Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus annuus L.) is typically found in ruderal environments, but crop-wild hybridization may facilitate the evolution of weedy populations. Using 1 crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of a recently discovered weedy population of sunflower (named BRW). Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild populations 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines and low differentiation with one wild population, suggesting that wild hybridization increased their genetic diversity. We found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Our results highlight the importance of seed dormancy during the earliest stages of adaptation and show that crop-wild hybrids can evolve quickly in agricultural environments.

Sex determination mechanisms vary widely across animals, but show remarkable degrees of recurrent evolution. Recurrent features of sex determination have largely been attributed to recurrent cooption of shared ancestral regulatory circuits. However, a new study on sex determination in Daphnia magna reveals both recurrent evolution of specific regulatory logic and apparently recurrent recruitment of a regulator, suggesting a role for optimization in recurrent patterns of sex determination mechanisms.

Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on 2 theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.

Salvia miltiorrhiza Bunge is an outcross-pollinated plant with diverse flower colors, ranging from white to purple. To clarify the genetic basis of S. miltiorrhiza flower color, we crossed white-flowered S. miltiorrhiza f. alba with dark violet-flowered S. miltiorrhiza, and selfed F1 to obtain an F2 population. The RGB color system was used to describe the flower color of the parents, F1 progeny, and F2 individuals. Afterward, we used genotyping-by-sequencing technology to construct a high-density linkage map of S. miltiorrhiza based on the F2 population. Finally, the linkage map was used to locate the QTLs of the genes that control flower color in S. miltiorrhiza. Through measurement and cluster analysis of the R, G, and B values of flowers from the parents, F1, and F2 individuals, it was found that the purple flower color of S. miltiorrhiza is a quantitative trait controlled by 2 loci of major genes. The genetic map contained 605 SNPs with a total length of 738.3 cM in 8 linkage groups (LGs), and the average distance between 2 markers was 1.22 cM. Based on the constructed genetic map and the flower R, G, B, and R+G+B values, 2 QTLs were detected for flower color, located on LG4 and LG5. The results of this study lay the foundation for cloning genes that control flower color and studying the molecular mechanism of flower color regulation in S. miltiorrhiza.

Formica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here, we performed a standard DNA extraction from a single, field-collected Formica aquilonia × Formica polyctena haploid male and assembled its genome using ~60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenopteran BUSCOs and was pseudo-scaffolded using the assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one-third of the genome consists of repeats, and 17 426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.

Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.

Synthesized chemical defenses have broadly evolved across countless taxa and are important in shaping evolutionary and ecological interactions within ecosystems. However, the underlying genomic mechanisms by which these organisms synthesize and utilize their toxins are relatively unknown. Herein, we use comparative transcriptomics to uncover potential toxin synthesizing genes and pathways, as well as interspecific patterns of toxin synthesizing genes across 10 species of North American true toads (Bufonidae). Upon assembly and annotation of the 10 transcriptomes, we explored patterns of relative gene expression and possible protein-protein interactions across the species to determine what genes and/or pathways may be responsible for toxin synthesis. We also tested our transcriptome dataset for signatures of positive selection to reveal how selection may be acting upon potential toxin producing genes. We assembled high-quality transcriptomes of the bufonid parotoid gland, a tissue not often investigated in other bufonid-related RNAseq studies. We found several genes involved in metabolic and biosynthetic pathways (e.g., steroid biosynthesis, terpenoid backbone biosynthesis, isoquinoline biosynthesis, and glucosinolate biosynthesis) that were functionally enriched and/or relatively expressed across the 10 focal species that may be involved in the synthesis of alkaloid and steroid toxins, as well as other small metabolic compounds that cause distastefulness in bufonids. We hope that our study lays a foundation for future studies to explore the genomic underpinnings and specific pathways of toxin synthesis in toads, as well as at the macroevolutionary scale across numerous taxa that produce their own defensive toxins.

