Human Genome News -  page 17
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-- Scientists Create “Virtual Fossil” - 12/18/15
-- Ancient British DNA Analyzed - 1/20/16
-- route taken out of Africa is still unclear - 11/10/15
-- Human Sperm Gene Traced to Dawn of Animal Evolution - 7/13/10
-- The Peopling of the New World - 7/22/15
-- Environmental Stresses Left Marks on Ancient Genes - 2/10/14
-- Our Tangled Ancestry - 2/10/14
-- Most European men from a handful of Bronze Age forefathers - 5/19/15
-- New DNA Analysis Technique Aids in Study of Early Human Migrations - 1/22/13
-- Oldest DNA Scrambles Human Origins - 12/04/13

 Ancient British DNA Analyzed

Wednesday, January 20, 2016

Anglo Saxon DNA

CAMBRIDGESHIRE, ENGLAND—An international team of scientists obtained whole genome sequences from ten skeletons unearthed near Cambridge. The skeletons ranged from the Iron Age, early Anglo-Saxon, and Middle Anglo-Saxon periods.

The scientists then compared the ancient genomes with those from modern Europeans by looking at rare mutations. “We estimate that 38 percent of the ancestors of the English were Anglo-Saxons. This is the first direct estimate of the impact of immigration into Britain from the fifth to seventh centuries A.D. and the traces left in modern England,” Stephan Schiffels of the Wellcome Trust Sanger Institute and the Max Plank Institute said in a press release. The genetic evidence, when combined with archaeological evidence, offers more information on how Anglo-Saxon immigrants adapted to life in Britain. “Genome sequences from four individuals from a cemetery in Oakington indicated that, genetically, two were migrant Anglo-Saxons, one was a native, and one was a mixture of both. The archaeological evidence shows that these individuals were treated the same way in death, and proves they were all well integrated into the Oakington Anglo-Saxon community despite their different biological heritage,” added Duncan Sayer of the University of Central Lancashire. To read in-depth about Anglo-Saxons, go to "The Kings of Kent."

 The predominantly African origin of all modern human populations is well established, but the route taken out of Africa is still unclear. Two alternative routes, via Egypt and Sinai or across the Bab el Mandeb strait into Arabia, have traditionally been proposed as feasible gateways in light of geographic, paleoclimatic, archaeological, and genetic evidence. Distinguishing among these alternatives has been difficult. We generated 225 whole-genome sequences (225 at 8× depth, of which 8 were increased to 30×; Illumina HiSeq 2000) from six modern Northeast African populations (100 Egyptians and five Ethiopian populations each represented by 25 individuals). West Eurasian components were masked out, and the remaining African haplotypes were compared with a panel of sub-Saharan African and non-African genomes. We showed that masked Northeast African haplotypes overall were more similar to non-African haplotypes and more frequently present outside Africa than were any sets of haplotypes derived from a West African population. Furthermore, the masked Egyptian haplotypes showed these properties more markedly than the masked Ethiopian haplotypes, pointing to Egypt as the more likely gateway in the exodus to the rest of the world. Using five Ethiopian and three Egyptian high-coverage masked genomes and the multiple sequentially Markovian coalescent (MSMC) approach, we estimated the genetic split times of Egyptians and Ethiopians from non-African populations at 55,000 and 65,000 years ago, respectively, whereas that of West Africans was estimated to be 75,000 years ago. Both the haplotype and MSMC analyses thus suggest a predominant northern route out of Africa via Egypt.

This is an open access article under the CC BY-NC-ND license (
Received: January 21, 2015; Accepted: April 29, 2015; Published Online: May 28, 2015
© 2015 The Authors. Published by Elsevier Inc.

 Human Sperm Gene Traced to Dawn of Animal Evolution

July 16, 2010 By Christine Dell'Amore, National Geographic News

Gene is in all sexual animals:

Human sperm.

The production of human sperm depends on a 600-million-year old gene, a new study says.   The gene responsible for sperm in all sexual creatures dates to the beginning of animal evolution.   The Boule gene, first discovered in humans in 2001, is linked to sperm production in humans and, the study says, is likely responsible for making sperm in every other sexual animal too.

