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Climate change is increasing drought intensity, threatening biodiversity. Rapid evolution of drought adaptations might be required for population persistence, particularly in rear-edge populations that may already be closer to physiological limits. Resurrection studies are a useful tool to assess adaptation to climate change, yet these studies rarely encompass the geographic range of a species. Here, we sampled 11 populations of scarlet monkeyflower (Mimulus cardinalis), collecting seeds across the plants’ northern, central, and southern range to track trait evolution from the lowest to the greatest moisture anomaly over a 7-year period. We grew families generated from these populations across well-watered and terminal drought treatments in a greenhouse and quantified five traits associated with dehydration escape and avoidance. When considering pre-drought to peak-drought phenotypes, we find that later date of flowering evolved across the range of M. cardinalis, suggesting a shift away from dehydration escape. Instead, traits consistent with dehydration avoidance evolved, with smaller and/or thicker leaves evolving in central and southern regions. The southern region also saw a loss of plasticity in these leaf traits by the peak of the drought, whereas flowering time remained plastic across all regions. This observed shift in traits from escape to avoidance occurred only in certain regions, revealing the importance of geographic context when examining adaptations to climate change.

Although persistent efforts have identified and characterized a few candidate genes and related biological processes with potential functions in the adaptation of many species to extreme environments, few works have been conducted to determine the genomic basis of adaptation in endangered livestock breeds that have been living in extreme conditions for more than thousands of years. To fill this gap, we sequenced the whole genomes of nine individuals from three Chinese native endangered cattle breeds that are living in high‐altitude or arid environments. Phylogenetic and evolutionary history analyses of these three and other six breeds showed that the genetic structure of the cattle populations is primarily related to geographic location. Interestingly, we identified pervasive introgression from the yak to Zhangmu cattle (ZMC) that cover several genes (e.g., NOS2, EGLN1 and EPAS1) involved in the hypoxia response and previously identified as positive selection genes in other species, which suggested that the adaptive introgression from yak may have contributed to the adaptation of ZMC to high‐altitude environments. In addition, by contrasting the breeds in opposite living conditions, we revealed a set of candidate genes with various functions from hypoxia response, water metabolism, immune response and body shape change to embryo development and skeletal system development, etc., that may be related to high‐altitude or arid adaptation. Our research provides new insights into the recovery and adaptation of endangered native cattle and other species in extreme environments and valuable resources for future research on animal husbandry to cope with climate change.

Resident microbes (microbiota) can shape host organismal function and adaptation in the face of environmental change. Invasion of new habitats exposes hosts to novel selection pressures, but little is known about the impact on microbiota and the host–microbiome relationship (e.g., how rapidly new microbial associations are formed, whether microbes influence invasion success). We used high‐throughput 16S rRNA sequencing of New Zealand (native) and European (invasive) populations of the freshwater snail Potamopyrgus antipodarum and found that while invaders do carry over some core microbial taxa from New Zealand, their microbial community is largely distinct. This finding highlights that invasions can result in the formation of novel host–microbiome relationships. We further show that the native microbiome is composed of fewer core microbes than the microbiome of invasive snails, suggesting that the microbiota is streamlined to a narrower set of core members. Furthermore, native snails exhibit relatively low alpha diversity but high inter‐individual variation, whereas invasive snails have higher alpha diversity but are relatively similar to each other. Together, our findings demonstrate that microbiota comparisons across native and invasive populations can reveal the impact of a long coevolutionary history and specialization of microbes in the native host range, as well as new associations occurring after invasion. We lay essential groundwork for understanding how microbial relationships affect invasion success and how microbes may be utilized in the control of invasive hosts.

Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human‐mediated hybridization between a domesticated species and its wild relative. We analysed whole‐genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and Admixture showed that wolves and dogs were well‐separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had

Biological invasion is a global problem with large negative impacts on ecosystems and human societies. When a species is introduced, individuals will first have to pass through the invasion stages of uptake and transport, before actual introduction in a non‐native range. Selection is predicted to act during these earliest stages of biological invasion, potentially influencing the invasiveness and/or impact of introduced populations. Despite this potential impact of pre‐introduction selection, empirical tests are virtually lacking. To test the hypothesis of pre‐introduction selection, we followed the fate of individuals during capture, initial acclimation, and captivity in two bird species with several invasive populations originating from the international trade in wild‐caught pets (the weavers Ploceus melanocephalus and Euplectes afer). We confirm that pre‐introduction selection acts on a wide range of physiological, morphological, behavioral, and demographic traits (incl. sex, age, size of body/brain/bill, bill shape, body mass, corticosterone levels, and escape behavior); these are all traits which likely affect invasion success. Our study thus comprehensively demonstrates the existence of hitherto ignored selection acting before the actual introduction into non‐native ranges. This could ultimately change the composition and functioning of introduced populations, and therefore warrants greater attention. More knowledge on pre‐introduction selection also might provide novel targets for the management of invasive species, if pre‐introduction filters can be adjusted to change the quality and/or quantity of individuals passing through such that invasion probability and/or impacts are reduced.

Background:- \ud \ud People with visual impairment have benefitted from recent developments of assistive technology that aim to decrease socio-economic inequality. However, access to post-secondary education is still extremelly challenging, especially for scientific areas. The under representation of people with visual impairment in the evolution research community is connected with the vision-based communication of evolutionary biology knowledge and the accompanying lack of multisensory alternatives for learning.\ud \ud Results:- \ud \ud Here, we describe the development of an inclusive outreach activity based on a multisensory phylogeny representing 20 taxonomic groups. We provide a tool kit of materials and ideas that allow both the replication of this activity and the adaptation of others, to include people with visual impairment. Furthermore, we provide activity evaluation data, a discussion of the lessons learned and an inclusive description of all figures and visual data presented.\ud \ud The presented baseline data show that people with visual impairment indeed have lack of access to education but are interested in and apt to understand evolutionary biology concepts and predict evolutionary change when education is inclusive.\ud \ud Conclusions:- \ud \ud We show that, with creative investment, basic evolutionary knowledge is perfectly possible to be transmitted through multisensory activities, which everyone can benefit from. Ultimately, we hope this case study will provide a baseline for future initiatives and a more inclusive outreach community.

Background To teach evolution efficiently teachers must be able to diagnose their students’ ideas and understanding of the phylogeny of organisms. This encompasses different facets of content-specific professional knowledge, that is, knowledge about core ideas and theories, as well as knowledge about respective misconceptions. However, as findings from the field of psychology have shown, diagnostic activities comprise a further facet, namely, teachers’ judgment accuracy. This refers to the question of whether achievement-irrelevant information about the student influences teachers’ diagnoses. Against this background we conducted a study (1) to assess trainee teachers’ abilities to diagnose (a) the scientific correctness of students’ written answers, (b) students’ misconceptions about evolution, and (2) to investigate the interplay of evolution specific and generic facets of professional knowledge during the diagnosis. For this purpose, we applied a digital instrument, the Student Inventory (SI). Using this instrument, the trainee teachers (N = 27) first diagnosed written answers (N = 6) from virtual students regarding their scientific correctness and regarding students’ misconceptions about the natural selection of the peppered moth. Second, to test for judgment accuracy, the trainee teachers received—via the SI—achievement-irrelevant information about each virtual student, that is, the previous result of a multiple-choice questionnaire about evolution, before diagnosing the written answers. Results The trainee teachers were able to distinguish between scientifically correct (90.8%) and scientifically incorrect (91.7%) written answers. Trainee teachers faced problems when diagnosing specific misconceptions categories. Anthropomorphic misconceptions were diagnosed significantly more often (61.1%) than teleological misconceptions (27.8%). The achievement-irrelevant information influenced the trainee teachers’ assessment of written answers (F [1,26] = 5.94, p < .022, η2 = .186) as they scored the written answers higher if the performance in the questionnaire was good and vice versa. Conclusion The findings indicate that the diagnosis is easier or more difficult depending on the particular misconception category. However, the findings also reveal that, besides the evolution-specific facets of professional knowledge, generic facets interrelate with the quality of the diagnosis result. We conclude from these findings that an integration of evolution-specific and generic knowledge into the education of biology teachers is critical.

