Isolation by environment

Desert landscape features influencing the microgeographic genetic structure of Nelson's pocket mouse Chaetodipus nelsoni

Elucidating the factors that drive the genetic patterns of natural populations is key in evolutionary biology, ecology and conservation. Hence, it is crucial to understand the role that environmental features play in species genetic diversity and structure. Landscape genetics measures functional connectivity and evaluates the effects of landscape composition, configuration, and heterogeneity on microevolutionary processes. Deserts constitute one of the world's most widespread biomes and exhibit a striking heterogeneity of microhabitats, yet few landscape genetics studies have been performed with rodents in deserts. We evaluated the relationship between landscape and functional connectivity, at a microgeographic scale, of the Nelson's pocket mouse Chaetodipus nelsoni in the Mapimí Biosphere Reserve (Chihuahuan desert). We used single-nucleotide polymorphisms and characterized the landscape based on on-site environmental data and from Landsat satellite images. We identified two distinct genetic clusters shaped by elevation, vegetation and soil. High elevation group showed higher connectivity in the elevated zones (1250-1350 m), with scarce vegetation and predominantly rocky soils; whereas that of Low elevation group was at <1200 m, with denser vegetation and sandy soils. These genetic patterns are likely associated with the species' locomotion type, feeding strategy and building of burrows. Interestingly, we also identified morphological differences, where hind foot size was significantly smaller in individuals from High elevation compared to Low elevation, suggesting the possibility of ecomorphs associated with habitat differences and potential local adaptation processes, which should be explored further. These findings improve our understanding of the genetics and ecology of C. nelsoni and other desert rodents.

Ice age-driven range shifts of diploids and expanding autotetraploids of Biscutella laevigata within a conserved niche

Early studies of the textbook mixed-ploidy system Biscutella laevigata highlighted diploids restricted to never-glaciated lowlands and tetraploids at high elevations across the European Alps, promoting the hypothesis that whole-genome duplication (WGD) is advantageous under environmental changes. Here we addressed long-held hypotheses on the role of hybridisation at the origin of the tetraploids, their single vs multiple origins, and whether a shift in climatic niche accompanied WGD. Climatic niche modelling together with spatial genetics and coalescent modelling based on ddRAD-seq genotyping of 17 diploid and 19 tetraploid populations was used to revisit the evolution of this species complex in space and time. Diploids differentiated into four genetic lineages corresponding to allopatric glacial refugia at the onset of the last ice age, whereas tetraploids displaying tetrasomic inheritance formed a uniform group that originated from southern diploids before the last glacial maximum. Derived from diploids occurring at high elevation, autotetraploids likely inherited their adaptation to high elevation rather than having evolved it through or after WGD. They further presented considerable postglacial expansion across the Alps and underwent admixture with diploids. Although the underpinnings of the successful expansion of autotetraploids remain elusive, differentiation in B. laevigata was chiefly driven by the glacial history of the Alps.

Influence of geographic isolation and the environment on gene flow among phenotypically diverse lizards

Lizards in the genus Anolis comprise hundreds of species that display a wide range of phenotypic variation closely related to their environment. One example is the Guadeloupean anole (Anolis marmoratus ssp.) that display extreme phenotypic variation, primarily in adult male color and pattern, with twelve described subspecies on the archipelago. Here we examine the relationship between phenotypic and genetic divergence among five subspecies on the two main islands and test the role of geographic isolation and the environment in reducing gene flow. We also examined two offshore island populations to assess the impact of complete geographic isolation on gene flow. We analyzed color phenotypes by measuring spectral reflectance and genomic diversity using SNPs. Genetic divergence was correlated with dorsolateral head and body color phenotypes, and slope and geographic distance were nearly equivalent at explaining this divergence. There was minimal genome-wide divergence at neutral loci among phenotypically disparate subspecies on the two main islands and their differentiation is consistent with a model of divergence with gene flow. Our spatial visualization of gene flow showed an impact of environmental features consistent with a hypothesis of ecologically driven divergence. Nonetheless, subspecies on the two main islands remain interconnected by substantial gene flow and their phenotypic variation is likely maintained at selection-gene flow equilibrium by divergent selection at loci associated with their color phenotypes. Greater isolation, such as inhabiting a remote island, may be required for reducing gene flow. Our findings highlight the role of the environment, adaptation, and geographic isolation on gene flow.

