The search for loci under selection: trends, biases and progress

Expression-environment associations in transcriptomic heat stress responses for a global plant lineage

The increasing frequency and severity of heatwaves will intensify stress on plants. Given regional variation in heatwave exposure and expected differences in thermal tolerance between species it is unlikely that all plant species will be affected equally by climate change. However, little is currently known about variation in the responses of plants to heat stress, or how those responses differ among closely related species adapted to different environments. Here we quantify the response of 17 Acacia species (175 RNA-seq libraries), from across Australia's diverse biomes, to a multi-day experimental heatwave treatment to identify variation in transcriptomic and physiological responses to heat stress. Genes with known heat response functions showed consistent responses across Acacia species. Up to 10% of all genes and over 100 gene families showed significant clinal variation in the magnitude of their expression plasticity across species. Specifically, gene families linked to the temperature stress response were overrepresented among significant relationships with home range temperature conditions. Gene expression responses seen on the first day of the heatwave were more frequently associated with home range climates, while expression responses by day four were more commonly related to photosystem II acclimation. Comparative transcriptomics on non-model species has the potential to provide key information on stress response plasticity, especially when linked with our understanding of model species. Our study indicates that the pressing challenge to identifying potentially vulnerable species to climate change could be benefited by the further exploration of clinal variation in transcriptome plasticity.

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.

Integrating very high resolution environmental proxies in genotype-environment association studies

Landscape genomic analyses associating genetic variation with environmental variables are powerful tools for studying molecular signatures of species' local adaptation and for detecting candidate genes under selection. The development of landscape genomics over the past decade has been spurred by improvements in resolutions of genomic and environmental datasets, allegedly increasing the power to identify putative genes underlying local adaptation in non-model organisms. Although these associations have been successfully applied to numerous species across a diverse array of taxa, the spatial scale of environmental predictor variables has been largely overlooked, potentially limiting conclusions to be reached with these methods. To address this knowledge gap, we systematically evaluated performances of genotype-environment association (GEA) models using predictor variables at multiple spatial resolutions. Specifically, we used multivariate redundancy analyses to associate whole-genome sequence data from the plant Arabis alpina L. collected across four neighboring valleys in the western Swiss Alps, with very high-resolution topographic variables derived from digital elevation models of grain sizes between 0.5 m and 16 m. These comparisons highlight the sensitivity of landscape genomic models to spatial resolution, where the optimal grain sizes were specific to variable type, terrain characteristics, and study extent. To assist in selecting variables at appropriate spatial resolutions, we demonstrate a practical approach to produce, select, and integrate multiscale variables into GEA models. After generalizing fine-grained variables to multiple spatial resolutions, a forward selection procedure is applied to retain only the most relevant variables for a particular context. Depending on the spatial resolution, the relevance for topographic variables in GEA studies calls for integrating multiple spatial scales into landscape genomic models. By carefully considering spatial resolutions, candidate genes under selection by a more realistic range of pressures can be detected for downstream analyses, with important applied implications for experimental research and conservation management of natural populations.

Managing invasive hybrids with pond hydroperiod manipulation in an endangered salamander system

When invasive and endangered native taxa hybridize, the resulting admixture introduces novel conservation challenges. Across a large region of central California, a hybrid swarm consisting of admixed endangered California tiger salamanders (CTS) (Ambystoma californiense) and introduced barred tiger salamanders (BTS) (Ambystoma mavortium) has replaced native populations, threatening the genetic integrity of CTS and the vernal pool systems they inhabit. We employed a large-scale, genomically informed field experiment to test whether shortening breeding pond hydroperiod would favor native CTS genotypes. We constructed 14 large, seminatural ponds to evaluate the effect of hydroperiod duration on larval survival and mass at metamorphosis. We tracked changes in non-native allele frequencies with a 5237-gene exon capture array and employed a combination of custom Bayesian and generalized linear models to quantify the effect of pond duration on salamander fitness. Earlier work on this system showed hybrid superiority under many conditions and suggested that hybrids are favored in human-modified ponds with artificially long hydroperiods. Consistent with these earlier studies, we found overwhelming evidence for hybrid superiority. Very short hydroperiods substantially reduced the mass (1.1-1.5 fold) and survival probability (10-13 fold) of both native and hybrid larvae, confirming that hydroperiod likely exerts a strong selective pressure in the wild. We identified 86 genes, representing 1.8% of 4723 screened loci, that significantly responded to this hydroperiod-driven selection. In contrast to earlier work, under our more natural experimental conditions, native CTS survival and size at metamorphosis were always less than hybrids, suggesting that hydroperiod management alone will not shift selection to favor native larval genotypes. However, shortening pond hydroperiod may limit productivity of hybrid ponds, complementing other strategies to remove hybrids while maintaining vernal pool ecosystems. This study confirms and expands on previous work that highlights the importance of hydroperiod management to control invasive aquatic species.

(Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions

Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.

Individual-based landscape genomics for conservation: An analysis pipeline

Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.

Capra hircus outliers markers in Brazil: Searching for genomic regions under the action of natural selection

Identifying genome regions subject to selection in local breeds of Brazil is an opportunity to elucidate the C. hircus genome plasticity, flowing the colonization history of the country. Using SNP Bead Chip Illumina 50K genotyping of Brazilian Anglo-Nubian (standardized breed) and Marota (local endangered population from the semiarid area of Brazil) to show outliers loci in genome regions subject to selection. After applying data quality control, 45,600 SNPs were included in this investigation. Principal component analysis (PCAdapt) and FDIST2 analysis signalized 14 genomic regions more affected by selection in the Brazilian dry zone environment. The genome study signalized regions that are close to the sequences of genes related to growth and embryonic skeletal development (FGF12, AMPD2, OSTN). In addition, flagged regions close to the genes UTSB2 and SLC5A2 contribute to research on functional adaptation with low water needs and poor nutritive diet to survive. Both genes encode proteins that act on osmotic pathways and avoid cell flooding on stress cell responses. Further studies on the genetic role and involvement of these outliers' genomic regions, building a robust conceptual high-resolution map of natural selection drives, help to achieve hardiness candidate genes linked to the evolutionary history of Capra hircus in the semiarid area of Brazil.

The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients

Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.

Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production

Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.

RAD-sequencing improves the genetic characterization of a threatened tree peony (Paeonia ludlowii) endemic to China: Implications for conservation

Compared with traditional genetic markers, genomic approaches have proved valuable to the conservation of endangered species. Paeonia ludlowii having rarely and pure yellow flowers, is one of the world's most famous tree peonies. However, only several wild populations remain in the Yarlung Zangbo Valley (Nyingchi and Shannan regions, Xizang) in China due to increasing anthropogenic impact on the natural habitats. We used genome-wide single nucleotide polymorphisms to elucidate the spatial pattern of genetic variation, population structure and demographic history of P. ludlowii from the fragmented region comprising the entire range of this species, aiming to provide a basis for conserving the genetic resources of this species. Unlike genetic uniformity among populations revealed in previous studies, we found low but varied levels of intra-population genetic diversity, in which lower genetic diversity was detected in the population in Shannan region compared to those in Nyingzhi region. These spatial patterns may be likely associated with different population sizes caused by micro-environment differences in these two regions. Additionally, low genetic differentiation among populations (Fst = 0.0037) were detected at the species level. This line of evidence, combined with the result of significant genetic differentiation between the two closest populations and lack of isolation by distance, suggested that shared ancestry among now remnant populations rather than contemporary genetic connectivity resulted in subtle population structure. Demographic inference suggested that P. ludlowii probably experienced a temporal history of sharp population decline during the period of Last Glacial Maximum, and a subsequent bottleneck event resulting from prehistoric human activities on the Qinghai-Tibet Plateau. All these events, together with current habitat fragment and excavation might contribute to the endangered status of P. ludlowii. Our study improved the genetic characterization of the endangered tree peony (P. ludlowii) in China, and these genetic inferences should be considered when making different in situ and ex situ conservation actions for P. ludlowii in this evolutionary hotspot region.

What Darwin could not see: island formation and historical sea levels shape genetic divergence and island biogeography in a coastal marine species

Oceanic islands play a central role in the study of evolution and island biogeography. The Galapagos Islands are one of the most studied oceanic archipelagos but research has almost exclusively focused on terrestrial organisms compared to marine species. Here we used the Galapagos bullhead shark (Heterodontus quoyi) and single nucleotide polymorphisms (SNPs) to examine evolutionary processes and their consequences for genetic divergence and island biogeography in a shallow-water marine species without larval dispersal. The sequential separation of individual islands from a central island cluster gradually established different ocean depths between islands that pose barriers to dispersal in H. quoyi. Isolation by resistance analysis suggested that ocean bathymetry and historical sea level fluctuations modified genetic connectivity. These processes resulted in at least three genetic clusters that exhibit low genetic diversity and effective population sizes that scale with island size and the level of geographic isolation. Our results exemplify that island formation and climatic cycles shape genetic divergence and biogeography of coastal marine organisms with limited dispersal comparable to terrestrial taxa. Because similar scenarios exist in oceanic islands around the globe our research provides a new perspective on marine evolution and biogeography with implications for the conservation of island biodiversity.