The population genetic structure of invasive species can be strongly affected by environmental and landscape barriers to dispersal. Disentangling the relative contributions of these factors to genetic divergence among invading populations is a fundamental goal of landscape genetics with important implications for invasion management. Here, we relate patterns of genetic divergence in a global invasive agricultural pest, Colorado potato beetle (CPB; Leptinotarsa decemlineata), to environmental and landscape factors along an invasion front in Northwestern China. We first used microsatellite markers and spatial‐temporal samples to assess broad patterns of genetic diversity as well as fine‐scale changes in patterns of genetic divergence. We then distinguished the relative contributions of five factors to genetic divergence among front populations: geographic distance (isolation by distance), climate dissimilarity (isolation by environment), and least‐cost distances (isolation by resistance) modeled with three factors: climate suitability, cropland cover, and road networks. Genetic diversity broadly decreased from West to East, with the exception being Eastern China. Low levels of genetic diversity and varying degrees of divergence were observed in Northwestern China, reflecting the potential effect of landscape heterogeneity. Least‐cost distance across cropland cover was most positively correlated with genetic divergence, suggesting a role of croplands in facilitating gene flow. The contribution of climate to genetic divergence was secondary, whether modeled in terms of local adaptability or connectivity of the climatic landscape, suggesting that constraints to CPB gene flow imposed by a harsh climate may be ameliorated in agricultural landscapes. No evidence was found for an obvious effect of road networks on genetic divergence and population structuring. Our study provides an example of how agricultural landscape connectivity can facilitate the spread of invasive pests, even across a broad climatic gradient. More broadly, our findings can guide decisions about future land management for mitigating further spread.

The human microbiome consists of five major regional biomes distributed in or on our five body sites including skin, oral, lung, gut, and reproductive tract. Its biogeography (the spatial and temporal distribution of its biodiversity) has far‐reaching implications to our health and diseases. Nevertheless, we currently have very limited understanding on the mechanisms shaping the biogeography, since it is often rather difficult to determine the relative importance of drift, dispersal, speciation, and selection, the four processes (mechanisms) determining the patterns of microbial biogeography and community dynamics according to a recent synthesis in community ecology and biogeography. To disentangle these mechanisms, I utilize multisite neutral (MSN) model and niche‐neutral hybrid (NNH) model to analyze large number of truly multisite microbiome samples covering all five major human microbiome habitats, including 699 metacommunities and 5,420 local communities. Approximately 89% of metacommunities and 92% local communities exhibit patterns indistinguishable from neutral, and 20% indistinguishable from niche‐neutral hybrid model, indicating the relative significance of stochastic neutral forces versus deterministic niche selection in shaping the biogeography of human microbiome. These findings cast supporting evidence to van der Gast's revision to classic Bass‐Becking doctrine of microbial biogeography: “Some things are everywhere and some things are not. Sometimes the environment selects and sometimes it doesn't,” offering the first educated guess for “some” and “sometimes” in the revised doctrine. Furthermore, the logistic/Cox regression models describing the relationships among community neutrality, niche differentiation, and key community/species characteristics (including community diversity, community/species dominance, speciation, and migration rates) were constructed to quantitatively describe the niche‐neutral continuum and the influences of community/species properties on the continuum.

Spatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome-wide distribution of summary statistics measuring genetic differentiation, such as FST, are often interpreted as evidence for alleles that contribute to local adaptation. However, theoretical studies have shown that in spatially structured populations the spread of beneficial mutations with spatially uniform fitness effects can also induce transient genetic differentiation. In recent years, numerous empirical studies have suggested that such species-wide, or global, adaptation makes a substantial contribution to molecular evolution. In this perspective, we discuss how commonly such global adaptation may influence the genome-wide distribution of FST and generate genetic differentiation patterns, which could be mistaken for local adaptation. To illustrate this, we use forward-in-time population genetic simulations assuming parameters for the rate and strength of beneficial mutations consistent with estimates from natural populations. We demonstrate that the spread of globally beneficial mutations in parapatric populations may frequently generate FST outliers, which could be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so in some cases, the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity within and between populations in addition to FST. However, when local adaptation has been only recently established, it may be much more difficult to distinguish from global adaptation, due to less accumulation of linkage disequilibrium at flanking sites. Through our discussion, we conclude that a large fraction of FST outliers that are presumed to arise from local adaptation may instead be due to global adaptation.

Various strains of the mycoparasitic fungal species Clonostachys rosea are used commercially as biological control agents for the control of fungal plant diseases in agricultural crop production. Further improvements of the use and efficacy of C. rosea in biocontrol require a mechanistic understanding of the factors that determines the outcome of the interaction between C. rosea and plant pathogenic fungi. Here, we determined the genome sequences of 11 Clonostachys strains, representing five species in Clonostachys subgenus Bionectria, and performed a comparative genomic analysis with the aim to identify gene families evolving under selection for gene gains or losses. Several gene families predicted to encode proteins involved in biosynthesis of secondary metabolites, including polyketide synthases, nonribosomal peptide syntethases and cytochrome P450s, evolved under selection for gene gains (p ≤ .05) in the Bionectria subgenus lineage. This was accompanied with gene copy number increases (p ≤ .05) in ATP‐binding cassette (ABC) transporters and major facilitator superfamily (MFS) transporters predicted to contribute to drug efflux. Most Clonostachys species were also characterized by high numbers of auxiliary activity (AA) family 9 lytic polysaccharide monooxygenases, AA3 glucose–methanol–choline oxidoreductases and additional carbohydrate‐active enzyme gene families with putative activity (or binding) towards xylan and rhamnose/pectin substrates. Particular features of the C. rosea genome included expansions (p ≤ .05) of the ABC‐B4 multidrug resistance transporters, the ABC‐C5 multidrug resistance‐related transporters and the 2.A.1.3 drug:H + antiporter‐2 MFS drug resistance transporters. The ABC‐G1 pleiotropic drug resistance transporter gene abcG6 in C. rosea was induced (p ≤ .009) by exposure to the antifungal Fusarium mycotoxin zearalenone (1121‐fold) and various fungicides. Deletion of abcG6 resulted in mutants with reduced (p

Divergence is mostly viewed as a progressive process often initiated by selection targeting individual loci, ultimately resulting in ever increasing genomic isolation due to linkage. However, recent studies show that this process may stall at intermediate stable equilibrium states without achieving complete genomic isolation. We tested the extent of genomic isolation between two recurrently hybridizing nonbiting midge sister taxa, Chironomus riparius and Chironomus piger, by analyzing the divergence landscape. Using a principal component‐based method, we estimated that only about 28.44% of the genomes were mutually isolated, whereas the rest was still exchanged. The divergence landscape was fragmented into isolated regions of on average 30 kb, distributed throughout the genome. Selection and divergence time strongly influenced lengths of isolated regions, whereas local recombination rate only had minor impact. Comparison of divergence time distributions obtained from several coalescence‐simulated divergence scenarios with the observed divergence time estimates in an approximate Bayesian computation framework favored a short and concluded divergence event in the past. Most divergence happened during a short time span about 4.5 million generations ago, followed by a stable equilibrium between mutual gene flow through ongoing hybridization for the larger part of the genome and isolation in some regions due to rapid purifying selection of introgression, supported by high effective population sizes and recombination rates. Impact Summary The process of speciation has fascinated biologists from early on. Prevailing theory suggested that gene flow among populations is the main obstacle for their divergence. Recently, it became clear that speciation with gene flow is possible under certain circumstances. However, it remains unclear how the divergence process proceeds in time, how widespread the phenomenon is, and whether it always and inevitably leads to complete isolation. Comparing the genomes of individuals of two regularly hybridizing sister taxa of nonbiting midges, we could show that they diverged during a short period millions of generations ago. Their divergence process apparently ceased before the entire genome was mutually isolated. The taxa remain distinct since, even though they share most of their genome. Our findings thus extend our view of the nature of species and the temporal dynamics of their divergence and describe novel approaches to analyze both current and past divergence processes.

Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter‐ and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.

Understanding the evolutionary impacts of harvest on fish populations is important for informing fisheries management and conservation and has become a growing research topic over the last decade. However, the dynamics of fish populations are highly complex, and phenotypes can be influenced by many biotic and abiotic factors. Therefore, it is vital to collect robust data and explore multiple alternative hypotheses before concluding that fish populations are influenced by harvest. In their recently published manuscript, Bowles et al, Evolutionary Applications, 13(6):1128 conducted age/growth and genomic analysis of walleye (Sander vitreus) populations sampled 13–15 years (1–2.5 generations) apart and hypothesized that observed phenotypic and genomic changes in this time period were likely due to harvest. Specifically, Bowles et al. (2020) documented differential declines in size‐at‐age in three exploited walleye populations compared to a separate, but presumably less‐exploited, reference population. Additionally, they documented population genetic differentiation in one population pair, homogenization in another, and outlier loci putatively under selection across time points. Based on their phenotypic and genetic results, they hypothesized that selective harvest had led to fisheries‐induced evolution (referred to as nascent changes) in the exploited populations in as little as 1–2.5 generations. We re‐analyzed their data and found that (a) sizes declined across both exploited and reference populations during the time period studied and (b) observed genomic differentiation in their study was the result of inadequate data filtering, including retaining individuals with high amounts of missing data and retaining potentially undersplit and oversplit loci that created false signals of differentiation between time points. This re‐analysis did not provide evidence for phenotypic or genetic changes attributable to harvest in any of the study populations, contrasting the hypotheses presented by Bowles et al. (2020). Our comment highlights the potential pitfalls associated with conducting age/growth analyses with low sample sizes and inadequately filtering genomic datasets.

Human-driven habitat fragmentation and loss have led to a proliferation of small and isolated plant and animal populations with high risk of extinction. One of the main threats to extinction in these populations is inbreeding depression, which is primarily caused by recessive deleterious mutations becoming homozygous due to inbreeding. The typical approach for managing these populations is to maintain high genetic diversity, increasingly by translocating individuals from large populations to initiate a “genetic rescue.” However, the limitations of this approach have recently been highlighted by the demise of the gray wolf population on Isle Royale, which declined to the brink of extinction soon after the arrival of a migrant from the large mainland wolf population. Here, we use a novel population genetic simulation framework to investigate the role of genetic diversity, deleterious variation, and demographic history in mediating extinction risk due to inbreeding depression in small populations. We show that, under realistic models of dominance, large populations harbor high levels of recessive strongly deleterious variation due to these mutations being hidden from selection in the heterozygous state. As a result, when large populations contract, they experience a substantially elevated risk of extinction after these strongly deleterious mutations are exposed by inbreeding. Moreover, we demonstrate that, although genetic rescue is broadly effective as a means to reduce extinction risk, its effectiveness can be greatly increased by drawing migrants from small or moderate-sized source populations rather than large source populations due to smaller populations harboring lower levels of recessive strongly deleterious variation. Our findings challenge the traditional conservation paradigm that focuses on maximizing genetic diversity in small populations in favor of a view that emphasizes minimizing strongly deleterious variation. These insights have important implications for managing small and isolated populations in the increasingly fragmented landscape of the Anthropocene.

Urbanization is a global phenomenon with major effects on species, the structure of community functional traits and ecological interactions. Body size is a key species trait linked to metabolism, life‐history and dispersal as well as a major determinant of ecological networks. Here, using a well‐replicated urban–rural sampling design in Central Europe, we investigate the direction of change of body size in response to urbanization in three common bumblebee species, Bombus lapidarius, Bombus pascuorum and Bombus terrestris, and potential knock‐on effects on pollination service provision. We found foragers of B. terrestris to be larger in cities and the body size of all species to be positively correlated with road density (albeit at different, species‐specific scales); these are expected consequences of habitat fragmentation resulting from urbanization. High ambient temperature at sampling was associated with both a small body size and an increase in variation of body size in all three species. At the community level, the community‐weighted mean body size and its variation increased with urbanization. Urbanization had an indirect positive effect on pollination services through its effects not only on flower visitation rate but also on community‐weighted mean body size and its variation. We discuss the eco‐evolutionary implications of the effect of urbanization on body size, and the relevance of these findings for the key ecosystem service of pollination.

Human activity continues to impact global ecosystems, often by altering the habitat suitability, persistence, and movement of native species. It is thus critical to examine the population genetic structure of key ecosystemservice providers across human‐altered landscapes to provide insight into the forces that limit wildlife persistence and movement across multiple spatial scales. While some studies have documented declines of bee pollinators as a result of human‐mediated habitat alteration, others suggest that some bee species may benefit from altered land use due to increased food or nesting resource availability; however, detailed population and dispersal studies have been lacking. We investigated the population genetic structure of the Eastern carpenter bee, Xylocopa virginica, across 14 sites spanning more than 450 km, including dense urban areas and intensive agricultural habitat. X. virginica is a large bee which constructs nests in natural and human‐associated wooden substrates, and is hypothesized to disperse broadly across urbanizing areas. Using 10 microsatellite loci, we detected significant genetic isolation by geographic distance and significant isolation by land use, where urban and cultivated landscapes were most conducive to gene flow. This is one of the first population genetic analyses to provide evidence of enhanced insect dispersal in human‐altered areas as compared to semi‐natural landscapes. We found moderate levels of regional‐scale population structure across the study system (GʹST = 0.146) and substantial co‐ancestry between the sampling regions, where co‐ancestry patterns align with major human transportation corridors, suggesting that human‐mediated movement may be influencing regional dispersal processes. Additionally, we found a signature of strong site‐level philopatry where our analyses revealed significant levels of high genetic relatedness at very fine scales (

Cities are often hotter and drier compared with nearby undeveloped areas, but how organisms respond to these multifarious stressors associated with urban heat islands is largely unknown. Terrestrial isopods are especially susceptible to temperature and aridity stress as they have retained highly permeable gills from their aquatic ancestors. We performed a two temperature common garden experiment with urban and rural populations of the terrestrial isopod, Oniscus asellus, to uncover evidence for plastic and evolutionary responses to urban heat islands. We focused on physiological tolerance traits including tolerance of heat, cold, and desiccation. We also examined body size responses to urban heat islands, as size can modulate physiological tolerances. We found that different mechanisms underlie responses to urban heat islands. While evidence suggests urban isopods may have evolved higher heat tolerance, urban and rural isopods had statistically indistinguishable cold and desiccation tolerances. In both populations, plasticity to warmer rearing temperature diminished cold tolerance. Although field‐collected urban and rural isopods were the same size, rearing temperature positively affected body size. Finally, larger size improved desiccation tolerance, which itself was influenced by rearing temperature. Our study demonstrates how multifarious changes associated with urban heat islands will not necessarily contribute to contemporary evolution in each of the corresponding physiological traits.

