting finding. It suggests the introduction of some of these Neanderthal mutations was harmful to the ancestors of non-Africans and that these mutations were later removed by the action of natural selection,” said lead author Dr Sriram Sankararaman from the Harvard and MIT’s Broad Institute and Harvard Medical School.

The team showed that the areas with reduced Neanderthal ancestry tend to cluster in two parts of our genomes: genes that are most active in the male germline and genes on the X chromosome. This pattern has been linked in many animals to a phenomenon known as hybrid infertility, where the offspring of a male from one subspecies and a female from another have low or no fertility.

Dr Reich explained: “this suggests that when ancient humans met and mixed with Neanderthals, the two species were at the edge of biological incompatibility.”

“Present-day human populations, which can be separated from one another by as much as 100,000 years, are fully compatible with no evidence of increased male infertility. In contrast, ancient human and Neanderthal populations apparently faced interbreeding challenges after 500,000 years of evolutionary separation.”

The second study, published online in the journal Science, tests an innovative, fossil-free method for sequencing archaic DNA.

Co-authors Dr Benjamin Vernot and Dr Joshua Akey, both from the University of Washington, analyzed whole-genome sequencing data from 379 Europeans and 286 East Asians to identify Neanderthal lineages that persist in the modern DNA.

“We found evidence that Neanderthal skin genes made Europeans and East Asians more evolutionarily fit, and that other Neanderthal genes were apparently incompatible with the rest of the modern human genome, and thus did not survive to present day human populations,” Dr Vernot said.

The scientists observed that certain chromosomes arms in humans are tellingly devoid of Neanderthal DNA sequences, perhaps due to mismatches between the two species along certain portions of their genetic materials. For example, they noticed a strong depletion of Neanderthal DNA in a region of human genomes that contains a gene for a factor thought to play an important role in human speech and language.

The results suggest that significant amounts of population-level DNA sequences might be obtained from extinct groups even in the absence of fossilized remains, because these ancient sequences might have been inherited by other individuals from whom scientists can gather genomic data. Therein lies the potential to discover and characterize previously unknown archaic humans that bred with early humans.

“The fossil free method of sequencing archaic genomes not only holds promise in revealing aspects of the evolution of now-extinct archaic humans and their characteristic population genetics, it also might provide insights into how interbreeding influenced current patterns of human diversity,” Dr Vernot said.

“In the future, I think scientists will be able to identify DNA from other extinct hominin, just by analyzing modern human genomes.”

“From our end, this was an entirely computational project. I think it’s really interesting how careful application of the correct statistical and computational tools can uncover important aspects of health, biology and human history. Of course, you need good data, too.”

Sriram Sankararaman et al. The genomic landscape of Neanderthal ancestry in present-day humans. Nature, published online January 29, 2014 doi: 10.1038/nature12961

Benjamin Vernot and Joshua M. Akey. Resurrecting Surviving Neandertal Lineages from Modern Human Genomes. Science, published online January 29, 2014 doi: 10.1126/science.1245938


Abundance of DNA evidence not enough to prevent wrongful convictions

Credit: IAEA Imagebank

As we enter an era in which DNA evidence is routinely used in criminal investigations, errors that led to wrongful convictions—including mistakes later corrected with DNA tests—may seem to be fading into history. This, however, isn't true, says law and criminal justice professor Daniel Medwed, who edited the book, Wrongful Convictions and the DNA Revolution, which was published last month.

Many of the underlying issues that plagued the U.S. criminal justice system before DNA evidence rose to the fore still exist, he says, and will continue to produce flawed convictions unless they're remedied.

Here, Medwed explores some of those procedural deficiencies as well as the deeply rooted sense of justice that animates his work.

Why do wrongful convictions occur, and what are some of the factors that lead to convicting an innocent person?

The phrase "wrongful convictions" could encompass a range of flawed convictions. Yet the concept typically refers to the case of a factually innocent person: Someone who simply didn't commit the crime for which she was convicted. I think innocence cases largely derive from good-faith mistakes rather than malevolence on the part of, say, police or prosecutors. Those mistakes include eyewitnesses who simply get it wrong zealous prosecutors who can't look objectively at contrary evidence because of tunnel vision suspects who falsely confess to crimes due to cognitive deficits defense lawyers who are overworked and underpaid and reliance on forensic "science" that lacks sufficient grounding in the scientific method.

In Wrongful Convictions and the DNA Revolution, you examine what we've learned after 25 years of exonerating innocent prisoners through DNA evidence. What are those lessons?

We've learned about the substantive factors that contribute to wrongful convictions, as mentioned earlier, but we've also unearthed the procedural deficiencies in our system. The more than 300 documented exonerations of innocent prisoners through post-conviction DNA tests from 1989 to 2014 show that the traditional mechanisms of error correction in our system are insufficient. The direct appeal (in which a defendant challenges a criminal conviction secured at the trial level to a higher court), is ill-suited to address errors based in fact as opposed to law. And classic "collateral" remedies, such as habeas corpus, are replete with statutes of limitations and other procedural hurdles too high even for the innocent to clear. Going forward, we need to address both the substantive and the procedural flaws that can yield miscarriages of justice.

