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The use of regression analysis has been instrumental in allowing evolutionary biologists to estimate the strength and mode of natural selection. Although directional and correlational selection gradients are equal to their corresponding regression coefficients, quadratic regression coefficients must be doubled to estimate stabilizing/disruptive selection gradients. Based on a sample of 33 papers published in Evolution between 2002 and 2007, at least 78% of papers have not doubled quadratic regression coefficients, leading to an appreciable underestimate of the strength of stabilizing and disruptive selection. Proper treatment of quadratic regression coefficients is necessary for estimation of fitness surfaces and contour plots, canonical analysis of the γ matrix, and modeling the evolution of populations on an adaptive landscape. [ABSTRACT FROM AUTHOR]

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus—NIDGS, and U. endemicus—SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single‐nucleotide polymorphisms (SNPs) from buccal swabs with restriction site‐associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter‐ and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype–environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographical barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species. [ABSTRACT FROM AUTHOR]

Background: Transmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown. Results: We sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation. Conclusions: Expression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival. [ABSTRACT FROM AUTHOR]

Identifying the genetic architecture of complex phenotypes is a central goal of modern biology, particularly for disease‐related traits. Genome‐wide association methods are a classical approach for identifying the genomic basis of variation in disease phenotypes, but such analyses are particularly challenging in natural populations due to sample size difficulties. Extensive mark–recapture data, strong linkage disequilibrium and a lethal transmissible cancer make the Tasmanian devil (Sarcophilus harrisii) an ideal model for such an association study. We used a RAD‐capture approach to genotype 624 devils at ~16,000 loci and then used association analyses to assess the heritability of three cancer‐related phenotypes: infection case–control (where cases were infected devils and controls were devils that were never infected), age of first infection and survival following infection. The SNP array explained much of the phenotypic variance for female survival (>80%) and female case–control (>61%). We found that a few large‐effect SNPs explained much of the variance for female survival (~5 SNPs explained >61% of the total variance), whereas more SNPs (~56) of smaller effect explained less of the variance for female case–control (~23% of the total variance). By contrast, these same SNPs did not account for a significant proportion of phenotypic variance in males, suggesting that the genetic bases of these traits and/or selection differ across sexes. Loci involved with cell adhesion and cell‐cycle regulation underlay trait variation, suggesting that the devil immune system is rapidly evolving to recognize and potentially suppress cancer growth through these pathways. Overall, our study provided necessary data for genomics‐based conservation and management in Tasmanian devils. [ABSTRACT FROM AUTHOR]

• We examine fitness and host use of hybrid biological control agents from the field. • Phenotypes paired with genomics can assess the risk of non-target attack by hybrids. • Fitness and host use are stable in hybrid and non-hybrid Diorhabda biocontrol agents. • Variation associated with non-target host use may be higher in hybrids. Releasing several ecotypes or species of biological control agent is common in many biological control programs. However, the consequences of hybridization for fitness and host use of the resulting hybrids are difficult to predict, especially for hybrids between more than two species and with varying levels of introgression. Hybridization of biocontrol agents may increase or decrease fitness, with consequences for control efficacy. Additionally, hybridization may lead to changes in host use patterns that may put non-target host species at increased risk. We collected genomic data to determine ancestry of individuals from ten collection sites across a hybrid zone of Diorhabda spp., the biological control agent of Tamarix spp. in North America. We paired genomic data with phenotypic data on fitness proxies of body size and early fecundity measured in a common garden, and host use for individuals from three of those sites. We found two originally released pure species and a wide range of introgression in hybrids between three Diorhabda species. Body size and early fecundity were similar in pure species and hybrids, indicating hybridization is not detrimental to insect fitness or the biocontrol program and may provide variation that allows populations to become locally adapted. Host use of hybrids was very similar to that of pure species, although some hybrid individuals had increased preference for Frankenia salina , a native non-target species. We find that hybridization has likely not been detrimental to the efficacy and safety of the Diorhabda biocontrol program, but possible impacts on F. salina should be monitored, considering ongoing hybridization and evolution in the field. [ABSTRACT FROM AUTHOR]