The sperm-production gene is apparently so critical to life that it hasn't changed since every animal's common evolutionary ancestor—likely just a blob of cells—arose some 600 million years ago, the researchers conclude.   The study team discovered that the gene is found in a wide range of sexually reproducing creatures, including flies and humans.   This means that Boule is found in all the evolutionary lineages that have branched off from that common ancestor, according to study leader Eugene Xu, a professor of obstetrics and gynecology at Northwestern University in Evanston, Illinois.

That the sperm-production gene remains the same "is surprising," Xu said, since most sex genes rapidly mutate under the pressures of evolution. "It really suggests a new perspective of how we look at humans and how sperm production evolved."  Sperm researcher Rhonda Snook agreed. The study "represents significant effort in understanding the evolution of sperm production," she said via email.

To find out Boule's age, Xu and colleagues had to show that the sperm gene arose only once, in a common ancestor. rather than forming independently in different evolutionary lineages.   To do so, the team collected sperm from a wide sample of different animals, including humans, roosters, flies, trout, and sea anemones—especially important because of their ancient lineage.  

Securing most of the sperm was a cinch, but the trout presented a sticky situation.   When Xu bought a trout from a Chicago fish seller, the man told him, "This is the best fish you could ever get—only a few hours old." Not so for Xu, who quickly realized the fish had been gutted. "I want their testicles," he told the seller.   No luck. Instead, Xu had no choice but to catch his own fully endowed rainbow trout on a family trip to a fishpond.   Back at the lab, Xu and colleagues discovered that each animal species mainly express the Boule gene in its testicles, he said.   The result is startling and, to Snook, of the U.K.'s University of Sheffield, enviable. "I couldn't help but think that the authors got 'lucky' in choosing Boule—although their rationale of choosing it was sound—and finding that it was so highly unchanged."

Until now, scientists hadn't known whether different species have different genes for making sperm. For instance, of hundreds of known sex genes, only a very small number can be found in more than one evolutionary lineage.   But since study leader Xu found Boule in different branches of the animal tree, from sea anemones to humans, he's confident that the sperm gene is widespread in every major lineage of the animal kingdom.   To finally prove Boule is a sexual animal's sole sperm-making powerhouse, the team had to disrupt the gene, according to the study, published July 15 in the journal PLoS Genetics.   When the scientists "disabled" the gene in lab mice, "boom ... everything was normal, [but] the male can't produce sperm," Xu said.   Turning off this sperm switch could someday help control disease-spreading pests such as mosquitoes, Xu pointed out. For instance scientists could genetically tweak males into becoming spermless.

Likewise, since Boule has only one function, using it to turn off sperm production would likely cause no adverse health effects in humans, he said.

This makes the Boule gene "an ideal target," Xu added, for the long-sought male birth control pill.

 The Peopling of the New World

Wednesday, July 22, 2015    Americas genetic migration    (Courtesy University of Copenhagen)

COPENHAGEN, DENMARK—A new large-scale genome study is adding to the debate over how the peopling of the Americas occurred. An international team of scientists sampled several present-day Native American and Siberian populations, in addition to ancient DNA samples from across the Americas. “Our study presents the most comprehensive picture of the genetic prehistory of the Americas to date. We show that all Native Americans, including the major sub-groups of Amerindians and Athabascans, descend from the same migration wave into the Americas. This was distinct from later waves that gave rise to the Paleo-Eskimo and Inuit populations in the New World Arctic region,” Maanasa Raghavan of the Centre for GeoGenetics at the University of Copenhagen said in a press release. The results also indicate that the initial migration took place no earlier than 23,000 years ago, when Native Americans split from East Asian and Siberian populations. Ancestral Native Americans may then have been isolated in Beringia for some 8,000 years, since the oldest archaeological evidence in the Americas is about 15,000 years old. The study also found that some 13,000 years ago, this population split into northern and southern branches. Gene flow between some Native American groups and present-day East Asians and Australo-Melanesians was also detected. “It is a surprising finding and it implies that New World populations were not completely isolated from the Old World after their initial migration. We cannot say exactly how and when this gene flow happened, but one possibility is that it came through the Aleutian Islanders living off the coast of Alaska,” added Eske Willerslev, who headed the study.

