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Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods. [ABSTRACT FROM AUTHOR]

Grasping the genetic structure ofmarine fish populations is vital for comprehending species connectivity patterns and determining the appropriate spatiotemporal scales for conservation management strategies. Here, we analyzed the population genetics of the Orangefin Ponyfish (Photopectoralis bindus Valenciennes, 1835) by examining a portion of the gene coding for the mitochondrial cytochrome c oxidase subunit I. The aim was to evaluate the haplotype pattern, genetic structure, demographic history, as well as the influence of ecological connectivity through the Qiongzhou Strait on the distribution patterns of this species in the northern South China Sea and the Beibu Gulf. In total, 257 specimens yielded only 13 haplotypes, with the predominant haplotype present at all sampling locations. The analysis revealed a "star-like" haplotype pattern, indicating low levels of both haplotype and nucleotide diversity. Additionally, a small but significant genetic structure was observed between the coastal regions flanking the Leizhou Peninsula. These patterns in the haplotype network and genetic structure may be significantly influenced by contemporary currents, particularly through the connectivity of the Qiongzhou Strait. Tajima's D and Fu's Fs demonstrated pronouncedly negative values, along with a unimodal mismatch distribution, suggested a recent demographic expansion of Photopectoralis bindus during the late Pleistocene, likely influenced by fluctuations in sea levels. [ABSTRACT FROM AUTHOR]

Grasping the genetic structure of marine fish populations is vital for comprehending species connectivity patterns and determining the appropriate spatiotemporal scales for conservation management strategies. Here, we analyzed the population genetics of the Orangefin Ponyfish (Photopectoralis bindus Valenciennes, 1835) by examining a portion of the gene coding for the mitochondrial cytochrome c oxidase subunit I. The aim was to evaluate the haplotype pattern, genetic structure, demographic history, as well as the influence of ecological connectivity through the Qiongzhou Strait on the distribution patterns of this species in the northern South China Sea and the Beibu Gulf. In total, 257 specimens yielded only 13 haplotypes, with the predominant haplotype present at all sampling locations. The analysis revealed a "star-like" haplotype pattern, indicating low levels of both haplotype and nucleotide diversity. Additionally, a small but significant genetic structure was observed between the coastal regions flanking the Leizhou Peninsula. These patterns in the haplotype network and genetic structure may be significantly influenced by contemporary currents, particularly through the connectivity of the Qiongzhou Strait. Tajima's D and Fu's Fs demonstrated pronouncedly negative values, along with a unimodal mismatch distribution, suggested a recent demographic expansion of Photopectoralis bindus during the late Pleistocene, likely influenced by fluctuations in sea levels. [ABSTRACT FROM AUTHOR]

Grasping the genetic structure ofmarine fish populations is vital for comprehending species connectivity patterns and determining the appropriate spatiotemporal scales for conservation management strategies. Here, we analyzed the population genetics of the Orangefin Ponyfish (Photopectoralis bindus Valenciennes, 1835) by examining a portion of the gene coding for the mitochondrial cytochrome c oxidase subunit I. The aim was to evaluate the haplotype pattern, genetic structure, demographic history, as well as the influence of ecological connectivity through the Qiongzhou Strait on the distribution patterns of this species in the northern South China Sea and the Beibu Gulf. In total, 257 specimens yielded only 13 haplotypes, with the predominant haplotype present at all sampling locations. The analysis revealed a "star-like" haplotype pattern, indicating low levels of both haplotype and nucleotide diversity. Additionally, a small but significant genetic structure was observed between the coastal regions flanking the Leizhou Peninsula. These patterns in the haplotype network and genetic structure may be significantly influenced by contemporary currents, particularly through the connectivity of the Qiongzhou Strait. Tajima's D and Fu's Fs demonstrated pronouncedly negative values, along with a unimodal mismatch distribution, suggested a recent demographic expansion of Photopectoralis bindus during the late Pleistocene, likely influenced by fluctuations in sea levels. [ABSTRACT FROM AUTHOR]