American Standardbreds were developed as a harness racing horse breed. The United States Trotting Association closed the studbook in 1973 and implemented a book size cap in 2009. This study aimed to investigate genetic diversity in the American Standardbred after the studbook cap was introduced using short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). Sixteen STRs from horses foaled from 2010 to 2015 and their sires and dams (n = 50 621) were utilized to examine allelic richness (Ar), expected heterozygosity (HE), observed heterozygosity (HO), unbiased heterozygosity (HU), inbreeding coefficient (FIS), and fixation index (FST). These analyses found that trotting and pacing sires were less genetically diverse than dams (HEPBonferroni = 0.029 and 6.3 × 10-5, respectively) and their offspring (ArPBonferroni = 0.034 and 6.9 × 10-6, respectively), and pacing offspring were significantly less diverse than their dams (HEPBonferroni = 2 × 10-3). Inbreeding coefficients for trotters (FIS = -0.014) and pacers (FIS = -0.012) suggest that breeding practices have maintained diversity. Moderate levels of genetic differentiation (0.066 < FST < 0.11) were found between pacing and trotting groups. Additionally, 10 of the most prolific trotting sires and their male offspring (n = 84) were genotyped on the 670K Axiom Equine HD Array. HO values higher than HE (P < 0.001), low inbreeding coefficients (mean F = -0.064), and mean FROH = 21% indicate relatively high levels of diversity in this cohort, further supporting the STR data. However, in contrast, HO values were higher for trotting sires (0.41) than their offspring (0.36). This observation warrants further monitoring of diversity over time. These data provide an updated foundation of diversity indices for further, long-term analysis in the breed.

In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.

Controlling extra fat deposition is economically favorable in modern swine industry. Understanding the genetic architecture of fat deposition traits such as body mass index (BMI) can help in improving genomic selection for such traits. We utilized a weighted single-step genome-wide association study (WssGWAS) to detect genetic regions and candidate genes associated with BMI in a Yorkshire pig population. Three extended haplotype homozygosity (EHH)-related statistics were also incorporated within a de-correlated composite of multiple signals (DCMS) framework to detect recent selection signatures signals. Overall, the full pedigree consisted of 7016 pigs, of which 5561 had BMI records and 598 pigs were genotyped with an 80 K single nucleotide polymorphism (SNP) array. Results showed that the most significant windows (top 15) explained 9.35% of BMI genetic variance. Several genes were detected in regions previously associated with pig fat deposition traits and treated as potential candidate genes for BMI in Yorkshire pigs: FTMT, SRFBP1, KHDRBS3, FOXG1, SOD3, LRRC32, TSKU, ACER3, B3GNT6, CCDC201, ADCY1, RAMP3, TBRG4, CCM2. Signature of selection analysis revealed multiple candidate genes previously associated with various economic traits. However, BMI genetic variance explained by regions under selection pressure was minimal (1.31%). In conclusion, candidate genes associated with Yorkshire pigs' BMI trait were identified using WssGWAS. Gene enrichment analysis indicated that the identified candidate genes were enriched in the insulin secretion pathway. We anticipate that these results further advance our understanding of the genetic architecture of BMI in Yorkshire pigs and provide information for genomic selection for fat deposition in this breed.

The California horn shark (Heterodontus francisci) is a small demersal species distributed from southern California and the Channel Islands to Baja California and the Gulf of California. These nocturnal reef predators maintain small home-ranges as adults and lay auger-shaped egg cases that become wedged into the substrate. While population trends are not well documented, this species is subject to fishing pressure through portions of its range and has been identified as vulnerable to overexploitation. Here, we present a survey of 318 specimens from across the range, using mtDNA control region sequences to provide the first genetic assessment of H. francisci. Overall population structure (ΦST = 0.266, P < 0.001) is consistent with limited dispersal as indicated by life history, with two distinct features. Population structure along the continuous coastline is low, with no discernable breaks from Santa Barbara, CA to Bahia Tortugas (Baja California Sur, Mexico); however, there is a notable partition at Punta Eugenia (BCS), a well-known biogeographic break between tropical and subtropical marine faunas. In contrast, population structure is much higher (max ΦST = 0.601, P < 0.05) between the coast and adjacent Channel Islands, a minimum distance of 19 km, indicating that horn sharks rarely disperse across deep habitat and open water. Population structure in most elasmobranchs is measured on a scale of hundreds to thousands of kilometers, but the California Horn Shark has population partitions on an unprecedented small scale, indicating a need for localized management strategies which ensure adequate protection of distinct stocks.

Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a comparative population genomic analysis of 13 species of Diospyros (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to determine priority localities for in situ and ex situ conservation efforts to maximize the genetic diversity of each Mascarene Diospyros species.

