PreColumbian Native Americans had 2nd Ghost Ancestry With Aboriginal Australian Affinities

Genetic evidence for two founding populations of the Americas

Authors:

Skoglund et al

Abstract:

Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia). Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.

multiple pop sci write-ups available.

Erk: Devil's Hole Pupfish Might be "Man Made"

Evaluating an icon of population persistence: the Devil's Hole pupfish

Authors:

Reed et al

Abstract:

The Devil's Hole pupfish Cyprinodon diabolis has iconic status among conservation biologists because it is one of the World's most vulnerable species. Furthermore, C. diabolis is the most widely cited example of a persistent, small, isolated vertebrate population; a chronic exception to the rule that small populations do not persist long in isolation. It is widely asserted that this species has persisted in small numbers (less than 400 adults) for 10 000–20 000 years, but this assertion has never been evaluated. Here, we analyse the time series of count data for this species, and we estimate time to coalescence from microsatellite data to evaluate this hypothesis. We conclude that mean time to extinction is approximately 360–2900 years (median 410–1800), with less than a 2.1% probability of persisting 10 000 years. Median times to coalescence varied from 217 to 2530 years, but all five approximations had wide credible intervals. Our analyses suggest that Devil's Hole pupfish colonized this pool well after the Pleistocene Lakes receded, probably within the last few hundred to few thousand years; this could have occurred through human intervention.

Basal Eurasians are a Third ANcestral Group to Modern Europeans, Related to Ancestral Native Americans

New studies of ancient DNA are shifting scientists' ideas of how groups of people migrated across the globe and interacted with one another thousands of years ago. By comparing nine ancient genomes to those of modern humans, Howard Hughes Medical Institute (HHMI) scientists have shown that previously unrecognized groups contributed to the genetic mix now present in most modern-day Europeans.

"There are at least three major, highly differentiated populations that have contributed substantial amounts of ancestry to almost everybody that has European ancestry today," says David Reich, an HHMI investigator at Harvard Medical School. Those include hunter-gatherers from western Europe, the early farmers who brought agriculture to Europe from the Near East, and a newly identified group of ancient north Eurasians who arrived in Europe sometime after the introduction of agriculture. That means there were major movements of people into Europe later than previously thought. The team, led by Reich and Johannes Krause at the University of Tübingen in Germany, reported their findings in the September 18, 2014, issue of the journal Nature.

In the last five years, genetic evidence has demonstrated that migrants from the Near East brought agriculture with them to Europe when they arrived about 8,500 years ago. But the genomes of present-day Europeans show signs that they come from more than just the indigenous hunter-gatherers and these early farmers.

Two years ago, Reich's group uncovered genetic evidence that most present-day Europeans are a mixture of groups related to southern Europeans, Near Easterners, and a third group most closely related to Native Americans. "That was a crazy observation, but it's very strong statistically," Reich says. "We argued that this is because of the contribution of an ancient north Eurasian population some of whose members contributed to the peopling of the Americas more than 15,000 years ago, and others of which later migrated to Europe."

To clarify that early history, Reich's team, including more than 100 collaborators worldwide, collected genetic data from nine ancient skeletons and 203 present-day populations living all over the world. Collaborators isolated human DNA and sequenced the complete genomes from the bones of a 7,000-year old skeleton found in Germany and eight skeletons of hunter-gatherers who lived in Luxembourg and Sweden about 8,000 years ago. They compared those genomes to those of the 2,345 people in their contemporary populations.

That required developing new computational methods for genetic analysis. "Figuring out how these populations are related is extremely hard," Reich says. "There's a lot that happened in Europe in the last 8,000 years, and this history acts like a veil, making it difficult to discern what happened at the beginning of this period. We had to find statistics that were able to tell us what happened deep in the past without getting confused by 8,000 years of intervening history, when massive and important events occurred."

"What we find is unambiguous evidence that people in Europe today have all three of these ancestries: early European farmers who brought agriculture to Europe, the indigenous hunter-gatherers who were in Europe prior to 8,000 years ago, and these ancient north Eurasians," Reich says. Further analyses showed that describing present-day Europeans as a mixture of the three populations is a good fit for most, although not all, populations.

When the study began, the ancient north Eurasian population was a "ghost population" – identified based on genetic patterns without any ancient DNA. But in 2013, another group analyzed DNA from two skeletons found in Siberia, one from 24,000 years ago and one from 17,000 years ago, and found that it shared genetic similarities with Europeans and North Americans. The ghost, Reich says, had been found.

