Survival and recovery of DNA from ancient teeth and bones

a b s t r a c t The recovery of genetic material from preserved hard skeletal remains is an essential part of ancient DNA, archaeological and forensic research. However, there is little understanding about the relative concentrations of DNA within different tissues, the impact of sampling methods on extracted DNA, or the role of environmentally-determined degradation rates on DNA survival in specimens. We examine these issues by characterizing the mitochondrial DNA (mtDNA) content of different hard and soft tissues in 42 ancient human and bovid specimens at a range of fragment lengths (77e235 bp) using real-time PCR. Remarkably, the standard drill speeds used to sample skeletal material (c. 1000 RPM) were found to decrease mtDNA yields up to 30 times (by 3.1 Â 10 5 mtDNA copies on average) compared to pulverization in a bone mill. This dramatic negative impact appears to relate to heat damage, and disappeared at very low drill speeds (e.g. 100 RPM). Consequently, many ancient DNA and forensic studies may have obtained false negative results, especially from important specimens which are commonly sampled with drills to minimize signs of damage. The mtDNA content of tooth cementum was found to be five times higher than the commonly used dentine (141 bp, p ¼ 0.01), making the cementum-rich root tip the best sample for ancient human material. Lastly, mtDNA was found to display a consistent pattern of exponential fragmentation across many depositional environments, with different rates for geographic areas and tissue types, improving the ability to predict and understand DNA survival in preserved specimens. Crow

Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy

Background: The Brokpas are an isolated tribal population of the Dah-Hanu villages of the Leh district of India. They speak Dardic, a sub-branch of the Indo-European language family, and are putatively identified as “pure Aryan,” a hegemonic impression perpetuated by foreign tourism. Aim: To determine if the above is true by looking for an appreciable frequency of NRY-HG-R1a1(M17) signatures which are common to Indo-European language speakers of mainland India and elsewhere. Subjects and methods: We studied 75 random Brokpa males from the Dah-Hanu region, on the northern bank of the Indus river. Results: Interestingly, the Brokpa males possessed a high proportion of NRY-HG-L1a2(M357) (62.7%) that are found sporadically in India and her neighbourhood. A global analysis of this clade (present study, 214 of 3327 men from 63 populations; from the literature 56 of 873) suggested that they originated from southern India. Conclusion: The Y chromosomal studies suggest the Brokpa to be pre-Vedic settlers of the Himalayas, 9000 ybp, with an isolated evolution. The mtDNA profile shows a predominance of mtDNA HG A4 that must have arrived from outside the Indian subcontinent

Geographic population structure analysis of worldwide human populations infers their biogeographical origins

The search for a method that utilizes biological information to predict humans’ place of origin has occupied scientists for millennia. Over the past four decades, scientists have employed genetic data in an effort to achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing data have achieved an accuracy of 700 km in Europe, they were inaccurate elsewhere. Here we describe the Geographic Population Structure (GPS) algorithm and demonstrate its accuracy with three data sets using 40,000–130,000 SNPs. GPS placed 83% of worldwide individuals in their country of origin. Applied to over 200 Sardinians villagers, GPS placed a quarter of them in their villages and most of the rest within 50 km of their villages. GPS’s accuracy and power to infer the biogeography of worldwide individuals down to their country or, in some cases, village, of origin, underscores the promise of admixture-based methods for biogeography and has ramifications for genetic ancestry testing.E.E is supported in part by Genographic grant GP 01/n-/n12. L.P, C.T.S and Y.X were/nsupported by The Wellcome Trust (098051). O.B. was supported in part by Presidium/nRAS (MCB programme) and RFBR (13-04-01711). T.T. was supported by grants from/nThe National Institute for General Medical Studies (GM068968), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD070996). S.T. is supported by a PRIN2009 grant. The Genographic Project is supported by the National Geographic Society IBM and the Waitt Foundation. We are grateful to all Genographic participants who contributed their DNA samples for this stud

A new method to reconstruct recombination events at a genomic scale

Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have fine-tuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation.This study is part of the Genographic project (https://genographic.nationalgeographic.com/genographic/index.html), an initiative of National Geographic and IBM. Additional support comes from the Spanish Ministry of Innovation and Research grants BFU2007-63657 and SAF-2007-63171, and a scholarship to M.M. (AP2006-03268). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip

Mitochondrial genome sequencing in mesolithic North East Europe unearths a new sub-clade within the broadly distributed human haplogroup C1

Entre els membres del The Genographic Consortium es troben els autors: Jaume Bertranpetit, David Comas, Marc Haber i Begoña Martínez CruzThe 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.This research was supported by The Genographic Project, which is supported by funding from the National Geographic Society, IBM, and the Waitt Family Foundation. PB was funded by the Australian Research Council Linkage Project LP0882622 awarded to AC, and the Discovery Projects DP1095782 and DP130102158 awarded to WH and BL. OB was funded by the RAS Programmes ‘‘Molecular and cell biology’’, ‘‘Gene pool dynamics’’ and RFBR grants 13-04-01711, Cover Letter 13-06-006