 Environmental Stresses Left Marks on Ancient Genes

AUSTIN, TEXAS—Chemical modifications, known as epigenetic marks, can be added to or removed from a person’s DNA in response to environmental factors such as diet, disease, and climate. These changes can influence which genes are turned on or off during a person’s life, shaping physical traits and health, and can even be passed on to offspring if the changes occur in sperm and egg DNA. Anthropologists from The University of Texas at Austin have shown that epigenetic marks on DNA can be detected in ancient human remains using techniques that are normally used to measure changes in modern DNA. They looked for an epigenetic mark known as cytosine methylation on the remains of 30 individuals who lived in five different places in North America between 230 to more than 4,500 years ago. They were able to identify methylation in 29 of the samples. “By studying methylation in ancient DNA from archaeological populations, not just isolated samples, we may gain insights into how past environments affected ancient societies. Future research in ancient epigenetics should open a new window into the lives and experiences of people who lived long ago,” anthropologist Deborah Bolnick explained in a press release. To read about the first people to reach the New World, see "America, in the Beginning."

 Our Tangled Ancestry

February 10, 2014    By ZACH ZORICH

Homo heidelbergensis skeleton
(Courtesy Javier Trueba, Madrid Scientific Films)
Homo heidelbergensisWhen scientists attempt to draw the evolutionary family tree of the human race, they would like to be able to use straight lines to show the relationships between hominin groups: one species leads to another, and so on. But this isn’t always possible. Three recent studies of ancient DNA have uncovered unique genetic markers in unexpected places, showing that our ancestors got around and interbred more than anyone had previously thought. The result is a convoluted set of relationships among early humans where once there was a simpler family tree.

The story of this new work begins in northern Spain. There, a group of Spanish researchers at the site of Sima de los Huesos teamed up with geneticists from the Max Planck Institute for Evolutionary Anthropology to examine the oldest known hominin DNA sample, which comes from a 400,000-year-old Homo heidelbergensis thigh bone. They sequenced the bone’s mitochondrial DNA (mtDNA), which is passed from mother to child. “What we were expecting to see was Neanderthal mitochondrial DNA,” says Matthias Meyer of the Max Planck Institute, as Neanderthals would later occupy that part of Europe and might be expected to carry genetic material from the previous inhabitants. Surprisingly, the mtDNA is instead more closely related to that of a hominin who lived more than 50,000 years ago in Siberia’s Denisova Cave than it is to that of Neanderthals. The Denisovans were related to, but genetically distinct from, Neanderthals.

According to Meyer, the Sima de los Huesos sample is old enough that it could represent an ancestor to both Denisovans and Neanderthals. However, it is also possible that H. heidelbergensis is not ancestral to either group, but later interbred with the Denisovan lineage. Studies of nuclear DNA, which contains genetic information from both parents, will be needed to clarify the relationship, Meyer believes.

Max Planck Institute scientists also recently sequenced the genome of a second individual who lived at Denisova more than 50,000 years ago. They discovered that the individual was actually a Neanderthal, not a Denisovan. It is the most complete Neanderthal genome yet recovered, and it has given geneticists a novel point of comparison among various human lineages. The new analysis shows that occasional interbreeding between Neanderthals, Denisovans, and Homo sapiens probably took place in more than one time and place, and that the Denisovans also interbred with an unknown archaic hominin group—possibly H. heidelbergensis.

According to another new study with surprising results, a small percentage of the Denisovans’ unique DNA still lives on in the indigenous people of Australia, New Guinea, and the eastern islands of Indonesia—all places that are separated from the Asian mainland by strong ocean currents that form a migratory barrier called the Wallace Line. Based on the lack of Denisovan DNA markers in ancient and modern populations on the Asian side of the line, and their relative abundance on the other, Alan Cooper of the University of Adelaide and Christopher Stringer of London’s Natural History Museum believe that Denisovans may have boated to locations across the Wallace Line and interbred with the H. sapiens already living there.

