The power and promise of population genomics: from genotyping to genome typing

Genetic Differentiation of a New World Screwworm Fly Population from Uruguay Detected by SNPs, Mitochondrial DNA and Microsatellites in Two Consecutive Years

The New World screwworm (NWS) fly, Cochliomyia hominivorax (Diptera: Calliphoridae), is an economically important ectoparasite currently distributed in South America and in the Caribbean basin. The successful eradication of this species in USA, Mexico and continental Central America was achieved by a control program based on the sterile insect technique (SIT). In order to implement a genetic control strategy over the NWS fly's current area of occurrence, first, it is necessary to understand the species dynamics and population structure. In order to address this objective, the spatial genetic structure of the NWS fly was previously reported in South America based on different genetic markers; however, to date, no study has investigated temporal changes in the genetic composition of its populations. In the current study, the temporal genetic structure of a NWS fly population from Uruguay was investigated through two consecutive samplings from the same locality over an interval of approximately 18 generations. The genetic structure was accessed with neutral and under selection SNPs obtained with genotyping-by-sequencing. The results gathered with these data were compared to estimates achieved with mitochondrial DNA sequences and eight microsatellite markers. Temporal changes in the genetic composition were revealed by all three molecular markers, which may be attributed to seasonal changes in the NWS fly's southern distribution. SNPs were employed for the first time for estimating the genetic structure in a NWS fly population; these results provide new clues and perspectives on its population genetic structure. This approach could have significant implications for the planning and implementation of management programs.

EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

BACKGROUND

The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers.

METHODS

In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms.

RESULTS

Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported.

CONCLUSION

This deep EST-SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

Population Genomics Reveals Demographic History and Genomic Differentiation of Populus davidiana and Populus tremula

Forest trees can increase our understanding of how evolutionary processes drive the genomic landscape and understand speciation due to the majority of forest trees being distributed widely and able to adapt to different climates and environments. Populus davidiana and Populus tremula are among the most geographically widespread and ecologically important tree species in Northern Hemisphere. Whole-genome resequencing data of 41 individuals of P. davidiana and P. tremula throughout Eurasia was conducted, finding that genetic differentiation was evident between the two species, the F_ST values between P. davidiana and P. tremula was 0.3625. The ancestors of the two aspen diverged into P. davidiana and P. tremula species approximately 3.60 million years ago (Mya), which was in accordance with the rapid uplift of Qinghai-Tibet Plateau (QTP) around the Miocene/Pliocene boundary. The two species experienced a considerable long-term bottleneck after divergence, with population expansion beginning approximately 20,000 years ago after the end of the last glacial maximum. Although the majority of regions of genomic differentiation between the two species can be explained by neutral evolutionary processes, some outlier regions have also been tested that are significantly influenced by natural selection. We found that the highly differentiated regions of the two species exhibited significant positive selection characteristics, and also identified long-term balancing selection in the poorly differentiated regions in both species. Our results provide strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between P. davidiana and P. tremula. These results provide the detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in P. davidiana and P. tremula.

Incorporating the Connectivity Timescale in Metapopulation Partitioning

The often complex spatial patterns of propagule dispersal across a metapopulation present a challenge for species management, motivating efforts to represent the connectivity in simpler but meaningful ways. The reduction of complexity may be achieved by partitioning the metapopulation into groups of highly connected patches called "subpopulations." To have relevance for management, these subunits must be defined from ecological or evolutionary principles. The probabilities of dispersal-mediated propagule interchange between sites, commonly organized into a connectivity matrix, entail a timescale that is usually ignored in subpopulation analyses, limiting their utility and possibly leading to misinterpretation and wrong management decisions. Recognition of the essentially dynamical role played by metapopulation connectivity naturally leads to the incorporation of the generational timescale into the partitioning analysis. An algorithm is proposed to determine the subpopulations-both their cardinality and their composition-as a function of the generational timescale and of a limiting probability of connection, illustrated with a novel empirical estimate of mesopelagic connectivity. The proposed framework allows the unambiguous determination of the timescales corresponding to dispersal barriers and the identification of effective ecological units across the spectrum of management-relevant time horizons.

Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River

Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.

Molecular and phenotypic diversity of groundnut (Arachis hypogaea L.) cultivars in Togo

Diversity assessment of 94 groundnut accessions from Togo and Senegal, using agro-morphological and SNP markers, revealed high variability for many quantitative traits such as late leaf spot (LLS) incidence, number of pods per plant and yield per plant. For qualitative traits, the Simpson Index showed high diversity for primary seed colour (0.75), stem pigmentation (0.60), and Growth habit (0.59). Principal component analysis underscored quantitative traits such as hundred seed weight, days to maturity, and LLS incidence, as the main traits contributing to the divergence. Correlation and path coefficient analysis showed that the number of pods per plant was the main yield-related trait positively affecting yield (r = 0.95, PC = 0.84; p = 0.01). Overall, 990 SNP markers revealed moderate genetic variability in the genotypes and the percentage of heterozygous genotypes varied from 0 to 50% for all loci. Analysis of molecular variance revealed that only 1.1% of the total molecular variance accounted for geographical contribution to the diversity. Co-analysis of phenotypic and SNP data delineated three clusters harbouring useful alleles and interesting phenotypic features such as LLS resistance, large number of pods per plant and early maturity indicating that differences observed at the phenotypic level are underlined by genotypic differences. The phenotypic and genotypic diversity observed could be exploited for the identification of parents with preferred traits for use in the breeding program. However, the low population structure highlights the necessity to improve groundnut diversity in Togo through introduction from various sources.

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)

Understanding the processes that shape neutral and adaptive genomic variation is a fundamental step to determine the demographic and evolutionary dynamics of pest species. Here, we use genomic data obtained via restriction site-associated DNA sequencing to investigate the genetic structure of Moroccan locust (Dociostaurus maroccanus) populations from the westernmost portion of the species distribution (Iberian Peninsula and Canary Islands), infer demographic trends, and determine the role of neutral versus selective processes in shaping spatial patterns of genomic variation in this pest species of great economic importance. Our analyses showed that Iberian populations are characterized by high gene flow, whereas the highly isolated Canarian populations have experienced strong genetic drift and loss of genetic diversity. Historical demographic reconstructions revealed that all populations have passed through a substantial genetic bottleneck around the last glacial maximum (~21 ka BP) followed by a sharp demographic expansion at the onset of the Holocene, indicating increased effective population sizes during warm periods as expected from the thermophilic nature of the species. Genome scans and environmental association analyses identified several loci putatively under selection, suggesting that local adaptation processes in certain populations might not be impeded by widespread gene flow. Finally, all analyses showed few differences between outbreak and nonoutbreak populations. Integrated pest management practices should consider high population connectivity and the potential importance of local adaptation processes on population persistence.

Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon

The introduction of wild Atlantic salmon into captivity, and their subsequent artificial selection for production traits, has caused phenotypic differences between domesticated fish and their wild counterparts. Identification of regions of the genome underling these changes offers the promise of characterizing the early biological consequences of domestication. In the current study, we sequenced a population of farmed European Atlantic salmon and compared the observed patterns of SNP variation to those found in conspecific wild populations. This identified 139 genomic regions that contained significantly elevated SNP homozygosity in farmed fish when compared to their wild counterparts. The most extreme was adjacent to versican, a gene involved in control of neural crest cell migration. To control for false positive signals, a second and independent dataset of farmed and wild European Atlantic salmon was assessed using the same methodology. A total of 81 outlier regions detected in the first dataset showed significantly reduced homozygosity within the second one, strongly suggesting the genomic regions identified are enriched for true selection sweeps. Examination of the associated genes identified a number previously characterized as targets of selection in other domestic species and that have roles in development, behavior and olfactory system. These include arcvf, sema6, errb4, id2-like, and 6n1-like genes. Finally, we searched for evidence of parallel sweeps using a farmed population of North American origin. This failed to detect a convincing overlap to the putative sweeps present in European populations, suggesting the factors that drive patterns of variation under domestication and early artificial selection were largely independent. This is the first analysis on domestication of aquaculture species exploiting whole-genome sequence data and resulted in the identification of sweeps common to multiple independent populations of farmed European Atlantic salmon.

Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin (Kajikia audax), a broadly distributed and highly migratory pelagic species

Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site-associated DNA to characterize genome-wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual-based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F ST = 0.0137-0.0819). F ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m R ≤ 0.37) compared with most populations in the Pacific Ocean (m R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long-distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome-wide markers enable inference of population-level relationships using sample sizes practical for large pelagic fishes of conservation concern.

Emerging Frontiers in the Study of Molecular Evolution

A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.

Current State and Perspectives in Population Genomics of the Common Bean

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Proteomic similarity of the Littorinid snails in the evolutionary context

BACKGROUND

The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.

METHODS

Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation.

RESULTS

Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.

RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics

Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site-associated DNA sequencing (RAD-Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00-0.018) were concordant with previous microsatellite-based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age-1 and age-2 families of full and half-siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non-native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.

Genet assignment and population structure analysis in a clonal forest-floor herb, Cardamine leucantha, using RAD-seq

To study the genetic structure of clonal plant populations, genotyping and genet detection using genetic markers are necessary to assign ramets to corresponding genets. Assignment is difficult as it involves setting a robust threshold of genetic distance for genet distinction as neighbouring genets in a plant population are often genetically related. Here, we used restriction site-associated DNA sequencing (RAD-seq) for a rhizomatous clonal herb, Cardamine leucantha [Brassicaceae] to accurately determine genet structure in a natural population. We determined a draft genome sequence of this species for the first time, which resulted in 66 617 scaffolds with N₅₀ = 6086 bp and an estimated genome size of approximately 253 Mbp. Using genetic distances based on the RAD-seq analysis, we successfully distinguished ramets that belonged to distinct genets even from a half-sib family. We applied these methods to 372 samples of C. leucantha collected at 1-m interval grids within a 20 × 20 m plot in a natural population in Hokkaido, Japan. From these samples, we identified 61 genets with high inequality in terms of genet size and patchy distribution. Spatial autocorrelation analyses indicated significant aggregation within 7 and 4 m at ramet and genet levels, respectively. An analysis of parallel DNA microsatellite loci (simple sequence repeats) suggested that RAD-seq can provide data that allows robust genet assignment. It remains unclear whether the large genets identified here became dominant stochastically or deterministically. Precise identification of genets will assist further study and characterization of dominant genets.

A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia

Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.

Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude

Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.

Genomic biosurveillance of forest invasive alien enemies: A story written in code

The world's forests face unprecedented threats from invasive insects and pathogens that can cause large irreversible damage to the ecosystems. This threatens the world's capacity to provide long-term fiber supply and ecosystem services that range from carbon storage, nutrient cycling, and water and air purification, to soil preservation and maintenance of wildlife habitat. Reducing the threat of forest invasive alien species requires vigilant biosurveillance, the process of gathering, integrating, interpreting, and communicating essential information about pest and pathogen threats to achieve early detection and warning and to enable better decision-making. This process is challenging due to the diversity of invasive pests and pathogens that need to be identified, the diverse pathways of introduction, and the difficulty in assessing the risk of establishment. Genomics can provide powerful new solutions to biosurveillance. The process of invasion is a story written in four chapters: transport, introduction, establishment, and spread. The series of processes that lead to a successful invasion can leave behind a DNA signature that tells the story of an invasion. This signature can help us understand the dynamic, multistep process of invasion and inform management of current and future introductions. This review describes current and future application of genomic tools and pipelines that will provide accurate identification of pests and pathogens, assign outbreak or survey samples to putative sources to identify pathways of spread, and assess risk based on traits that impact the outbreak outcome.

Machine learning and its applications in plant molecular studies

The advent of high-throughput genomic technologies has resulted in the accumulation of massive amounts of genomic information. However, biologists are challenged with how to effectively analyze these data. Machine learning can provide tools for better and more efficient data analysis. Unfortunately, because many plant biologists are unfamiliar with machine learning, its application in plant molecular studies has been restricted to a few species and a limited set of algorithms. Thus, in this study, we provide the basic steps for developing machine learning frameworks and present a comprehensive overview of machine learning algorithms and various evaluation metrics. Furthermore, we introduce sources of important curated plant genomic data and R packages to enable plant biologists to easily and quickly apply appropriate machine learning algorithms in their research. Finally, we discuss current applications of machine learning algorithms for identifying various genes related to resistance to biotic and abiotic stress. Broad application of machine learning and the accumulation of plant sequencing data will advance plant molecular studies.

