Utility of pooled sequencing for association mapping in nonmodel organisms

Population-specific thermal responses contribute to regional variability in arbovirus transmission with changing climates

Temperature is increasing globally, and vector-borne diseases are particularly responsive to such increases. While it is known that temperature influences mosquito life history traits, transmission models have not historically considered population-specific effects of temperature. We assessed the interaction between Culex pipiens population and temperature in New York State (NYS) and utilized novel empirical data to inform predictive models of West Nile virus (WNV) transmission. Genetically and regionally distinct populations from NYS were reared at various temperatures, and life history traits were monitored and used to inform trait-based models. Variation in Cx. pipiens life history traits and population-dependent thermal responses account for a predicted 2.9°C difference in peak transmission that is reflected in regional differences in WNV prevalence. We additionally identified genetic signatures that may contribute to distinct thermal responses. Together, these data demonstrate how population variation contributes to significant geographic variability in arbovirus transmission with changing climates.

Rapid vertebrate speciation via isolation, bottlenecks, and drift

Speciation is often driven by selective processes like those associated with viability, mate choice, or local adaptation, and "speciation genes" have been identified in many eukaryotic lineages. In contrast, neutral processes are rarely considered as the primary drivers of speciation, especially over short evolutionary timeframes. Here, we describe a rapid vertebrate speciation event driven primarily by genetic drift. The White Sands pupfish (Cyprinodon tularosa) is endemic to New Mexico's Tularosa Basin where the species is currently managed as two Evolutionarily significant units (ESUs) and is of international conservation concern (Endangered). Whole-genome resequencing data from each ESU showed remarkably high and uniform levels of differentiation across the entire genome (global FST ≈ 0.40). Despite inhabiting ecologically dissimilar springs and streams, our whole-genome analysis revealed no discrete islands of divergence indicative of strong selection, even when we focused on an array of candidate genes. Demographic modeling of the joint allele frequency spectrum indicates the two ESUs split only ~4 to 5 kya and that both ESUs have undergone major bottlenecks within the last 2.5 millennia. Our results indicate the genome-wide disparities between the two ESUs are not driven by divergent selection but by neutral drift due to small population sizes, geographic isolation, and repeated bottlenecks. While rapid speciation is often driven by natural or sexual selection, here we show that isolation and drift have led to speciation within a few thousand generations. We discuss these evolutionary insights in light of the conservation management challenges they pose.

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data

BACKGROUND

Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-coverage whole genome sequencing or pooled sequencing (pool-seq) data.

RESULTS

We developed new methods for estimating microhaplotype allele frequency from low-coverage whole genome sequence and pool-seq data. We validated these methods using datasets from three non-model organisms. These methods allowed estimation of allele frequency and expected heterozygosity at depths routinely achieved from pooled sequencing.

CONCLUSIONS

These new methods will allow microhaplotype panels to be designed using low-coverage WGS and pool-seq data to discover and evaluate candidate loci. The python script implementing the two methods and documentation are available at https://www.github.com/delomast/mhFromLowDepSeq .

Characterization of the male-specific region containing the candidate sex-determining gene in Amur catfish (Silurus asotus) using third-generation- and pool-sequencing data

Amur catfish (Silurus asotus) is an ecologically and economically important fish species in Asia. Here, we assembled the female and male Amur catfish genomes, with genome sizes of 757.15 and 755.44 Mb, respectively, at the chromosome level using nanopore and Hi-C technologies. Consistent with the known diploid chromosome count, both genomes contained 29 chromosome-size scaffolds covering 98.80 and 98.73 % of the complete haplotypic assembly with scaffold N50 of 28.87 and 27.29 Mb, respectively. The female (n = 40) and male (n = 40) pools were re-sequenced. Comparative analysis of sequencing and re-sequencing data from both sexes confirmed the presence of an XX/XY sex determination system in Amur catfish and revealed Chr5 as the sex chromosome containing an approximately 400 kb Y-specific region (MSY). Gene annotation revealed a male-specific duplicate of amhr2, namely amhr2y, in MSY, which is male-specific in different wild populations and expressed only in the testes. Amur catfish shared partially syntenic MSY and amhr2y genes with the southern catfish (S. meridionalis, Chr24), which were located on different chromosomes. High sequence divergence between amhr2y and amhr2 and high sequence similarity with amhr2y were observed in both species. These results indicate the common origin of the sex-determining (SD) gene and transition of amhr2y in the two Silurus species. Accumulation of repetitive elements in the MSY of both species may be the main driver of the transition of amhr2y. Overall, our study provides valuable catfish genomic resources. Moreover, determination of amhr2y as the candidate SD gene in Amur catfish provides another example of amhr2 as the SD gene in fish.