While these studies paint a complex picture of our genetic past, Meyer believes the relationships between ancient humans will become clear as methods for recovering ancient DNA improve. “In the next year or two,” he says, “we will have a much, much higher-resolution picture of human migrations out of Africa and within Eurasia.”

 Most European men descend from a handful of Bronze Age forefathers

May 19, 2015

Geneticists from the University of Leicester have discovered a European male-specific population explosion that occurred between 2,000 and 4,000 years ago.

Most European men descend from just a handful of Bronze Age forefathers, due to a 'population explosion' several thousand years ago.

The project, which was funded by the Wellcome Trust, was led by Professor Mark Jobling from the University of Leicester's Department of Genetics and the study is published in the prestigious journal Nature Communications.

The research team determined the DNA sequences of a large part of the Y chromosome, passed exclusively from fathers to sons, in 334 men from 17 European and Middle Eastern populations, using new methods for analysing DNA variation that provides a less biased picture of diversity, and also a better estimate of the timing of population events. This allowed the construction of a genealogical tree of European Y chromosomes that could be used to calculate the ages of branches. Three very young branches, whose shapes indicate recent expansions, account for the Y chromosomes of 64% of the men studied.

Professor Jobling said: "The population expansion falls within the Bronze Age, which involved changes in burial practices, the spread of horse-riding and developments in weaponry. Dominant males linked with these cultures could be responsible for the Y chromosome patterns we see today."

In addition, past population sizes were estimated, and showed that a continuous swathe of populations from the Balkans to the British Isles underwent an explosion in male population size between 2,000 and 4,000 years ago.

This contrasts with previous results for the Y chromosome, and also with the picture presented by maternally-inherited mitochondrial DNA, which suggests much more ancient population growth.

Europe during the late bronze age (1100 BC). Xoil, Wikimedia Commons

Previous research has focused on the proportion of modern Europeans descending from Paleolithic—Old Stone Age—hunter-gatherer populations or more recent Neolithic farmers, reflecting a transition that began about 10,000 years ago.
Chiara Batini from the University of Leicester's Department of Genetics, lead author of the study, added: "Given the cultural complexity of the Bronze Age, it's difficult to link a particular event to the population growth that we infer. But Y-chromosome DNA sequences from skeletal remains are becoming available, and this will help us to understand what happened, and when."

The study 'Large-scale recent expansion of European patrilineages shown by population resequencing' is published in Nature Communications.

Adapted and edited from the University of Leicester press release.

*The Wellcome Trust is a global charitable foundation dedicated to improving health. It provides more than £700 million a year to support scolarship in science, the humanities and the social sciences, as well as education, public engagement and the application of research to medicine.   The £18 billion investment portfolio provides the independence to support such transformative work as the sequencing and understanding of the human genome, research that established front-line drugs for malaria, and Wellcome Collection, the free venue for exploring medicine, life and art.

 New DNA Analysis Technique Aids in Study of Early Human Migrations

January 22, 2013

LEIPZIG, GERMANY—A new technique that identifies ancient human DNA even when large amounts of DNA from soil bacteria are also present has been used to study a 40,000-year-old modern-human leg bone. The findings suggest that the remains, which were found in China’s Tianyuan Cave in 2003, came from an ancestor of present-day Asians and Native Americans. The DNA tests also indicate that this ancestor had already split from the ancestors of present-day Europeans. “More analyses of additional early modern humans across Eurasia will further define our understanding of when and how modern humans spread across Europe and Asia,” said Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology.

 Discovery of Oldest DNA Scrambles Human Origins Picture

Published December 4, 2013    By Karl Gruber    for National Geographic        

Scientists reveal the surprising genetic identity of early human remains from roughly 400,000 years ago in Spain.

The bones were first thought to belong to European Neanderthals, but analysis showed they are genetically closer to the Siberian Denisovans.

