Phylogeographic history of mitochondrial haplogroup J in Scandinavia

Background

Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach.

Methods

Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates.

Results

Haplogroup J originated approximately 42.6 kya (95% CI: 30.0–64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers.

Conclusions

Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.

     

Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B

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QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major causative mutation and epistatic effects

The pursuits of white features and white fleeces free of pigmented fibre have been important selection objectives for many sheep breeds. The cause and inheritance of non‐white colour patterns in sheep has been studied since the early 19th century. Discovery of genetic causes, especially those which predispose pigmentation in white sheep, may lead to more accurate selection tools for improved apparel wool. This article describes an extended QTL study for 13 skin and fibre pigmentation traits in sheep. A total of 19 highly significant, 10 significant and seven suggestive QTL were identified in a QTL mapping experiment using an Awassi × Merino × Merino backcross sheep population. All QTL on chromosome 2 exceeded a LOD score of greater than 4 (range 4.4–30.1), giving very strong support for a major gene for pigmentation on this chromosome. Evidence of epistatic interactions was found for QTL for four traits on chromosomes 2 and 19. The ovine TYRP1 gene on OAR 2 was sequenced as a strong positional candidate gene. A highly significant association (P < 0.01) of grandparental haplotypes across nine segregating SNP/microsatellite markers including one non‐synonymous SNP with pigmentation traits could be shown. Up to 47% of the observed variation in pigmentation was accounted for by models using TYRP1 haplotypes and 83% for models with interactions between two QTL probabilities, offering scope for marker‐assisted selection for these traits.     

Postglacial population expansion of Dacrydium pectinatum(Podocarpaceae)in Hainan,southern China,based on cpDNA tmL-F nocoding sequence data

This study determined the sequences of chloro plast DNA(cpDNA)trnL-F non-coding regions of indiViduals of a tropical coniferous species,Dacrydium pectinatum,collected from 12 natural populations located in Hainan Province,southern China.Sequence length varied from 868 bp to 876 bp,indicating length polymorphism.Base composition in the sequences was high in A+T content between 64.17% and 64.95%.and no recombination event occurred (Rm=0).Thirty haplotypes were identified based on statistical parsimony algorithm by running the TCS program.Populations of D.pectinatum in Hainan were lacking genetic differentiation.Such a deduction was supported by the observed FST values(0.00),AMOVA(24.17% of molecular variance attributed to difference among populations,P＞0.05),high values of Nm(ranging from 1.92 to 2.50)and the branching structure in neighbor-joining(NJ)tree conin the TCS network of trnL-F haplotypes,and majority of the haplotypes coalesced near the tips in NJ tree.Gene genealogies of cpDNA haplotypes proposed a recent population expansion of D.pectinatum in Hainan,which was further supported by the results from Tajima's D test and mismatch distribution analysis.Our data.in COnjunction with geological and palynological evidences,showed that in the Holocene,due to global warming,refugee populations of D.pectinatum in Hainan might experience a range expansion.     

Promoter and functional polymorphisms of HTR2C and suicide victims

In Europe, the countries with the highest suicide rates form a so-called J-curve, which starts in Finland and extends down to Slovenia—a country with one of the world's highest suicide rates. So far, the strongest association between suicide and genes has been shown for the serotonergic system. A functional polymorphism 68G>C (Cys23Ser) and a promoter polymorphism–995G>A of serotonin receptor 2C (HTR2C) have already been investigated, but no associations with suicide were determined. In the present study 334 suicide victims and 211 controls of Slovenian origin were genotyped for the above-mentioned polymorphisms using standard methods. In the case of the polymorphism–995G>A no association with suicide was found. However, a significant association was observed between female suicide victims and polymorphism 68G>C. The significance remained when we combined alleles of female and male populations. An excess of GG genotype and allele G was observed. However, no statistically important differences were present when only males were analyzed. Haplotype analysis on female population showed marginal association of haplotype G-C with suicide. The present study speaks for the plausible implication of the HTR2C in suicide susceptibility.     

Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates

The ability to gather genetic information using DNA metabarcoding of bulk samples obtained directly from the environment is crucial to determine biodiversity baselines and understand population dynamics in the marine realm. While DNA metabarcoding is effective in evaluating biodiversity at community level, genetic patterns within species are often concealed in metabarcoding studies and overlooked for marine invertebrates. In the present study, we implement recently developed bioinformatics tools to investigate intraspecific genetic variability for invertebrate taxa in the Mediterranean Sea. Using metabarcoding samples from Autonomous Reef Monitoring Structures (ARMS) deployed in three locations, we present haplotypes and diversity estimates for 145 unique species. While overall genetic diversity was low, we identified several species with high diversity records and potential cryptic lineages. Further, we emphasize the spatial scale of genetic variability, which was observed from locations to individual sampling units (ARMS). We carried out a population genetic analysis of several important yet understudied species, which highlights the current knowledge gap concerning intraspecific genetic patterns for the target taxa in the Mediterranean basin. Our approach considerably enhances biodiversity monitoring of charismatic and understudied Mediterranean species, which can be incorporated into ARMS surveys.