Comparative genomics of rainbow trout (Oncorhynchus mykiss): Is the genetic architecture of migratory behavior conserved among populations?

Rainbow trout (Oncorhynchus mykiss) are a partially migratory species wherein some individuals undergo long-distance anadromous migrations, and others stay as residents in their native freshwater streams. The decision to migrate is known to be highly heritable, and yet, the underlying genes and alleles associated with migration are not fully characterized. Here we used a pooled approach of whole-genome sequence data from migratory and resident trout of two native populations-Sashin Creek, Alaska and Little Sheep Creek, Oregon-to obtain a genome-wide perspective of the genetic architecture of resident and migratory life history. We calculated estimates of genetic differentiation, genetic diversity, and selection between the two phenotypes to locate regions of interest and then compared these associations between populations. We identified numerous genes and alleles associated with life history development in the Sashin Creek population with a notable area on chromosome 8 that may play a critical role in the development of the migratory phenotype. However, very few alleles appeared to be associated with life history development in the Little Sheep Creek system, suggesting population-specific genetic effects are likely important in the development of anadromy. Our results indicate that a migratory life history is not controlled by a singular gene or region but supports the idea that there are many independent ways for a migratory phenotype to emerge in a population. Therefore, conserving and promoting genetic diversity in migratory individuals is paramount to conserving these populations. Ultimately, our data add to a growing body of literature that suggests that population-specific genetic effects, likely mediated through environmental variation, contribute to life history development in rainbow trout.

Genomic architecture of phenotypic extremes in a wild cervid

Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.

Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing

Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole-genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (Salvelinus fontinalis) populations using whole-genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7-41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed nonconvergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%-0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load; (ii) observed differentiation among introduced populations can be idiosyncratic, population-specific, or stochastic; and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.

Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature

Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants-Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae-in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.

A Chromosome-Level Genome Assembly of Mozambique Tilapia (Oreochromis mossambicus) Reveals the Structure of Sex Determining Regions

The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Many species that undergo long breeding migrations, such as anadromous fishes, face highly heterogeneous environments along their migration corridors and at their spawning sites. These environmental challenges encountered at different life stages may act as strong selective pressures and drive local adaptation. However, the relative influence of environmental conditions along the migration corridor compared with the conditions at spawning sites on driving selection is still unknown. In this study, we performed genome-environment associations (GEA) to understand the relationship between landscape and environmental conditions driving selection in seven populations of the anadromous Chinook salmon (Oncorhynchus tshawytscha)-a species of important economic, social, cultural, and ecological value-in the Columbia River basin. We extracted environmental variables for the shared migration corridors and at distinct spawning sites for each population, and used a Pool-seq approach to perform whole genome resequencing. Bayesian and univariate GEA tests with migration-specific and spawning site-specific environmental variables indicated many more candidate SNPs associated with environmental conditions at the migration corridor compared with spawning sites. Specifically, temperature, precipitation, terrain roughness, and elevation variables of the migration corridor were the most significant drivers of environmental selection. Additional analyses of neutral loci revealed two distinct clusters representing populations from different geographic regions of the drainage that also exhibit differences in adult migration timing (summer vs. fall). Tests for genomic regions under selection revealed a strong peak on chromosome 28, corresponding to the GREB1L/ROCK1 region that has been identified previously in salmonids as a region associated with adult migration timing. Our results show that environmental variation experienced throughout migration corridors imposed a greater selective pressure on Chinook salmon than environmental conditions at spawning sites.

Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Background

While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus).

Results

Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases.

Conclusions

The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07899-2.

