New DNA Papers

[Jean M]

Lanka Ranaweera et al., Mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations, Journal of Human Genetics (2014) 59, 28–36.

http://www.nature.com/jhg/journal/v5...g2013112a.html

Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil (Sri Lankan and Indian); their history of settlements on the island and the biological relationships among them have remained obscure. It has been hypothesized that the Vedda was probably the earliest inhabitants of the area, followed by Sinhalese and Tamil from the Indian mainland. This study, in which 271 individuals, representing the Sri Lankan ethnic populations mentioned, were typed for their mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) and part of hypervariable segment 2 (HVS-2), provides implications for their settlement history on the island. From the phylogenetic, principal coordinate and analysis of molecular variance results, the Vedda occupied a position separated from all other ethnic people of the island, who formed relatively close affiliations among themselves, suggesting a separate origin of the former. The haplotypes and analysis of molecular variance revealed that Vedda people’s mitochondrial sequences are more related to the Sinhalese and Sri Lankan Tamils’ than the Indian Tamils’ sequences. MtDNA haplogroup analysis revealed that several West Eurasian haplogroups as well as Indian-specific mtDNA clades were found amongst the Sri Lankan populations. Through a comparison with the mtDNA HVS-1 and part of HVS-2 of Indian database, both Tamils and Sinhalese clusters were affiliated with Indian subcontinent populations than Vedda people who are believed to be the native population of the island of Sri Lanka.

This was online last November, so some of you may have seen it already.

[Humanist]

Posts discussing and related to the La Brana paper have been moved here: Full Genome of Mesolithic Man from La Braña

[Humanist]

Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region

Hernández et al.

Abstract
Background
The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region.

Results
The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population.

Conclusions
The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia.

[soulblighter]

Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar, Summerer et.al.


"Background
Myanmar is the largest country in mainland Southeast Asia with a population of 55 million
people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and
dynasties and lying on the trade route between India and China, Myanmar was influenced by
numerous cultures. Since its independence from British occupation, tensions between the
ruling Bamar and ethnic minorities increased.

Results
Our aim was to search for genetic footprints of Myanmar’s geographic, historic and
sociocultural characteristics and to contribute to the picture of human colonization by
describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we
sequenced the mtDNA control region of 327 unrelated donors and the complete
mitochondrial genome of 44 selected individuals according to highest quality standards.

Conclusion
Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and
three unclassified basal M-lineages. The multi-ethnic population and the complex history of
Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of
Burmese control region sequences combined with population data from neighboring countries
revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern,
but also Northeast Asian and Indian influences. The population structure of the
extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of
genetic isolation. Migration analyses indicated a considerable genetic exchange with an
overall positive migration balance from Myanmar to neighboring countries. Age estimates of
the newly described haplogroups point to the existence of evolutionary windows where
climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia."

[R.Rocca]

Mitochondrial DNA Haplogroup Confers Genetic Susceptibility to Nasopharyngeal Carcinoma in Chaoshanese from Guangdong, China

http://www.plosone.org/article/info%...l.pone.0087795

Recent studies have shown association of mtDNA background with cancer development. We analyzed mitochondrial DNA (mtDNA) control region variation of 201 patients with nasopharyngeal carcinoma (NPC) and of 201 normal controls from Chaoshan Han Chinese to discern mtDNA haplogroup effect on the disease onset. Binary logistic regression analysis with adjustment for gender and age revealed that the haplogroup R9 (P = 0.011, OR = 1.91, 95% CI = 1.16–3.16), particularly its sub-haplogroup F1 (P = 0.015, OR = 2.43, 95% CI = 1.18–5.00), were associated significantly with increased NPC risk. These haplogroups were further confirmed to confer high NPC risk in males and/or individuals ≥40 years of age, but not in females or in subjects <40 years old. Our results indicated that mtDNA background confers genetic susceptibility to NPC in Chaoshan Han Chinese, and R9, particularly its sub-haplogroup F1, is a risk factor for NPC.

[Jean M]

Benazzi et al., A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy, Journal of Human Evolution, Volume 66, January 2014, Pages 89–94
http://www.sciencedirect.com/science...4724841300239X