THE EMERGING COMPLEXITY OF GENOMIC ARCHITECTURE IN HUMAN POPULATION ISOLATES

Each population isolate has a unique demographic history in terms of initial size , time since foundation and growth rate. These factors can shape their genetic makeup both at the individual and population level. However, is it possible to identify patterns relating genomic diversity and demographic history? To answer this question we analyzed approximately 90,000 autosomal ancestry informative markers (AIMs) as part of the Genochip (National Geographic Society, Washington, DC & Family Tree DNA, Houston, Texas, USA) in eight Italian populations, all subject to geographic and/or cultural isolation factors. Four were from Sardinia (old and large isolates) and as many from the eastern Alps (young and small isolates). The same panel of AIMs was analyze d in literature data relative to both open and isolated European groups, for a total of 24 populations. Alpine isolates (German-speaking linguistic islands of Sappada, Sauris and Timau) showed stronger signals of genetic isolation [i.e. frequency and size of Runs of Homozygosity, LD decay and intra-group distributions of Identity by State (IBS)] than older and larger groups (Sardinians, Basques and Orcadians). Rather unexpectedly, the ADMIXTURE and PCA analyses, as well as the comparison of intra-group IBS distributions, highlighted a noticeable genetic heterogeneity within Sappada, Sauris and Timau, likely due to relatively recent admixture events. This pattern, undetected in any other population sample, is at odds with the conventional view of a substantial genetic homogeneity within population isolates. Significance and implications of our results are discussed in relation to both micro-evolutionary aspects and bio-medical applications

Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast

We have examined the male-specific phylogeography of the Levant and its surroundings by analyzing Y-chromosomal haplogroup distributions using 5874 samples (885 new) from 23 countries. The diversity within some of these haplogroups was also examined. The Levantine populations showed clustering in SNP and STR analyses when considered against a broad Middle-East and North African background. However, we also found a coastal-inland, east-west pattern of diversity and frequency distribution in several haplogroups within the small region of the Levant. Since estimates of effective population size are similar in the two regions, this strong pattern is likely to have arisen mainly from differential migrations, with different lineages introduced from the east and west

Antiquity and diversity of aboriginal Australian Y-chromosomes

Objective: Understanding the origins of Aboriginal Australians is crucial in reconstructing the evolution and spread of Homo sapiens as evidence suggests they represent the descendants of the earliest group to leave Africa. This study analyzed a large sample of Y‐chromosomes to answer questions relating to the migration routes of their ancestors, the age of Y‐haplogroups, date of colonization, as well as the extent of male‐specific variation. Methods: Knowledge of Y‐chromosome variation among Aboriginal Australians is extremely limited. This study examined Y‐SNP and Y‐STR variation among 657 self‐declared Aboriginal males from locations across the continent. 17 Y‐STR loci and 47 Y‐SNPs spanning the Y‐chromosome phylogeny were typed in total. Results: The proportion of non‐indigenous Y‐chromosomes of assumed Eurasian origin was high, at 56%. Y lineages of indigenous Sahul origin belonged to haplogroups C‐M130*(xM8,M38,M217,M347) (1%), C‐M347 (19%), K‐M526*(xM147,P308,P79,P261,P256,M231,M175,M45,P202) (12%), S‐P308 (12%), and M‐M186 (0.9%). Haplogroups C‐M347, K‐M526*, and S‐P308 are Aboriginal Australian‐specific. Dating of C‐M347, K‐M526*, and S‐P308 indicates that all are at least 40,000 years old, confirming their long‐term presence in Australia. Haplogroup C‐M347 comprised at least three sub‐haplogroups: C‐DYS390.1del, C‐M210, and the unresolved paragroup C‐M347*(xDYS390.1del,M210). Conclusions: There was some geographic structure to the Y‐haplogroup variation, but most haplogroups were present throughout Australia. The age of the Australian‐specific Y‐haplogroups suggests New Guineans and Aboriginal Australians have been isolated for over 30,000 years, supporting findings based on mitochondrial DNA data. Our data support the hypothesis of more than one route (via New Guinea) for males entering Sahul some 50,000 years ago and give no support for colonization events during the Holocene, from either India or elsewhere. Am J Phys Anthropol 159:367–381, 2016. © 2015 Wiley Periodicals, Inc.No Full Tex

Afghanistan's ethnic groups share a y-chromosomal heritage structured by historical events

Afghanistan has held a strategic position throughout history. It has been inhabited since the Paleolithic and later became a crossroad for expanding civilizations and empires. Afghanistan's location, history, and diverse ethnic groups present a unique opportunity to explore how nations and ethnic groups emerged, and how major cultural evolutions and technological developments in human history have influenced modern population structures. In this study we have analyzed, for the first time, the four major ethnic groups in present-day Afghanistan: Hazara, Pashtun, Tajik, and Uzbek, using 52 binary markers and 19 short tandem repeats on the non-recombinant segment of the Y-chromosome. A total of 204 Afghan samples were investigated along with more than 8,500 samples from surrounding populations important to Afghanistan's history through migrations and conquests, including Iranians, Greeks, Indians, Middle Easterners, East Europeans, and East Asians. Our results suggest that all current Afghans largely share a heritage derived from a common unstructured ancestral population that could have emerged during the Neolithic revolution and the formation of the first farming communities. Our results also indicate that inter-Afghan differentiation started during the Bronze Age, probably driven by the formation of the first civilizations in the region. Later migrations and invasions into the region have been assimilated differentially among the ethnic groups, increasing inter-population genetic differences, and giving the Afghans a unique genetic diversity in Central Asia.This study is supported by the Waitt Family Foundatio