An evaluation of the potential factors affecting lifetime reproductive success in salmonids

Lifetime reproductive success (LRS), the number of offspring produced over an organism's lifetime, is a fundamental component of Darwinian fitness. For taxa such as salmonids with multiple species of conservation concern, understanding the factors affecting LRS is critical for the development and implementation of successful conservation management practices. Here, we reviewed the published literature to synthesize factors affecting LRS in salmonids including significant effects of hatchery rearing, life history, and phenotypic variation, and behavioral and spawning interactions. Additionally, we found that LRS is affected by competitive behavior on the spawning grounds, genetic compatibility, local adaptation, and hybridization. Our review of existing literature revealed limitations of LRS studies, and we emphasize the following areas that warrant further attention in future research: (1) expanding the range of studies assessing LRS across different life-history strategies, specifically accounting for distinct reproductive and migratory phenotypes; (2) broadening the variety of species represented in salmonid fitness studies; (3) constructing multigenerational pedigrees to track long-term fitness effects; (4) conducting LRS studies that investigate the effects of aquatic stressors, such as anthropogenic effects, pathogens, environmental factors in both freshwater and marine environments, and assessing overall body condition, and (5) utilizing appropriate statistical approaches to determine the factors that explain the greatest variation in fitness and providing information regarding biological significance, power limitations, and potential sources of error in salmonid parentage studies. Overall, this review emphasizes that studies of LRS have profoundly advanced scientific understanding of salmonid fitness, but substantial challenges need to be overcome to assist with long-term recovery of these keystone species in aquatic ecosystems.

Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the "Mame Shiba Inu" breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including F _ST, H _p and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.

Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations

Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species' genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine, through simulation, the sampling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.

Pooled Sequencing Analysis of Geese (Anser cygnoides) Reveals Genomic Variations Associated With Feather Color

During the domestication of the goose a change in its feather color took place, however, the molecular mechanisms responsible for this change are not completely understood. Here, we performed whole-genome resequencing on three pooled samples of geese (feral and domestic geese), with two distinct feather colors, to identify genes that might regulate feather color. We identified around 8 million SNPs within each of the three pools and validated allele frequencies for a subset of these SNPs using PCR and Sanger sequencing. Several genomic regions with signatures of differential selection were found when we compared the gray and white feather color populations using the F_ST and Hp approaches. When we combined previous functional studies with our genomic analyses we identified 26 genes (KITLG, MITF, TYRO3, KIT, AP3B1, SMARCA2, ROR2, CSNK1G3, CCDC112, VAMP7, SLC16A2, LOC106047519, RLIM, KIAA2022, ST8SIA4, LOC106044163, TRPM6, TICAM2, LOC106038556, LOC106038575, LOC106038574, LOC106038594, LOC106038573, LOC106038604, LOC106047489, and LOC106047492) that potentially regulate feather color in geese. These results substantially expand the catalog of potential feather color regulators in geese and provide a basis for further studies on domestication and avian feather coloration.

Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data

Population genomics is a fast-developing discipline with promising applications in a growing number of life sciences fields. Advances in sequencing technologies and bioinformatics tools allow population genomics to exploit genome-wide information to identify the molecular variants underlying traits of interest and the evolutionary forces that modulate these variants through space and time. However, the cost of genomic analyses of multiple populations is still too high to address them through individual genome sequencing. Pooling individuals for sequencing can be a more effective strategy in Single Nucleotide Polymorphism (SNP) detection and allele frequency estimation because of a higher total coverage. However, compared to individual sequencing, SNP calling from pools has the additional difficulty of distinguishing rare variants from sequencing errors, which is often avoided by establishing a minimum threshold allele frequency for the analysis. Finding an optimal balance between minimizing information loss and reducing sequencing costs is essential to ensure the success of population genomics studies. Here, we have benchmarked the performance of SNP callers for Pool-seq data, based on different approaches, under different conditions, and using computer simulations and real data. We found that SNP callers performance varied for allele frequencies up to 0.35. We also found that SNP callers based on Bayesian (SNAPE-pooled) or maximum likelihood (MAPGD) approaches outperform the two heuristic callers tested (VarScan and PoolSNP), in terms of the balance between sensitivity and FDR both in simulated and sequencing data. Our results will help inform the selection of the most appropriate SNP caller not only for large-scale population studies but also in cases where the Pool-seq strategy is the only option, such as in metagenomic or polyploid studies.

Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss)

Background

Identifying ecologically significant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhynchus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fish per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence.

