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Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p

AimThe Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to post-glacial bedrock rebound around 9,000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. Our main aim was to evaluate the role of the 20th century bottleneck in the erosion of genetic diversity in the Saimaa seal population. We also evaluated connections with other ringed seals from the Baltic Sea, Lake Ladoga, North America, Svalbard and the White Sea.LocationLake Saimaa, Finland, together with the Baltic Sea and the Arctic Ocean.MethodsWe sequenced sections of the mitochondrial control region from 60 up to 125 years old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies, and how it is phylogenetically related to other ringed seal populations.ResultsWe observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation shows also affinities to North American ringed seals.Main conclusionsOur results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seals do not represent well the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.

Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1,000 generations, is alarmingly low. The population is further divided into semi-isolated subpopulations in the labyrinthine landscape of the lake, which exposes the population to deleterious genomic effects. We performed whole-genome sequencing on Saimaa ringed seals (N=30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p

Human ancient DNA studies have revealed high mobility in Europe’s past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300–1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns. Results - Authenticity of ancient-DNA results. - Radiocarbon datings. - MtDNA data and haplotypic variation. - MtDNA haplogroup composition at the ancient sites. - Differences in haplogroup composition between the sites. - Genetic distances among sites and to contemporary Finns. - Main haplogroup frequencies in space and time. - Genetic affinities of ancient Finns to other ancient and contemporary populations. Discussion - Genetic layers of mitochondrial variation among the Iron Age and Medieval Finns. - The ancient distribution of mtDNA lineages contradicts the contemporary east-west divergence. - Bidirectional expansion of agriculturally oriented populations into Finland?. Materials and methods - Sample selection. - Reference populations used in comparative analyses. - Sampling. - Extraction of ancient DNA. - Mitochondrial capture and sequencing. - Processing of the sequence data. - Authentication of ancient DNA and haplogroup assignments. - Radiocarbon dating. - Statistical analyses.

Autosomal DNA data from Peru for human identity testing purposes are scarce in the scientific literature, which hinders obtaining an appropriate portrait of the genetic variation of the resident populations. In this study we genetically characterize five populations from the Northeastern Peruvian Andes (Chachapoyas, Awajun, Wampis, Huancas and Cajamarca). Autosomal short tandem repeat (aSTR) and identity informative single nucleotide polymorphism (iiSNP) data from a total of 233 unrelated individuals are provided, and forensic genetic parameters are calculated for each population and for the combined set Northeastern Peruvian Andes. After correction for multiple testing in the whole dataset of the Northeastern Peruvian Andes, the only departure from Hardy-Weinberg equilibrium was observed in locus rs2111980. Twenty one out of 27 aSTR loci exhibited an increased number of alleles due to sequence variation in the repeat motif and flanking regions. For iiSNPs 33% of the loci displayed flanking region variation. The combined random match probability (RMP), assuming independence of all loci (aSTRs and iiSNPs), in the Chachapoyas, the population with the largest samples size (N = 172), was 8.14 x 10(-62) for length-based data while for sequence-based was 4.15 x 10(-67). In the merged dataset (Northeastern Peruvian Andes; N = 233), the combined RMP when including all markers were 2.96 x 10(-61) (length-based) and 3.21 x 10(-66) (sequence-based). These new data help to fill up some of the gaps in the genetic canvas of South America and provide essential length- and sequence-based background information for other forensic genetic studies in Peru.

This study aimed to provide a better understanding of the population history of the Chachapoyas by assessing 1) the amount and nature of genetic diversity in the modern Chachapoya and their immediate neighbors (Huancas, Jivaro, and Cajamarca), 2) the genetic affinities of the Chachapoya and populations from Andean and Amazonian pools, and 3) whether a severe reduction of the genetic diversity in the Chachapoya occurred since ethnohistorical documents report a drastic population decline in the region. We studied mitochondrial (HVRI and HVRII sequences) and Y-chromosomal (23 STR loci) diversity in four populations (Chachapoya=276, Jivaro=47, Huancas=21, and Cajamarca=34) from the Amazonas region. Our findings show asymmetrical European gene flow in the region (Chachapoya: mtDNA=11%; Y-Chromosome=43%). When examining the Native American component only, the Chachapoya population displayed relatively high levels of genetic diversity and large Tajima’s D and Fu’s Fs values. This suggests that no drastic reduction in the effective population size has taken place in the past. In the context of cultural transformations in the region, the basal position of the Chachapoya amidst the South American populations may suggest that civilizations which developed along the Andes-Amazon divide played a more important role among the societies in the Northeast Andes.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas. Analyses of 34 ancient genomes from northeastern Siberia, dating to between 31,000 and 600 years ago, reveal at least three major migration events in the late Pleistocene population history of the region.