Evolutionary and ecological consequences of hybridization between native and invasive species are notoriously complicated because patterns of selection acting on non-native alleles can vary throughout the genome and across environments. Rapid advances in genomics now make it feasible to assess locus-specific and genome-wide patterns of natural selection acting on invasive introgression within and among natural populations occupying diverse environments. We quantified genome-wide patterns of admixture across multiple independent hybrid zones of native westslope cutthroat trout and invasive rainbow trout, the world's most widely introduced fish, by genotyping 339 individuals from 21 populations using 9380 species-diagnostic loci. A significantly greater proportion of the genome appeared to be under selection favouring native cutthroat trout (rather than rainbow trout), and this pattern was pervasive across the genome (detected on most chromosomes). Furthermore, selection against invasive alleles was consistent across populations and environments, even in those where rainbow trout were predicted to have a selective advantage (warm environments). These data corroborate field studies showing that hybrids between these species have lower fitness than the native taxa, and showthat these fitness differences are due to selection favouring many native genes distributed widely throughout the genome. [ABSTRACT FROM AUTHOR]

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics. [ABSTRACT FROM AUTHOR]

The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient technique to determine the fine-scale phylogenetic relationships among recently diverged populations in a species. This application of restriction site-associated DNA tags (RAD tags) reveals previously unresolved genetic structure and direction of evolution in the pitcher plant mosquito, Wyeomyia smithii, from a southern Appalachian Mountain refugium following recession of the Laurentide Ice Sheet at 22,000-19,000 B.P. The RAD tag method can be used to identify detailed patterns of phylogeography in any organism regardless of existing genomic data, and, more broadly, to identify incipient speciation and genome-wide variation in natural populations in general. [ABSTRACT FROM AUTHOR]

[Display omitted] • Restriction Site Associated DNA Sequencing (RAD-seq) revealed fine-scale genetic relationships among entomopathogenic nematodes. • Heterorhabditis bacteriophora and Steinernema feltiae grew increasingly less related with greater distance between collection sites. • Yet, intraspecific genetic diversity at a site could be high and distant strains could be closely related. • RAD-seq provides a powerful approach to inferring natural enemy movement within agricultural landscapes. Natural enemies often move among habitats to track prey and resources. Indeed, biocontrol often depends on natural enemies dispersing into crops after disturbances such as tillage and pesticide applications. However, the small size of many natural enemies makes it difficult to observe such movements. Here we used genetic relatedness among entomopathogenic nematodes, tiny, soil-dwelling, and thus cryptic natural enemies, to infer their movement across an agricultural landscape. We collected strains of two nematode species, Heterorhabditis bacteriophora and Steinernema feltiae , by placing sentinel hosts into eight irrigated Solanum tuberosum fields across arid central Washington State. We then used restriction site associated DNA sequencing to generate single nucleotide polymorphisms and infer relatedness among strains across our study sites. We identified 3,367 and 138,286 polymorphic loci for H. bacteriophora and S. feltiae , respectively. Genetic differentiation for both species increased with greater distance between sites, although there was considerable variation. While strains collected from the same field were generally more closely related than those from different sites, for both species, strains from different fields were sometimes quite closely related. Altogether, our results suggest a surprising amount of genetic similarity among nematodes from distant sites, despite the presumably limited distances that can be traversed by individual worms. This is consistent with the nematodes moving, at least occasionally, between far-apart locations. More generally, we suggest that recent advances in population genomics are providing powerful new tools for mapping natural enemy movement across broad landscapes. [ABSTRACT FROM AUTHOR]

The larvae of click beetles (Coleoptera: Elateridae), known as "wireworms," are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies. Andrews et al. sequenced and assembled the genome of a wireworm, or click beetle (Limonius californicus), an agricultural pest. Their data suggest the presence of multiple genetically distinct cryptic species in addition to population structure and a local adaptive response to pesticide use. [ABSTRACT FROM AUTHOR]

In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing divergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil's geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex. [ABSTRACT FROM AUTHOR]