Variable habitat use supports fine-scale population differentiation of a freshwater piscivore (northern pike, Esox lucius) along salinity gradients in brackish lagoons

In mobile animals, selection pressures resulting from spatio-temporally varying ecological factors often drive adaptations in migration behavior and associated physiological phenotypes. These adaptations may manifest in ecologically and genetically distinct ecotypes within populations. We studied a meta-population of northern pike (Esox lucius) in brackish environments and examined intrapopulation divergence along environmental gradients. Behavioral phenotypes in habitat use were characterized via otolith microchemistry in 120 individuals sampled from brackish lagoons and adjacent freshwater tributaries. We genotyped 1514 individual pike at 33 highly informative genetic markers. The relationship between behavioral phenotype and genotype was examined in a subset of 101 pikes for which both phenotypic and genomic data were available. Thermosaline differences between juvenile and adult life stages indicated ontogenetic shifts from warm, low-saline early habitats towards colder, higher-saline adult habitats. Four behavioral phenotypes were found: Freshwater residents, anadromous, brackish residents, and cross-habitat individuals, the latter showing intermediary habitat use between brackish and freshwater areas. Underlying the behavioral phenotypes were four genotypes, putative freshwater, putative anadromous, and two putatively brackish genotypes. Through phenotype-genotype matching, three ecotypes were identified: (i) a brackish resident ecotype, (ii) a freshwater ecotype expressing freshwater residency or anadromy, and (iii) a previously undescribed intermediary cross-habitat ecotype adapted to intermediate salinities, showing limited reliance on freshwater. Life-time growth of all ecotypes was similar, suggesting comparable fitness. By combining genetic data with lifelong habitat use and growth as a fitness surrogate, our study revealed strong differentiation in response to abiotic environmental gradients, primarily salinity, indicating ecotype diversity in coastal northern pike is higher than previously believed.

Testing concordance and conflict in spatial replication of landscape genetics inferences

The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses with a total of 119 individuals in five areas within the Sierra Nevada mountain range. Genetic distances calculated from thousands of ddRAD markers were used to optimize landscape resistance surfaces and infer the effects of landscape and topographic features on genetic connectivity. Across study areas, we found a great deal of consistency in the primary environmental gradients impacting genetic connectivity, along with some site-specific differences, and a range in the proportion of genetic variance explained by environmental factors across study sites. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Across study areas, canyon valleys were always implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity, though the relative importance varied in different areas. We emphasize that spatial data layers are complex and multidimensional, and careful consideration of spatial data correlation structure and robust analytic frameworks will be critical to our continued understanding of spatial genetics processes.

Limited Migration From Physiological Refugia Constrains the Rescue of Native Gastropods Facing an Invasive Predator