What has motivated you to study wrongful convictions and DNA evidence, and what inspires you to keep studying it?

First, inspiration comes from deeply-held personal beliefs. In my view, the hallmark of a civilized society is the extent to which we protect those in the weakest position to defend themselves—most notably, criminal suspects facing the potentially massive power of the government. All too often, criminal suspects are people of color with limited financial resources. This dynamic not infrequently produces disturbing outcomes for the individual, and sometimes results in the conviction of an innocent person. Imagine what it must be like to have the system fail you so dramatically, to have your cries of innocence fall on deaf, cynical ears. Thinking about that provides all the motivation I need.

Second, I feel as if we're at a unique stage in history. DNA testing is now commonly used at the front end of the criminal process to weed out the innocent before a case even gets to trial. That means post-conviction DNA exonerations of inmates will inevitably dwindle to almost nothing many of the DNA cases that generate headlines concern prisoners convicted years ago. But a decline in DNA exonerations will not signify that the system has become error-proof. Rather, the factors that initially gave rise to those wrongful convictions will remain and infect criminal cases that lack biological evidence suitable for DNA testing at all. Only an estimated 10 to 20 percent of criminal cases have testable biological evidence at all what's more, that evidence is often lost, destroyed, or degraded over time. So, I think we need to capitalize on the lessons learned from the DNA era to reform the underlying sources of error for all cases. And we need to do this before the rate of DNA exonerations wanes too much and the public gets the misimpression that the innocence problem is fixed.


Neanderthal in our skin

Most Neanderthal variants exist in only around 2 percent of modern people of Eurasian descent. But some archaic DNA is much more common, an indication that it was beneficial to ancient humans as they moved from Africa into Eurasia, which Neanderthals had called home for more than 300,000 years. In their 2014 study, Vernot and Akey found several sequences of Neanderthal origin that were present in more than half of the genomes from living humans they studied. The regions that contained high frequencies of Neanderthal sequences included genes that could yield clues to their functional effect. Base-pair differences between Neanderthal and human variants rarely fall in protein-coding sequences, but rather in regulatory ones, suggesting the archaic sequences affect gene expression. (See “Denisovans in the Mix” below.)

A number of segments harbor genes that relate to skin biology, such as a transcription factor that regulates the development of epidermal cells called keratinocytes. These variants may underlie traits that were adaptive in the different climatic conditions and lower levels of ultraviolet light exposure at more northern latitudes. Reich’s group similarly found genes involved in skin biology enriched in Neanderthal ancestry—that is, more than just a few percent of people carried Neanderthal DNA in these parts of the genome.

No one has actually shown yet in culture that a human and Neanderthal allele have a different physiological function. That will be exciting when someone does.

It was unclear, however, what specific effect the Neanderthal variants had on phenotype. For that, researchers needed phenotypic data on many different kinds of traits, paired with genetic information, for thousands of people. Vanderbilt University evolutionary geneticist Tony Capra has access to such a resource: the Electronic Medical Records and Genomics (eMERGE) Network. Right around the time the scientific community was beginning to map Neanderthal DNA in the genomes of living people, eMERGE organizers were compiling electronic health records and associated genetic data for tens of thousands of patients from nine health-care centers across the US. “We felt like we had a chance to evaluate some of those hypotheses [about functionality] on a larger scale in a real human population where we had rich phenotype data,” says Capra.

In collaboration with Akey and Vernot, who helped identify Neanderthal variants in the genetic data included in the database, Capra’s group looked for links between the archaic DNA and more than 1,000 phenotypes across some 28,000 people of European ancestry. They reported in 2016 that Neanderthal DNA at various sites in the genome influences a range of immune and autoimmune traits, and there was some association with obesity and malnutrition, pointing to potential metabolic effects. The researchers also saw an association between Neanderthal ancestry and two types of noncancerous skin growths associated with dysfunctional keratinocyte biology—supporting the idea that the Neanderthal DNA was at one point selected for its effects on skin. 4

“This was crazy to me,” says Capra. “What these other groups had predicted based on just the pattern of occurrence—the presence and absence of Neanderthal ancestry around certain types of genes—we were actually seeing in a real human population, that having Neanderthal ancestry influenced traits related to those types of skin cells.” What remains unclear, however, is what the benefits of the Neanderthal sequences were for those early humans.

At the same time, Kelso and her postdoc Michael Dannemann were taking a similar approach with a relatively new database called the UK Biobank (UKB), which includes data from around half a million British volunteers who filled out questionnaires about themselves, underwent medical exams, and gave blood samples for genotyping. Formally launched in 2006, the UKB published its 500,000-person-strong resource in 2015, and Kelso and Dannemann decided to see what information they could extract. Conveniently, the genotyping data specifically includes SNPs that can identify variants of Neanderthal origin, thanks to Reich’s group, which provided UKB architects with a list of 6,000 Neanderthal variants.

