Widespread evidence for incipient ecological speciation: a meta-analysis of isolation-by-ecology

The succession of ecological divergence and reproductive isolation in adaptive radiations

Adaptive radiation is a major source of biodiversity but the way in which known components of ecological opportunity, ecological differentiation, and reproductive isolation underpin such biodiversity patterns remains elusive. Much is known about the evolution of ecological differentiation and reproductive isolation during single speciation events, but exactly how those processes scale up to complete adaptive radiations is less understood. Do we expect complete reproductive barriers between newly formed species before the ecological differentiation continues, or does proper species formation occur much later, long after the ecological diversification? Our goal is to improve our mechanistic understanding of adaptive radiations by analyzing an individual-based model that includes a suite of mechanisms that are known to contribute to biodiversity. The model includes variable biogeographic settings, ecological opportunities, and types of mate choice, which makes several different scenarios of an adaptive radiation possible. We find that evolving clades tend to exploit ecological opportunities early whereas reproductive barriers evolve later, demonstrating a decoupling of ecological differentiation and species formation. In many cases, we also find a long-term trend where assortative mating associated with ecological traits is replaced by sexual selection of neutral display traits as the primary mechanism for reproductive isolation. Our results propose that reticulate phylogenies are likely common and stem from initially low reproductive barriers, rather than the previously suggested idea of repeated hybridization events between well-separated species.

RIDGE, a tool tailored to detect gene flow barriers across species pairs

Characterizing the processes underlying reproductive isolation between diverging lineages is central to understanding speciation. Here, we present RIDGE-Reproductive Isolation Detection using Genomic polymorphisms-a tool tailored for quantifying gene flow barrier proportion and identifying the relevant genomic regions. RIDGE relies on an Approximate Bayesian Computation with a model-averaging approach to accommodate diverse scenarios of lineage divergence. It captures heterogeneity in effective migration rate along the genome while accounting for variation in linked selection and recombination. The barrier detection test relies on numerous summary statistics to compute a Bayes factor, offering a robust statistical framework that facilitates cross-species comparisons. Simulations revealed RIDGE's efficiency in capturing signals of ongoing migration. Model averaging proved particularly valuable in scenarios of high model uncertainty where no migration or migration homogeneity can be wrongly assumed, typically for recent divergence times <0.1 2Ne generations. Applying RIDGE to four published crow data sets, we first validated our tool by identifying a well-known large genomic region associated with mate choice patterns. Second, while we identified a significant overlap of outlier loci using RIDGE and traditional genomic scans, our results suggest that a substantial portion of previously identified outliers are likely false positives. Outlier detection relies on allele differentiation, relative measures of divergence and the count of shared polymorphisms and fixed differences. Our analyses also highlight the value of incorporating multiple summary statistics including our newly developed outlier ones that can be useful in challenging detection conditions.

The role of neutral and adaptive evolutionary processes on patterns of genetic diversity across small cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus)

Understanding the adaptability of small populations in the face of environmental change is a central problem in evolutionary biology. Solving this problem is challenging because neutral evolutionary processes that operate on historical and contemporary timescales can override the effects of selection in small populations. We assessed the effects of isolation by colonization (IBC), isolation by dispersal limitation (IBDL) as reflected by a pattern of isolation by distance (IBD), and isolation by adaptation (IBA) and the roles of genetic drift and gene flow on patterns of genetic differentiation among 19 cave-dwelling populations of Icelandic Arctic charr (Salvelinus alpinus). We detected evidence of IBC based on the genetic affinity of nearby cave populations and the genetic relationships between the cave populations and the presumed ancestral population in the lake. A pattern of IBD was evident regardless of whether high-level genetic structuring (IBC) was taken into account. Genetic signatures of bottlenecks and lower genetic diversity in smaller populations indicate the effect of drift. Estimates of gene flow and fish movement suggest that gene flow is limited to nearby populations. In contrast, we found little evidence of IBA as patterns of local ecological and phenotypic variation showed little association with genetic differentiation among populations. Thus, patterns of genetic variation in these small populations likely reflect localized gene flow and genetic drift superimposed onto a larger-scale structure that is largely a result of colonization history. Our simultaneous assessment of the effects of neutral and adaptive processes in a tractable and replicated system has yielded novel insights into the evolution of small populations on both historical and contemporary timescales and over a smaller spatial scale than is typically studied.

Genomic signatures of climate adaptation in bank voles

Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.

Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula

Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.

The effect of divergent and parallel selection on the genomic landscape of divergence

While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.

Weak Genetic Isolation and Putative Phenotypic Selection in the Wild Carnation Dianthus virgineus (Caryophyllaceae)

By relating genetic divergence at neutral loci, phenotypic variation, and geographic and environmental distances, it is possible to dissect micro-evolutionary scenarios involving natural selection and neutral evolution. In this work, we tested the patterns of intraspecific genetic and phenotypic variation along an elevational gradient, using Dianthus virgineus as study system. We genotyped genome-wide SNPs through ddRAD sequencing and quantified phenotypic variation through multivariate morphological variation. We assessed patterns of variation by testing the statistical association between genetic, phenotypic, geographic, and elevational distances and explored the role of genetic drift and selection by comparing the Fst and Pst of morphometric traits. We revealed a weak genetic structure related to geographic distance among populations, but we excluded the predominant role of genetic drift acting on phenotypic traits. A high degree of phenotypic differentiation with respect to genetic divergence at neutral loci allowed us to hypothesize the effect of selection, putatively fuelled by changing conditions at different sites, on morphological traits. Thus, natural selection acting despite low genetic divergence at neutral loci can be hypothesized as a putative driver explaining the observed patterns of variation.

Gene-network analysis predicts clinical response to immunotherapy in patients affected by NSCLC

OBJECTIVES

Predictive biomarkers of response to immune checkpoint inhibitors (ICIs) have been extensively studied in non-small cell lung cancer (NSCLC) with controversial results. Recently, gene-network analysis emerged as a new tool to address tumor biology and behavior, representing a potential tool to evaluate response to therapies.