Biological invasions have caused the loss of freshwater biodiversity worldwide. The interplay between adaptive responses and demographic characteristics of populations impacted by invasions is expected to be important for their resilience, but the interaction between these factors is poorly understood. The freshwater gastropod Amnicola limosus is native to the Upper St. Lawrence River and distributed along a water calcium concentration gradient within which high-calcium habitats are impacted by an invasive predator fish (Neogobius melanostomus, round goby), whereas low-calcium habitats provide refuges for the gastropods from the invasive predator. Our objectives were to (1) test for adaptation of A. limosus to the invasive predator and the low-calcium habitats, and (2) investigate if migrant gastropods could move from refuge populations to declining invaded populations (i.e., demographic rescue), which could also help maintain genetic diversity through gene flow (i.e., genetic rescue). We conducted a laboratory reciprocal transplant of wild F0 A. limosus sourced from the two habitat types (high calcium/invaded and low calcium/refuge) to measure adult survival and fecundity in home and transplant treatments of water calcium concentration (low/high) and round goby cue (present/absent). We then applied pooled whole-genome sequencing of 12 gastropod populations from across the calcium/invasion gradient. We identified patterns of life-history traits and genetic differentiation across the habitats that are consistent with local adaptation to low-calcium concentrations in refuge populations and to round goby predation in invaded populations. We also detected restricted gene flow from the low-calcium refugia towards high-calcium invaded populations, implying that the potential for demographic and genetic rescue is limited by natural dispersal. Our study highlights the importance of considering the potentially conflicting effects of local adaptation and gene flow for the resilience of populations coping with invasive predators.

Understanding species limits through the formation of phylogeographic lineages

The outcomes of speciation across organismal dimensions (e.g., ecological, genetic, phenotypic) are often assessed using phylogeographic methods. At one extreme, reproductively isolated lineages represent easily delimitable species differing in many or all dimensions, and at the other, geographically distinct genetic segments introgress across broad environmental gradients with limited phenotypic disparity. In the ambiguous gray zone of speciation, where lineages are genetically delimitable but still interacting ecologically, it is expected that these lineages represent species in the context of ontology and the evolutionary species concept when they are maintained over time with geographically well-defined hybrid zones, particularly at the intersection of distinct environments. As a result, genetic structure is correlated with environmental differences and not space alone, and a subset of genes fail to introgress across these zones as underlying genomic differences accumulate. We present a set of tests that synthesize species delimitation with the speciation process. We can thereby assess historical demographics and diversification processes while understanding how lineages are maintained through space and time by exploring spatial and genome clines, genotype-environment interactions, and genome scans for selected loci. Employing these tests in eight lineage-pairs of snakes in North America, we show that six pairs represent 12 "good" species and that two pairs represent local adaptation and regional population structure. The distinct species pairs all have the signature of divergence before or near the mid-Pleistocene, often with low migration, stable hybrid zones of varying size, and a subset of loci showing selection on alleles at the hybrid zone corresponding to transitions between distinct ecoregions. Locally adapted populations are younger, exhibit higher migration, and less ecological differentiation. Our results demonstrate that interacting lineages can be delimited using phylogeographic and population genetic methods that properly integrate spatial, temporal, and environmental data.

Machine learning provides insights for spatially explicit pest management strategies by integrating information on population connectivity and habitat use in a key agricultural pest

BACKGROUND

Insect pests have garnered increasing interest because of anthropogenic global change, and their sustainable management requires knowledge of population habitat use and spread patterns. To enhance this knowledge for the prevalent tea pest Empoasca onukii, we utilized a random forest algorithm and a bivariate map to develop and integrate models of its habitat suitability and genetic connectivity across China.

RESULTS

Our modeling revealed heterogeneous spatial patterns in suitability and connectivity despite the common key environmental predictor of isothermality. Analyses indicated that tea cultivation in areas surrounding the Tibetan Plateau and the southern tip of China may be at low risk of population outbreaks because of their predicted low suitability and connectivity. However, regions along the middle and lower reaches of the Yangtze River should consider the high abundance and high recolonization potential of E. onukii, and thus the importance of control measures. Our results also emphasized the need to prevent dispersal from outside regions in the areas north of the Yangtze River and highlighted the effectiveness of internal management efforts in southwestern China and along the southeastern coast. Further projections under future conditions suggested the potential for increased abundance and spread in regions north of the Yangtze River and the southern tip of China, and indicated the importance of long-term monitoring efforts in these areas.

CONCLUSION

These findings highlighted the significance of combining information on habitat use and spread patterns for spatially explicit pest management planning. In addition, the approaches we used have potential applications in the management of other pest systems and the conservation of endangered biological resources. © 2024 Society of Chemical Industry.