Genomic data reveal similar genetic differentiation in aquifer species with different dispersal capabilities and life histories

Little is known about the life histories, genetic structure and population connectivity of shallow groundwater organisms. We used next-generation sequencing (RAD-seq) to analyse population genomic structure in two aquifer species: Paraperla frontalis (Banks, 1902), a stonefly with groundwater larvae and aerial (winged) adults; and Stygobromus sp., a groundwater-obligate amphipod. We found similar genetic differentiation in each species between floodplains separated by ~70 river km in the Flathead River basin of north-west Montana, USA. Given that Stygobromus lacks the above-ground life stage of P. frontalis, our findings suggest that connectivity and the magnitude of genetic structure cannot be definitively assumed from life history differences.

Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics

Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.

The combined use of raw and phylogenetically independent methods of outlier detection uncovers genome-wide dynamics of local adaptation in a lizard

Local adaptation is a dynamic process by which different allele combinations are selected in different populations at different times, and whose genetic signature can be inferred by genome-wide outlier analyses. We combined gene flow estimates with two methods of outlier detection, one of them independent of population coancestry (CIOA) and the other one not (ROA), to identify genetic variants favored when ecology promotes phenotypic convergence. We analyzed genotyping-by-sequencing data from five populations of a lizard distributed over an environmentally heterogeneous range that has been changing since the split of eastern and western lineages ca. 3 mya. Overall, western lizards inhabit forest habitat and are unstriped, whereas eastern ones inhabit shrublands and are striped. However, one population (Lerma) has unstriped phenotype despite its eastern ancestry. The analysis of 73,291 SNPs confirmed the east-west division and identified nonoverlapping sets of outliers (12 identified by ROA and 9 by CIOA). ROA revealed ancestral adaptive variation in the uncovered outliers that were subject to divergent selection and differently fixed for eastern and western populations at the extremes of the environmental gradient. Interestingly, such variation was maintained in Lerma, where we found high levels of heterozygosity for ROA outliers, whereas CIOA uncovered innovative variants that were selected only there. Overall, it seems that both the maintenance of ancestral variation and asymmetric migration have counterbalanced adaptive lineage splitting in our model species. This scenario, which is likely promoted by a changing and heterogeneous environment, could hamper ecological speciation of locally adapted populations despite strong genetic structure between lineages.

Genome Assembly of the Common Pheasant Phasianus colchicus: A Model for Speciation and Ecological Genomics

The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history.

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics

Motivation

Genotyping a set of variants from a database is an important step for identifying known genetic traits and disease-related variants within an individual. The growing size of variant databases as well as the high depth of sequencing data poses an efficiency challenge. In clinical applications, where time is crucial, alignment-based methods are often not fast enough. To fill the gap, Shajii et al. propose LAVA, an alignment-free genotyping method which is able to more quickly genotype single nucleotide polymorphisms (SNPs); however, there remains large room for improvements in running time and accuracy.

Results

We present the VarGeno method for SNP genotyping from Illumina whole genome sequencing data. VarGeno builds upon LAVA by improving the speed of k-mer querying as well as the accuracy of the genotyping strategy. We evaluate VarGeno on several read datasets using different genotyping SNP lists. VarGeno performs 7-13 times faster than LAVA with similar memory usage, while improving accuracy.

Availability and implementation

VarGeno is freely available at: https://github.com/medvedevgroup/vargeno.