In 1986–1987, three human remains were unearthed from macro-unit II of San Bernardino Cave (Berici Hills, Veneto, Italy), a deposit containing a late Mousterian lithic assemblage. The human remains (a distal phalanx, a lower right third molar and a lower right second deciduous incisor) do not show diagnostic morphological features that could be used to determine whether they were from Homo neanderthalensis or Homo sapiens. Despite being of small size, and thus more similar to recent H. sapiens, the specimens were attributed to Neandertals, primarily because they were found in Mousterian layers. We carried out a taxonomic reassessment of the lower right third molar (LRM3; San Bernardino 4) using digital morphometric analysis of the root, ancient DNA analysis, carbon and nitrogen isotope analyses, and direct accelerator mass spectrometry (AMS) radiocarbon dating of dentine collagen. Mitochondrial DNA analysis and root morphology show that the molar belongs to a modern human and not to a Neandertal. Carbon 14 (14C) dating of the molar attributes it to the end of the Middle Ages (1420–1480 cal AD, 2 sigma). Carbon and nitrogen isotope analyses suggest that the individual in question had a diet similar to that of Medieval Italians. These results show that the molar, as well as the other two human remains, belong to recent H. sapiens and were introduced in the Mousterian levels post-depositionally.

File under "Embarrassing".

[Jean M]

Joseph K. Pickrell et al., Ancient west Eurasian ancestry in southern and eastern Africa, PNAS, Early Edition
http://www.pnas.org/content/early/20...87111.abstract

The history of southern Africa involved interactions between indigenous hunter–gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.

[GailT]

Mitochondrial DNA Haplogroup Confers Genetic Susceptibility to Nasopharyngeal Carcinoma in Chaoshanese from Guangdong, China

http://www.plosone.org/article/info%...l.pone.0087795

Another case of poor or non-existent peer review. They primarily relied on an analysis of the control region and made no effort to identify a mechanism to explain their results. And then there is this statement: "mtDNA variants T16362C, T16519C and mtDNA microsatellite instability at D310 (a poly-C stretch between mtDNA nucleotide position 303 and 315) are thought to be the risk factors for familial NPC".

[jeanL]

Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade within the Broadly Distributed Human Haplogroup C1

The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined “C1f”. We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.

[Jean M]

Hafid Laayouni et al., Convergent evolution in European and Rroma populations reveals pressure exerted by plague on Toll-like receptors, PNAS, early edition.
http://www.pnas.org/content/early/2014/01/30/1317723111

Recent historical periods in Europe have been characterized by severe epidemic events such as plague, smallpox, or influenza that shaped the immune system of modern populations. This study aims to identify signals of convergent evolution of the immune system, based on the peculiar demographic history in which two populations with different genetic ancestry, Europeans and Rroma (Gypsies), have lived in the same geographic area and have been exposed to similar environments, including infections, during the last millennium. We identified several genes under evolutionary pressure in European/Romanian and Rroma/Gipsy populations, but not in a Northwest Indian population, the geographic origin of the Rroma. Genes in the immune system were highly represented among those under strong evolutionary pressures in Europeans, and infections are likely to have played an important role. For example, Toll-like receptor 1 (TLR1)/TLR6/TLR10 gene cluster showed a strong signal of adaptive selection. Their gene products are functional receptors for Yersinia pestis, the agent of plague, as shown by overexpression studies showing induction of proinflammatory cytokines such as TNF, IL-1β, and IL-6 as one possible infection that may have exerted evolutionary pressures. Immunogenetic analysis showed that TLR1, TLR6, and TLR10 single-nucleotide polymorphisms modulate Y. pestis–induced cytokine responses. Other infections may also have played an important role. Thus, reconstruction of evolutionary history of European populations has identified several immune pathways, among them TLR1/TLR6/TLR10, as being shaped by convergent evolution in two human populations with different origins under the same infectious environment.

Coverage by Science:

http://news.sciencemag.org/biology/2...k-human-genome

The Black Death didn’t just wipe out millions of Europeans during the 14th century. It left a mark on the human genome, favoring those who carried certain immune system genes, according to a new study. Those changes may help explain why Europeans respond differently from other people to some diseases and have different susceptibilities to autoimmune disorders.

Geneticists know that human populations evolve in the face of disease. Certain versions of our genes help us fight infections better than others, and people who carry those genes tend to have more children than those who don’t. So the beneficial genetic versions persist, while other versions tend to disappear as those carrying them die. This weeding-out of all but the best genes is called positive selection. But researchers have trouble pinpointing positively selected genes in humans, as many genes vary from one individual to the next.

Enter Mihai Netea, an immunologist at Radboud University Nijmegen Medical Centre in the Netherlands. He realized that in his home country, Romania, the existence of two very distinct ethnic groups provided an opportunity to see the hand of natural selection in the human genome. A thousand years ago, the Rroma people—commonly known as gypsies—migrated into Europe from north India. But they intermarried little with European Romanians and thus have very distinct genetic backgrounds. Yet, by living in the same place, both of these groups experienced the same conditions, including the Black Plague, which did not reach northern India. So the researchers sought genes favored by natural selection by seeking similarities in the Rroma and European Romanians that are not found in North Indians...