Monthly Archives: February 2014

The Digital Universe: A Cosmic Genome Project
Astronomers are about to embark on the grandest map of the universe ever made: the first large digital survey of the sky. A database of more than 100 million...

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DNA UA. People with the Ukrainian genome. Episode 2. Close to maturity
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DNA UA. People with the Ukrainian genome. Episode 2. Close to maturity - Video

Out of Asia: ancient genome lays to rest origins of Americas #39; first humans
The genome of a child who died some 12600 years ago in Montana -- the oldest known human remains from North America -- has been sequenced for the first time...

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Out of Asia: ancient genome lays to rest origins of Americas' first humans - Video

Genome and Transcriptome Dynamics in Cancer Cells - Thomas Ried
February 7, 2014 - The 2013-2014 Genomics in Medicine Lecture Series More: http://www.genome.gov/27553517.

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Genome and Transcriptome Dynamics in Cancer Cells - Thomas Ried - Video

Presentation from Large-Scale Genome Sequencing and Analysis Centers #39; Investigators - Richard Gibbs
February 10, 2014 - National Advisory Council for Human Genome More: http://www.genome.gov/27556133.

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Presentation from Large-Scale Genome Sequencing and Analysis Centers' Investigators - Richard Gibbs - Video

Presentation from Large-Scale Genome Sequencing and Analysis Centers #39; Investigators - Eric Lander
February 10, 2014 - National Advisory Council for Human Genome More: http://www.genome.gov/27556133.

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Presentation from Large-Scale Genome Sequencing and Analysis Centers' Investigators - Eric Lander - Video

Les Efants Terribles: Cloning The Genome Soldiers
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The new analysis of "Clovis boy" DNA also stirs an ethics debate about the handling of tribal remains

Humans from the Clovis culture used characteristic stone points (brown) and rod-shaped bone tools. Credit:Robert L. Walker

The remains of a young boy, ceremonially buried some 12,600years ago in Montana, have revealed the ancestry of one of the earliest populations in the Americas, known as the Clovis culture.

Published in this issue ofNature, the boys genome sequence shows that todays indigenous groups spanning North and South America are all descended from a single population that trekked across the Bering land bridge from Asia (M.Rasmussenet al. Nature506,225229; 2014). The analysis also points to an early split between the ancestors of the Clovis people and a second group, whose DNA lives on in populations in Canada and Greenland (seepage162).

But the research underscores the ethical minefield of studying ancient Native American remains, and rekindles memories of a bruising legal fight over a different human skeleton in the 1990s.

To avoid such a controversy, Eske Willerslev, a paleobiologist at the University of Copenhagen who led the latest study, attempted to involve Native American communities. And so he embarked on a tour of Montanas Indian reservations last year, talking to community members to explain his work and seek their support. I didnt want a situation where the first time they heard about this study was when its published, he says.

Construction workers discovered the Clovis burial site on a private ranch near the small town of Wilsall in May 1968 (see Ancient origins). About 100 stone and bone artefacts, as well as bone fragments from a male child aged under two, were subsequently recovered.

The boys bones were found to date to the end of the Clovis culture, which flourished in the central and western United States between about 13,000 and 12,600 years ago. Carved elk bones found with the boys remains were hundreds of years older, suggesting that they were heirlooms. The ranch, owned by Melvyn and Helen Anzick, is the only site yet discovered at which Clovis objects exist alongside human bones. Most of the artefacts now reside in a museum, but researchers returned the human remains to the Anzick family in the late 1990s.

At that time, the Anzicks daughter, Sarah, was conducting cancer and genome research at the National Institutes of Health in Bethesda, Maryland, and thought about sequencing genetic material from the bones. But she was wary of stoking a similar debate to the one surrounding Kennewick Man, a human skeleton found on the banks of the Columbia River in Kennewick, Washington, in July 1996. Its discovery sparked an eight-year legal battle between Native American tribes, who claimed that they were culturally connected to the individual, and researchers, who said that the roughly 9,000-year-old remains pre-dated the tribes.

The US government sided with the tribes, citing the federal Native American Graves Protection and Repatriation Act (NAGPRA). The act requires that human remains discovered on federal lands as Kennewick Man was are returned to affiliated tribes for reburial. But a court ruled that the law did not apply, largely because of the age of the remains, and ordered that Kennewick Man be stored away from public view in a museum.

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Ancient Genome Suggests Native Americans Really Did Descend from the First Americans

The sequencing of DNA from the earliest known North American remains has provided the first genetic confirmation of Native American ancestry, quashed a controversial alternative theory and hinted at possible migration patterns that may revise our understanding of population dispersal from modern-day Alaska to the southern tip of Chile.

Whew. Pretty impressive achievements for a baby.

Researchers today announced the successful whole-genome sequencing of Anzick-1, the remains of an infant boy who lived roughly 12,600 years ago. The remains were discovered in central Montana in 1968 during a construction project. Anzick-1 was a crucial find for archaeologists even before scientists completed the DNA analysis the childs remains are the oldest known burial in North America and the only human remains ever found that are definitively associated with the Clovis people, the continents first known indigenous culture.