METHODS

Clinical data and genetic profiles of 644 advanced NSCLCs were retrieved from cBioPortal and the Cancer Genome Atlas (TCGA); 243 ICI-treated NSCLCs were used to identify an immunotherapy response signatures via mutated gene network analysis and K-means unsupervised clustering. Signatures predictive values were tested in an external dataset of 242 cases and assessed versus a control group of 159 NSCLCs treated with standard chemotherapy.

RESULTS

At least two mutations in the coding sequence of genes belonging to the chromatin remodelling pathway (A signature), and/or at least two mutations of genes involved in cell-to-cell signalling pathways (B signature), showed positive prediction in ICI-treated advanced NSCLC. Signatures performed best when combined for patients undergoing first-line immunotherapy, and for those receiving combined ICIs.

CONCLUSIONS

Alterations in genes related to chromatin remodelling complexes and cell-to-cell crosstalk may force dysfunctional immune evasion, explaining susceptibility to immunotherapy. Therefore, exploring mutated gene networks could be valuable for determining essential biological interactions, contributing to treatment personalization.

Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle

Organisms living in mountains contend with extreme climatic conditions, including short growing seasons and long winters with extensive snow cover. Anthropogenic climate change is driving unprecedented, rapid warming of montane regions across the globe, resulting in reduced winter snowpack. Loss of snow as a thermal buffer may have serious consequences for animals overwintering in soil, yet little is known about how variability in snowpack acts as a selective agent in montane ecosystems. Here, we examine genomic variation in California populations of the leaf beetle Chrysomela aeneicollis, an emerging natural model system for understanding how organisms respond to climate change. We used a genotype-environment association approach to identify genomic signatures of local adaptation to microclimate in populations from three montane regions with variable snowpack and a coastal region with no snow. We found that both winter-associated environmental variation and geographical distance contribute to overall genomic variation across the landscape. We identified non-synonymous variation in novel candidate loci associated with cytoskeletal function, ion transport and membrane stability, cellular processes associated with cold tolerance in other insects. These findings provide intriguing evidence that variation in snowpack imposes selective gradients in montane ecosystems.

Ecological and evolutionary drivers of phenotypic and genetic variation in the European crabapple [Malus sylvestris (L.) Mill.], a wild relative of the cultivated apple

BACKGROUND AND AIMS

Studying the relationship between phenotypic and genetic variation in populations distributed across environmental gradients can help us to understand the ecological and evolutionary processes involved in population divergence. We investigated the patterns of genetic and phenotypic diversity in the European crabapple, Malus sylvestris, a wild relative of the cultivated apple (Malus domestica) that occurs naturally across Europe in areas subjected to different climatic conditions, to test for divergence among populations.

METHODS

Growth rates and traits related to carbon uptake in seedlings collected across Europe were measured in controlled conditions and associated with the genetic status of the seedlings, which was assessed using 13 microsatellite loci and the Bayesian clustering method. Isolation-by-distance, isolation-by-climate and isolation-by-adaptation patterns, which can explain genetic and phenotypic differentiation among M. sylvestris populations, were also tested.

KEY RESULTS

A total of 11.6 % of seedlings were introgressed by M. domestica, indicating that crop-wild gene flow is ongoing in Europe. The remaining seedlings (88.4 %) belonged to seven M. sylvestris populations. Significant phenotypic trait variation among M. sylvestris populations was observed. We did not observe significant isolation by adaptation; however, the significant association between genetic variation and the climate during the Last Glacial Maximum suggests that there has been local adaptation of M. sylvestris to past climates.

CONCLUSIONS

This study provides insight into the phenotypic and genetic differentiation among populations of a wild relative of the cultivated apple. This might help us to make better use of its diversity and provide options for mitigating the impact of climate change on the cultivated apple through breeding.

Speciation without gene-flow in hybridizing deer

Under the ecological speciation model, divergent selection acts on ecological differences between populations, gradually creating barriers to gene flow and ultimately leading to reproductive isolation. Hybridisation is part of this continuum and can both promote and inhibit the speciation process. Here, we used white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) to investigate patterns of speciation in hybridizing sister species. We quantified genome-wide historical introgression and performed genome scans to look for signatures of four different selection scenarios. Despite ample modern evidence of hybridisation, we found negligible patterns of ancestral introgression and no signatures of divergence with gene flow, rather localized patterns of allopatric and balancing selection were detected across the genome. Genes under balancing selection were related to immunity, MHC and sensory perception of smell, the latter of which is consistent with deer biology. The deficiency of historical gene-flow suggests that white-tailed and mule deer were spatially separated during the glaciation cycles of the Pleistocene and genome wide differentiation accrued via genetic drift. Dobzhansky-Muller incompatibilities and selection against hybrids are hypothesised to be acting, and diversity correlations to recombination rates suggests these sister species are far along the speciation continuum.

Landscape genetics across the Andes mountains: Environmental variation drives genetic divergence in the leaf-cutting ant Atta cephalotes

Distinguishing among the mechanisms underlying the spatial distribution of genetic variation resulting from the environmental or physical barriers from those arising due to simple geographic distance is challenging in complex landscapes. The Andean uplift represents one of the most heterogeneous habitats where multiple mechanisms may interact, confounding their relative roles. We explore this broad question in the leaf-cutting ant Atta cephalotes, a species that is distributed across the Andes mountains, using nuclear microsatellite markers and mtCOI gene sequences. We investigate spatial genetic divergence across the western range of the northern Andes in Colombia by testing the relative role of alternative scenarios of population divergence, including isolation by geographic distance (IBD), climatic conditions (IBE), and the physical barriers presented by the Andes mountains (IBB). Our results reveal substantial genetic differentiation among A. cephalotes populations for both types of markers, but only nuclear divergence followed a hierarchical pattern with multiple models of genetic divergence imposed by the western range. Model selection showed that the IBD, IBE (temperature and precipitation), and IBB (Andes mountains) models, often proposed as individual drivers of genetic divergence, interact, and explain up to 33% of the genetic divergence in A. cephalotes. The IBE model remained significant after accounting for IBD, suggesting that environmental factors play a more prominent role than IBB. These factors, in combination with the idiosyncratic dispersal patterns of ants, appear to determine the hierarchical patterns of gene flow. This study enriches our understanding of the forces shaping population divergence in complex habitat landscapes.