Introduction Rapid environmental change driven by urbanization offers a unique insight into the adaptive potential of urban‐dwelling organisms. Urban‐driven phenotypic differentiation is increasingly often demonstrated, but the impact of urbanization (here modelled as the percentage of impervious surface (ISA) around each nestbox) on offspring developmental rates and subsequent survival remains poorly understood. Furthermore, the role of selection on urban‐driven phenotypic divergence was rarely investigated to date. Methods and Results Data on nestling development and body mass were analysed in a gradient of urbanization set in Warsaw, Poland, in two passerine species: great tits (Parus major) and blue tits (Cyanistes caeruleus). Increasing levels of impervious surface area (ISA) delayed the age of fastest growth in blue tits. Nestling body mass was also negatively affected by increasing ISA 5 and 10 days after hatching in great tits, and 10 and 15 days in blue tits, respectively. High levels of ISA also increased nestling mortality 5 and 10 days after hatching in both species. An analysis of selection differentials performed for two levels of urbanization (low and high ISA) revealed a positive association between mass at day 2 and survival at fledging. Discussion This study confirms the considerable negative impact of imperviousness—a proxy for urbanization level—on offspring development, body mass and survival, and highlights increased selection on avian mass at hatching in a high ISA environment.

Urbanization has recently emerged as an exciting new direction for evolutionary research founded on our growing understanding of rapid evolution paired with the expansion of novel urban habitats. Urbanization can influence adaptive and nonadaptive evolution in urban‐dwelling species, but generalized patterns and the predictability of urban evolutionary responses within populations remain unclear. This editorial introduces the special feature “Evolution in Urban Environments” and addresses four major emerging themes, which include: (a) adaptive evolution and phenotypic plasticity via physiological responses to urban climate, (b) adaptive evolution via phenotype–environment relationships in urban habitats, (c) population connectivity and genetic drift in urban landscapes, and (d) human–wildlife interactions in urban spaces. Here, we present the 16 articles (12 empirical, 3 review, 1 capstone) within this issue and how they represent each of these four emerging themes in urban evolutionary biology. Finally, we discuss how these articles address previous questions and have now raised new ones, highlighting important new directions for the field.

Ongoing adaptive evolution, and resulting “evolutionary rescue” of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration-selection balance and micro-evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counteracts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long-term data from free-living song sparrows (Melospiza melodia) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro-evolutionary change should be expected given nonzero additive genetic variance and consistent directional selection. However, this evolutionary increase was counteracted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration-selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change.

Natural landscape heterogeneity and barriers resulting from urbanization can reduce genetic connectivity between populations. The evolutionary, demographic, and ecological effects of reduced connectivity may lead to population isolation and ultimately extinction. Alteration to the terrestrial and aquatic environment caused by urban influence can affect gene flow, specifically for stream salamanders who depend on both landscapes for survival and reproduction. To examine how urbanization affects a relatively common stream salamander species, we compared genetic connectivity of Eurycea bislineata (northern two‐lined salamander) populations within and between streams in an urban, suburban, and rural habitat around the New York City (NYC) metropolitan area. We report reduced genetic connectivity between streams within the urban landscape found to correspond with potential barriers to gene flow, that is, areas with more dense urbanization (roadways, industrial buildings, and residential housing). The suburban populations also exhibited areas of reduced connectivity correlated with areas of greater human land use and greater connectivity within a preserve protected from development. Connectivity was relatively high among neighboring rural streams, but a major roadway corresponded with genetic breaks even though the habitat contained more connected green space overall. Despite greater human disturbance across the landscape, urban and suburban salamander populations maintained comparable levels of genetic diversity to their rural counterparts. Yet small effective population size in the urban habitats yielded a high probability of loss of heterozygosity due to genetic drift in the future. In conclusion, urbanization impacted connectivity among stream salamander populations where its continual influence may eventually hinder population persistence for this native species in urban habitats.

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re‐visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community—from practicing biologists to funding agencies and professional societies—must make adjustments that prioritize the collection and deposition of urban specimens.

Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond‐reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life‐history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.

Based on specimens collected in historical times and stored in the insect collections of the Natural History Museum London and the Zoological Museum Hamburg two new subgenera are established Robustaccasubgen. nov. of the genus Peracca Griffini, 1897 and Indoliarasubgen. nov. of the genus Liara Redtenbacher, 1891. Five new species are described: Peracca (Robustacca) nigrifronssp. nov. from Sumatra, Liara (Acanthocoryphus) duratasp. nov. from Hongkong, Liara (Indoliara) dividatasp. nov. from South India, Pseudosubria assamensissp. nov. from Assam and Depressacca kinabalusp. nov. from Sabah. The species Odontoconus robustus Karny, 1923 is newly combined as Peracca (Robustacca) robustus (Karny, 1923) comb. nov. An extended and updated key to the subgenera of the genus Peracca Griffini, 1897 is provided. All specimens are deposited in the original collections.

Tree breeding has focused on increasing stem volume growth with a cost to fecundity. However, fecundity is important in maintaining the fitness in natural stands and facilitating cross‐pollination to advance breeding populations. Understanding the inheritance of fecundity and the genetic relationship between fecundity and growth is essential to understand the constraints of evolution in natural population and design an optimal selection strategy to balance breeding for growth and fecundity. Inheritance of female fecundity and the genetic relationship between fecundity and growth in radiata pine were investigated using a large Australia‐wide progeny test, planted on eight sites involving 279 control‐pollinated families. It was found that fecundity of female cones was highly heritable with an estimated heritability of 0.39–0.61, but genetically correlated with growth (−0.30 to −0.39). This indicates that improvement in tree growth alone could reduce the fecundity, thus to break the possible evolutionary constraint in natural population. To maintain fecundity for breeding purposes and minimize the interruption of the evolutionary constraint between fecundity and growth, use of a restraint selection index to impose no change of fecundity is developed in current breeding, while dissecting the genetic basis of adversely correlated traits at loci level is required for optimal long‐term strategy.

Lycodon deccanensisGanesh, Deuti, Punith, Achyuthan, Mallik, Adhikari, Vogel, 2020 was recently described from the Mysore plateau of Karnataka based solely on morphology but lacking in-depth descriptions and comparisons. A scrutiny of the description reveals that the type series, of two specimens, comprise specimens of two different species along with discrepancies throughout the paper. Surveys conducted near the type locality of the species led to the discovery of additional specimens, which allow us to provide an elaborate description of the species and present data on its phylogenetic relationship with members of the genus and comments on the systematics ofLycodonof India. Results from molecular phylogenetics suggest thatLycodon deccanensisis a member of theL. aulicusclade based on molecular data for mitochondrial cytochrome b gene and shows an un-corrected p-distance (sequence divergence) of 14–17% from other members of theLycodon aulicusclade.

Women have up to a fourfold increase in risk for autoimmune disease compared to men. Many explanations have been proposed, including sex hormones, the X chromosome, microchimerism, environmental factors, and the microbiome. However, the mechanism for this autoimmune sex bias remains obscure. In this manuscript, we evaluate the hypothesis that qualitative or quantitative differences in circulating antibodies may explain, at least in part, the pathogenesis of autoimmune disease and its sex bias—especially when considering an evolutionary perspective. Indeed, women have higher absolute levels of antibodies than men, and (auto)antibodies are also associated with most autoimmune diseases. Several facts suggest differences in antibodies may cause increased prevalence of autoimmune disease in women. First, the association between increased quantities of serum antibodies and increased prevalence of autoimmunity is found not only in women, but also in men with Klinefelter syndrome. Second, both serum antibody levels and autoimmunity spike in the postpartum period. Third, a dose–response effect exists between parity and both serum antibodies and prevalence of autoimmune disease. Fourth, many biologically plausible mechanisms explain the association, such as T cell‐dependent activation of B cells and/or VGLL3. The evolutionary underpinning of increased antibodies in women is likely to be protection of offspring from infections. Overall, this evolutionary paradigm can help explain why the phenomenon of autoimmunity occurs preferentially in women and raises the possibility of new treatment options.