Many native populations in South America have been severely impacted by two relatively recent historical events, the Inca and the Spanish conquest. However decisive these disruptive events may have been, the populations and their gene pools have been shaped markedly also by the history prior to the conquests. This study focuses mainly on the Chachapoya peoples that inhabit the montane forests on the eastern slopes of the northern Peruvian Andes, but also includes three distinct neighboring populations (the Jívaro, the Huancas and the Cajamarca). By assessing mitochondrial, Y-chromosomal and autosomal diversity in the region, we explore questions that have emerged from archaeological and historical studies of the regional culture (s). These studies have shown, among others, that Chachapoyas was a crossroads for Coast-Andes-Amazon interactions since very early times. In this study, we examine the following questions: 1) was there pre-Hispanic genetic population substructure in the Chachapoyas sample? 2) did the Spanish conquest cause a more severe population decline on Chachapoyan males than on females? 3) can we detect different patterns of European gene flow in the Chachapoyas region? and, 4) did the demographic history in the Chachapoyas resemble the one from the Andean area? Despite cultural differences within the Chachapoyas region as shown by archaeological and ethnohistorical research, genetic markers show no significant evidence for past or current population substructure, although an Amazonian gene flow dynamic in the northern part of this territory is suggested. The data also indicates a bottleneck c. 25 generations ago that was more severe among males than females, as well as divergent population histories for populations in the Andean and Amazonian regions. In line with previous studies, we observe high genetic diversity in the Chachapoyas, despite the documented dramatic population declines. The diverse topography and great biodiversity of the northeastern Peruvian montane forests are potential contributing agents in shaping and maintaining the high genetic diversity in the Chachapoyas region.

Levanluhta is a unique archaeological site with the remains of nearly a hundred Iron Age individuals found from a water burial in Ostrobothnia, Finland. The strongest climatic downturn of the Common Era, resembling the great Fimbulvinter in Norse mythology, hit these people during the 6th century AD. This study establishes chronological, dietary, and livelihood synthesis on this population based on stable carbon and nitrogen isotopic and radiocarbon analyses on human remains, supported by multidisciplinary evidence. Extraordinarily broad stable isotopic distribution is observed, indicating three subgroups with distinct dietary habits spanning four centuries. This emphasizes the versatile livelihoods practiced at this boundary of marine, freshwater, and terrestrial ecosystems. While the impact of the prolonged cold darkness of the 6th century was devastating for European communities relying on cultivation, the broad range of livelihoods provided resilience for the Levanluhta people to overcome the abrupt climatic decline.

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of “Ancient North Siberians” (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the “Neosiberians” from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

Genetic analyses of non-invasively collected samples are increasingly being used in the monitoring of wildlife populations and individuals. This study is the first describing the use of placentas as non-invasive genetic samples from a natural population. We collected 66 placentas from birth-lair sites of Saimaa ringed seals (Phoca hispida saimensis) after the breeding seasons, with the aim of obtaining DNA from both the pup and the mother. Umbilical cord samples proved to yield the pup genotypes, but mothers could not be genotyped with confidence. Comparisons with existing mtDNA and microsatellite reference data sets showed that placentas can be used for inferring population-level genetic parameters. Our microsatellite panel provided sufficient resolution for genetic identification of individuals but, due to the extremely low variability of the population, parentage and sibship could not be inferred reliably. Field-collected placentas could provide means for genetic monitoring of many other seal species a...

In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000–5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the ‘local’ Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the ‘immigrant’ haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.