Although DNA from ancient north Eurasians is present in nearly all modern Europeans, Reich's team did not find it in their ancient hunter-gatherers or the ancient farmers. That means the north Eurasian line of ancestry was introduced into Europe after agriculture had been established, a scenario most archaeologists had thought unlikely.

"We have this amazing observation that only two ancestries are represented among the first farmers, from about 7,000 to 5,000 years ago. And then suddenly everybody today has ancient north Eurasian ancestry," Reich says. "So there must have been a later movement of this ancestry into Europe."

Anthropologists have long thought that densely settled populations would be resistant to the arrival of new groups. "But this is hard evidence that exactly such a major migration occurred," Reich says. "It's very important because it's a major contributor to Europeans today." The time of the ancient north Eurasians' arrival remains to be determined, but Reich says their later-than-expected movement into Europe might help explain the complex mix of languages that exists there today.

The team's data also reveals that the first farmers to reach Europe from the Near East had ancestors from a previously unidentified lineage, which Reich's group named the Basal Eurasians. Basal Eurasians were the first people to separate from the larger group of non-Africans, before other non-African groups diversified. Reich says that attempts to identify the first group to split from the non-Africans had always been puzzling: genetic evidence indicates that this is likely to be Europeans or Near Easterners, even though some archaeological evidence has indicated that people were in New Guinea and Australia before they were Europe.

The new analysis shows that the Near Easterners who came into Europe 8,000 years ago brought with them a strand of ancestry that had separated before the ancestors of Australian aborigines separated from the indigenous people of Europe. "That population must have been hanging out somewhere in the Near East for a very long time," Reich says. Now he would like to know how that population fits into the archaeological history of the region. Ancient DNA from Basal Europeans, if found, might lead to new revelations about early human history.

link.

2nd link.

paper link.

Orcas Went Through Population Bottleneck During the Tarantian Pleistocene Quaternary

Whole genome sequencing has revealed a global fall in the numbers of killer whales during the last Ice Age, at a time when ocean productivity may have been widely reduced, according to researchers at Durham University.

The scientists studied the DNA sequences of killer whale communities across the world.

They found a severe decline in whale numbers leading to a bottleneck and consequent loss of genetic diversity approximately 40,000 years ago when large parts of the Earth were covered in ice.

The only exception to this was found in a killer whale population off the coast of South Africa that retained high variations in genetic diversity.

As greater genetic diversity indicates larger population size, the researchers believe the South African community of killer whales escaped the bottleneck faced by other communities.

They said an important factor could have been the Bengeula upwelling system – which delivers nutrient rich cold water to the oceans off South Africa – remaining stable despite the last glacial period.

This nutrient rich water would have been able to sustain the supplies of fish and dolphins that killer whales in this part of the world feed on.

link.

Siberian Skeleton Hints Native Americans Have Some PreColumbian, PreViking European Roots

Where did the first Americans come from? Most researchers agree that Paleoamericans moved across the Bering Land Bridge from Asia sometime before 15,000 years ago, suggesting roots in East Asia. But just where the source populations arose has long been a mystery.

Now comes a surprising twist, from the complete nuclear genome of a Siberian boy who died 24,000 years ago—the oldest complete genome of a modern human sequenced to date. His DNA shows close ties to those of today's Native Americans. Yet he apparently descended not from East Asians, but from people who had lived in Europe or western Asia. The finding suggests that about a third of the ancestry of today's Native Americans can be traced to "western Eurasia," with the other two-thirds coming from eastern Asia, according to a talk at a meeting* here by ancient DNA expert Eske Willerslev of the University of Copenhagen. It also implies that traces of European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots.

"I'm still processing that Native Americans are one-third European," says geneticist Connie Mulligan of the University of Florida in Gainesville. "It's jaw-dropping." At the very least, says geneticist Dennis O'Rourke of the University of Utah in Salt Lake City, "this is going to stimulate a lot of discussion."

Researchers have been trying to parse the origins of the first Americans for decades. Most agree that people moved across Beringia, via a vast ice age land bridge (see map p. 410), and began spreading through the Americas, reaching Chile by 14,500 years ago. But the origins of the source populations are not clear, and some archaeologists have even suggested that ancient Europeans crossing the Atlantic were part of the mix (Science, 16 March 2012, p. 1289). Others have contended that early skeletons found in the Americas, such as the 9000-year-old Kennewick Man, show some European features (Science, 10 April 1998, p. 190). In his talk, Willerslev argued that the ancient genome "can actually explain a lot of these inconsistencies," by offering glimpses of prehistoric populations before more recent migrations and other demographic events blurred the picture.