Drivers of population divergence and genetic variation in Elymus breviaristatus (Keng) Keng f. (Poaceae: Triticeae), an endemic perennial herb of the Qinghai-Tibet plateau

Elymus breviaristatus, a rare grass species with excellent resistance and ecological importance, is narrowly distributed on the Qinghai-Tibet plateau. Populations of E. breviaristatus are declining due to habitat fragmentation, and thus far, characteristics of genetic differentiation and adaptive responses to climate change remain poorly understood in this species. Here, we explored the genetic structure of 18 natural populations (269 individuals) in the transition zone between Tibet and the Hengduan Mountains using 15 expressed sequence tag (EST)-SSR primer pairs and identified possible barriers to gene flow that might have caused genetic discontinuities. Additional analyses were performed to identify the environmental factors affecting genetic diversity and to test whether the patterns of genetic variation among populations were more consistent with the isolation by distance (IBD) or isolation by environment (IBE) model. Multiple measures of genetic diversity revealed that intra-population genetic variation was low, while inter-population genetic variation was high. Clustering, structure, and principal coordinate analyses identified three genetic groups: (a) Eastern Qamdo, (b) Nagqu and Western Qamdo, and (c) Lhasa and Nyingchi. A clear physical barrier to gene flow was formed by the Yarlung Zangbo Grand Canyon and the Tanggula Mountains. We found that both IBD and IBE contributed to the observed patterns of genetic variation, and the IBE model played a leading role. In addition, precipitation-related variables, soil phosphorus content and soil K:P ratio significantly affected population genetic variation. Overall, our results emphasized the genetic fragility of E. breviaristatus populations and showed that this species requires attention, as future climate changes and human activities may further threaten its survival. In addition, the genetic differences among E. breviaristatus populations should be considered when formulating conservation measures for E. breviaristatus populations in the study area.

Eco-Geography and Phenology Are the Major Drivers of Reproductive Isolation in the Royal Irises, a Species Complex in the Course of Speciation

The continuous nature of speciation implies that different species are found at different stages of divergence, from no- to complete reproductive isolation. This process and its underlying mechanisms are best viewed in incipient species. Moreover, the species complex can offer unique insight into how reproductive isolation (RI) has evolved. The royal irises (Iris section Oncocyclus) are a young group of species in the course of speciation, providing an ideal system for speciation study. We quantified pre- and post-zygotic reproductive barriers between the eight Israeli species of this complex and estimated the total RI among them. We tested for both pre-pollination and post-pollination reproductive barriers. Pre-pollination barriers, i.e., eco-geographic divergence and phenological differentiation were the major contributors to RI among the Iris species. On the other hand, post-pollination barriers, namely pollen-stigma interactions, fruit set, and seed viability had negligible contributions to total RI. The strength of RI was not uniform across the species complex, suggesting that species may have diverged at different rates. Overall, this study in a young, recently diverged group of species provides insight into the first steps of speciation, suggesting a crucial role of the pre-zygotic barriers.

Landscape genomics of the American lobster (Homarus americanus)

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive loci to reliably infer population structure and thus more rigorously delineating biological management units in marine exploited species. Toward this end, we genotyped 14,893 single nucleotide polymorphism (SNPs) in 4190 lobsters sampled across 96 sampling sites distributed along 1000 km in the northwest Atlantic in both Canada and the USA. As typical for most marine species, we observed a weak, albeit highly significant genetic structure. We also found that adaptive genetic variation allows detecting fine-scale population structure not resolved by neutral genetic variation alone. Using the recent genome assembly of the American lobster, we were able to map and annotate several SNPs located in functional genes potentially implicated in adaptive processes such as thermal stress response, salinity tolerance and growth metabolism pathways. Taken together, our study indicates that weak population structure in high gene flow systems can be resolved at various spatial scales, and that putatively adaptive genetic variation can substantially enhance the delineation of biological management units of marine exploited species.

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.

Host association, environment, and geography underlie genomic differentiation in a major forest pest

Diverse geographic, environmental, and ecological factors affect gene flow and adaptive genomic variation within species. With recent advances in landscape ecological modelling and high‐throughput DNA sequencing, it is now possible to effectively quantify and partition their relative contributions. Here, we use landscape genomics to identify determinants of genomic differentiation in the forest tent caterpillar, Malacosoma disstria, a widespread and irruptive pest of numerous deciduous tree species in North America. We collected larvae from multiple populations across Eastern Canada, where the species experiences a diversity of environmental gradients and feeds on a number of different host tree species, including trembling aspen (Populus tremuloides), sugar maple (Acer saccharum), red oak (Quercus rubra), and white birch (Betula papyrifera). Using a combination of reciprocal causal modelling (RCM) and distance‐based redundancy analyses (dbRDA), we show that differentiation of thousands of genome‐wide single nucleotide polymorphisms (SNPs) among individuals is best explained by a combination of isolation by distance, isolation by environment (spatial variation in summer temperatures and length of the growing season), and differences in host association. Configuration of suitable habitat inferred from ecological niche models was not significantly related to genomic differentiation, suggesting that M. disstria dispersal is agnostic with respect to habitat quality. Although population structure was not discretely related to host association, our modelling framework provides the first molecular evidence of host‐associated differentiation in M. disstria, congruent with previous documentation of reduced growth and survival of larvae moved between natal host species. We conclude that ecologically mediated selection is contributing to variation within M. disstria, and that divergent adaptation related to both environmental conditions and host association should be considered in ongoing research and management of this important forest pest.

Genetic structure of wild rice Zizania latifolia in an expansive heterogeneous landscape along a latitudinal gradient

Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (HE = 0.125–0.433) and high genetic differentiation (FST = 0.641, Øpt = 0.654) were found. Higher historical gene flow (MH = 0.212–2.354) than contemporary gene flow (MC = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.