Few doubt that effective population size (Ne) is one of the most important parameters in evolutionary biology, but how many can say they really understand the concept? Ne is the evolutionary analog of the number of individuals (or adults) in the population, N. Whereas ecological consequences of population size depend on N, evolutionary consequences (rates of loss of genetic diversity and increase in inbreeding; relative effectiveness of selection) depend on Ne. Formal definitions typically relate effective size to a key population genetic parameter, such as loss of heterozygosity or variance in allele frequency. However, for practical application to real populations, it is more useful to define Ne in terms of 3 demographic parameters: number of potential parents (adult N), and mean and variance in offspring number. Defined this way, Ne determines the rate of random genetic drift across the entire genome in the offspring generation. Other evolutionary forces (mutation, migration, selection)-together with factors such as variation in recombination rate-can also affect genetic variation, and this leads to heterogeneity across the genome in observed rates of genetic change. For some, it has been convenient to interpret this heterogeneity in terms of heterogeneity in Ne, but unfortunately, this has muddled the concepts of genetic drift and effective population size. A commonly repeated misconception is that Ne is the number of parents that actually contribute genes to the next generation (NP). In reality, NP can be smaller or larger than Ne, and the NP/Ne ratio depends on the sex ratio, the mean and variance in offspring number, and whether inbreeding or variance Ne is of interest.

According to Haldane's Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane's Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e., mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e., autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked, and mitochondrial loci. Although most studies reported introgression rates in line with Haldane's Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane's Rule.

R/glmnet has been successfully applied to jointly mapped multiple quantitative trait loci for linkage analysis, along with statistical inference for quantitative trait loci candidates with nonzero genetic effects using R/lm for normally distributed traits, R/glm for discrete traits, and R/coxph for survival times. In this study, we extended R/glmnet to a genome-wide association study by means of parallel computation. A multi-locus genome-wide association study for high-throughput single-nucleotide polymorphisms was implemented in the "Multi-Runking" software written within the R workspace. This software can better detect common and large quantitative trait nucleotides and more accurately estimate than genome-wide mixed model analysis for one single-nucleotide polymorphism at a time and linear mixed models-least absolute shrinkage and selection operator. Its applicability and utility were demonstrated by multi-locus genome-wide association studies for the simulated and real traits distributed normally, binary traits, and survival times.

Cervids are distinguished by the shedding and regrowth of antlers. Furthermore, they provide insights into prion and other diseases. Genomic resources can facilitate studies of the genetic underpinnings of deer phenotypes, behavior, and disease resistance. Widely distributed in North America, the white-tailed deer (Odocoileus virginianus) has recreational, commercial, and food source value for many households. We present a genome generated using DNA from a single Illinois white-tailed sequenced on the PacBio Sequel II platform and assembled using Wtdbg2. Omni-C chromatin conformation capture sequencing was used to scaffold the genome contigs. The final assembly was 2.42 Gb, consisting of 508 scaffolds with a contig N50 of 21.7 Mb, a scaffold N50 of 52.4 Mb, and a BUSCO complete score of 93.1%. Thirty-six chromosome pseudomolecules comprised 93% of the entire sequenced genome length. A total of 20 651 predicted genes using the BRAKER pipeline were validated using InterProScan. Chromosome length assembly sequences were aligned to the genomes of related species to reveal corresponding chromosomes.

Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here, we report the complete mt genomes of 3 trematomin notothenioids: the bald notothen (Trematomus (Pagothenia) borchgrevinki), the spotted notothen (T. nicolai), and the emerald notothen (T. bernacchii). The 3 mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (Pleuragramma antarctica), we found a large gene inversion in the 3 trematomin mt genomes that included tRNAIle, ND1, tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe, and the control region. The trematomin mt genomes contained 3 intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although short-read next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.

Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.