The impact of geographic isolation and host shifts on population divergence of the rare cicada Subpsaltria yangi

The contributions of divergent selection and spatial isolation to population divergence are among the main focuses of evolutionary biology. Here we employed integrated methods to explore genomic divergence, demographic history and calling-song differentiation in the cicada Subpsaltria yangi, and compared the genotype and calling-song phenotype of different populations occurring in distinct habitats. Our results indicate that this species comprises four main lineages with unique sets of haplotypes and calling-song structure, which are distinctly associated with geographic isolation and habitats. The populations occurring on the Loess Plateau underwent substantial expansion at ∼0.130-0.115 Ma during the Last Interglacial. Geographic distance and host shift between pairs of populations predict genomic divergence, with geographic distance and acoustical signal together explaining > 60% of the divergence among populations. Differences in calling songs could reflect adaptation of populations to novel environments with different host plants, habitats and predators, which may have resulted from neutral divergence at the molecular level followed by natural selection. Geomorphic barriers and climate oscillations associated with Pleistocene glaciation may have been primary factors in shaping the population genetic structure of this species. Ultimately this may couple with a host shift in leading toward allopatric speciation in S. yangi, i.e., isolation by distance. Our findings improve understanding of divergence in allopatry of herbivorous insects, and may inform future studies on the molecular mechanisms underlying the association between genetic/phenotypic changes and adaptation of insects to novel niches and host plants.

Temperature is a cryptic factor shaping the geographical pattern of genetic variation in Ceratophyllum demersum across a subtropical freshwater lake

Macrophyte habitats exhibit remarkable heterogeneity, encompassing the spatial variation of abiotic and biotic components such as changes in water conditions and weather as well as anthropogenic stressors. Environmental factors are thought to be important drivers shaping the genetic and epigenetic variation of aquatic plants. However, the links among genetic diversity, epigenetic variation, and environmental variables remain largely unclear, especially for clonal aquatic plants. Here, we performed population genetic and epigenetic analyses in conjunction with habitat discrimination to elucidate the environmental factors driving intraspecies genetic and epigenetic variation in hornwort (Ceratophyllum demersum) in a subtropical lake. Environmental factors were highly correlated with the genetic and epigenetic variation of C. demersum, with temperature being a key driver of the genetic variation. Lower temperature was detected to be correlated with greater genetic and epigenetic variation. Genetic and epigenetic variation were positively driven by water temperature, but were negatively affected by ambient air temperature. These findings indicate that the genetic and epigenetic variation of this clonal aquatic herb is not related to the geographic feature but is instead driven by environmental conditions, and demonstrate the effects of temperature on local genetic and epigenetic variation in aquatic systems.

Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.)

Species that repeatedly evolve phenotypic clines across environmental gradients have been highlighted as ideal systems for characterizing the genomic basis of local environmental adaptation. However, few studies have assessed the importance of observed phenotypic clines for local adaptation: conspicuous traits that vary clinally may not necessarily be the most critical in determining local fitness. The present study was designed to fill this gap, using a plant species characterized by repeatedly evolved adaptive phenotypic clines. White clover is naturally polymorphic for its chemical defence cyanogenesis (HCN release with tissue damage); climate-associated cyanogenesis clines have evolved throughout its native and introduced range worldwide. We performed landscape genomic analyses on 415 wild genotypes from 43 locations spanning much of the North American species range to assess the relative importance of cyanogenesis loci vs. other genomic factors in local climatic adaptation. We find clear evidence of local adaptation, with temperature-related climatic variables best describing genome-wide differentiation between sampling locations. The same climatic variables are also strongly correlated with cyanogenesis frequencies and gene copy number variations (CNVs) at cyanogenesis loci. However, landscape genomic analyses indicate no significant contribution of cyanogenesis loci to local adaptation. Instead, several genomic regions containing promising candidate genes for plant response to seasonal cues are identified - some of which are shared with previously identified QTLs for locally adaptive fitness traits in North American white clover. Our findings suggest that local adaptation in white clover is likely determined primarily by genes controlling the timing of growth and flowering in response to local seasonal cues. More generally, this work suggests that caution is warranted when considering the importance of conspicuous phenotypic clines as primary determinants of local adaptation.