Among the many links Kelso and Dannemann identified as they dug into data from more than 112,000 individuals in the UKB was, once again, an association between certain Neander-thal variants and aspects of skin biology. 5 Specifically, the archaic sequences spanning the BNC2 gene—a stretch of the genome that Vernot and Akey had identified as having Neanderthal origin in some 70 percent of non-Africans—were very clearly associated with skin color. People who carried Neanderthal DNA there tended to have pale skin that burned instead of tanned, Kelso says. And the stretch that included BNC2 was just one of many, she adds: around 50 percent of Neanderthal variants linked with phenotype in her study have something to do with skin or hair color.

The effect that Neanderthal DNA might have on skin appearance and function is “fascinating,” says Akey. “Something that we’re still really interested in and starting to do some experimental work on is: Can we understand what these genes do and then maybe what the selective pressure was that favored the Neanderthal version?”

See “Effects of Neanderthal DNA on Modern Humans”


Baffling Genetic Barrier Prevents Similar Animals from Interbreeding

Most people don&rsquot get to use the tree-climbing skills they perfected as children once they&rsquore adults. But for Jochen Wolf, an evolutionary biologist at Uppsala University in Sweden, climbing trees is an essential part of his job. He regularly shimmies 60 feet up into the treetops, where he gingerly plucks fledgling crows from their nests and lowers them to his team below.

Wolf&rsquos climbing exploits have focused on two species of birds &mdash carrion crows, which predominate in western Germany, and the closely related hooded crows that prevail further to the east, in Sweden and Poland. The two groups can mate with each other, but they look very different &mdash carrion crows are black, and hooded crows have black-and-gray bodies &mdash and the birds strongly prefer mates of their own kind. For a long as anyone can remember, the two groups have remained distinct, save for a narrow band of habitat stretching from Denmark through eastern Germany to northern Italy where they sometimes intermingle.

The crows present a puzzling question to biologists, which gets to the heart of what it means to be a species: Given that hooded and carrion crows can mate and swap genes, how do the two groups maintain their individual identities? It&rsquos as if you mixed red and yellow paint in a bucket but the two colors stubbornly refused to make orange.

In new research published in June in the journal Science, Wolf&rsquos team has found that a surprisingly small chunk of DNA may hold the answer. A comparison of the carrion and hooded-crow genomes showed that the sequences are almost identical. Differences in just 82 DNA letters, out of a total of about 1.2 billion, appear to separate the two groups.

Almost all of them are clustered in a small part of one chromosome. &ldquoMaybe just a few genes make a species what they are,&rdquo said Chris Jiggins, a biologist at the University of Cambridge in England, who was not involved in the study. &ldquoMaybe the rest of genome can flow, so species are much more fluid than we imagined before.&rdquo

The findings are striking because they suggest that just a few genes can keep two populations apart. Something within that segment of DNA stops black crows from mating with gray ones and vice versa, creating a tenuous mating barrier that could represent one of the earliest steps in the formation of new species. &ldquoThey look very different and prefer to mate with their own kind, and all of that must be controlled by these narrow regions,&rdquo Jiggins said.

Crows aren&rsquot alone in their behavior. A deluge of genetic data in recent years suggests that interbreeding between species is more widespread than scientists ever imagined. &ldquoI think people will be surprised and the view of species will be challenged as more data comes along,&rdquo Jiggins said. &ldquoI think it will lead to a fundamental shift in how they view what a species is.&rdquo

Unknown Species
The traditional way to define two related organisms as distinct species is by their inability to mate. The Swedish naturalist Carl Linnaeus, who wandered the halls of Uppsala University more than 250 years ago, employed this definition when he created the classification system we still use today. But scientists have been arguing over what makes a species for more than a century.

Charles Darwin himself declined to define the concept in his landmark book &ldquoOn the Origin of Species.&rdquo &ldquoDarwin, when he proved that species evolved, also proved there was no such thing as species,&rdquo said James Mallet, an evolutionary biologist at Harvard University. If organisms are constantly evolving, then drawing a precise dividing line between two different species will necessarily be difficult.

Indeed, evolutionary biologists tend to take a more pragmatic approach to defining species, one that depends on their avenue of study. A distinction could be based on morphological or genetic differences, for example. &ldquoWhen we start speaking of species, it&rsquos in the eye of the beholder,&rdquo Wolf said.

The more interesting and important question, biologists say, is what drives two populations to diverge, a process known as speciation. That question has heated up over the last five years with the rapid advance of genomic technology. Until recently, the study of speciation has focused on ecology and behavior out in the field, as well as mating experiments, but scientists now find themselves able to analyze the genomes of a menagerie of wild creatures, including closely related ones. &ldquoJust a few years ago, it wasn&rsquot possible to sequence the genome of wild organisms,&rdquo Wolf said. &ldquoNow we can, and that&rsquos fantastic.&rdquo

The results &mdash from studies of crows, butterflies, mosquitoes, fish and other organisms &mdash suggest that the concept of species is even more muddled than we thought, and that genetic changes don&rsquot always align with more visible ones, such as appearance. &ldquoIn some cases, species have big morphological and behavioral changes with only a few genetic changes, and in other cases, there is lots of genetic change with few visible results,&rdquo said Matthew Hahn, a biologist at Indiana University.