New tests on human bones hidden in a Spanish cave for some 400,000 years set a new record for the oldest human DNA sequence ever decoded—and may scramble the scientific picture of our early relatives.

Analysis of the bones challenges conventional thinking about the geographical spread of our ancient cousins, the early human species called Neanderthals and Denisovans.   Until now, these sister families of early humans were thought to have resided in prehistoric Europe and Siberia, respectively. (See also: "The New Age of Exploration.")

But paleontologists write in a new study that the bones of what they thought were European Neanderthals appear genetically closer to the Siberian Denisovans, as shown by maternally inherited "mitochondrial" DNA found in a fossil thighbone uncovered at Spain's Sima de los Huesos cave.

"The fact that they show a mitochondrial genome sequence similar to that of Denisovans is irritating," says Matthias Meyer of Germany's Max Planck Institute for Evolutionary Anthropology in Leipzig, lead author of the study, published Wednesday in Nature.

"Our results suggest that the evolutionary history of Neanderthals and Denisovans may be very complicated and possibly involved mixing between different archaic human groups," he said.

Neanderthals and Denisovans arose hundreds of thousands of years before modern-looking humans spread worldwide from Africa more than 60,000 years ago. The small traces of their genes now found in modern humans are signs of interbreeding among ancient human groups.

Previously, the oldest human DNA sequenced came from bones that were less than 120,000 years old.

Meyer said stable temperatures in the cave helped preserve the mitochondrial DNA, and credited recent advances in gene-sequencing technology for establishing the basis for the new milestone.

Mixed Up or Mixing It Up?

For humanity's tangled past, the new mitochondrial DNA results raise an unexpected question: How does a Spanish early human species end up with Siberian DNA?

The authors propose several possible scenarios. For instance, Sima hominins could simply be close relatives of the Denisovans. But that would mean they lived right alongside Neanderthals without having close genetic ties to them.

The Sima hominins could also be a completely independent group that mingled with Denisovans, passing on their mitochondrial DNA, but it would be hard to explain why they also have Neanderthal features.

Another possibility, suggested by anthropologist Chris Stringer of the Natural History Museum in London, is that mitochondrial DNA from the Sima people reached the Denisovans thanks to interspecies sexual adventures among early humans, which introduced the DNA to both the Sima and Denisovans.

In the end, the identity of these ancient people remains a mystery, and further work is needed to clarify their identity. "The current genetic data [mitochondrial DNA] is too limited to conclude much about their population history," Meyer says.

As with the Denisovans, only the decoding of the full genetic map or genome, and not just the mitochondrial DNA, will provide convincing evidence of Sima family history, Meyer says.

New Piece of the Puzzle

In recent years, paleogeneticists have released surprising reports about such early human species, notably the interspecies breeding that likely occurred among Neanderthals, Denisovans, and modern humans.

Uncovered only in 2010, Denisovans are known solely from a pinkie and a tooth found in 30,000- to 50,000-year-old rock layers in Siberia's Denisova cave. DNA from those Siberian bones first established their owners as genetically distinct from Neanderthals and modern people.

(Read "The Case of the Missing Ancestor" in National Geographic magazine.)

"The fact that the Sima de los Huesos [mitochondrial DNA] shares a common ancestor with Denisovan rather than Neanderthal [mitochondrial DNA] is unexpected in light of the fact that the Sima de los Huesos fossils carry Neanderthal-derived features," says the study.

But paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not part of the study, says "there's not really anything very surprising" about the Spanish bones' bearing mitochondrial DNA that is not an earlier version of Neanderthal genes.

Ancient mitochondrial DNA from many other species—"bison, mammoths, cave bears, and others"—doesn't resemble that of more recent species, he notes.

Hawks is more cautious than the study authors about regarding the Spanish genes and younger Denisovan ones as being closely related: "The difference between Sima and Denisova [gene] sequences is about as large as the difference between Neanderthal and living human sequences.

"It would not be fair to say that Denisova and Sima represent a single population, any more than that Neandertals and living people do."