Results

Genomic divergence was high between sympatric insectivores and piscivores (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.188), and in fact higher than between insectivorous populations from Kootenay Lake and the Blackwater River (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST = 0.159) that are > 500 km apart. A window-based \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST analysis did not reveal “islands” of genomic differentiation; however, the window with highest \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{\text{ST}}$$\end{document}FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simulations revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identified several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small effect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs.

Conclusion

Our results reveal a high degree of genomic differentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large effect. Rather, the piscivore phenotype may be controlled by several loci of small effect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01795-9.

Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field

A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.

Heterogeneous genetic basis of age at maturity in salmonid fishes

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10^-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.

Steelhead (Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age-at-maturity traits with two genomic regions

As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139-0.170; females R 2 = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock-specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

Y-chromosome haplotypes are associated with variation in size and age at maturity in male Chinook salmon

Variation in size and age at maturity is an important component of life history that is influenced by both environmental and genetic factors. In salmonids, large size confers a direct reproductive advantage through increased fecundity and egg quality in females, while larger males gain a reproductive advantage by monopolizing access to females. In addition, variation in size and age at maturity in males can be associated with different reproductive strategies; younger smaller males may gain reproductive success by sneaking among mating pairs. In both sexes, there is a trade-off between older age and increased reproductive success and increased risk of mortality by delaying reproduction. We identified four Y-chromosome haplogroups that showed regional- and population-specific variation in frequency using RADseq data for 21 populations of Alaska Chinook salmon. We then characterized the range-wide distribution of these haplogroups using GT-seq assays. These haplogroups exhibited associations with size at maturity in multiple populations, suggesting that lack of recombination between X and Y-chromosomes has allowed Y-chromosome haplogroups to capture different alleles that influence size at maturity. Ultimately, conservation of life history diversity in Chinook salmon may require conservation of Y-chromosome haplotype diversity.

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.

A mobile sex-determining region, male-specific haplotypes and rearing environment influence age at maturity in Chinook salmon

Variation in age at maturity is an important contributor to life history and demographic variation within and among species. The optimal age at maturity can vary by sex, and the ability of each sex to evolve towards its fitness optimum depends on the genetic architecture of maturation. Using GWAS of RAD sequencing data, we show that age at maturity in Chinook salmon exhibits sex-specific genetic architecture, with age at maturity in males influenced by large (up to 20 Mb) male-specific haplotypes. These regions showed no such effect in females. We also provide evidence for translocation of the sex-determining gene between two different chromosomes. This has important implications for sexually antagonistic selection, particularly that sex linkage of adaptive genes may differ within and among populations based on chromosomal location of the sex-determining gene. Our findings will facilitate research into the genetic causes of shifting demography in Chinook salmon as well as a better understanding of sex determination in this species and Pacific salmon in general.

A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus)

Oestrogenic wastewater treatment works (WwTW) effluents discharged into UK rivers have been shown to affect sexual development, including inducing intersex, in wild roach (Rutilus rutilus). This can result in a reduced breeding capability with potential population level impacts. In the absence of a sex probe for roach it has not been possible to confirm whether intersex fish in the wild arise from genetic males or females, or whether sex reversal occurs in the wild, as this condition can be induced experimentally in controlled exposures to WwTW effluents and a steroidal oestrogen. Using restriction site-associated DNA sequencing (RAD-seq), we identified a candidate for a genetic sex marker and validated this marker as a sex probe through PCR analyses of samples from wild roach populations from nonpolluted rivers. We also applied the sex marker to samples from roach exposed experimentally to oestrogen and oestrogenic effluents to confirm suspected phenotypic sex reversal from males to females in some treatments, and also that sex-reversed males are able to breed as females. We then show, unequivocally, that intersex in wild roach populations results from feminisation of males, but find no strong evidence for complete sex reversal in wild roach at river sites contaminated with oestrogens. The discovered marker has utility for studies in roach on chemical effects, wild stock assessments, and reducing the number of fish used where only one sex is required for experimentation. Furthermore, we show that the marker can be applied nondestructively using a fin clip or skin swab, with animal welfare benefits.

