ASHG 2014 titles and abstracts

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The titles and abstracts of some of the papers that will be made available at the American Society of Human Genetics annual meeting in October were posted on Dienekes's Anthropology blog. A few of these seem quite interesting and promising. I have added some of the ones that could be relevant to the research that has been done on the forum.

_http://dienekes.blogspot.com/2014/08/ashg-2014-titles.html

Capture of 390,000 SNPs in dozens of ancient central Europeans reveals a population turnover in Europe thousands of years after the advent of farming.
I. Lazaridis, W. Haak, N. Patterson, N. Rohland, S. Mallick, B. Llamas, S. Nordenfelt, E. Harney, A. Cooper, K. W. Alt, D. Reich.

To understand the population transformations that took place in Europe since the early Neolithic, we used a DNA capture technique to obtain reads covering ~390 thousand single nucleotide polymorphisms (SNPs) from a number of different archaeological cultures of central Europe (Germany and Hungary). The samples spanned the time period from 7,500 BP to 3,500 BP (Early Neolithic to Early Bronze Age periods) and most of them were previously studied using mtDNA (Brandt, Haak et al., Science, 2013). The captured SNPs include about 360,000 SNPs from the Affymetrix Human Origins Array that were discovered in African individuals, as well as about 30,000 SNPs chosen for other reasons (that are thought to have been affected by natural selection, or to have phenotypic effects, or are useful in determining Y-chromosome haplogroups).By analyzing this data together with a dataset of 2,345 present-day humans and other published ancient genomes, we show that late Neolithic inhabitants of central Europe belonging to the Corded Ware culture were not a continuation of the earlier occupants of the region. Our results highlight the importance of migration and major population turnover in Europe long after the arrival of farming. * Contributed equally to this work.

Discussion: _http://www.eupedia.com/forum/threads/30424-Corded-Ware-Culture-Signals-Population-Change-in-Europe

Insights into British and European population history from ancient DNA sequencing of Iron Age and Anglo-Saxon samples from Hinxton, England.
S. Schiffels, W. Haak, B. Llamas, E. Popescu, L. Loe, R. Clarke, A. Lyons, P. Paajanen, D. Sayer, R. Mortimer, C. Tyler-Smith, A. Cooper, R. Durbin.

British population history is shaped by a complex series of repeated immigration periods and associated changes in population structure. It is an open question however, to what extent each of these changes is reflected in the genetic ancestry of the current British population. Here we use ancient DNA sequencing to help address that question. We present whole genome sequences generated from five individuals that were found in archaeological excavations at the Wellcome Trust Genome Campus near Cambridge (UK), two of which are dated to around 2,000 years before present (Iron Age), and three to around 1,300 years before present (Anglo-Saxon period). Good preservation status allowed us to generate one high coverage sequence (12x) from an Iron Age individual, and four low coverage sequences (1x-4x) from the other samples. By providing the first ancient whole genome sequences from Britain, we get a unique picture of the ancestral populations in Britain before and after the Anglo-Saxon immigrations. We use modern genetic reference panels such as the 1000 Genomes Project to examine the relationship of these ancient samples with present day population genetic data. Results from principal component analysis suggest that all samples fall consistently within the broader Northern European context, which is also consistent with mtDNA haplogroups. In addition, we obtain a finer structural genetic classification from rare genetic variants and haplotype based methods such as FineStructure. Reflecting more recent genetic ancestry, results from these methods suggest significant differences between the Iron Age and the Anglo-Saxon period samples when compared to other European samples. We find in particular that while the Anglo-Saxon samples resemble more closely the modern British population than the earlier samples, the Iron Age samples share more low frequency variation than the later ones with present day samples from southern Europe, in particular Spain (1000GP IBS). In addition the Anglo-Saxon period samples appear to share a stronger older component with Finnish (1000GP FIN) individuals. Our findings help characterize the ancestral European populations involved in major European migration movements into Britain in the last 2,000 years and thus provide more insights into the genetic history of people in northern Europe.

Discussion: _http://www.eupedia.com/forum/threads/30425-Ancient-DNA-Study-of-Iron-Age-vs-Anglo-Saxon-Era-British-populations

The population structure and demographic history of Sardinia in relationship to neighboring populations.
J. Novembre, C. Chiang, J. Marcus, C. Sidore, M. Zoledziewska, M. Steri, H. Al-asadi, G. Abecasis, D. Schlessinger, F. Cucca.

Numerous studies have made clear that Sardinian populations are relatively isolated genetically from other populations of the Mediterranean, and more recently, intriguing connections between Sardinian ancestry and early Neolithic ancient DNA samples have been made. In this study, we analyze a whole-genome low-coverage sequencing dataset from 2120 Sardinians to more fully characterize patterns of genetic diversity in Sardinia. The study contains one subsample that contains individuals from across Sardinia and a second subsample that samples 4 villages from the more isolated Ogliastra region. We also merge the data with published reference data from Europe and North Africa. Overall Fst values of Sardinia to other European populations are low (less than 0.015); however using a novel method for visualizing genetic differentiation on a geographic map, we formally show how Sardinia is more differentiated than would be expected given its geographic distance from the mainland, consistent with periods of isolation. Applications of the software Admixture show how Sardinia populations differ in the levels of recent admixture with mainland European populations and that there are only minor contributions from North African populations to Sardinian ancestry. Notably the Sardinians from Ogliastra contain a distinct genetic cluster with minimal evidence of recent admixture with mainland Europe. We found frequency-based f3 tests and the tree-based algorithm Treemix both also show minimal evidence of recent admixture. Given the relative isolation, one might expect to see a unique demographic history from neighboring populations. Using coalescent-based approaches, we find Sardinian populations have had more constant effective sizes over the past several thousand years than mainland European populations, which typically show evidence for rapid growth trajectories in the recent past. This unique demographic history has consequences for the abundance of putatively damaging and deleterious variants, and we use our data to address the prediction that the genetic architecture of disease traits is expected to involve fewer loci with a greater proportion of variants at common frequencies in Sardinia.