Supervised structural learning of semiparametric regression on high-dimensional correlated covariates with applications to eQTL studies

Expression quantitative trait loci (eQTL) studies utilize regression models to explain the variance of gene expressions with genetic loci or single nucleotide polymorphisms (SNPs). However, regression models for eQTL are challenged by the presence of high dimensional non-sparse and correlated SNPs with small effects, and nonlinear relationships between responses and SNPs. Principal component analyses are commonly conducted for dimension reduction without considering responses. Because of that, this non-supervised learning method often does not work well when the focus is on discovery of the response-covariate relationship. We propose a new supervised structural dimensional reduction method for semiparametric regression models with high dimensional and correlated covariates; we extract low-dimensional latent features from a vast number of correlated SNPs while accounting for their relationships, possibly nonlinear, with gene expressions. Our model identifies important SNPs associated with gene expressions and estimates the association parameters via a likelihood-based algorithm. A GTEx data application on a cancer related gene is presented with 18 novel eQTLs detected by our method. In addition, extensive simulations show that our method outperforms the other competing methods in bias, efficiency, and computational cost.

Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree

Human activity has diminished forests in different terrestrial ecosystems. This is well illustrated in the Brazilian Atlantic Forest, which still hosts high levels of species richness and endemism, even with only 28% of its original extent remaining. The consequences of such forest loss in remaining populations can be investigated with several approaches, including the genomic perspective, which allows a broader understanding of how human disturbance influences the genetic variability in natural populations. In this context, our study investigated the genomic responses of Euterpe edulis Martius, an endangered palm tree, in forest remnants located in landscapes presenting different forest cover amount and composed by distinct bird assemblage that disperse its seeds. We sampled 22 areas of the Brazilian Atlantic Forest in four regions using SNP markers inserted into transcribed regions of the genome of E. edulis, distinguishing neutral loci from those putatively under natural selection (outlier). We demonstrate that populations show patterns of structure and genetic variability that differ between regions, as a possible reflection of deforestation and biogeographic histories. Deforested landscapes still maintain high neutral genetic diversity due to gene flow over short distances. Overall, we not only support previous evidence with microsatellite markers, but also show that deforestation can influence the genetic variability outlier, in the scenario of selective pressures imposed by these stressful environments. Based on our findings, we suggest that, to protect genetic diversity in the long term, it is necessary to reforest and enrich deforested areas, using seeds from populations in the same management target region.

Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish

The responses of marine species to environmental changes and anthropogenic pressures (e.g., fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Using a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. The contemporary genomic structure showed three populations-two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects on fisheries that depend on this resource.

Global patterns of genomic and phenotypic variation in the invasive harlequin ladybird

BACKGROUND

The harlequin ladybird Harmonia axyridis (Coleoptera: Coccinellidae), native to Asia, has been introduced to other major continents where it has caused serious negative impacts on local biodiversity. Though notable advances to understand its invasion success have been made during the past decade, especially with then newer molecular tools, the conclusions reached remain to be confirmed with more advanced genomic analyses and especially using more samples from larger geographical regions across the native range. Furthermore, although H. axyridis is one of the best studied invasive insect species with respect to life history traits (often comparing invasive and native populations), the traits responsible for its colonization success in non-native areas warrant more research.

RESULTS

Our analyses of genome-wide nuclear population structure indicated that an eastern Chinese population could be the source of all non-native populations and revealed several putatively adaptive candidate genomic loci involved in body color variation, visual perception, and hemolymph synthesis. Our estimates of evolutionary history indicate (1) asymmetric migration with varying population sizes across its native and non-native range, (2) a recent admixture between eastern Chinese and American populations in Europe, (3) signatures of a large progressive, historical bottleneck in the common ancestors of both populations and smaller effective sizes of the non-native population, and (4) the southwest origin and subsequent dispersal routes within its native range in China. In addition, we found that while two mitochondrial haplotypes-Hap1 and Hap2 were dominant in the native range, Hap1 was the only dominant haplotype in the non-native range. Our laboratory observations in both China and USA found statistical yet slight differences between Hap1 and Hap2 in some of life history traits.