Birds of a Feather
When Wolf pulls himself up a branch toward a nest, the young birds aren&rsquot particularly startled to see him. Instead, &ldquothey open their mouths, waiting to be fed,&rdquo Wolf said. Their parents feel differently, however, calling out from nearby treetops. &ldquoThey always come back to them,&rdquo said Christen Bossu, a postdoctoral researcher in Wolf&rsquos lab.

Wolf&rsquos team measures the young birds&rsquo wing length and color and collects blood samples for genomic studies before returning them to the nest. In their recent paper, the researchers not only looked at the genetic code, but also studied how gene activity varied between the two populations. They found the biggest difference in the genes that make pigment, which are active in the skin tissue and control feather color. Many of these genes lie within the DNA segment that differs between carrion and hooded crows, suggesting that somehow the pigment genes that give the two groups their unique appearance are also keeping the species separate. But how?

The most obvious explanation is that genes within this region also influence how the birds choose their mates. So-called assortative mating, in which animals that look similar are more likely to mate with each other, is one of the causes of new species development. Simple imprinting is one way to drive this phenomenon if you were raised by a gray crow, you might prefer a gray crow as a mate.

A second possibility ties together mate choice, color palette and vision. Maybe black crows can see other black crows more easily than they can see hooded crows and are thus more likely to mate with them, Wolf said. If the genes related to color and the genes involved in this aspect of vision sit near each other on the genome, they are more likely to be inherited together. (The further apart two genes lie on the genome, the more probable it is that they will be separated when they are passed down.) Two neighboring genes with this kind of synergistic effect on mate choice could easily drive the separation of the species. Indeed, researchers have found a gene in the region that is likely linked to vision. They believe it influences how well the birds perceive contrast, a hypothesis they are now testing in captive crows.

Adult crows are too clever to be captured, so in May, just before his paper appeared in Science, Wolf embarked on another tree-climbing excursion. In addition to blood and feathers, he collected about a dozen baby birds. They are now being raised in a new aviary in Sweden, where they are eating scientists out of house and home. (Cattle hearts are one of their favorite meals.) Researchers will train the birds to respond to visual cues, such as flashing lights, and then figure out whether hooded and carrion crows can detect different visual contrasts. According to Wolf, it&rsquos possible that black crows detect strong visual contrasts differently from hooded crows, which could explain why they seek out other black crows as mates.

Butterfly Effect
Wolf&rsquos crows aren&rsquot the only set of interbreeding species that maintain their distinct identity. Across the Atlantic, two species of heliconius butterfly &mdash the cydno longwing (Heliconius cydno) and the postman butterfly (H. melpomene) &mdash reside in overlapping locales in South America and can mate with each other despite their different appearance, though it happens rarely. The cydno longwing is black with white or yellow markings, and the postman is black with red and yellow markings. Each has evolved to mimic the wing pattern of a different poisonous butterfly, which helps protect them from predation. But like Wolf&rsquos crows, the cydno longwing and postman prefer to mate with their own kind.

Genome analysis suggests that the two species are swapping genes at a surprising rate. But each species has genome segments unique to its own kind, which seem to persist despite the mixing of the rest of the genome. It&rsquos as if these parts of the genome were made of oil and the rest of water the water easily mixes but the oil remains in distinct droplets.

Scientists have dubbed such regions of the genome &ldquoislands of speciation.&rdquo The persistence of such islands is a phenomenon that has been observed in a variety of organisms. Natural selection appears to put evolutionary pressure on these regions, which keeps both the genes and their corresponding traits distinct even in the face of interbreeding, while the rest of the genome can mix. Scientists theorize that these areas do the bulk of the work in maintaining individual species, perhaps by preserving different color patterns or mating behavior. Jiggins and others are now trying to figure out what kinds of genes reside within these islands, and how they drive two populations apart. &ldquoWhen you do start to diverge, what types of genes diverge first? Which genes drive speciation? What are the first things that become differentiated?&rdquo Hahn asked.

A major driver of this process may be genes that control multiple traits. &ldquoThere often seem to be a few genes in the genome that have large effects, often on multiple things,&rdquo said Ole Seehausen, an evolutionary ecologist at the University of Bern in Switzerland. &ldquoA gene that affects how well an individual does in one environment or the other might affect how they see each other and how they mate with each other.&rdquo Genes that lie close together on the genome (such as the crows&rsquo pigment and vision genes) may have the same effect, since they tend to be inherited together.

The behavior of heliconius butterflies supports this idea. After scientists observed years of mating in the lab, they pinpointed a gene linked to wing patterning, which differs between the two species. A neighboring gene is linked to mating preference, though scientists have not yet identified the specific gene.

Taken together, the research is beginning to create a picture of the process of speciation. It might start with a small region of the genome, likely housing genes linked to mating, as seems to be the case with crows. Then that region expands, and new islands harboring other divergent genes emerge, creating islands of speciation across the genome.