Improved genomic resources for the black tiger prawn (Penaeus monodon)

World production of farmed crustaceans was 7.8 million tons in 2016. While only making up approximately 10% of world aquaculture production, crustaceans are generally high-value species and can earn significant export income for producing countries. Viet Nam is a major seafood producing country earning USD 7.3 billion in 2016 in export income with shrimp as a major commodity. However, there is a general lack of genomic resources available for shrimp species, which is challenging to obtain due to the need to deal with large repetitive genomes, which characterize many decapod crustaceans. The first tiger prawn (P. monodon) genome assembly was assembled in 2016 using the standard Illumina PCR-based pair-end reads and a computationally-efficient but relatively suboptimal assembler, SOAPdenovo v2. As a result, the current P. monodon draft genome is highly fragmented (> 2 million scaffolds with N₅₀ length of <1000 bp), exhibiting only moderate genome completeness (< 35% BUSCO complete single-copy genes). We sought to improve upon the recently published P. monodon genome assembly and completeness by generating Illumina PCR-free pair-end sequencing reads to eliminate genomic gaps associated with PCR-bias and performing de novo assembly using the updated MaSurCA de novo assembler. Furthermore, we scaffolded the assembly with low coverage Nanopore long reads and several recently published deep Illumina transcriptome paired-end sequencing data, producing a final genome assembly of 1.6 Gbp (1,211,364 scaffolds; N₅₀ length of 1982 bp) with an Arthropod BUSCO completeness of 96.8%. Compared to the previously published P. monodon genome assembly from China (NCBI Accession Code: NIUS01), this represents an almost 20% increase in the overall BUSCO genome completeness that now consists of more than 90% of Arthropod BUSCO single-copy genes. The revised P. monodon genome assembly (NCBI Accession Code: VIGR01) will be a valuable resource to support ongoing functional genomics and molecular-based breeding studies in Vietnam.

Wild GWAS-association mapping in natural populations

The increasing affordability of sequencing and genotyping technologies has transformed the field of molecular ecology in recent decades. By correlating marker variants with trait variation using association analysis, large-scale genotyping and phenotyping of individuals from wild populations has enabled the identification of genomic regions that contribute to phenotypic differences among individuals. Such "gene mapping" studies are enabling us to better predict evolutionary potential and the ability of populations to adapt to challenges, such as changing environment. These studies are also allowing us to gain insight into the evolutionary processes maintaining variation in natural populations, to better understand genotype-by-environment and epistatic interactions and to track the dynamics of allele frequency change at loci contributing to traits under selection. Gene mapping in the wild using genomewide association scans (GWAS) do, however, come with a number of methodological challenges, not least the population structure in space and time inherent to natural populations. We here provide an overview of these challenges, summarize the exciting methodological advances and applications of association mapping in natural populations reported in this special issue and provide some guidelines for future "wild GWAS" research.

Selection at a genomic region of major effect is responsible for evolution of complex life histories in anadromous steelhead

BACKGROUND

Disparity in the timing of biological events occurs across a variety of systems, yet the understanding of genetic basis underlying diverse phenologies remains limited. Variation in maturation timing occurs in steelhead trout, which has been associated with greb1L, an oestrogen target gene. Previous techniques that identified this gene only accounted for about 0.5-2.0% of the genome and solely investigated coastal populations, leaving uncertainty on the genetic basis of this trait and its prevalence across a larger geographic scale.

RESULTS

We used a three-tiered approach to interrogate the genomic basis of complex phenology in anadromous steelhead. First, fine scale mapping with 5.3 million SNPs from resequencing data covering 68% of the genome confirmed a 309-kb region consisting of four genes on chromosome 28, including greb1L, to be the genomic region of major effect for maturation timing. Second, broad-scale characterization of candidate greb1L genotypes across 59 populations revealed unexpected patterns in maturation phenology for inland fish migrating long distances relative to those in coastal streams. Finally, genotypes from 890 PIT-tag tracked steelhead determined associations with early versus late arrival to spawning grounds that were previously unknown.

CONCLUSIONS

This study clarifies the genetic bases for disparity in phenology observed in steelhead, determining an unanticipated trait association with premature versus mature arrival to spawning grounds and identifying multiple candidate genes potentially contributing to this variation from a single genomic region of major effect. This illustrates how dense genome mapping and detailed phenotypic characterization can clarify genotype to phenotype associations across geographic ranges of species.

Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon

A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.

Complex signatures of genomic variation of two non-model marine species in a homogeneous environment

BACKGROUND

Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist.

RESULTS

Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region.

CONCLUSIONS

Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.