CONCLUSIONS

Our study on H. axyridis provides new insights into its invasion processes into other major continents from its native Asian range, reconstructs a geographic range evolution across its native region China, and tentatively suggests that its invasiveness may differ between mitochondrial haplotypes.

Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data

Knowledge on the genetic composition of Quercus petraea in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-seq loci to the Quercus robur reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of Q. petraea were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north-southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4-16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined Q. petraea populations.

Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau

KEY MESSAGE

Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.

Population genomics of helminth parasites

Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.

Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.

Molecular advances to study the function, evolution and spectral tuning of arthropod visual opsins

Visual opsins of vertebrates and invertebrates diversified independently and converged to detect ultraviolet to long wavelengths (LW) of green or red light. In both groups, colour vision largely derives from opsin number, expression patterns and changes in amino acids interacting with the chromophore. Functional insights regarding invertebrate opsin evolution have lagged behind those for vertebrates because of the disparity in genomic resources and the lack of robust in vitro systems to characterize spectral sensitivities. Here, we review bioinformatic approaches to identify and model functional variation in opsins as well as recently developed assays to measure spectral phenotypes. In particular, we discuss how transgenic lines, cAMP-spectroscopy and sensitive heterologous expression platforms are starting to decouple genotype–phenotype relationships of LW opsins to complement the classical physiological-behavioural-phylogenetic toolbox of invertebrate visual sensory studies. We illustrate the use of one heterologous method by characterizing novel LW Gq opsins from 10 species, including diurnal and nocturnal Lepidoptera, a terrestrial dragonfly and an aquatic crustacean, expressing them in HEK293T cells, and showing that their maximum absorbance spectra (λ_max) range from 518 to 611 nm. We discuss the advantages of molecular approaches for arthropods with complications such as restricted availability, lateral filters, specialized photochemistry and/or electrophysiological constraints.

This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.

Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard (Ctenotus pantherinus)

Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.

Utility and challenges of using whole‐genome resequencing to detect emerging insect and mite resistance in agroecosystems

Arthropods that invade agricultural ecosystems systematically evolve resistance to the control measures used against them, and this remains a significant and ongoing challenge for sustainable food production systems. Early detection of resistance evolution could prompt remedial action to slow the spread of resistance alleles in the landscape. Historical approaches used to detect emerging resistance included phenotypic monitoring of agricultural pest populations, as well as monitoring of allele frequency changes at one or a few candidate pesticide resistance genes. In this article, I discuss the successes and limitations of these traditional monitoring approaches and then consider whether whole‐genome scanning could be applied to samples collected from agroecosystems over time for resistance monitoring. I examine the qualities of agroecosystems that could impact application of this approach to pesticide resistance monitoring and describe a recent retrospective analysis where genome scanning successfully detected an oligogenic response to selection by pesticides years prior to pest management failure. I conclude by considering areas of further study that will shed light on the feasibility of applying whole‐genome scanning for resistance risk monitoring in agricultural pest species.

Signals of adaptation to agricultural stress in the genomes of two European bumblebees

Human-induced environmental impacts on wildlife are widespread, causing major biodiversity losses. One major threat is agricultural intensification, typically characterised by large areas of monoculture, mechanical tillage, and the use of agrochemicals. Intensification leads to the fragmentation and loss of natural habitats, native vegetation, and nesting and breeding sites. Understanding the adaptability of insects to these changing environmental conditions is critical to predicting their survival. Bumblebees, key pollinators of wild and cultivated plants, are used as model species to assess insect adaptation to anthropogenic stressors. We investigated the effects of agricultural pressures on two common European bumblebees, Bombus pascuorum and B. lapidarius. Restriction-site Associated DNA Sequencing was used to identify loci under selective pressure across agricultural-natural gradients over 97 locations in Europe. 191 unique loci in B. pascuorum and 260 in B. lapidarius were identified as under selective pressure, and associated with agricultural stressors. Further investigation suggested several candidate proteins including several neurodevelopment, muscle, and detoxification proteins, but these have yet to be validated. These results provide insights into agriculture as a stressor for bumblebees, and signal for conservation action in light of ongoing anthropogenic changes.