Emerging infectious diseases increasingly threaten wildlife populations. Most studies focus on managing short‐term epidemic properties, such as controlling early outbreaks. Predicting long‐term endemic characteristics with limited retrospective data is more challenging. We used individual‐based modeling informed by individual variation in pathogen load and transmissibility to predict long‐term impacts of a lethal, transmissible cancer on Tasmanian devil (Sarcophilus harrisii) populations. For this, we employed approximate Bayesian computation to identify model scenarios that best matched known epidemiological and demographic system properties derived from 10 yr of data after disease emergence, enabling us to forecast future system dynamics. We show that the dramatic devil population declines observed thus far are likely attributable to transient dynamics (initial dynamics after disease emergence). Only 21% of matching scenarios led to devil extinction within 100 yr following devil facial tumor disease (DFTD) introduction, whereas DFTD faded out in 57% of simulations. In the remaining 22% of simulations, disease and host coexisted for at least 100 yr, usually with long‐period oscillations. Our findings show that pathogen extirpation or host–pathogen coexistence are much more likely than the DFTD‐induced devil extinction, with crucial management ramifications. Accounting for individual‐level disease progression and the long‐term outcome of devil–DFTD interactions at the population‐level, our findings suggest that immediate management interventions are unlikely to be necessary to ensure the persistence of Tasmanian devil populations. This is because strong population declines of devils after disease emergence do not necessarily translate into long‐term population declines at equilibria. Our modeling approach is widely applicable to other host–pathogen systems to predict disease impact beyond transient dynamics. [ABSTRACT FROM AUTHOR]

The threatened eastern wolf is found predominantly in protected areas of central Ontario and has an evolutionary history obscured by interbreeding with coyotes and gray wolves, which challenges its conservation status and subsequent management. Here, we used a population genomics approach to uncover spatial patterns of variation in 281 canids in central Ontario and the Great Lakes region. This represents the first genome-wide single nucleotide polymorphism (SNP) dataset with substantial sample sizes of representative populations. Although they comprise their own genetic cluster, we found evidence of eastern wolf dispersal outside of the boundaries of protected areas, in that the frequency of eastern wolf genetic variation decreases with increasing distance from provincial parks. We detected eastern wolf alleles in admixed coyotes along the northeastern regions of Lake Huron and Lake Ontario. Our analyses confirm the unique genomic composition of eastern wolves, which are mostly restricted to small fragmented patches of protected habitat in central Ontario. We hope this work will encourage an innovative discussion regarding a plan for managed introgression, which could conserve eastern wolf genetic material in any genome regardless of their potential mosaic ancestry composition and the habitats that promote them. [ABSTRACT FROM AUTHOR]

Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar's biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework., (© 2024. The Author(s).)

Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north-central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic-environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post-introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping-in-thousands by sequencing (GT-seq) is a powerful amplicon sequencing method that can genotype large numbers of variable-quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT-seq panel for the federally threatened northern Idaho ground squirrel ( Urocitellus brunneus ) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT-seq panel by measuring genotype discordance rates compared to RADseq and whole-genome sequencing. GT-seq and other sequencing methods had similar population diversity and F ST estimates, but GT-seq consistently called more heterozygotes than expected, resulting in negative F IS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT-seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT-seq for minimally invasive DNA sampling techniques in other rare animals., (© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Statistical estimation of parameters in large models of evolutionary processes is often too computationally inefficient to pursue using exact model likelihoods, even with single-nucleotide polymorphism (SNP) data, which offers a way to reduce the size of genetic data while retaining relevant information. Approximate Bayesian Computation (ABC) to perform statistical inference about parameters of large models takes the advantage of simulations to bypass direct evaluation of model likelihoods. We develop a mechanistic model to simulate forward-in-time divergent selection with variable migration rates, modes of reproduction (sexual, asexual), length and number of migration-selection cycles. We investigate the computational feasibility of ABC to perform statistical inference and study the quality of estimates on the position of loci under selection and the strength of selection. To expand the parameter space of positions under selection, we enhance the model by implementing an outlier scan on summarized observed data. We evaluate the usefulness of summary statistics well-known to capture the strength of selection, and assess their informativeness under divergent selection. We also evaluate the effect of genetic drift with respect to an idealized deterministic model with single-locus selection. We discuss the role of the recombination rate as a confounding factor in estimating the strength of divergent selection, and emphasize its importance in break down of linkage disequilibrium (LD). We answer the question for which part of the parameter space of the model we recover strong signal for estimating the selection, and determine whether population differentiation-based summary statistics or LD-based summary statistics perform well in estimating selection., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole-genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (N e ) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation., (© 2023 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Grossfurthner, Milano, Hohenlohe, Waits and Richardson.)