Interactions With Plant Defences Isolate Sympatric Populations of an Herbivorous Mite

Host plant specialisation can promote evolutionary divergence between herbivore populations associated with different plant species. While the mechanisms by which specialist species exploit their hosts have been studied widely across taxa, less is known about the mechanisms that allow intraspecific variants to arise and to be maintained across spatial and temporal scales. To understand whether adaptations to plant defences against herbivory contribute to the co-existence of genetically distinct populations of an herbivore, we investigate the interaction between honeysuckle (Lonicera periclymenum) and sympatric specialist and generalist populations of the spider mite Tetranychus urticae. We found that mite folivory induces the production of sticky droplets on honeysuckle, which have a defensive role: they increase mite mortality directly, and potentially indirectly by increasing the arrestment of a predator. We show that droplet induction and the preference to feed on honeysuckle depend on mite genotype, where the generalist avoids this host and the specialist suppresses droplet production. These traits are heritable and dominant in F1 hybrids between generalists and specialists. Selection pressure from honeysuckle and differences in host preference likely reduce the opportunity of mating encounters on this host. We propose that the interplay between selection from host plant defences and ecological barriers to hybridisation contribute to the persistence of genetically distinct populations of a single species in sympatry.

Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence

In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.

Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot

BACKGROUND

Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation.

RESULTS

The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (h_T) = 0.498; unbiased expected heterozygosity (UH_E) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods.

CONCLUSIONS

Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.

Hybridization boosts dispersal of two contrasted ecotypes in a grass species

Genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes and influence rates of hybridization. How these dynamics affect the emergence and spread of novel phenotypes remains only partially understood. Here, we use phylogenomics and population genomics to retrace the origin and spread of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. In addition to an ecotype inhabiting wetlands, we report the existence of a previously undescribed ecotype inhabiting Miombo woodlands and grasslands. The two ecotypes are consistently associated with different nuclear groups, which represent an advanced stage of divergence with secondary low-level gene flow. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can enter the seeds of the other via occasional pollen movements with sorting of nuclear groups in subsequent generations. The contrasting ecotypes of A. angusta can thus use each other as a gateway to new locations across a large part of Africa, showing that hybridization can facilitate the geographical dispersal of distinct ecotypes of the same grass species.

Demography and selection analysis of the incipient adaptive radiation of a Hawaiian woody species

Ecological divergence in a species provides a valuable opportunity to study the early stages of speciation. We focused on Metrosideros polymorpha, a unique example of the incipient radiation of woody species, to examine how an ecological divergence continues in the face of gene flow. We analyzed the whole genomes of 70 plants collected throughout the island of Hawaii, which is the youngest island with the highest altitude in the archipelago and encompasses a wide range of environments. The continuous M. polymorpha forest stands on the island of Hawaii were differentiated into three genetic clusters, each of which grows in a distinctive environment and includes substantial genetic and phenotypic diversity. The three genetic clusters showed signatures of selection in genomic regions encompassing genes relevant to environmental adaptations, including genes associated with light utilization, oxidative stress, and leaf senescence, which are likely associated with the ecological differentiation of the species. Our demographic modeling suggested that the glaberrima cluster in wet environments maintained a relatively large population size and two clusters split: polymorpha in the subalpine zone and incana in dry and hot conditions. This ecological divergence possibly began before the species colonized the island of Hawaii. Interestingly, the three clusters recovered genetic connectivity coincidentally with a recent population bottleneck, in line with the weak reproductive isolation observed in the species. This study highlights that the degree of genetic differentiation between ecologically-diverged populations can vary depending on the strength of natural selection in the very early phases of speciation.

Knowledge about how genetic barriers are formed between populations in distinct environments is valuable to understand the processes of speciation and conserve biodiversity. Metrosideros polymorpha, an endemic woody species in the Hawaiian Islands, is a good system to study developing genetic barriers in a species, because it colonized the diverse environments and diversified the morphology for a relatively short period of time. We analyzed the genomes of 70 M. polymorpha plants from a broad range of environments on the island of Hawaii to infer the current and past genetic barriers among them. Currently, M. polymorpha plants growing in different environments have substantially different genomes, especially at the genomic regions with genes putatively controlling physiology to fit in distinct environment. However, in its history, they had hybridized with one another, possibly because plants formerly growing in different environments came into close contact due to the climate changes. It is suggested that genetic barriers can easily strengthen or weaken depending on environments splitting the ecology of a species before reproductive isolation becomes complete.

Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila Alpestris)

Genetic structure and phenotypic variation among populations is affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD dataset of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.

Ecological divergence and synchronous Pleistocene diversification in the widespread South American butter frog complex

Phylogeographic studies primarily focus on the major role of landscape topography in driving lineage diversification. However, populational phylogeographic breaks may also occur as a result of either niche conservatism or divergence, in the absence of geographic barriers to gene flow. Furthermore, these two factors are not mutually exclusive and can act in concert, making it challenging to evaluate their relative importance on explaining genetic variation in nature. Herein, we use sequences of two mitochondrial and four nuclear genes to investigate the timing and diversification patterns of species pertaining to the Leptodactylus latrans complex, which harbors four morphologically cryptic species with broad distributions across environmental gradients in eastern South America. The origin of this species complex dates back to the late Miocene (ca. 5.5 Mya), but most diversification events occurred synchronically during the late Pleistocene likely as the result of ecological divergence driven by Quaternary climatic oscillations. Further, significant patterns of environmental niche divergences among species in the L. latrans complex imply that ecological isolation is the primary mode of genetic diversification, mostly because phylogenetic breaks are associated with environmental transitions rather than topographic barriers at both species and populational scale. We provided new insights about diversification patterns and processes within a species complex of broadly and continuously distributed group of frogs along South America.

Adaptive divergence and the evolution of hybrid trait mismatch in threespine stickleback

Selection against mismatched traits in hybrids is the phenotypic analogue of intrinsic hybrid incompatibilities. Mismatch occurs when hybrids resemble one parent population for some phenotypic traits and the other parent population for other traits, and is caused by dominance in opposing directions or from segregation of alleles in recombinant hybrids. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to test the theoretical prediction that trait mismatch in hybrids should increase with the magnitude of phenotypic divergence between parent populations. We measured morphological traits in parents and hybrids in crosses between a marine population representing the ancestral form and twelve freshwater populations that have diverged from this ancestral state to varying degrees according to their environments. We found that trait mismatch was greater in more divergent crosses for both F₁ and F₂ hybrids. In the F₁, the divergence–mismatch relationship was caused by traits having dominance in different directions, whereas it was caused by increasing segregating phenotypic variation in the F₂. Our results imply that extrinsic hybrid incompatibilities accumulate as phenotypic divergence proceeds.

Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation

Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of nonsignificant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e., loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST-based outlier detection tests. Instead, our analyses confirmed the lack of genome-wide differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.

Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental variation. Here, we analyze both genomic and phenotypic variation of rubber rabbitbrush (Ericameria nauseosa), a foundational shrub species of western North America. To quantify landscape genomic structure and provide perspective on patterns of local adaptation, we generated reduced representation sequencing data for 17 wild populations (222 individuals; 38,615 loci) spanning a range of environmental conditions. Population genetic analyses illustrated pronounced landscape genomic structure jointly shaped by geography and environment. Genetic-environment association (GEA) analyses using both redundancy analysis (RDA) and a machine-learning approach (Gradient Forest) indicated environmental variables (precipitation seasonality, slope, aspect, elevation, and annual precipitation) influenced spatial genomic structure and were correlated with allele frequency shifts indicative of local adaptation at a consistent set of genomic regions. We compared our GEA-based inference of local adaptation with phenotypic data collected by growing seeds from each population in a greenhouse common garden. Population differentiation in seed weight, emergence, and seedling traits was associated with environmental variables (e.g., precipitation seasonality) that were also implicated in GEA analyses, suggesting complementary conclusions about the drivers of local adaptation across different methods and data sources. Our results provide a baseline understanding of spatial genomic structure for E. nauseosa across the western Great Basin and illustrate the utility of GEA analyses for detecting the environmental causes and genetic signatures of local adaptation in a widely distributed plant species of restoration significance.

Genetic and morphological data demonstrate hybridization and backcrossing in a pair of salamanders at the far end of the speciation continuum

Deeply diverged yet hybridizing species provide a system to investigate the final stages of the speciation process. We study a hybridizing pair of salamander species-the morphologically and genetically drastically different newts Triturus cristatus and T. marmoratus-with a panel of 32 nuclear and mitochondrial genetic markers. Morphologically identified hybrids are mostly of the F1 generation and mothered by T. cristatus. The sex ratio of the F1 hybrid class is reciprocally skewed, with a preponderance of females in T. cristatus-mothered hybrids and males in T. marmoratus-mothered hybrids. This amounts to the Haldane effect operating in one direction of the cross. Deeper generation hybrids are occasionally produced, possibly including F1 hybrid × backcross hybrid offspring. Interspecific gene flow is low, yet skewed toward T. cristatus. This asymmetry may be caused by hybrid zone movement, with the superseding species being predisposed to introgression. The persisting gene flow between deeply differentiated species supports the notion that full genetic isolation may be selected against. Conversely, published morphological data suggest that introgressive hybridization is detrimental, with digital malformations occurring more frequently in the area of sympatry. Finally, to assist field identification, both within the area of natural range overlap and concerning anthropogenic introductions elsewhere, we document the phenotypical variation of two generations of hybrids compared with both parental species. We suggest that fluctuating range boundaries, ecological segregation, cytonuclear incompatibilities and hybrid breakdown through Bateson-Dobzhansky-Muller incompatibilities all contribute to species integrity, despite incomplete isolation during secondary contact.

Varying Intensities of Introgression Obscure Incipient Venom-Associated Speciation in the Timber Rattlesnake (Crotalus horridus)

Ecologically divergent selection can lead to the evolution of reproductive isolation through the process of ecological speciation, but the balance of responsible evolutionary forces is often obscured by an inadequate assessment of demographic history and the genetics of traits under selection. Snake venoms have emerged as a system for studying the genetic basis of adaptation because of their genetic tractability and contributions to fitness, and speciation in venomous snakes can be associated with ecological diversification such as dietary shifts and corresponding venom changes. Here, we explored the neurotoxic (type A)–hemotoxic (type B) venom dichotomy and the potential for ecological speciation among Timber Rattlesnake (Crotalus horridus) populations. Previous work identified the genetic basis of this phenotypic difference, enabling us to characterize the roles geography, history, ecology, selection, and chance play in determining when and why new species emerge or are absorbed. We identified significant genetic, proteomic, morphological, and ecological/environmental differences at smaller spatial scales, suggestive of incipient ecological speciation between type A and type B C. horridus. Range-wide analyses, however, rejected the reciprocal monophyly of venom type, indicative of varying intensities of introgression and a lack of reproductive isolation across the range. Given that we have now established the phenotypic distributions and ecological niche models of type A and B populations, genome-wide data are needed and capable of determining whether type A and type B C. horridus represent distinct, reproductively isolated lineages due to incipient ecological speciation or differentiated populations within a single species.

Rules of Plant Species Ranges: Applications for Conservation Strategies

Earth is changing rapidly and so are many plant species’ ranges. Here, we synthesize eco-evolutionary patterns found in plant range studies and how knowledge of species ranges can inform our understanding of species conservation in the face of global change. We discuss whether general biogeographic “rules” are reliable and how they can be used to develop adaptive conservation strategies of native plant species across their ranges. Rules considered include (1) factors that set species range limits and promote range shifts; (2) the impact of biotic interactions on species range limits; (3) patterns of abundance and adaptive properties across species ranges; (4) patterns of gene flow and their implications for genetic rescue, and (5) the relationship between range size and conservation risk. We conclude by summarizing and evaluating potential species range rules to inform future conservation and management decisions. We also outline areas of research to better understand the adaptive capacity of plants under environmental change and the properties that govern species ranges. We advise conservationists to extend their work to specifically consider peripheral and novel populations, with a particular emphasis on small ranges. Finally, we call for a global effort to identify, synthesize, and analyze prevailing patterns or rules in ecology to help speed conservation efforts.