Contrasting population differentiation in two sympatric Triplophysa loaches on the Qinghai–Tibet Plateau

Genetic differentiation in aquatic organisms is usually shaped by drainage connectivity. Sympatric aquatic species are thus expected to show similar population differentiation patterns and similar genetic responses to their habitats. Water bodies on the Qinghai–Tibet Plateau (QTP) have recently experienced dramatic physicochemical changes, threatening the biodiversity of aquatic organisms on the “roof of the world.” To uncover ecological genetics in Tibetan loaches (Triplophysa)—the largest component of the QTP ichthyofauna—we characterized population differentiation patterns and adaptive mechanisms to salinity change in two sympatric and phylogenetically closely related Tibetan loaches, T. stewarti and T. stenura, by integrating population genomic, transcriptomic, and electron probe microanalysis approaches. Based on millions of genome-wide SNPs, the two Tibetan loach species show contrasting population differentiation patterns, with highly geographically structured and clear genetic differentiation among T. stewarti populations, whereas there is no such observation in T. stenura, which is also supported by otolith microchemistry mapping. While limited genetic signals of parallel adaption to salinity changes between the two species are found from either genetic or gene expression variation perspective, a catalog of genes involved in ion transport, energy metabolism, structural reorganization, immune response, detoxification, and signal transduction is identified to be related to adaptation to salinity change in Triplophysa loaches. Together, our findings broaden our understanding of the population characteristics and adaptive mechanisms in sympatric Tibetan loach species and would contribute to biodiversity conservation and management of aquatic organisms on the QTP.

ddRAD‐Seq reveals evolutionary insights into population differentiation and the cryptic phylogeography of Hyporhamphus intermedius in Mainland China

Species differentiation and local adaptation in heterogeneous environments have attracted much attention, although little is known about the mechanisms involved. Hyporhamphus intermedius is an anadromous, brackish‐water halfbeak that is widely distributed in coastal areas and hyperdiverse freshwater systems in China, making it an interesting model for research on phylogeography and local adaptation. Here, 156 individuals were sampled at eight sites from heterogeneous aquatic habitats to examine environmental and genetic contributions to phenotypic divergence. Using double‐digest restriction‐site‐associated DNA sequencing (ddRAD‐Seq) in the specimens from the different watersheds, 5498 single nucleotide polymorphisms (SNPs) were found among populations, with obvious population differentiation. We find that present‐day Mainland China populations are structured into distinct genetic clusters stretching from southern and northern ancestries, mirroring geography. Following a transplant event in Plateau Lakes, there were virtually no variations of genetic diversity occurred in two populations, despite the fact two main splits were unveiled in the demographic history. Additionally, dorsal, and anal fin traits varied widely between the southern group and the others, which highlighted previously unrecognized lineages. We then explore genotype–phenotype‐environment associations and predict candidate loci. Subgroup ranges appeared to correspond to geographic regions with heterogeneous hydrological factors, indicating that these features are likely important drivers of diversification. Accordingly, we conclude that genetic and phenotypic polymorphism and a moderate amount of genetic differentiation occurred, which might be ascribed to population subdivision, and the impact of abiotic factors.

EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries

A fishery’s structure and connectivity are priors to its effective management. A successful description of such processes depends on both the sampling design and the choice of adequate genetic markers. EST markers are perfusing the studies of marine metapopulations and are believed to provide access to functional polymorphisms. However, the assumed adaptive role of outlier EST loci might not be generalizable. EST-microsatellites represent the upper polymorphic boundary in these regions because of their high mutation rate. We have subclassified the polymorphisms of EST-microsatellites to assess their structural contribution in the European hake, a paradigmatic and highly mobile marine species (HMMS). Because of the counterbalanced forces between directional markers (15%) and balanced markers (23%), the whole marker set offers the same structural situation as the one observed with neutral markers (62%), i.e., k = 2 gene pools. In contrast to outlier EST- microsatellites, neutral EST subsets allow one to measure crucial population phenomena for fisheries’ management. The high inter-population divergence of outlier EST-microsatellites is compatible with drifted post-selection genomic regions rather than with ongoing local selective pressures. The structural scenario in hake is explainable by a limited gene flow across the Almería-Oran Front (AOF) and by the within-basin IBD pattern of connectivity plus drift-related demographic events. This study highlights how polymorphic properties of EST-microsatellite types can be useful to address mutually excluding research tasks in fisheries, i.e., to address its evolutionary history (directional markers or FAPS: Fossil Adaptive Polymorphic Systems); to delineate management units (neutral markers or NAPS: Non Adaptive Polymorphic Systems); or to ensure sustainability (balanced markers or APS: Adaptive Polymorphic Systems).