Supplementary information

Supplementary data are available at Bioinformatics online.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Gene Introgression among Closely Related Species in Sympatric Populations: A Case Study of Three Walnut (Juglans) Species

Gene introgression usually results from natural hybridization occurring among closely related species in sympatric populations. In this study, we discussed two rare and frequent gene flow phenomena between three species of Juglans plants and analyzed the possible causes for the difference. We collected 656 individuals from 40 populations of Persian walnut (Juglans regia L.), Chinese walnut (J. cathayensis Dode), and Iron walnut (J. sigillata Dode) that were genotyped at 17 expressed sequence tag simple sequence repeat (EST-SSR) loci to analyze the introgressions between J. regia and J. cathayensis, and J. regia and J. sigillata. Our study compared the spatial patterns of expected heterozygosity (HE), allelic richness (Rs), and private allele richness (PAR) so as to vividly infer the biogeographic history of related species of Juglans in the two regions. The results of the PCoA, UPGMA, and STRUCTURE analyses showed that all J. regia and J. sigillata populations clustered into one group, and the J. cathayensis populations clustered into the other group. The results of the historical gene flow analysis indicated that J. regia and J. sigillata have no genetic barriers, and the directional gene flow is mainly from J. regia to J. sigillata. For the three species of Juglans, all the above results indicated that gene flow was common among the same group of Juglans, and only rare and low-level gene flow appeared in distinct groups. Therefore, our study revealed multiple phenomena of gene flow and introgression among closely related species in sympatric populations, thereby providing a theoretical basis for the genetic evolution of the genus Juglans.

Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach

An increasing number of studies are using landscape genomics to investigate local adaptation in wild and domestic populations. Implementation of this approach requires the sampling phase to consider the complexity of environmental settings and the burden of logistical constraints. These important aspects are often underestimated in the literature dedicated to sampling strategies. In this study, we computed simulated genomic data sets to run against actual environmental data in order to trial landscape genomics experiments under distinct sampling strategies. These strategies differed by design approach (to enhance environmental and/or geographical representativeness at study sites), number of sampling locations and sample sizes. We then evaluated how these elements affected statistical performances (power and false discoveries) under two antithetical demographic scenarios. Our results highlight the importance of selecting an appropriate sample size, which should be modified based on the demographic characteristics of the studied population. For species with limited dispersal, sample sizes above 200 units are generally sufficient to detect most adaptive signals, while in random mating populations this threshold should be increased to 400 units. Furthermore, we describe a design approach that maximizes both environmental and geographical representativeness of sampling sites and show how it systematically outperforms random or regular sampling schemes. Finally, we show that although having more sampling locations (between 40 and 50 sites) increase statistical power and reduce false discovery rate, similar results can be achieved with a moderate number of sites (20 sites). Overall, this study provides valuable guidelines for optimizing sampling strategies for landscape genomics experiments.

Divergent selection and genetic structure of Sideritis scardica populations from southern Balkan Peninsula as revealed by AFLP fingerprinting

Sideritis scardica Giseb. is a subalpine/alpine plant species endemic to the central part of the Balkan Peninsula. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) and environmental data to examine the adaptive genetic variations in S. scardica natural populations sampled in contrasting environments. A total of 226 AFLP loci were genotyped in 166 individuals from nine populations. The results demonstrated low gene diversity, ranging from 0.095 to 0.133 and significant genetic differentiation ranging from 0.115 to 0.408. Seven genetic clusters were revealed by Bayesian clustering methods as well as by Discriminant Analysis of Principal Components and each population formed its respective cluster. The exception were populations P02 Mt. Shara and P07 Mt. Vermio, that were admixed between two clusters. Both landscape genetic methods Mcheza and BayeScan identified a total of seven (3.10%) markers exhibiting higher levels of genetic differentiation among populations. The spatial analysis method Samβada detected 50 individual markers (22.12%) associated with bioclimatic variables, among them seven were identified by both Mcheza and BayeScan as being under directional selection. Four bioclimatic variables associated with five out of seven outliers were related to precipitation, suggesting that this variable is the key factor affecting the adaptive variation of S. scardica.

Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools

Recurrently invading pests provide unique challenges for pest management, but also present opportunities to utilize genomics to understand invasion dynamics and inform regulatory management through pathway analysis. In the southern United States, the Mexican fruit fly Anastrepha ludens is such a pest, and its incursions into Texas and California represent major threats to the agricultural systems of those regions. We developed a draft genome assembly for A. ludens, conducted range-wide population genomics using restriction site-associated DNA sequencing, and then developed and demonstrated a panel of highly differentiated diagnostic SNPs for source determination of intercepted flies in this system. Using 2,081 genomewide SNPs, we identified four populations across the range of A. ludens, corresponding to western Mexico, eastern Mexico/Texas, Guatemala/Belize/Honduras, and Costa Rica/Panama, with some intergradation present between clusters, particularly in Central America. From this population genomics framework, we developed a diagnostic panel of 28 highly differentiated SNPs that were able to recreate the genomewide population structure in this species. We demonstrated this panel on a set of test specimens, including specimens intercepted as part of regular trapping surveillance in Texas and California, and we were able to predict populations of origin for these specimens. This methodology presents a highly applied use of genomic techniques and can be implemented in any group of recurrently invading pests.

Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

This study is the first large-scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4-26°S and 33-48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale-across national borders.

The potential of genomics for restoring ecosystems and biodiversity

Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.

RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean

Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise F_ST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.

Ecological Divergence with Gene Flow in a Thermophilic Cyanobacterium

How ecological diversity is maintained and distributed within populations is a longstanding question in microbial ecology. In the thermophilic cyanobacterium Synechococcus B', high observed levels of recombination are predicted to maintain ecological variation despite the simultaneous action of diverse selective pressures on different regions of the genome. To investigate ecological diversity in these bacteria, we directly isolated laboratory strains of Synechococcus B' from samples collected along the thermal gradients of two geothermal environments in Yellowstone National Park. Extensive recombination was evident for a multi-locus sequence data set, and, consequently, our sample did not exhibit the sequence clustering expected for distinct ecotypes evolving by periodic clonal selection. Evidence for local selective sweeps at specific loci suggests that sweeps may be common but that recombination is effective for maintaining diversity of unlinked genomic regions. Thermal performance for strain growth was positively associated with the temperature of the environment, indicating that Synechococcus B' populations consist of locally adapted ecological specialists that occupy specific thermal niches. Because this ecological differentiation is observed despite the absence of dispersal barriers among sites, we conclude that these bacteria may freely exchange much of the genome but that barriers to gene flow exist for loci under direct temperature selection.

Exploration of Genetic Variations through Single-cell Whole-genome Sequencing in the Model Ciliate Tetrahymena thermophila

Ciliates are unicellular eukaryotes with separate germline and somatic genomes and diverse life cycles, which make them a unique model to improve our understanding of population genetics through the detection of genetic variations. However, traditional sequencing methods cannot be directly applied to ciliates because the majority are uncultivated. Single-cell whole-genome sequencing (WGS) is a powerful tool for studying genetic variation in microbes, but no studies have been performed in ciliates. We compared the use of single-cell WGS and bulk DNA WGS to detect genetic variation, specifically single nucleotide polymorphisms (SNPs), in the model ciliate Tetrahymena thermophila. Our analyses showed that (i) single-cell WGS has excellent performance regarding mapping rate and genome coverage but lower sequencing uniformity compared with bulk DNA WGS due to amplification bias (which was reproducible); (ii) false-positive SNP sites detected by single-cell WGS tend to occur in genomic regions with particularly high sequencing depth and high rate of C:G to T:A base changes; (iii) SNPs detected in three or more cells should be reliable (an detection efficiency of 83.4-97.4% was obtained for combined data from three cells). This analytical method could be adapted to measure genetic variation in other ciliates and broaden research into ciliate population genetics.

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e., presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population-specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as nonsynonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented data set, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.

Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection

Although efforts have been taken to exploit diversity for yield and quality improvements, limited progress on using beneficial alleles in domesticated and undomesticated cotton varieties is limited. Given the complexity and limited amount of genomic information since the completion of four cotton genomes, characterizing significant variations and haplotype block inheritance under artificial selection has been challenging. Here we sequenced Gossypium hirsutum L. cv CRI-12 (the cotton variety with the largest acreage in China), its parental cultivars, and progeny cultivars, which were bred by the different institutes in China. In total, 3.3 million SNPs were identified and 118, 126 and 176 genes were remarkably correlated with Verticillium wilt, salinity and drought tolerance in CRI-12, respectively. Transcriptome-wide analyses of gene expression, and functional annotations, have provided support for the identification of genes tied to these tolerances. We totally discovered 58 116 haplotype blocks, among which 23 752 may be inherited and 1029 may be recombined under artificial selection. This survey of genetic diversity identified loci that may have been subject to artificial selection and documented the haplotype block inheritance and recombination, shedding light on the genetic mechanism of artificial selection and guiding breeding efforts for the genetic improvement of cotton.

Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites

Background

Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush.

Methods

Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010-2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate.

Results

Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified.

Discussion

This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangered bird species. Furthermore, our results indicate that we cannot exclude the probability that the origin of the Hong Kong captive population was the wild population from Wuyuan. These results provide valuable knowledge that can help improve conservation management and planning for both captive and wild Blue-crowned Laughingthrush populations.

A novel transcriptome-derived SNPs array for tench (Tinca tinca L.)

Tench (Tinca tinca L.) has great economic potential due to its high rate of fecundity and long-life span. Population genetic studies based on allozymes, microsatellites, PCR-RFLP and sequence analysis of genes and DNA fragments have revealed the presence of Eastern and Western phylogroups. However, the lack of genomic resources for this species has complicated the development of genetic markers. In this study, the tench transcriptome and genome were sequenced by high-throughput sequencing. A total of 60,414 putative SNPs were identified in the tench transcriptome using a computational pipeline. A set of 96 SNPs was selected for validation and a total of 92 SNPs was validated, resulting in the highest conversion and validation rate for a non-model species obtained to date (95.83%). The validated SNPs were used to genotype 140 individuals belonging to two tench breeds (Tabor and Hungarian), showing low (FST = 0.0450) but significant (<0.0001) genetic differentiation between the two tench breeds. This implies that set of validated SNPs array can be used to distinguish the tench breeds and that it might be useful for studying a range of associations between DNA sequence and traits of importance. These genomic resources created for the tench will provide insight into population genetics, conservation fish stock management, and aquaculture.

Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda

Understanding the resistance and resilience of foundation plant species to climate change is a critical issue because the loss of these species would fundamentally reshape communities and ecosystem processes. High levels of population genetic diversity may buffer foundation species against climate disruptions, but the strong selective pressures associated with climatic shifts may also rapidly reduce such diversity. We characterized genetic diversity and its responsiveness to experimental drought in the foundation plant, black grama grass (Bouteloua eriopoda), which dominates many western North American grasslands and shrublands. Previous studies suggested that in arid ecosystems, black grama reproduces largely asexually via stolons, and thus is likely to have low genetic variability, which might limit its potential to respond to climate disruptions. Using genotyping-by-sequencing, we demonstrated unexpectedly high genetic variability among black grama plants in a 1 ha site within the Sevilleta National Wildlife Refuge in central New Mexico, suggesting some level of sexual reproduction. Three years of experimental, growing season drought reduced black grama survival and biomass (the latter by 96%), with clear genetic differentiation (higher F_ST) between plants succumbing to drought and those remaining alive. Reduced genetic variability in the surviving plants in drought plots indicated that the experimental drought had forced black grama populations through selection bottlenecks. These results suggest that foundation grass species, such as black grama, may experience rapid evolutionary change if future climates include more severe droughts.

Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada

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 F ST = 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.

Evolution of population structure in an estuarine-dependent marine fish

Restriction site-associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, Sciaenops ocellatus, an estuarine-dependent fish found in coastal waters along the southeastern coast of the United States (Atlantic) and the northern Gulf of Mexico (Gulf). Analyses of neutral and outlier loci revealed three genetically distinct regional clusters: one in the Atlantic and two in the northern Gulf. Divergence in neutral loci indicated gradual genetic change and followed a linear pattern of isolation by distance. Divergence in outlier loci was at least an order of magnitude greater than divergence in neutral loci, and divergence between the regions in the Gulf was twice that of divergence between other regions. Discordance in patterns of genetic divergence between outlier and neutral loci is consistent with the hypothesis that the former reflects adaptive responses to environmental factors that vary on regional scales, while the latter largely reflects drift processes. Differences in basic habitat, initiated by glacial retreat and perpetuated by contemporary oceanic and atmospheric forces interacting with the geomorphology of the northern Gulf, followed by selection, appear to have led to reduced gene flow among red drum across the northern Gulf, reinforcing differences accrued during isolation and resulting in continued divergence across the genome. This same dynamic also may pertain to other coastal or nearshore fishes (18 species in 14 families) where genetically or morphologically defined sister taxa occur in the three regions.