Climate change and associated shifts in temperature and precipitation patterns have become an increasing concern as drivers of ongoing biodiversity loss. The Mediterranean region is particularly vulnerable, being both a biodiversity hotspot and a region very prone to desertification. Freshwater mussels are amongst the most threatened invertebrate taxa worldwide. Unio tumidiformis is an endemic and endangered species restricted to the southern Iberian Peninsula, living in temporary Mediterranean-type streams. Freshwater mussels need a fish host for successful larval transformation, meaning U. tumidiformis must belong to the genus Squalius. The main objective of this study was to evaluate the vulnerability of U. tumidiformis to climate change, by studying its population genetics and evolutionary history, its current and future habitat suitability, and that of its hosts. Genetic population structure and diversity were assessed using Single-Nucleotide Polymorphisms through Genotyping by Sequencing and used to infer species evolutionary history. The species potential distribution was modeled using an ensemble forecasting approach, and future shifts in habitat suitability were assessed with the projected climate data layers from Worldclim. Most populations showed extreme genetic differentiation (Fst up to 0.745), even from close neighboring ones. Upper Guadiana populations were more diverse and less differentiated. We hypothesize that U. tumidiformis originated in Upper Guadiana and followed the same colonization routes as their hosts with numerous founder effects and bottlenecks. Our results also predicted a reduction of 99% of climatically suitable areas for U. tumidiformis in the Iberian Peninsula until 2040. For the fish hosts, a maximum 42% reduction in suitable areas was estimated throughout the century, with remaining adequate habitats in the north. Our results suggest that difficult conservation options are necessary, prioritizing the preservation of populations, translocations to the northern area of its historical range and stream engineering to increase resilience to droughts. [ABSTRACT FROM AUTHOR]

The tropical eastern Pacific (TEP) has been divided into several biogeographic provinces separated by two types of habitat gaps: stretches of sandy shoreline that separate rocky reefs on the mainland (Sinaloan and Central American gaps) and expanses of deep ocean between offshore TEP islands and the mainland. Those gaps are known to influence the distribution and evolution of TEP reef fishes by acting as barriers to gene flow. We investigated potential effects of those gaps on the genetic structure and connectivity of populations of five widely distributed TEP reef-fish species that have different modes of life, habitat preferences and reproductive strategies: Caranx caballus, Rypticus bicolor, Hypsoblennius brevipinnis, Plagiotremus azaleus and Stegastes flavilatus. We used the coxI mitochondrial DNA marker to make phylogeographic, population genetics, and coalescent analyses of geographic patterns of genetic variation in these species. Those analyses showed high variation in levels of genetic diversity. We found no geographic genetic differentiation relating to mainland gaps in any species. Such genetic homogeneity may relate to factors such as migratory behavior, high pelagic dispersal potential and wide environmental tolerance. In two species, differentiation across oceanic gaps separating oceanic islands from the mainland may reflect differences between insular and mainland environments. Historical population expansions that occurred between 400 and 100 thousand years ago in different species may have shaped by patterns of Pleistocene climatic dynamics. The lack of polymorphism of coxI in the damselfish Stegastes flavilatus may relate to the effects of a historical population collapse, although we were not able to detect that genetically. [ABSTRACT FROM AUTHOR]

Simple Summary: The yak is endemic to the Qinghai-Tibetan Plateau (QTP) and serves as an important livestock animal for Tibetan pastoral society. Phenotypic traits vary among domestic yaks. However, genomic characteristics, population structure, and the genetic relationship of domestic yaks with wild yaks have not been effectively characterized until now. In this study, six domestic populations were sequenced, and selective sweep regions involved in yak domestication were detected. Furthermore, divergence time for domestic and wild yaks was estimated. This study revealed new insight into selection for domestic and wild yaks. The yak (Bos grunniens) was domesticated in the high-altitude QTP. Research about their genetic diversity and population structure is limited. In this study, we resequenced the genome of 494 domestic yaks using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). The survey was conducted on six populations sampled from isolated locations in China in order to analyze their structure and genetic diversity. These six domestic populations were clearly grouped into two independent clusters, with Jinchuan, Changtai, and Jiulong showing a tight genetic relationship with the wild yak. Nerve development pathways were enriched with GO enrichment analysis of 334 domesticated genes. Major genomic regions associated with the differentiation of domestic yaks were detected. These findings provide preliminary information on the yak genome variability, useful to understand the genomic characteristics of different populations in QTP. [ABSTRACT FROM AUTHOR]