Island populations are on average smaller, genetically less diverse, and at a higher risk to go extinct than mainland populations. Low genetic diversity may elevate extinction probability, but the genetic component of the risk can be affected by the mode of diversity loss, which, in turn, is connected to the demographic history of the population. Here, we examined the history of genetic erosion in three Fennoscandian ringed seal subspecies, of which one inhabits the Baltic Sea ‘mainland’ and two the ‘aquatic islands’ composed of Lake Saimaa in Finland and Lake Ladoga in Russia. Both lakes were colonized by marine seals after their formation c. 9500 years ago, but Lake Ladoga is larger and more contiguous than Lake Saimaa. All three populations suffered dramatic declines during the 20th century, but the bottleneck was particularly severe in Lake Saimaa. Data from 17 microsatellite loci and mitochondrial control-region sequences show that Saimaa ringed seals have lost most of the genetic diversity present in their Baltic ancestors, while the Ladoga population has experienced only minor reductions. Using Approximate Bayesian computing analyses, we show that the genetic uniformity of the Saimaa subspecies derives from an extended founder event and subsequent slow erosion, rather than from the recent bottleneck. This suggests that the population has persisted for nearly 10,000 years despite having low genetic variation. The relatively high diversity of the Ladoga population appears to result from a high number of initial colonizers and a high post-colonization population size, but possibly also by a shorter isolation period and/or occasional gene flow from the Baltic Sea.

Blood samples preserved on FTA cards offer unique opportunities for genetic research. DNA recovered from these cards should be stable for long periods of time. However, it is not well established as how well the DNA stored on FTA card for substantial time periods meets the demands of forensic or genomic DNA analyses and especially so for from post-mortem (PM) samples in which the quality can vary upon initial collection. The aim of this study was to evaluate the time-dependent degradation on DNA quality and quantity extracted from up to 16 years old post-mortem bloodstained FTA cards. Four random FTA samples from eight time points spanning 1998 to 2013 (n = 32) were collected and extracted in triplicate. The quantity and quality of the extracted DNA samples were determined with Quantifiler (R) Human Plus (HP) Quantification kit. Internal sample and sample-to-sample variation were evaluated by comparing recovered DNA yields. The DNA from the triplicate samplings were subsequently combined and normalized for further analysis. The practical effect of degradation on DNA quality was evaluated from normalized samples both with forensic and pharmacogenetic target markers. Our results suggest that (1) a PM change, e.g. blood clotting prior to sampling, affects the recovered DNA yield, creating both internal and sample-to-sample variation; (2) a negative correlation between the FTA card storage time and DNA quantity (r = -0.836 at the 0.01 level) was observed; (3) a positive correlation (r = 0.738 at the level 0.01) was found between FTA card storage time and degradation levels. However, no inhibition was observed with the method used. The effect of degradation was manifested clearly with functional applications. Although complete STR-profiles were obtained for all samples, there was evidence of degradation manifested as decreased peak heights in the larger-sized amplicons. Lower amplification success was notable with the large 5.1 kb CYP2D6 gene fragment which strongly supports degradation of the stored samples. According to our results, DNA stored on FTA cards is rather stable over a long time period. DNA extracted from this storage medium can be used as human identification purposes as the method used is sufficiently sensitive and amplicon sizes tend to be

Medico-legal autopsy is the primary method in determining the cause and manner of death when the death is suspected to be unnatural. In some of these autopsies, the death remains ambiguous, even after a complete autopsy including histological investigation and toxicological screenings. In cases where there are no morphological abnormalities, medico-legal genetics may offer additional means to provide knowledge of possible genetic mutations, which may have initiated the process or predisposed the individual to stress risk conditions leading to death. One class of ambiguous deaths consists of drug-related deaths where the interpretation of the toxicological results are not clear. In such situations post mortem genotyping and the analysis of metabolite rations may provide an insight to the findings. A few cases demonstrating the potential strength of pharmacogenetics in medico-legal context has been published. However, there is a paramount need for serious scientific studies before the field of post mortem pharmacogenetics can be utilized in routine medico-legal analyses casework and brought routinely into courtroom.