Patterns of selection across gene regulatory networks

Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced consideration of the evolution of functional relationships between genes, especially in the context of their broader network interactions. Characterizing and comparing GRNs across traits and species in a more detailed way will allow us to determine how network position influences what genes drive adaptive evolution. In this perspective paper, we consider the architecture of developmental GRNs and how positive selection strength may vary across a GRN. We then propose several testable models for these patterns of selection and experimental approaches to test these models.

Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (N_e). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Finding the adaptive needles in a population-structured haystack: a case study in a New Zealand mollusc

Genetic adaptation to future environmental conditions is crucial to help species persist as the climate changes. Genome scans are powerful tools to understand adaptive landscapes, enabling us to correlate genetic diversity with environmental gradients while disentangling neutral from adaptive variation. However, low gene flow can lead to both local adaptation and highly structured populations, and is a major confounding factor for genome scans, resulting in an inflated number of candidate loci.

Here, we compared candidate locus detection in a marine mollusc (Onithochiton neglectus), taking advantage of a natural geographical contrast in the levels of genetic structure between its populations. O. neglectus is endemic to New Zealand and distributed throughout an environmental gradient from the subtropical north to the subantarctic south. Due to a brooding developmental mode, populations tend to be locally isolated. However, adult hitchhiking on rafting kelp increases connectivity among southern populations.

We applied two genome scans for outliers (Bayescan and PCAdapt) and two genotype–environment association (GEA) tests (BayeScEnv and RDA). To limit issues with false positives, we combined results using the geometric mean of q‐values and performed association tests with random environmental variables. This novel approach is a compromise between stringent and relaxed approaches widely used before, and allowed us to classify candidate loci as low confidence or high confidence.

Genome scans for outliers detected a large number of significant outliers in strong and moderately structured populations. No high‐confidence GEA loci were detected in the context of strong population structure. However, 86 high‐confidence loci were associated predominantly with latitudinally varying abiotic factors in the less structured southern populations. This suggests that the degree of connectivity driven by kelp rafting over the southern scale may be insufficient to counteract local adaptation in this species.

Our study supports the expectation that genome scans may be prone to errors in highly structured populations. Nonetheless, it also empirically demonstrates that careful statistical controls enable the identification of candidate loci that invite more detailed investigations. Ultimately, genome scans are valuable tools to help guide further research aiming to determine the potential of non‐model species to adapt to future environments.

Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km² island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.

Detecting steps in spatial genetic data: Which diversity measures are best?

Accurately detecting sudden changes, or steps, in genetic diversity across landscapes is important for locating barriers to gene flow, identifying selectively important loci, and defining management units. However, there are many metrics that researchers could use to detect steps and little information on which might be the most robust. Our study aimed to determine the best measure/s for genetic step detection along linear gradients using biallelic single nucleotide polymorphism (SNP) data. We tested the ability to differentiate between linear and step-like gradients in genetic diversity, using a range of diversity measures derived from the q-profile, including allelic richness, Shannon Information, G_ST, and Jost-D, as well as Bray-Curtis dissimilarity. To determine the properties of each measure, we repeated simulations of different intensities of step and allele proportion ranges, with varying genome sample size, number of loci, and number of localities. We found that alpha diversity (within-locality) based measures were ineffective at detecting steps. Further, allelic richness-based beta (between-locality) measures (e.g., Jaccard and Sørensen dissimilarity) were not reliable for detecting steps, but instead detected departures from fixation. The beta diversity measures best able to detect steps were: Shannon Information based measures, G_ST based measures, a Jost-D related measure, and Bray-Curtis dissimilarity. No one measure was best overall, with a trade-off between those measures with high step detection sensitivity (G_ST and Bray-Curtis) and those that minimised false positives (a variant of Shannon Information). Therefore, when detecting steps, we recommend understanding the differences between measures and using a combination of approaches.

Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice

The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between the island and mainland populations and moderate to high marker-based heritability estimates for overall variation in traits previously found to differ in line with the ISH between mainland and island locations. F_ST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between the island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

Simple Summary

Over the last century, genetic diversity in the cattle species has been affected by the replacement of many local, dual-purpose breeds with a few specialized, high-output dairy breeds. This replacement caused a sharp decline in the population size of local breeds. In the Netherlands, the local Dutch Friesian breed has gradually been replaced by the Holstein Friesian. This resulted in a rapid decrease in numbers of the Dutch Friesian breed with an associated risk of loss of genetic diversity due to drift. The objective of this study is to investigate genomewide genetic diversity between a group of historic and recent Dutch Friesian bulls and a group of recently used Holstein Friesian bulls. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has some unique genetic identity (12% of the single nucleotide polymorphism were group-specific). The genetic diversity of the Dutch Friesians reduced over time, but this did not lead to higher inbreeding levels—especially, inbreeding due to recent ancestors has not increased. Genetically, the recent Dutch Friesians were slightly more different from Holstein Friesians than the historic Dutch Friesians. Our results also highlighted the presence of several genomic regions that differentiated between the groups.

Abstract

Over the last century, genetic diversity in many cattle breeds has been affected by the replacement of traditional local breeds with just a few milk-producing breeds. In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF). The objective of this study is to investigate genomewide genetic diversity between a group of historically and recently used DF bulls and a group of recently used HF bulls. Genetic material of 12 historic (hDF), 12 recent DF bulls (rDF), and 12 recent HF bulls (rHF) in the Netherlands was sequenced. Based on the genomic information, different parameters—e.g., allele frequencies, inbreeding coefficient, and runs of homozygosity (ROH)—were calculated. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has a unique genetic identity (12% of the single nucleotide polymorphisms were group-specific). The rDF is slightly more diverged from rHF than hDF. The inbreeding coefficient based on runs of homozygosity (Froh) was higher for rDF (0.24) than for hDF (0.17) or rHF (0.13). Our results also displayed the presence of several genomic regions that differentiated between the groups. In addition, thirteen, forty-five, and six ROH islands were identified in hDF, rDF, and rHF, respectively. The genetic diversity of the DF breed reduced over time, but this did not lead to higher inbreeding levels—especially, inbreeding due to recent ancestors was not increased.

Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world's major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc's wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop's domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc's evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.

Signatures of natural selection in a foundation tree along Mediterranean climatic gradients

Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean‐type climates (MTC). Forest management that enhance forests’ resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex. For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South‐west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype‐association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (F_ST = 0.04), environmental association analyses found a total of 2336 unique SNPs associated with temperature and precipitation variables, with 1440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

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.

Genome-wide analysis reveals the genetic stock structure of hoki (Macruronus novaezelandiae)

The assessment of the genetic structuring of biodiversity is crucial for management and conservation. This is particularly critical for widely distributed and highly mobile deep-water teleosts, such as hoki (Macruronus novaezelandiae). This species is significant to Māori people and supports the largest commercial fishery in New Zealand, but uncertainty about its stock structure presents a challenge for management. Here, we apply a comprehensive genomic analysis to shed light on the demographic structure of this species by (1) assembling the genome, (2) generating a catalogue of genome-wide SNPs to infer the stock structure and (3) identifying regions of the genome under selection. The final genome assembly used short and long reads and is near complete, representing 93.8% of BUSCO genes, and consisting of 566 contigs totalling 501 Mb. Whole-genome re-sequencing of 510 hoki sampled from 14 locations around New Zealand and Australia, at a read depth greater than 10×, produced 227,490 filtered SNPs. Analyses of these SNPs were able to resolve the stock structure of hoki into two genetically and geographically distinct clusters, one including the Australian and the other one all New Zealand locations, indicating genetic exchange between these regions is limited. Location differences within New Zealand samples were much more subtle (global F ST  = 0.0006), and while small and significant differences could be detected, they did not conclusively identify additional substructures. Ten putative adaptive SNPs were detected within the New Zealand samples, but these also did not geographically partition the dataset further. Contemporary and historical N e estimation suggest the current New Zealand population of hoki is large yet declining. Overall, our study provides the first genomic resources for hoki and provides detailed insights into the fine-scale population genetic structure to inform the management of this species.

Museum Genomics

Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.