Cryptomeria japonica var. sinensis is a fast-growing coniferous species that is widely planted in southern China for landscaping and timber production. Large-scale afforestation is frequently associated with alien provenance invasion and could increase the likelihood of intraspecific hybridization, with potentially significant positive or negative effects on local forests. This study is the first investigation of the genetic background of planted C. japonica var. sinensis forests across their distribution. A synthetic approach integrating population genetics and species distribution modelling was used to evaluate the genetic consequences of widespread plantations and predict the species' future distribution. We found comparable levels of genetic diversity in 11 planted populations and seven ancient tree populations. Plantations in the species' native range in eastern China were sourced from nearby native forests or ancient trees, so clear genetic structure has been retained in this region. In colonized regions, planted materials were mostly introduced from Zhejiang province, the best-preserved habitat of C. japonica var. sinensis in China. Overall, the species has low genetic diversity compared to its conspecies, C. japonica, in Japan. Fortunately, Maxent modelling indicated that suitable habitats for this species will expand to the northeast and southwest gradually during the next 50 years, indicating promising applications in afforestation under climate change. However, seed transfer zones for the species should be delineated quickly to guard against risks of genetic pattern disruption and adaptation loss. Finally, our results show that rapidly increasing plantation of this species has a negligible impact on ancient trees and highlights an urgent need to conserve remaining genetic resources. [ABSTRACT FROM AUTHOR]

Despite the increasing accessibility of high‐throughput sequencing, obtaining high‐quality genomic data on non‐model organisms without proximate well‐assembled and annotated genomes remains challenging. Here, we describe a workflow that takes advantage of distant genomic resources and ingroup transcriptomes to select and jointly enrich long open reading frames (ORFs) and ultraconserved elements (UCEs) from genomic samples for integrative studies of microevolutionary and macroevolutionary dynamics. This workflow is applied to samples of the African unionid bivalve tribe Coelaturini (Parreysiinae) at basin and continent‐wide scales. Our results indicate that ORFs are efficiently captured without prior identification of intron‐exon boundaries. The enrichment of UCEs was less successful, but nevertheless produced substantial data sets. Exploratory continent‐wide phylogenetic analyses with ORF supercontigs (>515,000 parsimony informative sites) resulted in a fully resolved phylogeny, the backbone of which was also retrieved with UCEs (>11,000 informative sites). Variant calling on ORFs and UCEs of Coelaturini from the Malawi Basin produced ~2000 SNPs per population pair. Estimates of nucleotide diversity and population differentiation were similar for ORFs and UCEs. They were low compared to previous estimates in molluscs, but comparable to those in recently diversifying Malawi cichlids and other taxa at an early stage of speciation. Skimming off‐target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally‐inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. Overall, our workflow and results provide exciting perspectives for integrative genomic studies of microevolutionary and macroevolutionary dynamics in non‐model organisms. [ABSTRACT FROM AUTHOR]

Clubroot disease is a kind of soil-borne disease that seriously infects Brassica species. In this study, we collected 121 varieties of non-heading Chinese cabbages. In order to better understand the genetic variation and to screen suitable clubroot disease-resistant parental material, we re-sequenced them to examine the population genetic structure, population genetic diversity, population differentiation index, and selective sweep based on SNPs. The mapping rate with the reference genome was high, and data quality analysis revealed that the sequencing quality was good. The annotated data indicated that intronic and intergenic areas held the majority of SNPs and indels. Four subgroups of 121 non-heading Chinese cabbages were identified using principal component analysis, phylogenetic tree, and genetic structure analysis. An examination of genetic diversity revealed that while selfing may happen in subgroups C and D, heterozygosity may exist in subgroups A and B. In subgroup B, self-fertilization is not possible. There was a moderate degree of genetic differentiation between subgroups B and C (Fst = 0.0744347). For genes in certain sweep regions, we also ran GO enrichment and KEGG enrichment analysis. Two disease resistance-related genes, BraA01g042910.3.5C and BraA06g019360.3.5C, were examined. These findings will serve as a theoretical foundation for developing novel, clubroot disease-resistant types of non-heading Chinese cabbages. [ABSTRACT FROM AUTHOR]