Adaptation to current and future climates can be constrained by trade‐offs between fitness‐related traits. Early seedling emergence often enhances plant fitness in seasonal environments, but if earlier emergence in response to seasonal cues is genetically correlated with lower potential to spread emergence among years (i.e., bet‐hedging), then this functional trade‐off could constrain adaptive evolution. Consequently, selection favoring both earlier within‐year emergence and greater spread of emergence among years—as is expected in more arid environments—may constrain adaptive responses to trait value combinations at which a performance gain in either function (i.e., evolving earlier within‐ or greater among‐year emergence) generates a performance loss in the other. All such trait value combinations that cannot be improved for both functions simultaneously are described as Pareto optimal and together constitute the Pareto front. To investigate how this potential emergence timing trade‐off might constrain adaptation to increasing aridity, we sourced seeds of two grasses, Stipa pulchra and Bromus diandrus, from multiple maternal lines within populations across an aridity gradient in California and examined their performance in a greenhouse experiment. We monitored emergence and assayed ungerminated seeds for viability to determine seed persistence, a metric of potential among‐year emergence spread. In both species, maternal lines with larger fractions of persistent seeds emerged later, indicating a trade‐off between within‐year emergence speed and potential among‐year emergence spread. In both species, populations on the Pareto front for both earlier emergence and larger seed persistence fraction occupied significantly more arid sites than populations off the Pareto front, consistent with the hypothesis that more arid sites impose the strongest selection for earlier within‐year emergence and greater among‐year emergence spread. Our results provide an example of how evaluating genetically based correlations within populations and applying Pareto optimality among populations can be used to detect evolutionary constraints and adaptation across environmental gradients.

The tools provided by genetic engineering can fundamentally alter our technological approaches to medicine, agriculture, and ecology. Through their use, crops have been designed to increase yield while reducing loss from pests and disease (Pellegrino, Bedini, Nuti, & Ercoli, 2018). Critical medications, such as insulin and the mammalian growth hormone‐inhibiting hormone, are now produced using bio‐engineered organisms (Itakura et al., 1977). Genetically engineered organisms have been proposed to help facilitate adaptive responses to climate change, suppress undesirable or invasive populations, and reverse the fixation of deleterious mutations in at‐risk populations of endangered plants and animals (Thomas et al., 2013). In addition, genetic engineering has made vaccines safer, more effective, faster to produce, and could make them easier to disseminate (Basinski et al., 2018; Chahal et al., 2016). Although promising, these new technologies all confront a common challenge: unwanted evolution that may undermine the intent of engineering. Transgenes, stretches of foreign DNA inserted into a host genome, evolve in the same way as any other genetic material. Consequently, if a transgene compromises fitness, selection favors its potentially rapid removal from the population (Sleight, Bartley, Lieviant, & Sauro, 2010; Willemsen & Zwart, 2019). Even when the insert does not reduce fitness, mutations can accumulate, leading to loss of function. This “evolutionary half‐life” poses a significant challenge for the design of successful genetically modified organisms and motivates the identification of designs that slow or arrest evolution of genetic modifications (Bull & Barrick, 2017). One possible solution to suppress evolution in genetically modified organisms comes from population genetics theory demonstrating that gene flow can impede local adaptation (Akerman & Burger, 2014; Bolnick & Nosil, 2007; Crow & Kimura, 1970; Haldane, 1957; Lenormand, 2002; Levene, 1953; Slatkin, 1973; Wright, 1940). In the classic “mainland‐island” models, migration from a mainland to an island can suppress island adaptation. By suppressing local adaptation, immigration can maintain costly phenotypes that would otherwise be displaced by evolution. An interesting question is whether “migration” can be used to maintain essential functions of genetically modified populations in the face of countering selection. In this context, repeated re‐introduction of genetically modified individuals into an evolving population is analogous to a constant level of immigration from a source fixed for locally unfavorable mutations. To address this question, we develop and analyze mathematical models to evaluate the efficacy of repeated introduction (henceforth “supplementation”) as a tool for controlling unwanted evolution in three contexts of genetically engineered populations: bioreactors, gene drives, and transmissible vaccines. In the first, we identify the level of supplementation required to maintain a stable frequency of a desired but deleterious transgene in the microbial population of a bioreactor. In the second, we evaluate the effect of supplementation on the spread and stability of gene drives that experience resistance evolution. In the third, we identify the amount of supplemental direct vaccination required of a transmissible vaccine to prevent its evolutionary decay while maintaining a high enough vaccine coverage to also protect the population against a pathogen.

Uncertainty hampers innovative mixed-fisheries management by the scales at which connectivity dynamics are relevant to management objectives. The spatial scale of sustainable stock management is species-specific and depends on ecology, life history and population connectivity. One valuable approach to understand these spatial scales is to determine to what extent population genetic structure correlates with the oceanographic environment. Here, we compare the level of genetic connectivity in three codistributed and commercially exploited demersal flatfish species living in the North East Atlantic Ocean. Population genetic structure was analysed based on 14, 14 and 10 neutral DNA microsatellite markers for turbot, brill and sole, respectively. We then used redundancy analysis (RDA) to attribute the genetic variation to spatial (geographical location), temporal (sampling year) and oceanographic (water column characteristics) components. The genetic structure of turbot was composed of three clusters and correlated with variation in the depth of the pycnocline, in addition to spatial factors. The genetic structure of brill was homogenous, but correlated with average annual stratification and spatial factors. In sole, the genetic structure was composed of three clusters, but was only linked to a temporal factor. We explored whether the management of data poor commercial fisheries, such as in brill and turbot, might benefit from population-specific information. We conclude that the management of fish stocks has to consider species-specific genetic structures and may benefit from the documentation of the genetic seascape and life-history traits. ispartof: EVOLUTIONARY APPLICATIONS vol:14 issue:2 pages:536-552 ispartof: location:England status: published

If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value—notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and noncrop hosts and between experimental and natural host populations. Here, we used a meta-analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested. We synthesized the results of 102 studies, comprising 2004 effect sizes representing a diversity of approaches and host-parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ∼20% for noncrop hosts and by ∼50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.

Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade‐offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short‐ and long‐term strategies are integrated into a decision framework that also considers nongenetic aspects of management.

Hybridization between species can affect the strength of the reproductive barriers that separate those species. Two extensions of this effect are: (1) the expectation that asymmetric hybridization will have asymmetric effects on reproductive barrier strength and (2) the expectation that local hybridization will affect only local reproductive barrier strength and could therefore alter within-species compatibility. We tested these hypotheses in a pair of morning glory species that exhibit asymmetric gene flow from highly selfingIpomoea lacunosainto mixed matingI. cordatotrilobain regions where they co-occur. Because of the direction of this gene flow, we predicted that reproductive barrier strength would be more strongly affected inI. cordatotrilobathanI. lacunosa. We also predicted that changes to reproductive barriers in sympatricI. cordatotrilobapopulations would affect compatibility with allopatric populations of that species. We tested these predictions by measuring the strength of a reproductive barrier to seed set across the species’ ranges. Consistent with our first prediction, we found that sympatric and allopatricI. lacunosaproduce the same number of seeds in crosses withI. cordatotriloba, whereas crosses between sympatricI. cordatotrilobaandI. lacunosaare more successful than crosses between allopatricI. cordatotriloba and I. lacunosa.This difference in compatibility appears to reflect an asymmetric decrease in the strength of the barrier to seed set in sympatricI. cordatotriloba, which could be caused byI. lacunosaalleles that have introgressed intoI. cordatotriloba. We further demonstrated that changes to sympatricI. cordatotrilobahave decreased its ability to produce seeds with allopatric populations of the same species, in line with our second prediction. Thus, in a manner analogous to cascade reinforcement, we suggest that introgression associated with hybridization not only influences between-species isolation but can also contribute to isolation within a species.Impact StatementBiological diversity depends on traits that prevent different species from successfully interbreeding. However, these reproductive barriers are often imperfect, leading to hybrid matings and possible genetic exchange between species where they occur together. When this happens, the reproductive barriers that separate species can themselves evolve to become stronger or weaker. Understanding the effects of hybridization on reproductive barriers is key to predicting the potential for future hybridization between species and ultimately whether hybridizing species will diverge, persist, or merge in regions where they co-occur. Here we hypothesize and show that hybridization in only one direction causes unidirectional changes to reproductive barrier strength and that geographically restricted hybridization causes local changes to barrier strength that can affect interbreeding within a species. Specifically, we found that gene flow from one species of morning glory into another likely caused a reproductive barrier to decrease in regions where they co-occur. The decreased reproductive barrier is caused by changes in only the species that received gene flow. We also found that the locally reduced barriers in the species that received gene flow affected reproductive compatibility between populations within that species. Thus, a breakdown of barriers between species can cause a build-up of barriers within a species. Our work demonstrates critical and rarely explored interactions at species boundaries.

