Contrasting whole-genome and reduced representation sequencing for population demographic inference: an alpine mammal example

Genomic approaches to the study of population demography rely on accurate SNP calling and by-proxy the site frequency spectrum (SFS). Two main questions for the design of such studies remain poorly investigated: do reduced genomic sequencing summary statistics reflect that of whole genome, and how do sequencing strategies and derived summary statistics impact demographic inferences? To address those questions, we applied the ddRAD sequencing approach to 254 individuals and whole genome resequencing approach to 35 mountain goat (Oreamnos americanus) individuals across the species range with a known demographic history. We identified SNPs with 5 different variant callers and used ANGSD to estimate the genotype likelihoods (GLs). We tested combinations of SNP filtering by linkage disequilibrium (LD), minor allele frequency (MAF) and the genomic region. We compared the resulting suite of summary statistics reflective of the SFS and quantified the relationship to demographic inferences by estimating the contemporary effective population size (Ne), isolation-by-distance and population structure, FST, and explicit modelling of the demographic history with δaδi. Filtering had a larger effect than sequencing strategy, with the former strongly influencing summary statistics. Estimates of contemporary Ne and isolation-by-distance patterns were largely robust to the choice of sequencing, pipeline, and filtering. Despite the high variance in summary statistics, whole genome and reduced representation approaches were overall similar in supporting a glacial induced vicariance and low Ne in mountain goats. We discuss why whole genome resequencing data is preferable, and reiterate support the use of GLs, in part because it limits user-determined filters.

Habitat Adaptation Drives Speciation of a Streptomyces Species with Distinct Habitats and Disparate Geographic Origins

Both isolation by distance and isolation by environment occur in bacteria, and different diversification patterns may apply to different species. Streptomyces species, typified by producing useful natural products, are widespread in nature and possess high genetic diversity. However, the ecological processes and evolutionary mechanisms that shape their distribution are not well understood.

High Level of Phenotypic Differentiation of Common Yew (Taxus baccata L.) Populations in the North-Western Part of the Balkan Peninsula

Common or English yew (Taxus baccata L., Taxaceae) is a conifer species, native to Europe, northern Africa, Asia Minor and Caucasus. It is a dioecious, wind-pollinated and animal-dispersed tree, known for its high-quality wood and medicinal properties, albeit poisonous. The species is rare and has been legally protected at the European and national levels. In addition, its low population density and disjunct character of distribution have reinforced the need for its protection as regeneration is mostly lacking. The aim of this study was to phenotypically characterise the north-western Balkan yew populations. Phenotypic diversity was examined for seven populations, using morphometric analysis of nine phenotypic traits of needles. Descriptive and multivariate statistical analyses were conducted to evaluate the inter- and intrapopulation variability. In addition, to test correlations between geographic, climatic and phenotypic data, Mantel test was used. We identified a geographic structure across studied populations that exhibited high levels of variability on intra- and interpopulation levels. Two groups of populations have been defined and are consistent with previously described genetic divergent lineages from separate refugia. In addition, a significant correlation between phenotypic and geographic data were revealed, i.e., isolation by distance (IBD). However, the Mantel test revealed no significant correlation between morphometric and environmental data. In conclusion, our data reveal that the historical events and persistent IBD acted in combination to produce the morphological patterns observed in common yew populations in the north-western part of the Balkan Peninsula. Finally, we suggested conservation measures to be implemented on a stand level, with habitat preservation as the main goal. In addition, ex situ conservation should be considered, both in the form of collections and urban planting, as both provide additional gene pool reserves.

Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: insights into the recent Australian invasion

Liriomyza sativae, the vegetable leafminer, is a serious agricultural pest originally from the Americas which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double-digest restriction-site associated DNA sequencing (ddRAD-seq) to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our principal component analyses (PCA) results suggested that Australian mainland populations were genetically close to populations from the Torres Strait and had connections to Bali and Papua New Guinea (PNG), whereas populations from Asia and Africa were more distantly related. Hawaii was genetically distinct from populations from Asia, Africa and Australia. Co-ancestry analyses pointed to signals of gene flow from the Torres Strait into the Australian mainland, while Indonesia/PNG were the likely sources of the initial invasion into the Torres Strait. Admixture analyses further revealed that L. sativae from the Torres Strait had genetic diversity originating from multiple sources, which has now spread to the Australian mainland. The L. sativae lineages from Asia/Africa appear closely related and may share co-ancestry. Isolation by distance (IBD) was found at a broad global scale, but not within small regions, suggesting human-mediated factors contribute to the local spread of this pest. Overall, our findings highlight the challenges in quarantine measures aimed at restricting the distribution of this global pest.

Patterns in the Population History of Northern Eurasia from the Mesolithic to the Early Bronze Age, Based on Craniometry and Genetics

This study examines the craniometric differentiation of Northern Eurasian groups with reference to genetic and partly linguistic facts. Measurements of 66 series of male crania from that territory, dating to various periods from the Mesolithic to the Early Bronze Age, were subjected to statistical methods especially destined for detecting spatial patterns, specifi cally gradients. Using the nonmetric multidimensional scaling of the matrix of D2 distances corrected for sample size, a two-dimensional projection of group constellation was generated, and a minimum spanning tree, showing the shortest path between group centroids in the multivariate space, was constructed. East-west clines in Northern Eurasia, detected by both genetic and craniometric traits, likely indicate not so much gene fl ow as isolation by distance, resulting from an incomplete evolutionary divergence of various fi lial groups constituting the Boreal meta-population. The western fi lial component, which, in Siberia and Eastern Central Asia, is mostly represented by Afanasyevans, has evidently made little contribution to the genetic makeup of later populations. The eastern fi lial component, which had appeared in the Cis-Baikal region from across Lake Baikal no later than the Neolithic, admixed with the autochthonous Paleosiberian component. The latter’s principal marker—the ANE autosomal component—had been present in Siberia since the Upper Paleolithic. Likewise autochthonous were both Eurasian formations—Northern and Southern; statis tical analysis has made it possible to make these more inclusive, whereby the former has been expanded in the eastern direction to include the Kuznetsk Basin, and the latter westwards, to the Middle Irtysh. Nothing suggests that Eastern European groups had taken part in the origin of either the Northern Eurasian formation or the proto-Uralic groups.