With the global rise of human-mediated translocations and invasions, it is critical to understand the genomic consequences of hybridization and mechanisms of range expansion. Conventional wisdom is that high genetic drift and loss of genetic diversity due to repeated founder effects will constrain introduced species. However, reduced genetic variation can be countered by behavioral aspects and admixture with other distinct populations. As planned invasions, classical biological control (biocontrol) agents present important opportunities to understand the mechanisms of establishment and spread in a novel environment. The ability of biocontrol agents to spread and adapt, and their effects on local ecosystems, depends on genomic variation and the consequences of admixture in novel environments. Here, we use a biocontrol system to examine the genome-wide outcomes of introduction, spread, and hybridization in four cryptic species of a biocontrol agent, the tamarisk beetle ( Diorhabda carinata , D .  carinulata , D .  elongata , and D .  sublineata ), introduced from six localities across Eurasia to control the invasive shrub tamarisk ( Tamarix spp.) in western North America. We assembled a de novo draft reference genome and applied RADseq to over 500 individuals across laboratory cultures, the native ranges, and the introduced range. Despite evidence of a substantial genetic bottleneck among D .  carinulata in N. America, populations continue to establish and spread, possibly due to aggregation behavior. We found that D .  carinata , D .  elongata , and D .  sublineata hybridize in the field to varying extents, with D .  carinata × D .  sublineata hybrids being the most abundant. Genetic diversity was greater at sites with hybrids, highlighting potential for increased ability to adapt and expand. Our results demonstrate the complex patterns of genomic variation that can result from introduction of multiple ecotypes or species for biocontrol, and the importance of understanding them to predict and manage the effects of biocontrol agents in novel ecosystems., Competing Interests: The authors declare no conflict of interest., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Parallelism, the evolution of similar traits in populations diversifying in similar conditions, provides strong evidence of adaptation by natural selection. Many studies of parallelism focus on comparisons of different ecotypes or contrasting environments, defined a priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with components of environmental and phenotypic variation at an intercontinental scale across four freshwater adaptive radiations (Alaska, British Columbia, Iceland and Scotland) of the three-spined stickleback (Gasterosteus aculeatus). We combined large-scale biological sampling and phenotyping with restriction site associated DNA sequencing (RAD-Seq) data from 73 freshwater lake populations and four marine ones (1,380 fish) to associate genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. Our three main findings demonstrate that (1) quantitative variation in phenotypes and environments can predict genomic parallelism; (2) genomic parallelism at the early stages of adaptive radiations, even at large geographic scales, is founded on standing variation; and (3) similar environments are a better predictor of genome-wide parallelism than similar phenotypes. Overall, this study validates the importance and predictive power of major phenotypic and environmental factors likely to influence the emergence of common patterns of genomic divergence, providing a clearer picture than analyses of dichotomous phenotypes and environments.

Infectious diseases, including transmissible cancers, can have a broad range of impacts on host behaviour, particularly in the latter stages of disease progression. However, the difficulty of early diagnoses makes the study of behavioural influences of disease in wild animals a challenging task. Tasmanian devils ( Sarcophilus harrisii ) are affected by a transmissible cancer, devil facial tumour disease (DFTD), in which tumours are externally visible as they progress. Using telemetry and mark-recapture datasets, we quantify the impacts of cancer progression on the behaviour of wild devils by assessing how interaction patterns within the social network of a population change with increasing tumour load. The progression of DFTD negatively influences devils' likelihood of interaction within their network. Infected devils were more active within their network late in the mating season, a pattern with repercussions for DFTD transmission. Our study provides a rare opportunity to quantify and understand the behavioural feedbacks of disease in wildlife and how they may affect transmission and population dynamics in general.