Understanding the mechanisms of how urbanization influences the evolution of native species is vital for urban wildlife ecology and conservation in the Anthropocene. With thousands of years of agriculture‐dominated historical urbanization followed by 40 years of intensive and rapid urbanization, Shanghai provides an ideal environment to study how the two‐stage urbanization process influences the evolution of indigenous wildlife, especially of anuran species. Therefore, in this study, we used mitochondrial Cyt‐b gene, microsatellite (SSR), and single nucleotide polymorphism (SNP) data to evaluate the demographic history and genetic structure of the eastern golden frog (Pelophylax plancyi), by sampling 407 individuals from 15 local populations across Shanghai, China. All local populations experienced bottlenecks during historical urbanization, while the local populations in urban areas maintained comparable contemporary effective population sizes (N e) and genetic diversity with suburban and rural populations. Nevertheless, the rapid modern urbanization has already imposed significant negative effects to the integrity of populations. The 15 local populations were differentiated into eight genetic clusters, showing a spatial distribution pattern consistent with the current urbanization gradient and island–mainland geography. Although moderate gene flow still occurred from the rural peripheral cluster to urban and suburban clusters, population fragmentation was more serious in the urban and suburban populations, where higher urbanization levels within 2‐km radius areas showed significant negative relationships to the N e and genetic diversity of local populations. Therefore, to protect urban wildlife with limited dispersal ability, improving conditions in fragmented habitat remnants might be most essential for local populations living in more urbanized areas. Meanwhile, we highlight the need to preserve large unfragmented rural habitats and to construct corridor networks to connect discrete urban habitat remnants for the long‐term wildlife conservation in intensively urbanizing environments.

As part of sterile insect technique (SIT) programs, irradiation can effectively induce sterility in insects by damaging germline genomic DNA. However, irradiation also induces other off‐target side effects that reduce the quality and performance of sterilized males, including the formation of damaging free radicals that can reduce sterile male performance. Thus, treatments that reduce off‐target effects of irradiation on male performance while maintaining sterility can improve the feasibility and economy of SIT programs. We previously found that inducing a form of rapid, beneficial plasticity with a 1‐hr anoxic‐conditioning period (physiological conditioning hormesis) prior to and during irradiation improves male field performance in the laboratory while maintaining sterility in males of the cactus moth, Cactoblastis cactorum. Here, we extend this work by testing the extent to which this beneficial plasticity may improve male field performance and longevity in the field. Based on capture rates after a series of mark release–recapture experiments, we found that anoxia‐conditioned irradiated moths were active in the field longer than their irradiated counterparts. In addition, anoxia‐conditioned moths were captured in traps that were farther away from the release site than unconditioned moths, suggesting greater dispersal. These data confirmed that beneficial plasticity induced by anoxia hormesis prior to irradiation led to lower postirradiation damage and increased flight performance and recapture duration under field conditions. We recommend greater consideration of beneficial plasticity responses in biological control programs and specifically the implementation of anoxia‐conditioning treatments applied prior to irradiation in area‐wide integrated pest management programs that use SIT.

Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able to rapidly evolve resistance to them, but how they are able to do so is poorly understood. One possible but largely unexplored explanation is that exposure to sublethal doses of insecticides may alter epigenetic patterns that are heritable. For instance, epigenetic mechanisms, such as DNA methylation that modifies gene expression without changing the underlying genetic code, may facilitate the emergence of resistant phenotypes in complex ways. We assessed the effects of sublethal insecticide exposure, with the neonicotinoid imidacloprid, on DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata, examining both global changes in DNA methylation and specific changes found within genes and transposable elements. We found that exposure to insecticide led to decreases in global DNA methylation for parent and F2 generations and that many of the sites of changes in methylation are found within genes associated with insecticide resistance, such as cytochrome P450s, or within transposable elements. Exposure to sublethal doses of insecticide caused heritable changes in DNA methylation in an agricultural insect herbivore. Therefore, epigenetics may play a role in insecticide resistance, highlighting a fundamental mechanism of evolution while informing how we might better coexist with insect species in agroecosystems.

The adaptive value of phenotypic plasticity for performance under single stressors is well documented. However, plasticity may only truly be adaptive in the natural multifactorial environment if it confers resilience to stressors of a different nature, a phenomenon known as cross‐tolerance. An understanding of the mechanistic basis of cross‐tolerance is essential to aid prediction of species resilience to future environmental change. Here, we identified mechanisms underpinning cross‐tolerance between two stressors predicted to increasingly challenge aquatic ecosystems under climate change, chronic warming and hypoxia, in an ecologically‐important aquatic invertebrate. Warm acclimation improved hypoxic performance through an adaptive hypometabolic strategy and changes in the expression of hundreds of genes that are important in the response to hypoxia. These ‘frontloaded’ genes showed a reduced reaction to hypoxia in the warm acclimated compared to the cold acclimated group. Frontloaded genes included stress indicators, immune response and protein synthesis genes that are protective at the cellular level. We conclude that increased constitutive gene expression as a result of warm acclimation reduced the requirement for inducible stress responses to hypoxia. We propose that transcriptional frontloading contributes to cross‐tolerance between stressors and may promote fitness of organisms in environments increasingly challenged by multiple anthropogenic threats.

Natural history collections provide an unparalleled resource for documenting population responses to past anthropogenic change. However, in many cases, traits measured on specimens may vary temporally in response to a number of different anthropogenic pressures or demographic processes. While teasing apart these different drivers is challenging, approaches that integrate analyses of spatial and temporal series of specimens can provide a robust framework for examining whether traits exhibit common responses to ecological variation in space and time. We applied this approach to analyze bill morphology variation in California Savannah Sparrows (Passerculus sandwichensis). We found that bill surface area increased in birds from higher salinity tidal marshes that are hotter and drier. Only the coastal subspecies, alaudinus, exhibited a significant increase in bill size through time. As with patterns of spatial variation, alaudinus populations occupying higher salinity tidal marshes that have become warmer and drier over the past century exhibited the greatest increases in bill surface area. We also found a significant negative correlation between bill surface area and total evaporative water loss (TEWL) and estimated that observed increases in bill size could result in a reduction of up to 16.2% in daily water losses. Together, these patterns of spatial and temporal variation in bill size were consistent with the hypothesis that larger bills are favored in freshwater‐limited environments as a mechanism of dissipating heat, reducing reliance on evaporative cooling, and increasing water conservation. With museum collections increasingly being leveraged to understand past responses to global change, this work highlights the importance of considering the influence of many different axes of anthropogenic change and of integrating spatial and temporal analyses to better understand the influence of specific human impacts on population change over time.