The Finnish population in Northern Europe has been a target of extensive genetic studies during the last decades. The population is considered as a homogeneous isolate, well suited for gene mapping studies because of its reduced diversity and homogeneity. However, several studies have shown substantial differences between the eastern and western parts of the country, especially in the male-mediated Y chromosome. This divergence is evident in non-neutral genetic variation also and it is usually explained to stem from founder effects occurring in the settlement of eastern Finland as late as in the 16th century. Here, we have reassessed this population historical scenario using Y-chromosomal, mitochondrial and autosomal markers and geographical sampling covering entire Finland. The obtained results suggest substantial Scandinavian gene flow into south-western, but not into the eastern, Finland. Male-biased Scandinavian gene flow into the south-western parts of the country would plausibly explain the large inter-regional differences observed in the Y-chromosome, and the relative homogeneity in the mitochondrial and autosomal data. On the basis of these results, we suggest that the expression of 'Finnish Disease Heritage' illnesses, more common in the eastern/north-eastern Finland, stems from long-term drift, rather than from relatively recent founder effects.

Northwest Siberia is geographically remote territory, which has been settled by indigenous human populations probably since the Upper Paleolithic. To investigate the genetic landscape of Northwest Siberians, we have analyzed mitochondrial and Y chromosome DNA polymorphisms of 169 unrelated individuals from Khanty and Mansi ethnic groups in Northwest Siberia. In addition, HVS-I sequences (N = 3522) and Y chromosome SNP data (N = 2175), obtained from the literature, were used to elucidate the genetic relationships among the North Eurasian populations. The results show clinal distributions of mtDNA and Y chromosome haplogroups along East-West axis of Northern Eurasia. In this context, the Ugric-speaking Khanty and Mansi appear as unique intermediate populations carrying Upper Paleolithic and more recent haplotypes typical for both West and East Eurasian gene pools. This admixture indicates that the Khanty and Mansi populations have resided in the contact zone of genetically distinguishable eastern and western Eurasia.

We have analyzed the two hypervariable regions HVS-I and HVS-II of 200 Finnish male individuals for forensic purposes. The distribution of the haplotypes within Finland was determined by the geographical knowledge of the donors' maternal ancestors. In our population sample, we identified 135 different mtDNA haplotypes. Different mtDNA sequences were further divided to haplogroups using the EMPOP software. The most common haplogroups were H (40.0%) and U (27.5%). Subgroup U5b, which contains earlier described "Saami motif", consisted majority (65.5%) of the sample in the U haplogroup. Analysis of the mtDNA sequence hypervariable regions I and II showed that the mtDNA diversity within the Finnish population sample was comparable to other European populations and uniformly distributed. This is contrary to the Y-STR "minimal haplotype" diversity, which in Finland is lower than in any of the other European populations studied so far.

Analysis of partial ADP/ATP Translocase gene (Aat) sequences from 11 species of Ranid frogs (Amphibia: Ranidae) identified multiple Aat gene copies. All frog species examined had at least one of the 2 Aat gene copies differing mainly by presence or absence of an approximately 85-bp intron sequence. The sequence data suggest that the gene variant with intron is the ancestral Aat form, whereas the other variants are retroposed copies. Surprisingly, a phylogenetic analysis suggests that multiple reptroposition events have taken place in the Ranid frogs. An analysis including sequences from Drosophila, zebra fish, Xenopus, mouse, and human indicated that all the frog Aat sequences form a monophyletic group with mammalian X-chromosomal Ant2 as a sister unit. Furthermore, the selection test suggested that different variants of the Aat gene appear to have evolved under different modes of evolution (viz., neutral, purifying, and positive selection), and the evolutionary history of different AAT variants appears to differ even among different species.

It has previously been demonstrated that the advance of the Neolithic Revolution from the Near East through Europe was decelerated in the northernmost confines of the continent, possibly as a result of space and resource competition with lingering Mesolithic populations. Finland was among the last domains to adopt a farming lifestyle, and is characterized by substructuring in the form of a distinct genetic border dividing the northeastern and southwestern regions of the country. To explore the origins of this divergence, the geographical patterns of mitochondrial and Y-chromosomal haplogroups of Neolithic and Mesolithic ancestry were assessed in Finnish populations. The distribution of these uniparental markers revealed a northeastern bias for hunter-gatherer haplogroups, while haplogroups associated with the farming lifestyle clustered in the southwest. In addition, a correlation could be observed between more ancient mitochondrial haplogroup age and eastern concentration. These results coupled with prior archeological evidence suggest the genetic northeast/southwest division observed in contemporary Finland represents an ancient vestigial border between Mesolithic and Neolithic populations undetectable in most other regions of Europe.