Dispersal is generally difficult to directly observe. Instead, dispersal is often inferred from genetic markers and biophysical modelling where a correspondence indicates that dispersal routes and barriers explain a significant part of population genetic differentiation. Biophysical models are used for wind-driven dispersal in terrestrial environments and for propagules drifting with ocean currents in the sea. In the ocean, such seascape genetic or seascape genomic studies provide promising tools in applied sciences, as actions within management and conservation rely on an understanding of population structure, genetic diversity and presence of local adaptations, all dependent on dispersal within the metapopulation. Here, we surveyed 87 studies that combine population genetics and biophysical models of dispersal. Our aim was to understand if biophysical dispersal models can generally explain genetic differentiation. Our analysis shows that genetic differentiation and lack of genetic differentiation can often be explained by dispersal, but the realism of the biophysical model, as well as local geomorphology and species biology also play a role. The review supports the use of a combination of both methods, and we discuss our findings in terms of recommendations for future studies and pinpoint areas where further development is necessary, particularly on how to compare both approaches. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'. [ABSTRACT FROM AUTHOR]

Background: The interplay of animal dispersal and environmental heterogeneity is fundamental for the distribution of biodiversity on earth. In the ocean, the interaction of physical barriers and dispersal has primarily been examined for organisms with planktonic larvae. Animals that lack a planktonic life stage and depend on active dispersal are however likely to produce distinctive patterns. Methods: We used available literature on population genetics and phylogeography of elasmobranchs (sharks, rays and skates) to examine how marine barriers and dispersal ecology shape genetic connectivity in animals with active dispersal. We provide a global geographical overview of barriers extracted from the literature and synthesize the geographical and hydrological factors, spatial and temporal scales to characterize different types of barriers. The three most studied barriers were used to analyse the effect of elasmobranch dispersal potential and barrier type on genetic connectivity. Results: We characterized nine broad types of marine barriers, with the three most common barriers being related to ocean bathymetry. The maximum depth of occurrence, maximum body size and habitat of each species were used as proxies for dispersal potential, and were important predictors of genetic connectivity with varying effect depending on barrier type. Environmental tolerance and reproductive behaviour may also play a crucial role in population connectivity in animals with active dispersal. However, we find that studies commonly lack appropriate study designs based on a priori hypotheses to test the effect of physical barriers while accounting for animal behaviour. Main conclusions: Our synthesis highlights the relative contribution of different barrier types in shaping elasmobranch populations. We provide a new perspective on how barriers and dispersal ecology interact to rearrange genetic variation of marine animals with active dispersal. We illustrate methodological sources that can bias the detection of barriers and provide potential solutions for future research in the field. [ABSTRACT FROM AUTHOR]

Uncertainty hampers innovative mixed‐fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species‐specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population‐specific information. We conclude that the management of fish stocks has to consider species‐specific genetic structures and may benefit from the documentation of the genetic seascape and life‐history traits. [ABSTRACT FROM AUTHOR]

Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further. [ABSTRACT FROM AUTHOR]

Interactions between environmental factors and complex life‐history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype–environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster. [ABSTRACT FROM AUTHOR]

Recent advances in next-generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction site-associated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total of 88 individuals were sequenced on the Illumina MiSeq platform, and demultiplexed reads were used to create a reference catalog of loci. Individual reads were then mapped to the reference catalog, and variant calling was performed. We have characterized two single-nucleotide polymorphism (SNP) panels comprised in total of 656 SNPs. The first panel contained 535 neutral SNPs and the second, 121 outlier SNPs that were characteristic of being putatively under selection. Both neutral and outlier SNP panels showed significant differentiation between the two countries, with the outlier loci demonstrating much larger F values ( F outlier SNP panel = 0.134, P < 0.0001; F neutral SNP panel = 0.022, P < 0.0001). Assignment tests performed with the outlier SNP panel allocated 100 % of the individuals to country of origin, demonstrating the usefulness of these markers for food traceability of J. edwardsii. [ABSTRACT FROM AUTHOR]