Genetic Diversity and Population Structure of Chionanthus virginicus

The genus Chionanthus, known as fringetrees, is a member of the olive family (Oleaceae). Chionanthus virginicus is an understory tree or shrub with a wide range in forests of the eastern United States and is used as an ornamental tree that is known to be free of insects and disease in the wild. The species is tolerant of a wide range of environmental conditions, and there is interest in developing new cultivars with improved horticultural traits, such as tree form or upright growth habit and superior flowering display that are widely adapted. To identify genepools in the native range of C. virginicus for use in breeding programs, the genetic diversity and population structure were assessed for 274 individuals from 12 locations in four states (Florida, Maryland, North Carolina, and Texas) using 26 simple sequence repeats (SSRs). An average of 12.54 alleles/locus were detected, allelic richness averaged 2.80. Genetic differentiation was 0.11, indicating moderate differentiation among subpopulations. Despite the high genetic diversity and low population differentiation, Bayesian clustering analysis identified six genetic groups that match the geographic distribution of collection sites. Analysis of molecular variance indicated that most (82%) of the variation is explained within individuals, and 11% and 7% of the variation is due to differences among individuals within populations and among populations. Analysis of isolation by distance across all samples showed a weak positive relationship between geographic distance and genetic distance. The C. virginicus samples analyzed in this study indicate there is sufficient diversity for germplasm collection for use in breeding programs. Given the relatively moderate genetic differentiation, there are not likely to be unique islands of genetic diversity that may be missed when gathering parental materials for a breeding program

Chloroplast and Nuclear Genetic Diversity Explain the Limited Distribution of Endangered and Endemic Thuja sutchuenensis in China

Narrow-ranged species face challenges from natural disasters and human activities, and to address why species distributes only in a limited region is of great significance. Here we investigated the genetic diversity, gene flow, and genetic differentiation in six wild and three cultivated populations of Thuja sutchuenensis, a species that survive only in the Daba mountain chain, using chloroplast simple sequence repeats (cpSSR) and nuclear restriction site-associated DNA sequencing (nRAD-seq). Wild T. sutchuenensis populations were from a common ancestral population at 203 ka, indicating they reached the Daba mountain chain before the start of population contraction at the Last Interglacial (LIG, ∼120–140 ka). T. sutchuenensis populations showed relatively high chloroplast but low nuclear genetic diversity. The genetic differentiation of nRAD-seq in any pairwise comparisons were low, while the cpSSR genetic differentiation values varied with pairwise comparisons of populations. High gene flow and low genetic differentiation resulted in a weak isolation-by-distance effect. The genetic diversity and differentiation of T. sutchuenensis explained its survival in the Daba mountain chain, while its narrow ecological niche from the relatively isolated and unique environment in the “refugia” limited its distribution.

The antique genetic plight of the Mediterranean monk seal (Monachus monachus)

Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the world's most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Western-Sahara/Mauritania (Cabo Blanco), Madeira, Western Mediterranean (historical range) and Eastern Mediterranean regions segregate in four populations. This structure is likely the consequence of recent drift, combined with long-term isolation by distance (R2 = 0.7), resulting from prevailing short-distance (< 500 km) and infrequent long-distance dispersal (< 1,500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. Approximate Bayesian Computation analyses support a scenario combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled to the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.

The interacting effects of genetic variation in Geranium subg. Geranium (Geraniaceae) using scot molecular markers

One of the most crucial aspects of biological diversity for conservation strategies is genetic diversity, particularly in rare and narrow endemic species. Our study is the first attempt to utilize SCoT markers to check the genetic diversity in Iran. We used 115 plant samples. Our objectives were 1) to check genetic diversity among Geranium species 2) Genetic structure of the Geranium 3) Do the Geranium species exchange genes? 4) To detect isolation by distance among the Geranium species. We used traditional morphological and molecular methods to assess genetic diversity and genetic structure in the Geranium species. A total of 129 amplified polymorphic bands were generated across 13 Geranium species. The size of the amplified fragments ranged from 150 to 3000 bp. G. stepporum showed the highest values for the effective number of alleles (Ne = 1.30) and Shannon information index (I =0.35). Significant ANOVA results (P <0.01) showed differences in quantitative morphological characters in plant species. G. sylvaticum showed high genetic diversity. Mantel test showed a significant correlation (r = 0.17, p=0.0002) between genetic distance and geographical distance, so isolation by distance (IBD) occurred among the Geranium species. According to the SCoT markers analysis, G. kotschyi and G. dissectum had the lowest similarity, and the species of G. sylvaticum and G. pratense had the highest similarity. The present study revealed that a combination of morphological and SCoT methods could distinguish the species of Geranium.