The endemic seals of Lake Baikal ( Phoca sibirica ) and of the Caspian Sea ( Phoca caspica ) inhabit ancient continental basins that have remained isolated from primary marine seal habitats for millions of years. The species have been united with the Arctic ringed seal, Phoca hispida , into (sub)genus Pusa , but the age and route of invasions to/from the continental basins remain controversial. A phylogenetic analysis of nine northern phocines based on three mitochondrial genes (Cyt b , COI, COII, total 3369 bp) provided no support for the monophyly of the Pusa group. The three species are involved in an apparent polytomy with the boreal harbour seal, Phoca vitulina , and grey seal, Halichoerus grypus . From the average estimated interspecies divergence (4.1%), the radiation of this group plausibly took place in the Late Pliocene 2‐3 Mya. This dating does not fit the prevailing hypotheses on the origin of the landlocked taxa in association with Middle Pleistocene glacial events, or of the Caspian seal as a direct descendant of Miocene fossil phocines of the continental Paratethyan basin. The current phocine diversity more likely results from marine radiations, and the continental seals invaded their basins through Plio-Pleistocene (marine) connections from the north. The palaeohydrography that would have enabled the invasions at that time still remains an enigma. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 61‐72. ADDITIONAL KEYWORDS: glacial relicts ‐ Paratethys ‐ Phocidae ‐ phylogeography ‐ Pleistocene glaciations ‐ Pusa .

The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, > 94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colour from DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences. (c) 2014 Elsevier Ireland Ltd. All rights reserved.

[OBJECTIVE] Linkage disequilibrium (LD) and recombination rate variations are known to vary considerably between human genome regions and populations mostly because of the combined effects of mutation, recombination, and demographic history. Thus, the pattern of LD is a key issue to disentangle variants associated with complex traits. Here, we aim to describe the haplotype structure and LD variation at the pharmacogenetically relevant cytochrome P450 CYP2C and CYP2D gene regions among European populations. [METHODS] To assess the haplotype structure, LD pattern, and recombination rate variations in the clinically significant CYP2C and CYP2D regions, we genotyped 143 single-nucleotide polymorphisms (SNPs) across these two genome regions in a diverse set of 11 European population samples and one sub-Saharan African sample. [RESULTS] Our results showed extended patterns of LD and in general a low rate of recombination at these loci, and a low degree of allele differentiation for the two cytochrome P450 regions among Europeans, with the exception of the Sami and the Finns as European outliers. The Sami sample showed reduced haplotype diversity and higher LD for the two cytochrome P450 regions than the other Europeans, a feature that is proposed to enhance the LD mapping of underlying common complex traits. However, recombination hotspots and LD blocks at these two regions showed highly consistent structures across Europeans including Finns and Sami. Moreover, we showed that the CEPH sample has significantly higher tag transferability among Europeans and a more efficient tagging of both the rare CYP2C9 and the common CYP2C19 functional variants than the Sami. Our data set included CYP2C9*3 (rs1057910) and CYP2C19*2 (rs4244285) enzyme activity-altering variants associated in a recent genome-wide study with acenocoumarol-induced and warfarin-induced anticoagulation or to the antiplatelet effect of clopidogrel, respectively. Including these known activity-altering variants, we showed the haplotype variation and high derived allele frequencies of novel recently identified acenocoumarol genome-wide associated SNPs at CYP2C9 (rs4086116) and CYP2C18 (rs12772169, rs1998591, rs2104543, rs1042194) loci in a comprehensive set of 11 European populations. Furthermore, a significant frequency difference of a CYP2C19*2 gene mutation causing variable drug reactions was observed among Europeans. [CONCLUSION] The CEPH sample representing the general European population as such in the HapMap project seems to be the optimal population sample for the LD mapping of common complex traits among Europeans. Nevertheless, it is still argued that the unique pattern of LD in the Sami may offer an advantage for further association mapping, especially if multiple rare variants play a role in disease etiology. However, besides the activity-altering CYP2C9*3 (rs1057910) and CYP2C19*2 (rs4244285) variants, the high derived allele frequencies of novel recently identified acenocoumarol genome-wide associated SNPs at CYP2C9 (rs4086116) and CYP2C18 (rs12772169, rs1998591, rs2104543, rs1042194) loci variants indicated that the CYP2C region may have been influenced by selection. Thus, this fine-scale haplotype map of the CYP2C and CYP2D regions may help to choose markers for further association mapping of complex pharmacogenetic traits at these loci. © 2012 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Background Factors affecting the success of short tandem repeat (STR) amplification of poorly preserved samples are generally known, but as of yet, they have seldom been systematically assessed. Using two different maximum likelihood-based methods, the relative importance of DNA quantity, degradation and inhibition in STR genotyping was studied with DNA extracts from a set of old bone samples. First, the effects of different factors related to PCR amplification were estimated with a generalized linear mixed model. Second, error rates of allelic drop-out and drop-in were estimated on the basis of the frequency and nature of mismatches between replicates. Results In autosomal STR analyses, the most important factor was the DNA quantity, followed by the degradation, whereas in Y-chromosomal STR analysis, the most important factor was the degradation. Inhibition was a minor concern in STR analyses of poorly preserved bones. Conclusions The success of PCR amplification depends largely on the template DNA quality (amount and degradation), but these problems can be partly compensated for by different primer design and amplification chemistry. Consequently, the relative roles of the compromising factors differ according to the kit used.