Marine species live in a wide diversity of environments and yet, because of their pelagic life stages, are thought to be well-connected: they have high migration rates that inhibit significant population structure. Recent innovations in sequencing technologies now provide information on nucleotide polymorphisms at thousands to tens of thousands of loci based on whole genomes, reduced representative portions of genomes (0.1-1%) or a majority of expressed mRNAs. Data from these genomic approaches are used to define and quantify single-nucleotide polymorphisms (SNPs). These SNP data tend to agree with data from older technologies (allozymes or microsatellites), which support well-connected populations with few genetic differences among populations. However, these studies also find few percentages of SNPs (1-5%) that readily distinguish genetic differences among populations on relatively small geographic scales. The magnitudes of the genetic differences (FST values) suggest that hundreds of loci with significant differences are due to positive selective pressures. Thus, these data suggest that natural selection is effectively altering allele frequencies at 100s of loci in marine populations. In this manuscript, we provide examples of these studies, the strengths and weaknesses of different genomic approaches as well as important technical aspects associated with genomic approaches. [ABSTRACT FROM AUTHOR]

Background: The advent of next-generation sequencing has brought about an explosion of single nucleotide polymorphism (SNP) data in non-model organisms; however, profiling these SNPs across multiple natural populations still requires substantial time and resources. Results: Here, we introduce two cost-efficient quantitative High Resolution Melting (qHRM) methods for measuring allele frequencies at known SNP loci in pooled DNA samples: the 'peaks' method, which can be applied to large numbers of SNPs, and the 'curves' method, which is more labor intensive but also slightly more accurate. Using the reef-building coral Acropora millepora, we show that both qHRMmethods can recover the allele proportions from mixtures prepared using two or more individuals of known genotype. We further demonstrate advantages of each method over previously published methods; specifically, the 'peaks' method can be rapidly scaled to screen several hundred SNPs at once, whereas the 'curves' method is better suited for smaller numbers of SNPs. Conclusions: Compared to genotyping individual samples, these methods can save considerable effort and genotyping costs when relatively few candidate SNPs must be profiled across a large number of populations. One of the main applications of this method could be validation of SNPs of interest identified in population genomic studies. [ABSTRACT FROM AUTHOR]

Background Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultivated accessions was genotyped at 552 single-nucleotide polymorphism loci to search for signals of selection during and after domestication. Results The wild and cultivated populations were well differentiated from one another. Application of the Fst outlier test revealed 64 loci showing evidence for selection. Of these, 35 related to selection during domestication, while the other 29 likely gradually became monomorphic as a result of prolonged selection during post domestication. Two of the SNP locus outliers were associated with testa color. Conclusions Identifying genes controlling domestication-related traits is important for maintaining the diversity of crops. SNP locus outliers detected by a combined forward genetics and population genetics approach can provide markers with utility for the conservation of wild accessions and for trait improvement in the cultivated genepool. [ABSTRACT FROM AUTHOR]

The use of genetic information in conservation biology has become more widespread with genetic information more readily available for non-model organisms. It has also been recognized that genetic information from invasive species can inform their management and control. The red fox poses a significant threat to Australian native fauna and the agricultural industry. Despite this, there are few recently published studies investigating the population genetics of foxes in Australia. This study investigated the population genetics of 94 foxes across the Illawarra and Shoalhaven regions of New South Wales, Australia. Diversity Array sequencing technology was used to genotype a large number of single nucleotide polymorphisms (N = 33,375). Moderate genetic diversity and relatedness were observed across the foxes sampled. Low to moderate levels of inbreeding, high-levels of identity-by-state values, as well as high identity-by-descent values were also found. There was limited evidence for population genetic structure among the foxes across the landscape sampled, supporting the presence of a single population across the study area. This indicates that there may be no barriers hindering fox dispersal across the landscape. [ABSTRACT FROM AUTHOR]