The genome comes from the right upper arm bone of a boy aged about 4 years, who lived by Siberia's Belaya River. Those who buried him adorned his grave with flint tools, pendants, a bead necklace, and a sprinkling of ochre. In the 1920s, Russian archaeologists discovered the burial and other artifacts near a village called Mal'ta, which gave the celebrated site its name. Willerslev and co-author Kelly Graf of Texas A&M University in College Station, traveled to the State Hermitage Museum in St. Petersburg, Russia, where the boy's remains are housed, and took a bone sample.

Willerslev reported that the team was able to sequence the boy's genome, and also to radiocarbon date the bone. The team then used a variety of statistical methods to compare the genome with that of living populations. They found that a portion of the boy's genome is shared only by today's Native Americans and no other groups, showing a close relationship. Yet the child's Y chromosome belongs to a genetic group called Y haplogroup R, and its mitochondrial DNA to a haplogroup U. Today, those haplogroups are found almost exclusively in people living in Europe and regions of Asia west of the Altai Mountains, which are near the borders of Russia, China, and Mongolia.

One expected relationship was missing from the picture: The boy's genome showed no connection to modern East Asians. DNA studies of living people strongly suggest that East Asians—perhaps Siberians, Chinese, or Japanese—make up the major part of Native American ancestors. So how could the boy be related to living Native Americans, but not to East Asians? "This was kind of puzzling at first," Willerslev told the meeting. But there seemed little doubt that the finding was correct, he said, because nearly all Native Americans from North and South America were equally related to the Mal'ta child, indicating that he represented very deep Native American roots.

link.

Genetic Study of India Highlights Mixture, Origins of Caste

Scientists from Harvard Medical School and the CSIR-Centre for Cellular and Molecular Biology in Hyderabad, India, provide evidence that modern-day India is the result of recent population mixture among divergent demographic groups.

The findings, published August 8 in the American Journal of Human Genetics, describe how India transformed from a country where mixture between different populations was rampant to one where endogamy—that is, marrying within the local community and a key attribute of the caste system—became the norm.

"Only a few thousand years ago, the Indian population structure was vastly different from today," said co–senior author David Reich, professor of genetics at Harvard Medical School. "The caste system has been around for a long time, but not forever."

In 2009, Reich and colleagues published a paper based on an analysis of 25 different Indian population groups. The paper described how all populations in India show evidence of a genetic mixture of two ancestral groups: Ancestral North Indians (ANI), who are related to Central Asians, Middle Easterners, Caucasians, and Europeans; and Ancestral South Indians (ASI), who are primarily from the subcontinent.

However, the researchers wanted to glean clearer data as to when in history such admixture occurred. For this, the international research team broadened their study pool from 25 to 73 Indian groups.

The researchers took advantage of the fact that the genomes of Indian people are a mosaic of chromosomal segments of ANI and ASI descent. Originally when the ANI and ASI populations mixed, these segments would have been extremely long, extending the entire lengths of chromosomes. However, after mixture these segments would have broken up at one or two places per chromosome, per generation, recombining the maternal and paternal genetic material that occurs during the production of egg and sperm.

By measuring the lengths of the segments of ANI and ASI ancestry in Indian genomes, the authors were thus able to obtain precise estimates of the age of population mixture, which they infer varied about 1,900 to 4,200 years, depending on the population analyzed.

While the findings show that no groups in India are free of such mixture, the researchers did identify a geographic element. "Groups in the north tend to have more recent dates and southern groups have older dates," said co-first author Priya Moorjani, a graduate student in Reich's lab at Harvard Medical School. "This is likely because the northern groups have multiple mixtures."

"This genetic datatells us a three-part cultural and historical story," said Reich, who is also an associate member of the Broad Institute. "Prior to about 4000 years ago there was no mixture. After that, widespread mixture affected almost every group in India, even the most isolated tribal groups. And finally, endogamy set in and froze everything in place."

"The fact that every population in India evolved from randomly mixed populations suggests that social classifications like the caste system are not likely to have existed in the same way before the mixture," said co–senior author Lalji Singh, currently of Banaras Hindu University, in Varanasi, India, and formerly of the CSIR-Centre for Cellular and Molecular Biology. "Thus, the present-day structure of the caste system came into being only relatively recently in Indian history."*

But once established, the caste system became genetically effective, the researchers observed. Mixture across groups became very rare.

Razib has an interesting post up.  Not sure what to make of it.