The accuracy of predicting maladaptation to new environments with genomic data

Rapid environmental change poses unprecedented challenges to species persistence. To understand the extent that continued change could have, genomic offset methods have been used to forecast maladaptation of natural populations to future environmental change. However, while their use has become increasingly common, little is known regarding their predictive performance across a wide array of realistic and challenging scenarios. Here, we evaluate the performance of currently available offset methods (gradientForest, the Risk-Of-Non-Adaptedness, redundancy analysis with and without structure correction and LFMM2) using an extensive set of simulated data sets that vary demography, adaptive architecture and the number and spatial patterns of adaptive environments. For each data set, we train models using either all, adaptive or neutral marker sets and evaluate performance using in silico common gardens by correlating known fitness with projected offset. Using over 4,849,600 of such evaluations, we find that (1) method performance is largely due to the degree of local adaptation across the metapopulation (LA), (2) adaptive marker sets provide minimal performance advantages, (3) performance within the species range is variable across gardens and declines when offset models are trained using additional non-adaptive environments and (4) despite (1) performance declines more rapidly in globally novel climates (i.e. a climate without an analogue within the species range) for metapopulations with greater LA than lesser LA. We discuss the implications of these results for management, assisted gene flow and assisted migration.

A spatial approach to jointly estimate Wright's neighborhood size and long-term effective population size

Spatially continuous patterns of genetic differentiation, which are common in nature, are often poorly described by existing population genetic theory or methods that assume either panmixia or discrete, clearly definable populations. There is therefore a need for statistical approaches in population genetics that can accommodate continuous geographic structure, and that ideally use georeferenced individuals as the unit of analysis, rather than populations or subpopulations. In addition, researchers are often interested in describing the diversity of a population distributed continuously in space; this diversity is intimately linked to both the dispersal potential and the population density of the organism. A statistical model that leverages information from patterns of isolation by distance to jointly infer parameters that control local demography (such as Wright's neighborhood size), and the long-term effective size (Ne) of a population would be useful. Here, we introduce such a model that uses individual-level pairwise genetic and geographic distances to infer Wright's neighborhood size and long-term Ne. We demonstrate the utility of our model by applying it to complex, forward-time demographic simulations as well as an empirical dataset of the two-form bumblebee (Bombus bifarius). The model performed well on simulated data relative to alternative approaches and produced reasonable empirical results given the natural history of bumblebees. The resulting inferences provide important insights into the population genetic dynamics of spatially structured populations.

Scots pine - panmixia and the elusive signal of genetic adaptation

Scots pine is the foundation species of diverse forested ecosystems across Eurasia and displays remarkable ecological breadth, occurring in environments ranging from temperate rainforests to arid tundra margins. Such expansive distributions can be favored by various demographic and adaptive processes and the interactions between them. To understand the impact of neutral and selective forces on genetic structure in Scots pine, we conducted range-wide population genetic analyses on 2321 trees from 202 populations using genotyping-by-sequencing, reconstructed the recent demography of the species and examined signals of genetic adaptation. We found a high and uniform genetic diversity across the entire range (global FST 0.048), no increased genetic load in expanding populations and minor impact of the last glacial maximum on historical population sizes. Genetic-environmental associations identified only a handful of single-nucleotide polymorphisms significantly linked to environmental gradients. The results suggest that extensive gene flow is predominantly responsible for the observed genetic patterns in Scots pine. The apparent missing signal of genetic adaptation is likely attributed to the intricate genetic architecture controlling adaptation to multi-dimensional environments. The panmixia metapopulation of Scots pine offers a good study system for further exploration into how genetic adaptation and plasticity evolve under gene flow and changing environment.