One reason for caution is that mitochondrial DNA results in the past have pointed scholars in errant directions; for example, some early studies suggested that humans and Neanderthals did not share any common ancestry.

Mitochondrial DNA is a small part of the human genome that is generally transmitted only through the female line, from mothers to offspring. This has important implications for the study of past events.

For instance, ancient interspecies breeding events might not be picked up by mitochondrial DNA.

But mitochondrial DNA can be transferred between species when interspecies mingling events occur. Such scenarios have been observed for other groups, such as polar and brown bears, where it has been found that interspecies breeding led to mixed-up mitochondrial genomes.

The Mountain of Bones

The Atapuerca Mountains, where the human bones were found, is a world-famous archaeological site located in northern Spain; a group of caves there contain some of Western Europe's oldest known human remains.

The most famous of these caves, Sima de los Huesos, has been studied since 1997 and hosts more than 6,000 ancient bone samples belonging to 28 ancient humans that lived roughly 400,000 years ago. The exact origin of the bone pile is unclear.

"Could a natural catastrophe or carnivore activities explain the accumulation of so many bodies?" asks anthropologist Juan-Luis Arsuaga, a co-author of the study and lead excavator at the cave for the past 30 years. "Or were there hominins that accumulated the corpses of their relatives and friends in such a dark and remote place: a pit in a cave?

"I would like to live to know the answer."

The bones of the Sima people share the features of Neanderthals, notably their thick-browed skulls, as well as the features of a much older group of human ancestors called Homo heidelbergensis, which lived about 600,000 years ago.

That species is also considered an ancestor of modern humans, Denisovans, and Neanderthals.

Genetic Study Traces the Origins of the Irish

Tuesday, December 29, 2015

Ireland genomes sequenced (Barrie Hartwell) DUBLIN, IRELAND—Geneticists from Trinity College Dublin and archaeologists from Queen’s University Belfast sequenced the genomes of a Neolithic woman who lived near Belfast some 5,200 years ago, and three men who lived during the Bronze Age, some 4,000 years ago, on Rathlin Island. The team found that the early farmer had black hair and brown eyes, and her ancestors had originated in the Middle East. They probably brought agriculture with them across Europe to Ireland. The Bronze Age men had blue eye alleles, the most common Irish Y chromosome type, and the most important variant for the genetic disease haemochromatosis, which is now frequent in people of Irish descent and sometimes thought of as a Celtic disease. About a third of the ancestors of the Bronze Age men came from the northern shores of the Black Sea. “There was a great wave of genome change that swept into Europe from above the Black Sea into Bronze Age Europe and we now know it washed all the way to the shores of its most westerly island,” study leader Dan Bradley of Trinity College Dublin said in a press release. To read more about Bronze Age Ireland, go to "Bronze Age Ireland’s Taste in Gold."

 Scientists Create “Virtual Fossil”

Friday, December 18, 2015

CAMBRIDGE, ENGLAND—DNA studies have suggested that modern humans and Neanderthals split from a common ancestor some 400,000 years ago. But what did this ancestor look like? Researchers have created a “virtual fossil” of this last common ancestor by plotting a total of 797 “landmarks” on a modern skull and the fossilized skulls of human relatives spanning a range of two million years. These data points were used to predict a timeline for skull structure. “We wanted to try an innovative solution to deal with the imperfections of the fossil record: a combination of 3-D digital methods and statistical estimation techniques. This allowed us to predict mathematically and then recreate virtually skull fossils of the last common ancestor of modern humans and Neanderthals, using a simple and consensual ‘tree of life’ for the genus Homo,” Aurélien Mounier of Cambridge University said in a press release. Three possible ancestral skull shapes were generated for three possible times of the split. These skull shapes were then compared to the few available fossils in the range of 800,000 to 100,000 years old. The virtual skull that was the best fit for the fossils suggests that the split between Neanderthals and modern humans occurred some 700,000 years ago. To read more about our extinct ancestors, go to "Should We Clone Neanderthals?"

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