Maintenance of adaptive genetic variation has long been a goal of management of natural populations, but only recently have genomic tools allowed identification of specific loci associated with fitness-related traits in species of conservation concern. This raises the possibility of managing for genetic variation directly relevant to specific threats, such as those due to climate change or emerging infectious disease. Tasmanian devils (Sarcophilus harrisii) face the threat of a transmissible cancer, devil facial tumor disease (DFTD), that has decimated wild populations and led to intensive management efforts. Recent discoveries from genomic and modeling studies reveal how natural devil populations are responding to DFTD, and can inform management of both captive and wild devil populations. Notably, recent studies have documented genetic variation for disease-related traits and rapid evolution in response to DFTD, as well as potential mechanisms for disease resistance such as immune response and tumor regression in wild devils. Recent models predict dynamic persistence of devils with or without DFTD under a variety of modeling scenarios, although at much lower population densities than before DFTD emerged, contrary to previous predictions of extinction. As a result, current management that focuses on captive breeding and release for maintaining genome-wide genetic diversity or demographic supplementation of populations could have negative consequences. Translocations of captive devils into wild populations evolving with DFTD can cause outbreeding depression and/or increases in the force of infection and thereby the severity of the epidemic, and we argue that these risks outweigh any benefits of demographic supplementation in wild populations. We also argue that genetic variation at loci associated with DFTD should be monitored in both captive and wild populations, and that as our understanding of DFTD-related genetic variation improves, considering genetic management approaches to target this variation is warranted in developing conservation strategies for Tasmanian devils.

Admixture resulting from natural dispersal processes can potentially generate novel phenotypic variation that may facilitate persistence in changing environments or result in the loss of population-specific adaptations. Yet, under the US Endangered Species Act, policy is limited for management of individuals whose ancestry includes a protected taxon; therefore, they are generally not protected under the Act. This issue is exemplified by the recently re-established grey wolves of the Pacific Northwest states of Washington and Oregon, USA. This population was likely founded by two phenotypically and genetically distinct wolf ecotypes: Northern Rocky Mountain (NRM) forest and coastal rainforest. The latter is considered potentially threatened in southeast Alaska and thus the source of migrants may affect plans for their protection. To assess the genetic source of the re-established population, we sequenced a ~ 300 bp portion of the mitochondrial control region and ~ 5 Mbp of the nuclear genome. Genetic analysis revealed that the Washington wolves share ancestry with both wolf ecotypes, whereas the Oregon population shares ancestry with NRM forest wolves only. Using ecological niche modelling, we found that the Pacific Northwest states contain environments suitable for each ecotype, with wolf packs established in both environmental types. Continued migration from coastal rainforest and NRM forest source populations may increase the genetic diversity of the Pacific Northwest population. However, this admixed population challenges traditional management regimes given that admixture occurs between an adaptively distinct ecotype and a more abundant reintroduced interior form. Our results emphasize the need for a more precise US policy to address the general problem of admixture in the management of endangered species, subspecies, and distinct population segments.

High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.

Systems biology is accumulating a wealth of understanding about the structure of genetic regulatory networks, leading to a more complete picture of the complex genotype-phenotype relationship. However, models of multivariate phenotypic evolution based on quantitative genetics have largely not incorporated a network-based view of genetic variation. Here we model a set of two-node, two-phenotype genetic network motifs, covering a full range of regulatory interactions. We find that network interactions result in different patterns of mutational (co)variance at the phenotypic level (the M-matrix), not only across network motifs but also across phenotypic space within single motifs. This effect is due almost entirely to mutational input of additive genetic (co)variance. Variation in M has the effect of stretching and bending phenotypic space with respect to evolvability, analogous to the curvature of space-time under general relativity, and similar mathematical tools may apply in each case. We explored the consequences of curvature in mutational variation by simulating adaptation under divergent selection with gene flow. Both standing genetic variation (the G-matrix) and rate of adaptation are constrained by M, so that G and adaptive trajectories are curved across phenotypic space. Under weak selection the phenotypic mean at migration-selection balance also depends on M., (© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.)

Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bi-directional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations.

Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative genomics, and phylogeography that was unthinkable even a few years ago is now possible. More importantly, these next-generation sequencing studies can be performed in organisms for which few genomic resources presently exist. To speed this revolution in evolutionary genetics, we have developed Restriction site Associated DNA (RAD) genotyping, a method that uses Illumina next-generation sequencing to simultaneously discover and score tens to hundreds of thousands of single-nucleotide polymorphism (SNP) markers in hundreds of individuals for minimal investment of resources. In this chapter, we describe the core RAD-seq protocol, which can be modified to suit a diversity of evolutionary genetic questions. In addition, we discuss bioinformatic considerations that arise from unique aspects of next-generation sequencing data as compared to traditional marker-based approaches, and we outline some general analytical approaches for RAD-seq and similar data. Despite considerable progress, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types.

Natural selection shapes patterns of genetic variation among individuals, populations, and species, and it does so differentially across genomes. The field of population genomics provides a comprehensive genome-scale view of the action of selection, even beyond traditional model organisms. However, even with nearly complete genomic sequence information, our ability to detect the signature of selection on specific genomic regions depends on choosing experimental and analytical tools appropriate to the biological situation. For example, processes that occur at different timescales, such as sorting of standing genetic variation, mutation-selection balance, or fixed interspecific divergence, have different consequences for genomic patterns of variation. Inappropriate experimental or analytical approaches may fail to detect even strong selection or falsely identify a signature of selection. Here we outline the conceptual framework of population genomics, relate genomic patterns of variation to evolutionary processes, and identify major biological factors to be considered in studies of selection. As data-gathering technology continues to advance, our ability to understand selection in natural populations will be limited more by conceptual and analytical weaknesses than by the amount of molecular data. Our aim is to bring critical biological considerations to the fore in population genomics research and to spur the development and application of analytical tools appropriate to diverse biological systems.

Multiple cues, across multiple sensory modalities, are involved in mate choice in a wide range of animal taxa. This multiplicity leads to the prediction that, in adaptive radiations, sexual isolation results from divergence in multiple dimensions. However, difficulties in directly measuring preferences and detecting multiple effects limit our ability to empirically assess the number of independent traits contributing to mate choice and sexual isolation. We present an approach to estimate the dimensionality of sexual isolation using mating trials across groups of related populations. We analyze nine radiations: seven in fruit flies (Drosophila) and one each in salamanders (Desmognathus) and cichlid fishes (Pseudotropheus). We find strong evidence that multiple latent traits--linear combinations of phenotypic traits and preferences--are responsible for the patterns of sexual isolation in all nine radiations but that dimensionality has a strong upper limit. Just two latent traits are implicated in the majority of cases. Mapping along latent trait axes tests predictions of sexual-selection models and allows correlation with specific phenotypic traits and functional components of mate choice. We find support for the role of stabilizing natural selection on the sexually selected (male) traits. In the cichlids, latent-trait axes incorporate male-coloration patterns and exhibit convergence as well as divergence among populations. In the salamanders, temporal patterning in sensory modalities and male vs. female preferences are reflected in different latent-trait axes.

Despite the many triumphs of comparative biology during the past few decades, the field has remained strangely divorced from evolutionary genetics. In particular, comparative methods have failed to incorporate multivariate process models of microevolution that include genetic constraint in the form of the G matrix. Here we explore the insights that might be gained by such an analysis. A neutral model of evolution by genetic drift that depends on effective population size and the G matrix predicts a probability distribution for divergence of population trait means on a phylogeny. Use of a maximum likelihood (ML) framework then allows us to compare independent direct estimates of G with the ML estimates based on the observed pattern of trait divergence among taxa. We assess the departure from neutrality, and thus the role of different types of selection and other forces, in a stepwise hypothesis-testing procedure based on parameters for the size, shape, and orientation of G. We illustrate our approach with a test case of data on vertebral number evolution in garter snakes.