9 páginas, 3 figuras, 2 tablas.-- et al., Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene–disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309 790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls., This work was supported by the Netherlands Forensic Institute (M Ka), Affymetrix (M Ka and M Kr), the German National Genome Research Network and the German Federal Ministry of Education and Research (H-EW, SS, M Kr and PN); the Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg and the Munich Center of Health Sciences as part of LMUinnovativ (H-EW), the Netherlands Organization for Scientific Research (AGU: NWO 175.010.2005.011), the European Commission (AGU: GEFOS; 201865, AS: LD Europe; QLG2-CT-2001-00916); the Czech Ministry of Health (MM: VZFNM 00064203 and IGA NS/9488-3), Helse-Vest, Regional Health Authority Norway (LAB), the Swedish National Board of Forensic Medicine (GH: RMVFoU 99:22, 02:20) and the Academy of Finland (AS: 80578, OMLL, JP: 109265 and 111713).

Genetic variability and population structure of Baltic ringed seals and an Arctic reference population were assessed using eight microsatellite loci. Ringed seals colonized the Baltic Sea basin soon after deglaciation 11 500 years ago and are supposed to have remained largely isolated from the main Arctic stock since then, approximately 1000 generations. In the 1900s the Baltic population declined rapidly, and is now confined to three distinct breeding areas, with N < 6000 seals altogether. Microsatellite heterozygosity in ringed seals was higher than that in the closely related, boreal harbour seal and grey seal, for which the markers were initially developed. This is plausibly attributed to an overall greater population (species) size of ringed seals during the Quaternary. Allele frequency differentiation between the Baltic and Arctic ringed seals, conventionally treated as different subspecies, was weak. Assuming complete isolation, the divergence (FST=0.023) would imply a notably high postglacial effective population size, approximately 20 000 for the Baltic population. The isolation assumption however, seems unrealistic in the light of the data: a coalescent-based simulation approach to the likelihood of alternative demographic histories clearly favoured a scenario with recurrent gene flow to the Baltic, over one of complete isolation (drift only). Within the Baltic Sea, no differentiation was found between the Gulf of Finland and the Gulf of Bothnia breeding areas; the recent population decline and split have not yet affected the inbreeding levels of the disjunct breeding stocks.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent. Fil: Corach, Daniel. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Caputo, Mariela. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Servicio de Huellas Digitales Genéticas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Marino, Miguel Eduardo. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Analisis de ADN; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Purps, Josephine. Charité-Universitätsmedizin; Alemania Fil: Siegert, Sabine. University of Cologne; Alemania Fil: Willuweit, Sascha. Charité-Universitätsmedizin; Alemania Fil: Nagy, Marion. Charité-Universitätsmedizin; Alemania Fil: Alves, Cíntia. Universidad de Porto; Portugal Fil: Salazar, Renato. Universidad de Porto; Portugal Fil: Angustia, Sheila M. T.. Philippine National Police Crime Laboratory; Filipinas Fil: Santos, Lorna H.. Philippine National Police Crime Laboratory; Filipinas Fil: Anslinger, Katja. Universitat Genzentrum Der Ludwing-maximilians; Alemania Fil: Bayer, Birgit. Universitat Genzentrum Der Ludwing-maximilians; Alemania Fil: Ayub, Qasim. The Wellcome Trust Sanger Institute; Reino Unido Fil: Wei, Wei. The Wellcome Trust Sanger Institute; Reino Unido Fil: Xue, Yali. The Wellcome Trust Sanger Institute; Reino Unido Fil: Tyler Smith, Chris. The Wellcome Trust Sanger Institute; Reino Unido Fil: Baeta Bafalluy, Miriam. Universidad de Zaragoza; España Fil: Martínez Jarreta, Begoña. Universidad de Zaragoza; España Fil: Egyed, Balazs. Eotvos University, Budapest; Argentina Fil: Balitzki, Beate. Universidad de Basilea; Suiza Fil: Tschumi, Sibylle. Universidad de Basilea; Suiza Fil: Ballard, David. King; Reino Unido Fil: Syndercombe Court, Denise. King; Reino Unido Fil: Barrantes, Xinia. Poder Judicial, Forensic Sciences Department; Costa Rica Fil: Bäßler, Gerhard. Landeskriminalamt Baden-Württemberg; Alemania Fil: Berger, Burkhard. Universidad de Innsbruck; Austria Fil: Niederstätter, Haral. Universidad de Innsbruck; Austria Fil: Parson, Walther. Universidad de Innsbruck; Austria. University Park; Estados Unidos Fil: Davis, Carey. Department of Molecular and Medical Genetics; Estados Unidos. Institute of Applied Genetics; Estados Unidos Fil: Furfuro, Sandra. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Análisis de ADN; Argentina Fil: Locarno, Laura. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Laboratorio de Análisis de ADN; Argentina