Understanding local adaptation to climate is critical for managing ecosystems in the face of climate change. While there have been many provenance studies in trees, less is known about local adaptation in herbaceous species, including the perennial grasses that dominate arid and semiarid rangeland ecosystems. We used a common garden study to quantify variation in growth and drought resistance traits in 99 populations of Elymus elymoides from a broad geographic and climatic range in the western United States. Ecotypes from drier sites produced less biomass and smaller seeds, and had traits associated with greater drought resistance: small leaves with low osmotic potential and high integrated water use efficiency (δ13C). Seasonality also influenced plant traits. Plants from regions with relatively warm, wet summers had large seeds, large leaves, and low δ13C. Irrespective of climate, we also observed trade‐offs between biomass production and drought resistance traits. Together, these results suggest that much of the phenotypic variation among E. elymoides ecotypes represents local adaptation to differences in the amount and timing of water availability. In addition, ecotypes that grow rapidly may be less able to persist under dry conditions. Land managers may be able to use this variation to improve restoration success by seeding ecotypes with multiple drought resistance traits in areas with lower precipitation. The future success of this common rangeland species will likely depend on the use of tools such as seed transfer zones to match local variation in growth and drought resistance to predicted climatic conditions.

How males and females contribute to joint reproductive success has been a long-standing question in sexual selection. Under postcopulatory sexual selection, paternity success is predicted to derive from complex interactions among females engaging in cryptic female choice and males engaging in sperm competition. Such interactions have been identified as potential sources of genetic variation in sexually selected traits but are also expected to inhibit trait diversification. To date, studies of interactions between females and competing males have focused almost exclusively on genotypes and not phenotypic variation in sexually selected traits. Here, we characterize within- and between-sex interactions in Drosophila melanogaster using isogenic lines with heritable variation in both male and female traits known to influence competitive fertilization. We confirmed, and expanded on, previously reported genotypic interactions within and between the sexes, and showed that several reproductive events, including sperm transfer, female sperm ejection, and sperm storage, were explained by two- and three-way interactions among sex-specific phenotypes. We also documented complex interactions between the lengths of competing males’ sperm and the female seminal receptacle, which are known to have experienced rapid female-male co-diversification. Our results highlight the nonindependence of sperm competition and cryptic female choice and demonstrate that complex interactions between the sexes do not limit the ability of multivariate systems to respond to directional sexual selection.

Introduction Transcriptomic divergence drives plant ecological adaptation. Upland rice is differentiated in drought tolerance from lowland rice during its adaptation to the drought‐prone environment. They provide a good system to learn the evolution of drought tolerance in rice. Methods and Results We estimate morphological differences between the two rice ecotypes under well‐watered and drought conditions, as well as their genetic and transcriptomic divergences by the high‐throughput sequencing. Upland rice possesses higher expression diversity than lowland rice does. Thousands of genes exhibit expression divergences between the two rice ecotypes, which contributes to their morphological differences in drought tolerance. These transcriptomic divergences contribute to drought adaptation of upland rice during its domestication. Mutations in transcriptional regulatory regions, which cause presence and absence of cis‐elements, are the cause of expression divergence. About 15.3% transcriptionally selected genes also receive sequence‐based selection in upland or lowland ecotype. Some highly differentiated genes promote the transcriptomic divergence between rice ecotypes via gene co‐expression network. In addition, we also detected transcriptomic trade‐offs between drought tolerance and productivity. Discussion Many key genes, which promote transcriptomic adaptation to drought in upland rice, have great prospective in breeding water‐saving and drought‐resistant rice. Meanwhile, appropriate strategies are required in breeding to overcome the potential transcriptomic trade‐off.

Understanding the factors influencing the current distribution of genetic diversity across a species range is one of the main questions of evolutionary biology, especially given the increasing threat to biodiversity posed by climate change. Historical demographic processes such as population expansion or bottlenecks and decline are known to exert a predominant influence on past and current levels of genetic diversity, and revealing this demo‐genetic history can have immediate conservation implications. We used a whole‐exome capture sequencing approach to analyze polymorphism across the gene space of red spruce (Picea rubens Sarg.), an endemic and emblematic tree species of eastern North America high‐elevation forests that are facing the combined threat of global warming and increasing human activities. We sampled a total of 340 individuals, including populations from the current core of the range in northeastern USA and southeastern Canada and from the southern portions of its range along the Appalachian Mountains, where populations occur as highly fragmented mountaintop “sky islands.” Exome capture baits were designed from the closely relative white spruce (P. glauca Voss) transcriptome, and sequencing successfully captured most regions on or near our target genes, resulting in the generation of a new and expansive genomic resource for studying standing genetic variation in red spruce applicable to its conservation. Our results, based on over 2 million exome‐derived variants, indicate that red spruce is structured into three distinct ancestry groups that occupy different geographic regions of its highly fragmented range. Moreover, these groups show small Ne, with a temporal history of sustained population decline that has been ongoing for thousands (or even hundreds of thousands) of years. These results demonstrate the broad potential of genomic studies for revealing details of the demographic history that can inform management and conservation efforts of nonmodel species with active restoration programs, such as red spruce.

Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of a whole genome paired with reduced representation libraries (RAD-Seq) from samples collected across the species' range, we find evidence for panmixia using multiple methods, including PCA (no geographic clustering), admixture analyses (ADMIXTURE and TESS conclude K=1), and comparisons of genetic differentiation (average FST=0.029). Demographic modeling approaches recovered an ancient decline that had a strong impact on genetic diversity but did not detect any effect from the known recent decline. We also did not detect any evidence for selection, and hence adaptive variation, at any site, either geographic or genomic. These results indicate that species continues to have high vagility across its range despite population decline and habitat loss and should be managed as a single unit.

Sexually antagonistic (SA) genetic variation—in which genotypes favoured in one sex are disfavoured in the other—is predicted to be common and has been documented in several animal and plant populations, yet we currently know little about its pervasiveness among species or its population genetic basis. Recent applications of genomics in studies of SA genetic variation have highlighted considerable methodological challenges to the identification and characterisation of SA genes, raising questions about the feasibility of genomic approaches for inferring SA selection. The related fields of local adaptation and statistical genomics have previously dealt with similar challenges, and lessons from these disciplines can therefore help overcome current difficulties in applying genomics to study SA genetic variation. Here, we integrate theoretical and analytical concepts from local adaptation and statistical genomics research—includingFSTandFISstatistics, genome-wide association studies (GWAS), pedigree analyses, reciprocal transplant studies, and evolve-and-resequence (E&R) experiments—to evaluate methods for identifying SA genes and genome-wide signals of SA genetic variation. We begin by developing theoretical models for between-sexFSTandFIS, including explicit null distributions for each statistic, and using them to critically evaluate putative signals of sex-specific selection in previously published datasets. We then highlight new statistics that address some of the limitations ofFSTandFIS, along with applications of more direct approaches for characterising SA genetic variation, which incorporate explicit fitness measurements. We finish by presenting practical guidelines for the validation and evolutionary analysis of candidate SA genes and discussing promising empirical systems for future work.Impact SummaryGenome sequences carry a record of the evolutionary and demographic histories of natural populations. Research over the last two decades has dramatically improved our ability to detect genomic signals of adaptation by natural selection, including several widely-used methods for identifying genes underlying local adaptation and quantitative trait variation. Yet the application of these methods to identify sexually antagonistic (SA) genes—wherein variants that are adaptive for one sex are maladaptive for the other—remains under-explored, despite the potential importance of SA selection as a mechanism for maintaining genetic variation. Indeed, several lines of evidence suggest that SA genetic variation is common within animal and plant populations, underscoring the need for analytical methods that can reliably identify SA genes and genomic signals of SA genetic variation. Here, we integrate statistics and experimental designs that were originally developed within the fields of local adaptation and statistical genomics and apply them to the context of sex-specific adaptation and SA genetic variation. First, we evaluate and extend statistical methods for identifying signals of SA variation from genome sequence data alone. We then apply these methods to re-analyse previously published datasets on allele frequency differences between sexes—a putative signal of SA selection. Second, we highlight more direct approaches for identifying SA genetic variation, which utilise experimental evolution and statistical associations between individual genetic variants and fitness. Third, we provide guidelines for the biological validation, evolutionary analysis, and interpretation of candidate SA polymorphisms. By building upon the strong methodological foundations of local adaptation and statistical genomics research, we provide a roadmap for rigorous analyses of genetic data in the context of sex-specific adaptation, thereby facilitating insights into the role and pervasiveness of SA variation in adaptive evolution.