Phylogeography of the threatened tetraploid fish, Schizothorax waltoni, in the Yarlung Tsangpo River on the southern Qinghai-Tibet Plateau: implications for conservation

The phylogeography of Schizothorax waltoni, an endemic and endangered tetraploid schizothoracine fish in the Yarlung Tsangpo River (YLTR) on southern margin of Qinghai-Tibet Plateau (QTP), was investigated using two mitochondrial DNA regions and eleven microsatellite loci. Analyses of concatenated sequences of cytochrome b (1141 bp) and the control region (712 bp) revealed high haplotype diversity and moderate nucleotide diversity. High genetic diversity was observed based on microsatellite variation. Both mtDNA and microsatellite analyses revealed significant genetic differentiation between the eastern population (Mainling) and the other four populations to the west, and non-significant genetic differentiation amongst the three central populations in the west. Significant genetic differentiation was observed between the western population (Shigatse) and the three central populations based on microsatellite analyses alone. Bayesian skyline plot analyses showed that S. waltoni experienced a pronounced population expansion 0.05 to 0.10 Ma. Hierarchical structure analyses of microsatellite data indicated that S. waltoni could be split into three groups (western, central and eastern YLTR). The results indicate that three management units should be considered for S. waltoni. Our findings highlight the need for the conservation and effective management of S. waltoni, which is a key member of the endemic and highly threatened fishes of the QTP.

Towards a systematic understanding of differences between archaeal and bacterial diversity

In this crystal ball, we discuss emerging methodologies that can help reaching a synthesis on the biodiversity of Archaea and Bacteria and thereby inform a central enigma in microbiology, i.e. the fundamental split between these primary domains of life and the apparent lower diversity of the Archaea.

Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single-nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted resampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principal components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.

SNP variable selection by generalized graph domination

BACKGROUND

High-throughput sequencing technology has revolutionized both medical and biological research by generating exceedingly large numbers of genetic variants. The resulting datasets share a number of common characteristics that might lead to poor generalization capacity. Concerns include noise accumulated due to the large number of predictors, sparse information regarding the p≫n problem, and overfitting and model mis-identification resulting from spurious collinearity. Additionally, complex correlation patterns are present among variables. As a consequence, reliable variable selection techniques play a pivotal role in predictive analysis, generalization capability, and robustness in clustering, as well as interpretability of the derived models.

METHODS AND FINDINGS

K-dominating set, a parameterized graph-theoretic generalization model, was used to model SNP (single nucleotide polymorphism) data as a similarity network and searched for representative SNP variables. In particular, each SNP was represented as a vertex in the graph, (dis)similarity measures such as correlation coefficients or pairwise linkage disequilibrium were estimated to describe the relationship between each pair of SNPs; a pair of vertices are adjacent, i.e. joined by an edge, if the pairwise similarity measure exceeds a user-specified threshold. A minimum k-dominating set in the SNP graph was then made as the smallest subset such that every SNP that is excluded from the subset has at least k neighbors in the selected ones. The strength of k-dominating set selection in identifying independent variables, and in culling representative variables that are highly correlated with others, was demonstrated by a simulated dataset. The advantages of k-dominating set variable selection were also illustrated in two applications: pedigree reconstruction using SNP profiles of 1,372 Douglas-fir trees, and species delineation for 226 grasshopper mouse samples. A C++ source code that implements SNP-SELECT and uses Gurobi optimization solver for the k-dominating set variable selection is available (https://github.com/transgenomicsosu/SNP-SELECT).