Meeting Halfway
The crow hybrid zone &mdash the narrow strip of land where the carrion and hooded crows intermingle &mdash isn&rsquot dramatic in any way. No mountains set it apart, blocking one species from another. The landscape to the east and to the west is similar, with both species inhabiting the same type of forests. Exactly how the two groups carved out their territories is not yet clear.

The groups probably split during the ice ages, when glaciers repeatedly covered northern Europe. Crows and other animals moved south, likely taking refuge in two different locales. When the glaciers receded, the two populations moved north, meeting in the hybrid zone. But scientists don&rsquot yet know if this happened in the latest ice age, only about 10,000 to 20,000 years ago, or in an earlier one, as far back as two million years ago.

This uncertainty highlights one of the challenges of studying speciation. Sometimes two very different possible histories can produce the same genetic pattern. The shared regions of the genome surrounding islands of speciation, for example, may have other explanations, such as shared ancestry, as Hahn argued in a paper published in July. Two species might have similar genomes not only because they recently swapped genes, but because they share a distant parent species. &ldquoPeople went overboard with interpreting islands of speciation,&rdquo Hahn said.

Carrion and hooded crows could be quite old species whose genomes became similar through interbreeding. Or they could be quite young, having split off from a common ancestor relatively recently, with the small chunk of divergence the first sign of speciation. Wolf&rsquos group favors the latter interpretation but hopes to address the question directly with further genetic analysis.

So what does all this mean for the definition of species? Scientists still don&rsquot have a definitive answer. Simply defining species based on genetics doesn&rsquot solve the problem. As Wolf and others have shown, the answer depends on where in the genome you look. &ldquoIt&rsquos really hard to draw a boundary,&rdquo Wolf said. &ldquoDifferent parts of the genome tell you different things.&rdquo


Examiners report

There was much criticism of the cladogram from teachers in G2 forms and predictions that candidates would not understand it. In practice, most candidates realized for point A, they were expected to give a feature of fish that is absent in birds and mammals, the reverse of this for B, and for C a characteristic of mammals that is absent in birds and fish. This was an effective test of candidates&rsquo knowledge of the characteristics of these three chordate groups.

In this question candidates were expected to apply their understanding of evolution and speciation to the context of the early evolution of vertebrates. All that was expected was a methods of reproductive isolation, differential natural selection and divergence until the differences between populations and their gene pools were great enough to prevent interbreeding. Candidates mostly got at least part of this.

Question setters try to include some stimulus material to make questions more interesting but the first sentence of this question proved to be a distraction rather than a help. Candidates only really needed to think about the second sentences and so describe two structures and explain how they help the mitochondrion to carry out its function of producing ATP.


Denisovan Genome Reveals Interbreeding With Modern Humans

With the publishing of the Denisovan genome, the genetic profile of interfertile humans has widened considerably.

From a single fingerbone, scientists at Max Planck Institute were able to determine the complete genome of a surprising group of humans in Siberia that have been named the Denisovans. According to Scientific American on August 30 (reprinted by Nature News), the individual’s DNA can reveal traits of the entire population. The current interpretation is that the Denisovans were an isolated population group in Asia with low genetic diversity, living 74,000 to 82,000 years ago (earlier estimates were half that, about 30,000 to 50,000 years ago), but that “the modern human line diverged from what would become the Denisovan line as long as 700,000 years ago—but possibly as recently as 170,000 years ago.” Writer Katharine Harmon speculated that “the population on the whole seems to have been very small for hundreds of thousands of years, with relatively little genetic diversity throughout their history.

Enough commonality was found with modern humans – about 6% – that it shows the population must have interbred with them and with Neanderthals, with whom they share more commonality than with moderns. As for the owner of the fingerbone, analysis is “consistent with” dark hair and skin of a female. Charles Q. Choi at Live Science took that as a cue to proclaim, “Genome of Mysterious Extinct Human Reveals Brown-Eyed Girl.” Perhaps they will name her Denise.

That’s how the evolutionists are re-framing this find within their standard timeline. It should be remembered, however, that the Denisovan bones (a finger and two molars in a cave in Siberia) came as a complete surprise to Svante Pääbo, his team at the Max Planck Institute, and to anthropologists worldwide. John Hawks, a paleoanthropologist from the University of Wisconsin-Madison, who was not involved in the genome study, called Denisova a “big surprise.” Early genetic indications of interbreeding with modern humans were doubted by some, but the newly published genome appears to remove all doubt. That being the case, it is appropriate to consider Denisovans, Neanderthals and modern humans as a single interfertile species. Consider, by comparison, the diversity in dogs, all of which are members of a single species, Canis familiaris.

Several points in the Nature News article bear emphasis for their surprise effects. For one, this fingerbone retained a remarkable amount of DNA:

Most bone fragments would be expected to contain less than 5 percent of the individual’s endogenous DNA, but this fortuitous finger had a surprising 70 percent, the researchers noted in the study. And many Neandertal fragments have been preserved in vastly different states—many are far worse off than this Denisovan finger bone.