The enigma of genetic adaptation in a panmictic pine

This article is a Commentary on Bruxaux et al. (2024), 243: 1231–1246.

Isolation by environment and its consequences for range shifts with global change: Landscape genomics of the invasive plant common tansy

Invasive species are a growing global economic and ecological problem. However, it is not well understood how environmental factors mediate invasive range expansion. In this study, we investigated the recent and rapid range expansion of common tansy across environmental gradients in Minnesota, USA. We densely sampled individuals across the expanding range and performed reduced representation sequencing to generate a dataset of 3071 polymorphic loci for 176 individuals. We used non-spatial and spatially explicit analyses to determine the relative influences of geographic distance and environmental variation on patterns of genomic variation. We found no evidence for isolation by distance but strong evidence for isolation by environment, indicating that environmental factors may have modulated patterns of range expansion. Land use classification and soils were particularly important variables related to population structure although they operated on different spatial scales; land use classification was related to broad-scale patterns and soils were related to fine-scale patterns. All analyses indicated a distinctive genetic cluster in the most recently invaded portion of the range. Individuals from the far northwestern range margin were separated from the remainder of the range by reduced migration, which was associated with environmental resistance. This portion of the range was invaded primarily in the last 15 years. Ecological niche models also indicated that this cluster was associated with the expansion of the niche. While invasion is often assumed to be primarily influenced by dispersal limitation, our results suggest that ongoing invasion and range shifts with climate change may be strongly affected by environmental heterogeneity.

Environmental and anthropogenic factors mediating the functional connectivity of the mesquite lizard along the eastern Trans-Mexican Volcanic Belt

Functional connectivity, the extent to which a landscape facilitates or impedes the dispersal of individuals across the landscape, is a key factor for the survival of species. Anthropogenic activities, such as urbanization, agriculture and roads, negatively impact functional connectivity of most species, particularly low-vagility species like lizards. Here, we examine how a landscape modified by anthropogenic activities affects the functional connectivity, at both broad and fine scales, of a widely distributed generalist lizard Sceloporus grammicus in the eastern Trans-Mexican Volcanic Belt, Mexico. We estimated for the first time the species' genetic structure, gene flow and functional connectivity in agricultural and forest zones using genomic data, a comprehensive landscape characterization and novel methods including gravity models. Our results showed not only marked genetic differentiation across the study region but also that functional connectivity is maintained for tens of kilometres despite S. grammicus low vagility. Specifically, we found that substrate and air temperature facilitated connectivity over broad and fine scales, respectively, while agricultural cover, relative humidity and slope were important for connectivity and gene flow. Contrastingly, forest cover and roads favoured (broad-scale) and limited (fine-scale) connectivity, likely associated with movement facilitated by small forest patches and with thermoregulation. Altogether, these results support that S. grammicus alternates its thermoregulatory behaviour depending on the distance travelled and the habitat environmental conditions, and that it can disperse through relatively modified landscapes, mainly using agricultural zones. The information obtained is crucial to understanding the response of lizards to current anthropogenic pressures and their potential to adapt.

Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.

Patterns of Genetic Diversity and Gene Flow Associated With an Aridity Gradient in Populations of Common Mole-rats, Cryptomys hottentotus hottentotus