Phenotypic and genomic diversification with isolation by environment along elevational gradients in a neotropical treefrog

Understanding how geographic and environmental heterogeneity drive local patterns of genetic variation is a major goal of ecological genomics and a key question in evolutionary biology. The tropical Andes and inter-Andean valleys are shaped by markedly heterogeneous landscapes, where species experience strong selective processes. We examined genome-wide SNP data together with behavioural and ecological traits (mating calls and body size) known to contribute to genetic isolation in anurans in the banana tree-dwelling frog, Boana platanera, distributed across an environmental gradient in Central Colombia (northern South America). Here, we analysed the relationships between environmentally (temperature and precipitation) associated genetic and phenotypic differentiation and the potential drivers of isolation by environment along an elevation gradient. We identified candidate SNPs associated with temperature and body size, which follow a clinal pattern of genome-wide differentiation tightly coupled with phenotypic variation: as elevation increases, B. platanera exhibits larger body size and longer call duration with more pulses but lower pulse rate and frequency. Thus, the environmental landscape has rendered a scenario where isolation by environment and candidate loci show concordance with phenotypic divergence in this tropical frog along an elevation gradient in the Colombian Andes. Our study sets the basis for evaluating the role of temperature in the genetic structure and local adaptation in tropical treefrogs and its putative effect on life cycle (embryos, tadpoles, adults) along elevation gradients.

Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats

Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.

Taxonomy and Translocations of African Mammals: A Plea for a Cautionary Approach

Ecotourism can fuel an important source of financial income for African countries and can therefore help biodiversity policies in the continent. Translocations can be a powerful tool to spread economic benefits among countries and communities; yet, to be positive for biodiversity conservation, they require a basic knowledge of conservation units through appropriate taxonomic research. This is not always the case, as taxonomy was considered an outdated discipline for almost a century, and some plurality in taxonomic approaches is incorrectly considered as a disadvantage for conservation work. As an example, diversity of the genus Giraffa and its recent taxonomic history illustrate the importance of such knowledge for a sound conservation policy that includes translocations. We argue that a fine-grained conservation perspective that prioritizes all remaining populations along the Nile Basin is needed. Translocations are important tools for giraffe diversity conservation, but more discussion is needed, especially for moving new giraffes to regions where the autochthonous taxa/populations are no longer existent. As the current discussion about the giraffe taxonomy is too focused on the number of giraffe species, we argue that the plurality of taxonomic and conservation approaches might be beneficial, i.e., for defining the number of units requiring separate management using a (majority) consensus across different concepts (e.g., MU—management unit, ESU—evolutionary significant unit, and ECU—elemental conservation unit). The taxonomically sensitive translocation policy/strategy would be important for the preservation of current diversity, while also supporting the ecological restoration of some regions within rewilding. A summary table of the main translocation operations of African mammals that have underlying problems is included. Therefore, we call for increased attention toward the taxonomy of African mammals not only as the basis for sound conservation but also as a further opportunity to enlarge the geographic scope of ecotourism in Africa.

Temporal resource partitioning mitigates interspecific competition and promotes coexistence among insect parasites

A key to understanding life's great diversity is discerning how competing organisms divide limiting resources to coexist in diverse communities. While temporal resource partitioning has long been hypothesized to reduce the negative effects of interspecific competition, empirical evidence suggests that time may not often be an axis along which animal species routinely subdivide resources. Here, we present evidence to the contrary in the world's most biodiverse group of animals: insect parasites (parasitoids). Specifically, we conducted a meta-analysis of 64 studies from 41 publications to determine if temporal resource partitioning via variation in the timing of a key life-history trait, egg deposition (oviposition), mitigates interspecific competition between species pairs sharing the same insect host. When competing species were manipulated to oviposit at (or near) the same time in or on a single host in the laboratory, competition was common, and one species was typically inherently superior (i.e. survived to adulthood a greater proportion of the time). In most cases, however, the inferior competitor could gain a survivorship advantage by ovipositing earlier (or in a smaller number of cases later) into shared hosts. Moreover, this positive (or in a few cases negative) priority advantage gained by the inferior competitor increased as the interval between oviposition times became greater. The results from manipulative experiments were also correlated with patterns of life-history timing and demography in nature: the more inherently competitively inferior a species was in the laboratory, the greater the interval between oviposition times of taxa in co-occurring populations. Additionally, the larger the interval between oviposition times of competing taxa, the more abundant the inferior species was in populations where competitors were known to coexist. Overall, our findings suggest that temporal resource partitioning via variation in oviposition timing may help to facilitate species coexistence and structures diverse insect communities by altering demographic measures of species success. We argue that the lack of evidence for a more prominent role of temporal resource partitioning in promoting species coexistence may reflect taxonomic differences, with a bias towards larger-sized animals. For smaller species like parasitic insects that are specialized to attack one or a group of closely related hosts, have short adult lifespans and discrete generation times, compete directly for limited resources in small, closed arenas and have life histories constrained by host phenology, temporal resource subdivision via variation in life history may play a critical role in allowing species to coexist by alleviating the negative effects of interspecific competition.

Ecological adaptation drives wood frog population divergence in life history traits

Phenotypic variation among populations is thought to be generated from spatial heterogeneity in environments that exert selection pressures that overcome the effects of gene flow and genetic drift. Here, we tested for evidence of isolation by distance or by ecology (i.e., ecological adaptation) to generate variation in early life history traits and phenotypic plasticity among 13 wood frog populations spanning 1200 km and 7° latitude. We conducted a common garden experiment and related trait variation to an ecological gradient derived from an ecological niche model (ENM) validated to account for population density variation. Shorter larval periods, smaller body weight, and relative leg lengths were exhibited by populations with colder mean annual temperatures, greater precipitation, and less seasonality in precipitation and higher population density (high-suitability ENM values). After accounting for neutral genetic variation, the Q_ST-F_ST analysis supported ecological selection as the key process generating population divergence. Further, the relationship between ecology and traits was dependent upon larval density. Specifically, high-suitability/high-density populations in the northern part of the range were better at coping with greater conspecific competition, evidenced by greater postmetamorphic survival and no difference in body weight when reared under stressful conditions of high larval density. Our results support that both climate and competition selection pressures drive clinal variation in larval and metamorphic traits in this species. Range-wide studies like this one are essential for accurate predictions of population's responses to ongoing ecological change.