Is it plausible this bone retained its DNA for up to 82,000 years? or even 30,000? Another point is that Australian aborigines, Melanesians and inhabitants of Papua New Guinea share Denisovan DNA, but not modern residents of Asia:

Yet contemporary residents of mainland Asia do not seem to posses Denisovian traces in their DNA, a “very curious” fact,” Hawks says. “We’re looking at a very interesting population scenario“—one that does not jibe entirely with what we thought we knew about how waves modern human populations migrated into and through Asia and out to Oceania’s islands. This new genetic evidence might indicate that perhaps an early wave of humans moved through Asia, mixed with Denisovans and then relocated to the islands—to be replaced in Asia by later waves of human migrants from Africa. “It’s not totally obvious that that works really well with what we know about the diversity of Asians and Australians,” Hawks says.

A third point in the article regards the expanded variability now appreciated within the interfertile human line. Denisova may not be the last population of diverse humans to be found. Harmon revealed a little-known fact: there’s a lot of variability among living Africans:

The genomes of contemporary pygmy and hunter–gatherer tribes in Africa, for example, have roughly as many differences as do those of European modern humans and Neandertals. So “any ancient specimen that we find in Africa might be as different from us as Neandertals,” Hawks says. “Anything we find from the right place might be another Denisovan.”

With a new sequencing technique available that can discern a genome from one DNA strand rather than both, anthropologists approach additional fossil sequences with excitement, and perhaps some trepidation. What will the genome of H. floresiensis reveal? Will additional human populations be found in Asia? Pääbo said, “I would be surprised if there were not other groups to be found there in the future.”

To discern how scientists are doing, watch for surprised looks on their faces. The paleoanthropology community was caught completely off guard by the Denisova fossils (read those links to our five earlier reports about Denisovans to emphasize the point). Archaic hominids in a Siberian cave, far from Europe, who interbred who with modern humans? Impossible. Yet their own analysis brings them to that conclusion. Don’t be fooled when they recover their composure by switching from the surprised look to the excited look and say (like John Hawks, one of the more reasonable of the gang), “Going back further in time will be exciting. There’s a huge race on—it’s exciting.” Observe the plain fact: they were wrong! Their story of human evolution was false. Tell them to stop the spin doctoring within the Grand Tale of Human Evolution Story and face the facts.

We additionally know they were wrong because this finger had quality DNA. It’s highly implausible that this bone contained 70% of its original DNA after 30,000 years, to say nothing of 82,000 years. Who could possibly believe that? It’s much more likely that this individual lived just a few thousand years ago at most, like the Table of Nations timeline of Genesis describes. Fully modern, big-brained, ensouled humans spread across the globe after Babel and began to interbreed in groups that accentuated various traits without eliminating traces of their common ancestry from Mr. & Mrs. Noah. The more isolated groups became in more remote places, like Siberian caves, the more distinctive their genomes became. Notice also the ability of these people to travel far and wide around the globe. It doesn’t take tens or hundreds of thousands of years for these things to happen.

That interpretation fits the facts without requiring us to believe the impossible dream that Denisovans kept to themselves as an isolated small population for “hundreds of thousands of years” without ever thinking of making wheels, building cities or riding a horse, while flirting with modern humans from Europe once in awhile. The folly of their long-age scenario should sizzle in your brain till it “sheds light on evolution,” showing it to be complete baloney. How can anyone believe that? Why do they believe that? The answer: they have committed their souls to protecting Darwin from falsification.

It’s only a matter of time before history laughs these charlatans off the stage. Sure, they are intelligent, and good at sequencing DNA. They’ve had a lot of education. They can talk jargon and work phylogeny software. Fantastic. But when it comes to explaining the world, they are a sorry bunch. Get the jump on the historians of 2030 and start laughing now.


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How much difference in genome is enough to prevent interbreeding? - Biology

Interbreeding Between Species

From time to time I encounter the assertion that H. sapiens (and/or H. sapiens sapiens ) could not have interbred with H. erectus , because they are different species. I've also been told that, "If they could have produced fertile offspring, then they weren't really different species". These fairly common misconceptions proceed from a misunderstanding of the 'biological species concept', which makes species distinctions based on fertility. Most people leave school thinking that, if two creatures can produce fertile offspring, then they must belong to the same species. I wouldn't be surprised if many teachers actually tell students that, but it simply isn't so.

The biological species concept was developed by Ernst Mayr, in 1942. Here it is, as first formulated, and quoted in Douglas J. Futuyma's EVOLUTIONARY BIOLOGY (1998): "Species are groups of actually or potentially interbreeding populations that are reproductively isolated from other such groups". The "reproductive isolation" can be genetic (non-fertility), geographic, or behavioral there is NO criteria that says (as is commonly believed) that if two populations can interbreed they are the SAME species. There is NO criteria that says that two distinct species CAN'T interbreed. Consider the example of wolves, coyotes and dogs: three distinct species that can interbreed. In fact, all species of the genus Canis can mate and produce fertile offspring (Wayne et al., 1997, re: A. P. Gray, Mammalian Hybrids ). This is so common, that biologists actually use a different formulation of Mayr's definition: they say, "If two populations can NOT interbreed, they are NOT the same species." That is a very different statement. Note that this is an empirical definition, and gives no guidance in regard to extinct taxons, but the bottom line is: nothing in the biological species concept contradicts the idea that erectus and sapiens could and DID interbreed.

