//Nature Communications

Nature Communications

Publisher: Nature
Impact Factor: 11.470 (2014)
Years in Print: 2010 - Present
Journal Website: http://www.nature.com/ncomms/index.html

Articles of Interest

Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals

Journal: Nature Communications | Year: 2017

Abstract:

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals 270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.

Peoples: Neandertals | Places: Germany | Topics: mtDNA | DNA Type: Ancient DNA and mtDNA

Complete mitochondrial sequences from Mesolithic Sardinia

Journal: Nature Communications | Year: 2017

Abstract:

Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times.

Peoples: Sardinians | Places: Sardinia | Topics: Mesolithic, mtDNA, and Neolithic | DNA Type: Ancient DNA and mtDNA

Clustering of 770,000 genomes reveals post-colonial population structure of North America

Journal: Nature Communications | Year: 2017

Abstract:

Despite strides in characterizing human history from genetic polymorphism data, progress in identifying genetic signatures of recent demography has been limited. Here we identify very recent fine-scale population structure in North America from a network of over 500 million genetic (identity-by-descent, IBD) connections among 770,000 genotyped individuals of US origin. We detect densely connected clusters within the network and annotate these clusters using a database of over 20 million genealogical records. Recent population patterns captured by IBD clustering include immigrants such as Scandinavians and French Canadians; groups with continental admixture such as Puerto Ricans; settlers such as the Amish and Appalachians who experienced geographic or cultural isolation; and broad historical trends, including reduced north-south gene flow. Our results yield a detailed historical portrait of North America after European settlement and support substantial genetic heterogeneity in the United States beyond that uncovered by previous studies.

Peoples: African Americans and North American | Places: Americas | Topics: IBD | DNA Type: Autosomal DNA

A time transect of exomes from a Native American population before and after European contact

Journal: Nature Communications | Year: 2016

Abstract:

A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s.

Peoples: Native Americans | Places: North America | Topics: Effective population size, European-borne epidemics, HLA-DQA1, Negative selection, and Positive selection | DNA Type: Autosomal DNA and X-DNA

A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome

Journal: Nature Communications | Year: 2016

Abstract:

The African Diaspora in the Western Hemisphere represents one of the largest forced migrations in history and had a profound impact on genetic diversity in modern populations. To date, the fine-scale population structure of descendants of the African Diaspora remains largely uncharacterized. Here we present genetic variation from deeply sequenced genomes of 642 individuals from North and South American, Caribbean and West African populations, substantially increasing the lexicon of human genomic variation and suggesting much variation remains to be discovered in African-admixed populations in the Americas. We summarize genetic variation in these populations, quantifying the postcolonial sex-biased European gene flow across multiple regions. Moreover, we refine estimates on the burden of deleterious variants carried across populations and how this varies with African ancestry. Our data are an important resource for empowering disease mapping studies in African-admixed individuals and will facilitate gene discovery for diseases disproportionately affecting individuals of African ancestry.

Peoples: African-admixed individuals | Places: Africa, North America, and South America | Topics: African ancestry | DNA Type: Autosomal DNA

Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines

Journal: Nature Communications | Year: 2013

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra

Journal: Nature Communications | Year: 2011

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA and Y-DNA

Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages

Journal: Nature Communications | Year: 2006

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages

Journal: Nature Communications | Year: 2013

Abstract:

Peoples: | Places: | Topics: | DNA Type: mtDNA

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

Journal: Nature Communications | Year: 2013

Abstract:

Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.

Peoples: | Places: | Topics: | DNA Type: mtDNA

2016-06-23T17:57:47+00:00 June 23rd, 2016|