Genetic, Morphological, and Environmental Differentiation of an Arid-Adapted Oak with a Disjunct Distribution

The patterns of genetic and morphological diversity of a widespread species can be influenced by environmental heterogeneity and the degree of connectivity across its geographic distribution. Here, we studied Quercus havardii Rydb., a uniquely adapted desert oak endemic to the Southwest region of the United States, using genetic, morphometric, and environmental datasets over various geographic scales to quantify differentiation and understand forces influencing population divergence. First, we quantified variation by analyzing 10 eastern and 13 western populations from the disjunct distribution of Q. havardii using 11 microsatellite loci, 17 morphological variables, and 19 bioclimatic variables. We then used regressions to examine local and regional correlations of climate with genetic variation. We found strong genetic, morphological and environmental differences corresponding with the large-scale disjunction of populations. Additionally, western populations had higher genetic diversity and lower relatedness than eastern populations. Levels of genetic variation in the eastern populations were found to be primarily associated with precipitation seasonality, while levels of genetic variation in western populations were associated with lower daily temperature fluctuations and higher winter precipitation. Finally, we found little to no observed environmental niche overlap between regions. Our results suggest that eastern and western populations likely represent two distinct taxonomic entities, each associated with a unique set of climatic variables potentially influencing local patterns of diversity.

Experimental evolution of adaptive divergence under varying degrees of gene flow

Adaptive divergence is the key evolutionary process generating biodiversity by means of natural selection. Yet, the conditions under which it can arise in the presence of gene flow remain contentious. To address this question, we subjected 132 sexually reproducing fission yeast populations, sourced from two independent genetic backgrounds, to disruptive ecological selection and manipulated the level of migration between environments. Contrary to theoretical expectations, adaptive divergence was most pronounced when migration was either absent (allopatry) or maximal (sympatry), but was much reduced at intermediate rates (parapatry and local mating). This effect was apparent across central life-history components (survival, asexual growth and mating) but differed in magnitude between ancestral genetic backgrounds. The evolution of some fitness components was constrained by pervasive negative correlations (trade-off between asexual growth and mating), while others changed direction under the influence of migration (for example, survival and mating). In allopatry, adaptive divergence was mainly conferred by standing genetic variation and resulted in ecological specialization. In sympatry, divergence was mainly mediated by novel mutations enriched in a subset of genes and was characterized by the repeated emergence of two strategies: an ecological generalist and an asexual growth specialist. Multiple loci showed consistent evidence for antagonistic pleiotropy across migration treatments providing a conceptual link between adaptation and divergence. This evolve-and-resequence experiment shows that rapid ecological differentiation can arise even under high rates of gene flow. It further highlights that adaptive trajectories are governed by complex interactions of gene flow, ancestral variation and genetic correlations.

Drivers of population divergence and species differentiation in a recent group of indigenous orchids (Vanilla spp.) in Madagascar

With over 25,000 species, orchids are among families with remarkable high rate of diversification. Since Darwin's time, major advances attributed the exceptional diversity of orchids to plant-pollinator interactions. However, unraveling the processes and factors that determine the phenotypic and genotypic variation of natural orchid populations remains a challenge. Here, we assessed genetic population structure and floral differentiation in recently diverged leafless Vanilla species in a world biodiversity hotspot, Madagascar, using seven microsatellite loci and 26 morphometric variables. Additionally, analyses were performed to test for the occurrence of any patterns of isolation by distance, isolation by environment, and isolation by adaptation and to detect possible physical barriers that might have caused genetic discontinuities between populations. Positive inbreeding coefficients detected in 22 populations were probably due to the presence of null alleles, geitonogamy and/or some admixture (sympatric species). In contrast, the only high-altitude population showed an important rate of clonality leading to heterozygote excess. Genetic diversity was maximum in western populations, suggesting a postglacial colonization to the north and south. Clustering analyses identified seven genetic groups characterized by specific floral traits that matched five botanical descriptions in the literature. A contribution of montane refugia and river barriers on population differentiation was detected. We also detected combined effects of IBD/IBE and IBE/IBA on genetic differentiation and suggested this pattern is more likely determined by ecological isolation, although pollinator-mediated divergent selection could not be ruled out for some of the species. Overall, this study provides further insights on speciation in orchids, a group for which Madagascar shows one of the world's highest level of endemism and confirms the importance of the peculiar biogeography of the island in shaping species differentiation.

Intraspecific genomic variation and local adaptation in a young hybrid species

Hybridization increases genetic variation, hence hybrid species may have greater evolutionary potential once their admixed genomes have stabilized and incompatibilities have been purged. Yet, little is known about how such hybrid lineages evolve at the genomic level following their formation, in particular their adaptive potential. Here we investigate how the Italian sparrow (Passer italiae), a homoploid hybrid species, has evolved and locally adapted to its variable environment. Using restriction site-associated DNA sequencing (RAD-seq) on several populations across the Italian peninsula, we evaluate how genomic constraints and novel genetic variation have influenced population divergence and adaptation. We show that population divergence within this hybrid species has evolved in response to climatic variation, suggesting ongoing local adaptation. As found previously in other nonhybrid species, climatic differences appear to increase population differentiation. We also report strong population divergence in a gene known to affect beak morphology. Most of the strongly divergent loci among Italian sparrow populations do not seem to be differentiated between its parent species, the house and Spanish sparrows. Unlike in the hybrid, population divergence within each of the parental taxa has occurred mostly at loci with high allele frequency difference between the parental species, suggesting that novel combinations of parental alleles in the hybrid have not necessarily enhanced its evolutionary potential. Rather, our study suggests that constraints linked to incompatibilities may have restricted the evolution of this admixed genome, both during and after hybrid species formation.