I think it will come as a surprise to many that most scientists accept the fact that sapiens and erectus were so closely related that they could have interbred with each other. To begin with, some (probably most ) scientists don't think erectus and sapiens were genetically separate species at all. They consider them developmental 'grades' within a single taxon. Here is an example of that view, from Futuyma.

"The word species, however, is sometimes used simply as a name for a morphologically distinguishable form. This is especially true in paleontology, in which a single evolving lineage (gene pool) may be assigned several names for successive, phenotypically different forms. For example, Homo erectus and Homo sapiens are names for different, distinguishable stages in the same evolving lineage. They are chrono-species, rather than separate biological species. The two species names do not imply that speciation (bifurcation into two gene pools) occurred: in fact it probably DIDN'T in this case." [my emphasis on didn't]

Futuyma claims erectus is "human", probably because all those bad bones from Africa show such strong expression of erectus traits. The afrocentrists say they were erectus slouching toward humanity I say the more modern-looking fossils were erectus hybridized with sapiens . BOTH views imply that erectus and sapiens were able to interbreed. In fact, the afrocentrist position, that there was only a SINGLE gene pool, is a stronger statement of their capability for interbreeding than mine. Wolpoff, and other multiregionalists, exhibit similar thinking: he maintains that erectus was "human" and evolved into modern sapiens all over the world, while the afrocentrists say that process only culminated in Africa, from whence a modern human type radiated, displacing all other 'people' without interbreeding. They don't deny those (supposedly erectus -derived) moderns and Eurasian indigenes could have interbred, they just claim they didn't.

So, nearly everybody is in agreement that erectus could interbreed with sapiens : multiregionalists, afrocentrists, and even me. Note, however, that some people also say erectus was a distinct taxon. In fact, Rightmire, a recognized expert on erectus , says ( The Evolution of Homo Erectus , Cambridge, 1990) they were a distinct species I even agree with him. It is interesting to see why there is disagreement on the subject. Wolpoff, and others, compare the early African and Asian skulls with the most modern ones and show that there was an increase in cranial capacity, and a morphological tendency toward some sapiens characteristics. BUT, those recent skulls are the very ones I contend are hybrid specimens! Rightmire excludes the late, Southeast Asian skulls from Ngandong for very good reasons, and shows that the rest of the series reveals no statistically significant development toward becoming modern human. That is even with including later, African skulls that I think show some interbreeding with sapiens radiating out of Eurasia. When you get up to the recent African material, which shows significant sapiens influence, the afrocentrists claim those aren't erectus , but 'early sapiens'. For instance, they call the Herto skulls H. sapiens idaltu .

So, the real difference in viewpoint is whether: 1) erectus evolved into modern humans by a gradual process, with int RA -species gene flow (whether it occurred only in Africa or also elsewhere) or 2) erectus and sapiens interbred, founding some (tropical) modern populations, while Eurasian sapiens founded Eurasian populations, which is my interpretation of the data. None of these views preclude interbreeding between erectus and sapiens , and the multiregional position DEPENDS on it. Note how 'shifty' Wolpoff is. As a multiregionalist, he argues that "gene flow" (interbreeding) between advanced populations (who are called sapiens because of their clearly more-modern morphology) and less-advanced ( erectus 'grade') specimens caused all the world's 'people' to evolve into sapiens . YET, in attempting to refute my view (that the Ngandong skulls represent hybrids between erectus and sapiens ) he characterizes that as intER-species gene flow, as if it were not exactly what his own theory implies. Then to further obfuscate, he plays the race-card, saying my hypothesis, "raises the specter that some populations will be seen as differing because they have more genes from an extinct species" . Well, yes!

If H. sapiens or s. sapiens could interbreed with erectus , then they should certainly have been able to produce fertile offspring with other sapiens , such as H. sapiens neanderthalis , or with H. heidelbergensis , which may have been a direct ancestor. Consider that wolves and coyotes have been distinct species for nearly a million years, or more than 300 thousand generations. A similar number of generations would take the human ancestry back nearly to the last common ancestor of Homo and Pan.

A final consideration is the distinguishing characteristics that differentiate the various Homo species. If they were separated by potentially incompatible mutations, then there might have been diminished fertility between those species. However, it appears they have been distinguished by neoteny: ancestral forms were succeeded by juvenilized versions of themselves. While the effects of neoteny (such as increased intelligence, delayed maturation, progressive gracilization, and a diminution of some ancestral-adult characteristics) may be profound, the genetic changes are subtle. There seems to be little or no impediment to fertility, as the new type must have been fertile with the parent species in order to survive. Accordingly, the entire genus Homo has probably been int ER -fertile, just as the genus Canis is.