The hog deer (Axis porcinus) is an endangered cervid with drastic population declines. There are 2 recognized subspecies of hog deer: A. p. porcinus, ranging from Punjab Province in Pakistan, Nepal, and the Northern part of India to Myanmar, and A. p. annamiticus found in Indo-China, Thailand, Laos, Cambodia, and Vietnam. The current geographic range of A. p. annamiticus is still ambiguous. We analyzed variation in the mitochondrial DNA control region (mtDNA CR) to investigate the intra-species structure, differentiation, and demographic history of hog deer from Cambodia (Kratie Province), which we compared with the populations from India and Thailand. We also generated divergence time estimates using a concatenated dataset of complete Cyt b and partial CR. The CR data showed that Cambodian hog deer are genetically differentiated from the mainland Indian and Thai populations, forming a distinct basal clade. The time of divergence indicates that the Cambodian lineage split from the other 2 hog deer lineages around 0.51 Mya, during the Late Pleistocene. The results also suggest strong phylogeographic structure among hog deer: lineage A extends from Terai Arc (foothills of the Himalayas) to Assam, India (A. p. porcinus), lineage B from Manipur, India to Thailand (A. p. annamiticus), and lineage C is only known from Kratie Province, Cambodia. Lineage A exhibited a higher level of genetic diversity than lineages B and C, with recent demographic stability. Thus, the hog deer population in Kratie Province appears to be a distinct lineage that should be treated as an evolutionarily significant unit.

Premelanosome protein (pmel) is a key gene for melanogenesis. Mutations in this gene are responsible for white plumage in chicken, but its role in pigmentation of fish remains to be demonstrated. In this study, we found that most fishes have 2 pmel genes arising from the teleost-specific whole-genome duplication. Both pmela and pmelb were expressed at high levels in the eyes and skin of Nile tilapia. We mutated both genes in tilapia using CRISPR/Cas9. Homozygous mutation of pmela resulted in yellowish body color with weak vertical bars and a hypopigmented retinal pigment epithelium (RPE) due to significantly reduced number and size of melanophores. In contrast, we observed an increased number and size of xanthophores in mutants compared to wild-type fish. Homozygous mutation of pmelb resulted in a similar, but milder phenotype than pmela-/- mutants. Double mutation of pmela and pmelb resulted in loss of additional melanophores compared to the pmela-/- mutants, and also an increase in the number and size of xanthophores, producing a golden body color. The RPE pigmentation of pmela-/-;pmelb-/- was similar to pmela-/- mutants, with much less pigmentation than pmelb-/- mutants and wild-type fish. Taken together, our results indicate that, although both pmel genes are important for the formation of body color in tilapia, pmela plays a more important role than pmelb. To our knowledge, this is the first report on mutation of pmelb or both pmela;pmelb in fish. Studies on these mutants suggest new strategies for breeding golden tilapia, and also provide a new model for studies of pmel function in vertebrates.

Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the United States was evaluated in four ways: 1) using genetic relationships from pedigree data [(n = 64 310 animals recorded in the US National Sheep Improvement Program (NSIP)]; 2) using molecular data (n = 304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n = 109) and Irish (n = 55) Suffolk sheep to those in the United States using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n = 18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the US population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in US Suffolk sheep engaged in NSIP was proposed.

Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modeling to investigate how climatic and habitat variables relate to patterns of genetic variation in 2 stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO > 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis, but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.

Dareshouri, Arabian, and Akhal-Teke are 3 Middle Eastern horse breeds that have been selected for endurance and adaptation to harsh climates. Deciphering the genetic characteristics of these horses by tracing selection footprints and copy number of variations will be helpful in improving our understanding of equine breeds' development and adaptation. For this purpose, we sequenced the whole genome of 4 Dareshouri horses using Illumina Hiseq panels and compared them with publicly available whole-genome sequences of Arabian (n = 3) and Akhal-Teke (n = 3) horses. Three tests of FLK, hapFLK, and pooled heterozygosity were applied using a sliding window (window size = 100 kb, step size = 50 kb) approach to detect putative selection signals. Copy number variation analysis was applied to investigate copy number of variants (CNVs), and the results were used to suggest selection signatures involving CNVs. Whole-genome sequencing demonstrated 8 837 950 single-nucleotide polymorphisms (SNPs) in autosomal chromosomes. We suggested 58 genes and 3 quantitative trait loci, including some related to horse gait, insect bite hypersensitivity, and withers height, based on selective signals detected by adjusted P-value of Mahalanobis distance based on the rank-based P-values (Md-rank-P) method. We proposed 12 genomic regions under selection pressure involving CNVs that were previously reported to be associated with metabolism energy (SLC5A8), champagne dilution in horses (SLC36A1), and synthesis of polyunsaturated fatty acids (FAT2). Only 10 Middle Eastern horses were tested in this study; therefore, the conclusions are speculative. Our findings are useful to better understanding the evolution and adaptation of Middle Eastern horse breeds.