Y chromosome in forensic casework and paternity testing

Abstract. The aim of the study is to demonstrate the power obtained by combining autosomal and Y chromosome STRs in certain case scenarios. Although autosomal STRs are in use and highly informative, Y STRs are extremely useful and provide additional information that could not be provided by autosomal STRs alone.

Genetic Stratigraphy of Key Demographic Events in Arabia

The issue of admixture in human populations is normally addressed by genome-wide (GW) studies, and several approaches have been developed to date admixture events [1,2,3,4,5]. Admixed populations bear chromosomes with segments of DNA from all contributing source groups, the size of which decreases over successive generations until recombination renders them undetectably short. Several algorithms attempt to date admixture events by inferring the size of the nuclear ancestry segments, and these can work well when dating recent episodes in human history, such as the sub-Saharan African input into the New World [6], but they fail to detect several known episodes that took place at earlier times, such as the African input into Iberia [1] and genetic exchanges across the Red Sea [7]. Simulations with the suite of methods available at the ADMIXTOOLS package indicated that these methods could detect admixture events as early as 500 generation ago, but real data did not allow the tracing of such old events [8]. A recent improved algorithm, called GLOBETROTTER, has been used to tackle the detection of the co-occurrence of several mixture events by decomposing each chromosome into a series of haplotypic chunks and then analysing each chunk independently [3], but the problem of detecting ancient events remains. Its application to the systematic screening of worldwide admixture events was able to reveal around 100 events, but all occurring over only the past 4,000 years [3

Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe

Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europ

Online calculator for individual affiliation to a major population group

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification

Diploid and haploid markers and their distributions in sample populations from Dubai, South Arabian Peninsula and Iran

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The First Modern Human Dispersals across Africa

The emergence of more refined chronologies for climate change and archaeology in prehistoric Africa, and for the evolution of human mitochondrial DNA (mtDNA), now make it feasible to test more sophisticated models of early modern human dispersals suggested by mtDNA distributions. Here we have generated 42 novel whole-mtDNA genomes belonging to haplogroup L0, the most divergent clade in the maternal line of descent, and analysed them alongside the growing database of African lineages belonging to L0's sister clade, L1'6. We propose that the last common ancestor of modern human mtDNAs (carried by "mitochondrial Eve") possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations. Early modern human dispersals correlate with climate changes, particularly the tropical African "megadroughts" of MIS 5 (marine isotope stage 5, 135-75 ka) which paradoxically may have facilitated expansions in central and eastern Africa, ultimately triggering the dispersal out of Africa of people carrying haplogroup L3 ~60 ka. Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution

Local population structure in Arabian Peninsula revealed by Y-STR diversity

Genetic studies have been underway on Arabian Peninsula populations because of their pivotal geographic location for population migration and times of occurrence. To assist in better understanding population dynamics in this region, evidence is presented herein on local population structure in the Arabian Peninsula, based on Y-STR characterisation in four Arabian samples and its comparison in a broad geographical scale. Our results demonstrate that geography played an important role in shaping the genetic structure of the region around the Near-East. Populations are grouped regionally but none of these groups is significantly differentiated from others and all groups merge in the Near-East, in keeping with this important migration corridor for the human species. Focusing on the Arabian Peninsula, we show that Dubai and Oman share genetic affinities with other Near-Eastern populations, while Saudi Arabia and Yemen show a relative distinctive isolated background. Those two populations may have been kept relatively separated from migration routes, maybe due to their location in a desert area