Compilation and analysis of information from the literature regarding cross-species microsatellite amplification and polymorphism success, and relating this to source-target species genetic distance as estimated by pairwise cytochrome b (cytb) divergence, enabled an in-depth investigation of factors affecting avian cross-species microsatellite amplification. Source-target species cytb distances provided accurate estimates of cross-species microsatellite amplification/polymorphism success rates not only in birds, but also in taxa where microsatellites cross-amplify across contrasting levels of taxonomic classification (frogs and cetaceans). As cytb is one of the most commonly sequenced DNA regions, pairwise cytb genetic distances should therefore be useful for predicting cross-species microsatellite success across a range of taxonomic groups. While the most important factor affecting cross-species microsatellite amplification/polymorphism success was a negative association with source-target species genetic distance, associations with additional features affecting cross-species amplification/polymorphism success included: decreasing PCR annealing temperature significantly increasing the chance of successful cross-species amplification, and a significant positive association between source species polymorphism and the proportion of target species in which a locus revealed polymorphism. No association between cross-species amplification and repeat motif (di-, tri-, or tetranucelotide) or repeat structure (perfect, imperfect, or compound) was observed. A set of nine loci which cross-amplified across an unusually broad range of passerine bird species were also identified, and could serve as a good starting point for cross-species amplification testing in passerine species for which insufficient loci are available.

The additive genetic variance-covariance matrix (G) is a concept central to discussions about evolutionary change over time in a suite of traits. However, at the moment we do not know how fast G itself changes as a consequence of selection or how sensitive it is to environmental influences. We investigated possible evolutionary divergence and environmental influences on G using data from a factorial common-garden experiment where common frog (Rana temporaria) tadpoles from two divergent populations were exposed to three different environmental treatments. G-matrices were estimated using an animal model approach applied to data from a NCII breeding design. Matrix comparisons using both Flury and multivariate analysis of variance methods revealed significant differences in G matrices both between populations and between treatments within populations, the former being generally larger than the latter. Comparison of levels of population differentiation in trait means using Q(ST) indices with that observed in microsatellite markers (F(ST)) revealed that the former values generally exceeded the neutral expectation set by F(ST). Hence, the results suggest that intraspecific divergence in G matrix structure has occurred mainly due to natural selection.

Background Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland. Results Microsatellite diversity within the subspecies (HE = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (FST = 0.107) than in maternally inherited mtDNA (FST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females. Conclusions Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.