Cytoplasmic male sterility (CMS) is a widely used genetic tool in modern hybrid rice breeding. Most genes conferring rice gametophytic CMS are homologous to orf79 and co‐transcribe with atp6. However, the origin, differentiation and flow of these mitochondrial genes in wild and cultivated rice species remain unclear. In this study, we performed de novo assembly of the mitochondrial genomes of 221 common wild rice (Oryza rufipogon Griff.) and 369 Asian cultivated rice (Oryza sativa L.) accessions, and identified 16 haplotypes of atp6‐orf79‐like structures and 11 orf79 alleles. These homologous structures were classified into 4 distinct groups (AO‐I, AO‐II, AO‐III and AO‐IV), all of which were observed in O. rufipogon but only AO‐I was detected in O. sativa, causing a decrease in the frequency of atp6‐orf79‐like structures from 19.9% to 8.1%. Phylogenetic and biogeographic analyses revealed that the different groups of these gametophytic CMS‐related genes in O. rufipogon evolved in a multicentric pattern. The geographical origin of the atp6‐orf79‐like structures was further traced back, and a candidate region in north‐east of Gangetic Plain on the Indian Peninsula (South Asia) was identified as the origin centre of AO‐I. The orf79 alleles were detected in all three cytoplasmic types (Or‐CT0, Or‐CT1 and Or‐CT2) of O. rufipogon, but only two alleles (orf79a and orf79b) were observed in Or‐CT0 type of O. sativa, while no orf79 allele was found in other types of O. sativa. Our results also revealed that the orf79 alleles in cultivated rice originated from the wild rice population in South and South‐East Asia. In addition, strong positive selection pressure was detected on the sequence variations of orf79 alleles, and a special evolutionary strategy was noted in these gametophytic CMS‐related genes, suggesting that their divergence could be beneficial to their survival in evolution.

Despite being one of the most diverse families, scant attention has been paid to the seed dispersal system in Orchidaceae, owing to the widely accepted notion that wind dispersal is the dominant strategy. However, the indehiscent fruits, with seeds immersed in fleshy tissue, evoke the possibility of endozoochory in Apostasioideae, the earliest diverging lineage of orchids. In the present study, I investigated the seed dispersal system of Apostasia nipponica by direct observation, time-lapse photography, and investigation of the viability of seeds passing through the digestive tract of orthopterans. This study revealed a previously undocumented seed dispersal system in A. nipponica, in which the cricket, Eulandrevus ivani, and the camel cricket, Diestrammena yakumontana, consume the fruit and defecate viable seeds. Orthopterans are rarely considered seed dispersers, but the gross fruit morphology and pigmentation patterns of some Apostasia species parallel those seen in A. nipponica, suggesting that similar seed dispersal systems could be widespread among Apostasia species. Whether seed dispersal by orthopteran frugivores is common in Apostasioideae warrants further investigation.

Recent studies have begun to elucidate the genetic basis for phenotypic traits in salmonid species, but many questions remain before these candidate genes can be directly incorporated into conservation management. In Chinook Salmon (Oncorhynchus tshawytscha), a region of major effect for migration timing has been discovered that harbors two adjacent candidate genes (greb1L, rock1), but there has been limited work to examine the association between these genes and migratory phenotypes at the individual, compared to the population, level. To provide a more thorough test of individual phenotypic association within lineages of Chinook Salmon, 33 candidate markers were developed across a 220 Kb region on chromosome 28 previously associated with migration timing. Candidate and neutral markers were genotyped in individuals from representative collections that exhibit phenotypic variation in timing of arrival to spawning grounds from each of three lineages of Chinook Salmon. Association tests confirmed the majority of markers on chromosome 28 were significantly associated with arrival timing and the strongest association was consistently observed for markers within the rock1 gene and the intergenic region between greb1L and rock1. Candidate markers alone explained a wide range of phenotypic variation for Lower Columbia and Interior ocean‐type lineages (29% and 78%, respectively), but less for the Interior stream‐type lineage (5%). Individuals that were heterozygous at markers within or upstream of rock1 had phenotypes that suggested a pattern of dominant inheritance for early arrival across populations. Finally, previously published fitness estimates from the Interior stream‐type lineage enabled tests of association with arrival timing and two candidate markers, which revealed that fish with homozygous mature genotypes had slightly higher fitness than fish with premature genotypes, while heterozygous fish were intermediate. Overall, these results provide additional information for individual‐level genetic variation associated with arrival timing that may assist with conservation management of this species.

Sloths are notoriously slow and consequently have limited dispersal ability, which makes them particularly vulnerable to the effects of habitat fragmentation and degradation. Sloths in Costa Rica are considered of conservation concern due to habitat loss, livestock production and increasing urbanization. Reintroductions from rescue centres are commonplace across the country, yet their genetic diversity and population structure are unknown, and there is currently little consideration of the genetic background prior to intervention or releases. We used microsatellite analysis to undertake the first exploratory investigation into sloth population genetics in Costa Rica. Using data from 98 two‐fingered sloths (Choloepus hoffmanni) from four different geographic regions, we determined the presence of four potential genetic groups, three of them with minimal population structuring despite the limited dispersal ability and presence of physical barriers. Sloths from the North appear to represent a highly distinct population that we propose may require management as a discrete unit for conservation. We stress the need for additional analyses to better understand the genetic structure and diversity of North andWest regions and suggest that rescue facilities in Costa Rica should consider the genetic background of rehabilitated sloths when planning future reintroductions. Our results also highlight the threat posed by physical isolation due to widespread urbanization and agriculture expansion for a species with a weak dispersal ability.

Myxobacteria and dictyostelids are prokaryotic and eukaryotic multicellular lineages, respectively, that after nutrient depletion aggregate and develop into structures called fruiting bodies. The developmental processes and resulting morphological outcomes resemble one another to a remarkable extent despite their independent origins, the evolutionary distance between them and the lack of traceable homology in molecular mechanisms. We hypothesize that the morphological parallelism between the two lineages arises as the consequence of the interplay within multicellular aggregates betweengeneric processes, physical and physicochemical processes operating similarly in living and non-living matter at the mesoscale (~10–3–10–1 m) andagent-like behaviors, unique to living systems and characteristic of the constituent cells, considered as autonomous entities acting according to internal rules in a shared environment. Here, we analyze the contributions of generic and agent-like determinants in myxobacteria and dictyostelid development and their roles in the generation of their common traits. Consequent to aggregation, collective cell–cell contacts mediate the emergence of liquid-like properties, making nascent multicellular masses subject to novel patterning and morphogenetic processes. In both lineages, this leads to behaviors such as streaming, rippling, and rounding-up, as seen in non-living fluids. Later the aggregates solidify, leading them to exhibit additional generic properties and motifs. Computational models suggest that the morphological phenotypes of the multicellular masses deviate from the predictions of generic physics due to the contribution of agent-like behaviors of cells such as directed migration, quiescence, and oscillatory signal transduction mediated by responses to external cues. These employ signaling mechanisms that reflect the evolutionary histories of the respective organisms. We propose that the similar developmental trajectories of myxobacteria and dictyostelids are more due to shared generic physical processes in coordination with analogous agent-type behaviors than to convergent evolution under parallel selection regimes. Insights from the biology of these aggregative forms may enable a unified understanding of developmental evolution, including that of animals and plants.