Anzick-1s DNA allowed researchers to confirm genetically, for the first time, that all native peoples of North and South America descended from ancestors who arrived via land bridges from East Asia, possibly in a single migration. While there has been ample archeological evidence of the East Asian origin of Native Americans, conclusive proof based on DNA had been absent until now. Even a recent study comparing the genes of ancient Siberian remains with those of modern Native Americans had not been as conclusive.

The sequencing of Anzick-1s genome, however, revealed the child was part of a line that was directly ancestral to 80 percent of all American native peoples, and close cousins to the remaining 20 percent.

In addition, analysis of the childs mitochondrial DNA indicated Anzick-1 belonged to whats known as the D4h3a haplogroup, or lineage. The finding is important and surprising, according to researchers because the D4h3a line is considered to be a founder lineage, belonging to the first people to arrive in the Americas. Although rare in most Native Americans in the U.S. and Canada today, D4h3a genes are found more commonly in native people of South America, far from the Montana cliff beneath which Anzick-1 was laid to rest.

Placing Anzick-1 in the D4h3a haplogroup suggests greater genetic complexity among Native Americans than previously believed, including an early divergence in genetic lineage 13,000 years ago or more. One theory had suggested that after crossing into North America from Siberia, one group of early Americans, with the D4h3a lineage, moved south along the Pacific coast and eventually, over thousands of years, to Central and South America. Other groups may have moved inland, east of the Rockies, as ice sheets retreated.

Finding Anzick-1s D4h3a lineage in central Montana casts doubt on that theory, though researchers were quick to caution that we shouldnt draw conclusions about migration patterns more than 10,000 years ago by comparing one ancient genome with that of modern people. Only the discovery and genetic sequencing of other remains as old as Anzick-1 will clarify how and when populations spread from the far northwest of the Americas.

Anzick-1 was estimated to be 12-18 months old at the time of his death; a cause of death has not been identified. He was covered in red ochre, a natural pigment, and apparently buried with several tools made of bone or stone in the style of the Clovis people. The Clovis people are generally believed to be the first wholly indigenous culture of North America, though there is archaeological evidence some of it contentious of an earlier human presence in the Americas.

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Earliest American Genome Proves Siberian Origins of Native Peoples

Social insects, which usually have specialized behavioral groups (also called castes), are important models for social evolution and behavior researches. How division of labor in insect societies is regulated is an outstanding question and not fully understood yet. However, in many social insect species, experimental control over important factors that regulate division of labor, such as genotype and age, is limited. In a study published online on February 6th in Current Biology, researchers from Rockefeller University and BGI-Shenzhen have sequenced the genome of the queenless clonal raider ant Cerapachys biroi, a new model system to study the molecular mechanisms of social behaviors.

Ants of the genus Cerapachys are myrmecophagous and raid the nests of other ants. It belongs to the dorylomorph clade of ants, which also includes the infamous army ants. Since the early 1900s, introduced populations of C. biroi have become established on tropical and subtropical islands around the world, probably as a consequence of human traffic and trade. Like in many other army ants, colonies of C. biroi undergo two phases in their life cycles: one is for reproduction and the other for foraging and brood care. And more interestingly, colonies of C. biroi uniquely consist entirely of totipotent workers, all of which reproduce asexually.

The authors noted one of the most interesting findings of this study is that nestmates in a colony are almost clonally related and reproduce via an asexual way called automixis with central fusion, which was also found in the Cape honeybees. Asexual reproduction usually leads to loss of genomic heterozygosity, which is harmful in the long run. However, that genomic heterozygosity in C. biroi is lost extremely slowly. "It is not yet clear whether maintaining heterozygosity in C. biroi is through reduced recombination during meiosis, via selection against homozygous individuals, or both." said Dr. Peter Oxley, co-first author of this study, in Laboratory of Insect Social Evolution, Rockefeller University.

Nestmates of C. biroi can synchronously alternate between reproduction and brood care. The authors also found expression patterns of the genes associated with division of labor in other social insects are conserved in C. biroi and dynamically regulated during the colony cycle. "This suggests that the gene networks underlying reproduction and brood care in C. biroi are likely to be the same conserved networks underlying caste-specific behavior in other eusocial insects." said Dr. Daniel Kronauer, co-senior author of this study and head of Laboratory of Insect Social Evolution in Rockefeller University.

Because C. biroi colonies have totipotent workers and no queens, it is easy to conduct colony propagation and control the composition of arbitrarily sized experimental colonies. In addition, the colony cycle of C. biroi allows for precise selection of age-matched workers and experimental control over colony demography. "Ants represent one of the most successful exclusively eusocial insects, with at least 15,000 species have been recorded, they have evolved innumerous diversity. This is the fourth ant genome published in our group. The clonal raider ant is unique in many aspects compared to other ants. There are still many interesting questions related to the development and evolution of the queenless and reproductive cycle in this system that we don't know yet. The availability of this genome could pave the road for these future studies." said Dr. Guojie Zhang, co-senior author of this study, from China National Genebank, BGI-Shenzhen and Centre for Social Evolution in University of Copenhagen.

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Genome of clonal raider ant provides promising model to study social evolution and behavior