Geographical and environmental contributions to genomic divergence in mangrove forests

Assessing the relative importance of geographical and environmental factors to the spatial distribution of genetic variation can provide information about the processes that maintain genetic variation in natural populations. With a globally wide but very restricted habitat distribution, mangrove trees are a useful model for studies aiming to understand the contributions of these factors. Mangroves occur along the continent–ocean interface of tropical and subtropical latitudes, regions considered inhospitable to many other types of plants. Here, we used landscape genomics approaches to investigate the relative contributions of geographical and environmental variables to the genetic variation of two black mangrove species, Avicennia schaueriana and Avicennia germinans, along the South American coast. Using single nucleotide polymorphisms, our results revealed an important role of ocean currents and geographical distance in the gene flow of A. schaueriana and an isolation-by-environment pattern in the organization of the genetic diversity of A. germinans. Additionally, for A. germinans, we observed significant correlations between genetic variation with evidence of selection and the influence of precipitation regimens, solar radiation and temperature patterns. These discoveries expand our knowledge about the evolution of mangrove trees and provide important information to predict future responses of coastal species to the expected global changes during this century.

Harnessing landscape genomics to identify future climate resilient genotypes in a desert annual

Local adaptation features critically in shaping species responses to changing environments, complicating efforts to revegetate degraded areas. Rapid climate change poses an additional challenge that could reduce fitness of even locally sourced seeds in restoration. Predictive restoration strategies that apply seeds with favourable adaptations to future climate may promote long-term resilience. Landscape genomics is increasingly used to assess spatial patterns in local adaption and may represent a cost-efficient approach for identifying future-adapted genotypes. To demonstrate such an approach, we genotyped 760 plants from 64 Mojave Desert populations of the desert annual Plantago ovata. Genome scans on 5,960 SNPs identified 184 potentially adaptive loci related to climate and satellite vegetation metrics. Causal modelling indicated that variation in potentially adaptive loci was not confounded by isolation by distance or isolation by habitat resistance. A generalized dissimilarity model (GDM) attributed spatial turnover in potentially adaptive loci to temperature, precipitation and NDVI amplitude, a measure of vegetation green-up potential. By integrating a species distribution model (SDM), we find evidence that summer maximum temperature may both constrain the range of P. ovata and drive adaptive divergence in populations exposed to higher temperatures. Within the species' current range, warm-adapted genotypes are predicted to experience a fivefold expansion in climate niche by midcentury and could harbour key adaptations to cope with future climate. We recommend eight seed transfer zones and project each zone into its relative position in future climate. Prioritizing seed collection efforts on genotypes with expanding future habitat represents a promising strategy for restoration practitioners to address rapidly changing climates.

The Leafless Vanilla Species-Complex from the South-West Indian Ocean Region: A Taxonomic Puzzle and a Model for Orchid Evolution and Conservation Research

The pantropical genus Vanilla is a member of the Orchidaceae family, one of the largest and most diverse families of angiosperms in the world. It originated in America and differentiated in America, Africa, and Asia. About 132 species of Vanilla have now been accepted since the discovery of the genus. Within the Vanilla genus, leaflessness has appeared at least three independent times, in Africa, Asia, and America as an adaptation to drought conditions. The South-West Indian Ocean (SWIO) region, a biodiversity hotspot for orchids, is home to seven leafless species. Chloroplast markers failed to differentiate species within this recent SWIO clade. Morphological traits used for description are very similar between species and do not provide reliable identification. Moreover, some of the species have overlapping flowering periods and geographic distribution in Madagascar, increasing the probability of finding some sympatric species and, therefore, hybrids. Leafless Vanilla species from the SWIO islands are thus an excellent model for understanding the evolution of orchids. For their conservation, and to confirm the identity of these leafless species, an integrated approach with classical taxonomy using a large number of samples, intense fieldwork on biology and ecology, and molecular studies using variable markers is necessary.

Putative chromosomal rearrangements are associated primarily with ecotype divergence rather than geographic separation in an intertidal, poorly dispersing snail

Littorina saxatilis is becoming a model system for understanding the genomic basis of ecological speciation. The parallel formation of crab-adapted ecotypes that exhibit partial reproductive isolation from wave-adapted ecotypes has enabled genomic investigation of conspicuous shell traits. Recent genomic studies suggest that chromosomal rearrangements may enable ecotype divergence by reducing gene flow. However, the genomic architecture of traits that are divergent between ecotypes remains poorly understood. Here, we use 11,504 single nucleotide polymorphism (SNP) markers called using the recently released L. saxatilis genome to genotype 462 crab ecotype, wave ecotype and phenotypically intermediate Spanish L. saxatilis individuals with scored phenotypes. We used redundancy analysis to study the genetic architecture of loci associated with shell shape, shape corrected for size, shell size and shell ornamentation, and to compare levels of co-association among different traits. We discovered 341 SNPs associated with shell traits. Loci associated with trait divergence between ecotypes were often located inside putative chromosomal rearrangements recently characterized in Swedish L. saxatilis. In contrast, we found that shell shape corrected for size varied primarily by geographic site rather than by ecotype and showed little association with these putative rearrangements. We conclude that genomic regions of elevated divergence inside putative rearrangements were associated with divergence of L. saxatilis ecotypes along steep environmental axes-consistent with models of adaptation with gene flow-but were not associated with divergence among the three geographical sites. Our findings support predictions from models indicating the importance of genomic regions of reduced recombination allowing co-association of loci during ecological speciation with ongoing gene flow.

Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar (Calocedrus formosana)

Population diversification can be shaped by a combination of environmental factors as well as geographic isolation interacting with gene flow. We surveyed genetic variation of 243 samples from 12 populations of Calocedrus formosana using amplified fragment length polymorphism (AFLP) and scored a total of 437 AFLP fragments using 11 selective amplification primer pairs. The AFLP variation was used to assess the role of gene flow on the pattern of genetic diversity and to test environments in driving population adaptive evolution. This study found the relatively lower level of genetic diversity and the higher level of population differentiation in C. formosana compared with those estimated in previous studies of conifers including Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides occurring in Taiwan. BAYESCAN detected 26 F_ST outlier loci that were found to be associated strongly with various environmental variables using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression. We found several environmentally dependent adaptive loci with high frequencies in low- or high-elevation populations, suggesting their involvement in local adaptation. Ecological factors, including relative humidity and sunshine hours, that are generally not altitude related could have been the most important selective drivers for population divergent evolution in C. formosana. The present study provides fundamental information in relation to adaptive evolution and can be useful for assisted migration program of C. formosana in the future conservation of this species.

Limited divergent adaptation despite a substantial environmental cline in wild pea

Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.