Waste not, want not: Microsatellites remain an economical and informative technology for conservation genetics

Comparisons of microsatellites and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, questioning the continued utility of microsatellites in population and landscape genetics. Yet, highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated previous analyses that used microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source sites to the remaining sink sites. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.

Genetic structure of immunologically associated candidate genes suggests arctic rabies variants exert differential selection in arctic fox populations

Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. F_ST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.

Genomic Signatures of Domestication Selection in the Australasian Snapper (Chrysophrys auratus)

Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.

Adaptive divergence in bill morphology and other thermoregulatory traits is facilitated by restricted gene flow in song sparrows on the California Channel Islands

Disentangling the effects of neutral and adaptive processes in maintaining phenotypic variation across environmental gradients is challenging in natural populations. Song sparrows (Melospiza melodia) on the California Channel Islands occupy a pronounced east-west climate gradient within a small spatial scale, providing a unique opportunity to examine the interaction of genetic isolation (reduced gene flow) and the environment (selection) in driving variation. We used reduced representation genomic libraries to infer the role of neutral processes (drift and restricted gene flow) and divergent selection in driving variation in thermoregulatory traits with an emphasis on the mechanisms that maintain bill divergence among islands. Analyses of 22,029 neutral SNPs confirm distinct population structure by island with restricted gene flow and relatively large effective population sizes, suggesting bill differences are probably not a product of genetic drift. Instead, we found strong support for local adaptation using 3294 SNPs in differentiation-based and environmental association analyses coupled with genome-wide association tests. Specifically, we identified several putatively adaptive and candidate loci in or near genes involved in bill development pathways (e.g., BMP, CaM, Wnt), confirming the highly complex and polygenic architecture underlying bill morphology. Furthermore, we found divergence in genes associated with other thermoregulatory traits (i.e., feather structure, plumage colour, and physiology). Collectively, these results suggest strong divergent selection across an island archipelago results in genomic changes in a suite of traits associated with climate adaptation over small spatial scales. Future research should move beyond studying univariate traits to better understand multidimensional responses to complex environmental conditions.

Assessing signals of selection and historical demography to develop conservation strategies in the Chilean emblematic Araucaria araucana

Loss of genetic diversity reduces the ability of species to evolve and respond to environmental change. Araucaria araucana is an emblematic conifer species from southern South America, with important ethnic value for the Mapuche people (Pehuenche); the Chilean Government has catalogued its conservation status as vulnerable. Climatic fluctuations were potentially a major impact in the genetic variation within many tree species. In this context, the restricted geographic distribution of A. araucana in Chile appears to be a consequence of the Last Glacial Maximum (LGM). During the past two centuries, strong human intervention has also affected the geographical distribution and population sizes of A. araucana. Reduction of population size may cause loss of genetic diversity, which could affect frequency of adaptive loci. The aims of this study were to know the existence of potential loci under selection and populations with genetic, demographic disequilibrium in the Chilean distribution of A. araucana. Based on 268 polymorphic AFLP loci, we have investigated potential loci under selection and genetic, demographic disequilibrium within seven Chilean populations of Araucaria araucana. Correlation of 41 outlier loci with the environmental variables of precipitation and temperature reveals signatures of selection, whereas 227 neutral loci provide estimates of demographic equilibrium and genetic population structure. Three populations are recommended as priorities for conservation.

Divergent patterns of selection on metabolite levels and gene expression

Background

Natural selection can act on multiple genes in the same pathway, leading to polygenic adaptation. For example, adaptive changes were found to down-regulate six genes involved in ergosterol biosynthesis—an essential pathway targeted by many antifungal drugs—in some strains of the yeast Saccharomyces cerevisiae. However, the impact of this polygenic adaptation on metabolite levels was unknown. Here, we performed targeted mass spectrometry to measure the levels of eight metabolites in this pathway in 74 yeast strains from a genetic cross.

Results

Through quantitative trait locus (QTL) mapping we identified 19 loci affecting ergosterol pathway metabolite levels, many of which overlap loci that also impact gene expression within the pathway. We then used the recently developed v-test, which identified selection acting upon three metabolite levels within the pathway, none of which were predictable from the gene expression adaptation.

Conclusions

These data showed that effects of selection on metabolite levels were complex and not predictable from gene expression data. This suggests that a deeper understanding of metabolism is necessary before we can understand the impacts of even relatively straightforward gene expression adaptations on metabolic pathways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01915-5.