Clifford Jolly, writing in the American Journal of Physical Anthropology (2001 Supplement 33: 177-204) discusses the more apposite hybridization of hominins . He says,

'' Another source of phylogenetic uncertainty is the possibility of gene-flow by occasional hybridization between hominins belonging to ecologically and adaptively distinct species or even genera. Although the evidence is unsatisfactorily sparse, it suggests that among catarrhines generally, regardless of major chromosomal rearrangement, intersterility is roughly proportional to time since cladogenetic separation. '' And, '' any hominine species whose ancestries diverged less than 4 ma previously may well have been able to produce hybrid offspring ''

Four million years ago takes us back before Homo is recognized to have existed! And that is not even considering that Homo species have a longer generation time, so an equivalent number of generations would extend the potential hybridization period even further than 4 million years into the past. As an aside, this suggests that the genus Homo could have begun by hybridization. That would offer an explanation for why we are so closely related to the knuckle-walking chimps and gorillas, while Homo had bipedal ancestry. Of course, chimps and gorillas may have split off the line of descent from a common bipedal ancestor and reverted to knuckle-walking. The important point, with respect to interbreeding of species, is that hominin species separated by several million years of divergence can still produce fertile hybrid offspring.

By contrast, the divergence time separating erectus from sapiens, or the latter from Neanderthals, is much less. For instance, Krings, et al. (in DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen , PNAS 1999) estimates that Homo sapiens sapiens and H. neanderthalsis shared a common ancestor not more than 741, and perhaps as recently as 317 thousand years ago. Afrocentrists believe sapiens diverged from erectus only a couple of hundred thousand years ago. Even if sapiens shared no common ancestors with erectus after the earliest known Homo fossils in Eurasia, 1.8 million years ago, they should still have been inter-fertile. In fact, morphological features of the Nagandong, Kow Swamp, Herto, and other skulls suggest that sapiens and erectus did interbreed and produce offspring. I contend that view is confirmed by the genetic evidence cited in Age & Origin of the Human Species, Plural Lineages in the Human mtDNA Genome , and Australian Ancestry: Implications for the Origin of H. sapiens sapiens.

In Number of ancestral human species: a molecular perspective , (HOMO Vol. 53/3, pp. 201–224) D. CURNOE, and A. THORNE directly address the question of whether recent types of Homo would have been able to mate and produce viable and fertile offspring. They say, flatly:

”All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Distances calculated here for H. neanderthalensis versus H. sapiens and for H. erectus versus H. sapiens are around one-third and two-thirds, respectively, of the mammalian intrageneric mode.”

Some genetic data from humans, chimps, and orangutans suggest there were genetic speciation events in Homo’s history, resulting in populations that could not have interbred with their ancestors, but not many nor recently. This type of speciation, as a result of infertility by reason of genetic incompatibility, must be distinguished from the evolution of ” type ” morphology, leading to species designations such as erectus and neanderthalensis .

”Sumatran and Bornean orangutans differ by three chromosomal rearrangements but are known to be fully fertile, and common chimpanzees and bonobos differ by six chromosomal rearrangements, and although some workers regard them as distinct species (see above), they do produce apparently normal hybrid offspring (H. Vervaecke, pers. com.). Most types of rearrangements between orangutan subspecies and between common chimpanzees and bonobos are also seen in humans. This suggests that at least some of the rearrangements in humans might not represent reproductive isolation.”

”This observation is complicated by the fact that humans appear to possess even greater chromosomal instability than great apes. Humans possess a high level of chromosomal rearrangements, with 1 out of every 120 babies born being abnormal (Hook 1992). The figure rises to about 25% for 10-day old blastocysts (Gardner & Sutherland 1996). We conclude that chromosomal rearrangements were likely to have been important during human evolution, more so than among the great apes, making comparisons with them of limited value.”

”Given the chromosomal instability in humans, it seems likely that at least some of the chromosomal rearrangements may have had a significant impact on reproductive isolation when they occurred.”

Thus, it isn’t clear (from the ape evidence) that even chromosomal rearrangements would have rendered the different types of Homo infertile, but it is clear that there were fewer such events, which even might have caused reproductive isolation, than there are recognized taxons of Homo. In other words, just because erectus was different enough to be a recognized taxon doesn’t mean they could not interbreed with sapiens .

The cited authors state there have been five or fewer genetic-isolation-speciations since the last common ancestor with chimps:

”From the above evidence we conclude that the number of species on the DLMH, as inferred from human chromosome rearrangements, might be around 3 and cannot be more than 5.”

So all of the types of Homo living in the last few hundred thousand years would have been fertile with the other types. H. sapiens/sapiens and H. erectus and H. neanderthalensis would have all been able to interbreed … and the genetic evidence, as presented in the papers posted on this site, indicates they DID interbreed, resulting in the modern populations.


Affiliations

Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

W. Ford Doolittle & Tyler D. P. Brunet

Department of History and Philosophy of Science, University of Cambridge, Cambridge, UK

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Contributions

Both authors contributed to the writing of this paper, and have read and agreed to its contents.


Watch the video: viel und viele verstehen - Was ist der Unterschied zwischen viel und viele? (October 2022).