Genetic adaptation is the change of a population toward a phenotype that best fits the present ecological conditions of the environment it inhabits. As environmental conditions change, allele frequencies shift, resulting in different populations of the same species possessing genetic variation and divergent phenotypes. Cooperatively breeding common mole-rats (Cryptomys hottentotus hottentotus) inhabit environments along an aridity gradient in South Africa, which provides an opportunity for local genetic adaptations to occur. Using one mitochondrial gene (cytochrome b) and 3,540 SNP loci across the whole genome, we determined the phylogenetic relationship, population structure and genetic diversity of five populations of C. h. hottentotus located along an aridity gradient. Mitochondrial data identified population-specific clades that were less distinct in the two mesic populations, potentially indicating historical or recent gene flow, or the retention of ancestral haplotypes. Arid and semi-arid populations formed a distinct cluster from the non-arid populations. Genetic diversity and gene flow were higher in arid-dwelling individuals, suggesting greater connectivity and interactions between colonies in arid regions in comparison to mesic ones. Using an Aridity Index, we determined that isolation by environment, rather than isolation by geographical distance, best explains the genetic distance between the populations. Further analyses using target loci may determine if there are differing underlying genetic adaptations among populations of C. h. hottentotus. These analyses could help unravel population differences in response to environmental factors within a subspecies of bathyergid mole-rat and determine the adaptive capacity of this small nonmigratory subterranean rodent species in response to aridification in the face of climate change.

Phenotypic plasticity rather than ecotypic differentiation explains the broad realized niche of a Neotropical orchid species

Local adaptation is common in plant species, and knowing whether a population is locally adapted has fundamental and applied relevance. However, local adaptation in tropical plants remains largely less studied, and covering this gap is not simple since reciprocal transplantation - the gold standard for detecting local adaptation - is not feasible for most species. Here, we combined genetic, climatic and phenotypic data to investigate ecotypic differentiation, an important aspect of local adaptation, in coastal and inland populations of the orchid Epidendrum fulgens Brongn., a long-lived tropical plant for which reciprocal transplantation would not be feasible. We used nine microsatellite markers to estimate genetic divergence between inland and coastal populations. Moreover, occurrence data and climate data were used to test for differences in the realized niche of those populations. Finally, we assessed saturated water content, leaf specific area, height, and stomatal density in common garden and in situ to investigate the effects of ecotypic differentiation and plasticity on the phenotype. Coastal and inland groups' niches do not overlap, the former occupying a wetter and warmer area. However, this differentiation does not seem to be driven by ecotypic differentiation since there was no positive correlation between genetic structure and climate dissimilarity. Moreover, specific leaf area and leaf saturated water content, which are important phenotypic traits related to soil fertility and drought stress, were rather plastic. We conclude that ecotypic differentiation is absent, since phenotypic plasticity is an important mechanism explaining the niche broadness of this species.

Unraveling the genomic landscape of Campylorhynchus wrens along western Ecuador's precipitation gradient: Insights into hybridization, isolation by distance, and isolation by the environment

Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single-nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry-habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.

Patterns and effects of gene flow on adaptation across spatial scales: implications for management

Gene flow can have rapid effects on adaptation and is an important evolutionary tool available when undertaking biological conservation and restoration. This tool is underused partly because of the perceived risk of outbreeding depression and loss of mean fitness when different populations are crossed. In this article, we briefly review some theory and empirical findings on how genetic variation is distributed across species ranges, describe known patterns of gene flow in nature with respect to environmental gradients, and highlight the effects of gene flow on adaptation in small or stressed populations in challenging environments (e.g., at species range limits). We then present a case study involving crosses at varying spatial scales among mountain populations of a trigger plant (Stylidium armeria: Stylidiaceae) in the Australian Alps to highlight how some issues around gene flow effects can be evaluated. We found evidence of outbreeding depression in seed production at greater geographic distances. Nevertheless, we found no evidence of maladaptive gene flow effects in likelihood of germination, plant performance (size), and performance variance, suggesting that gene flow at all spatial scales produces offspring with high adaptive potential. This case study demonstrates a path to evaluating how increasing sources of gene flow in managed wild and restored populations could identify some offspring with high fitness that could bolster the ability of populations to adapt to future environmental changes. We suggest further ways in which managers and researchers can act to understand and consider adaptive gene flow in natural and conservation contexts under rapidly changing conditions.

"Isolation by Gentes with Asymmetric Migration" shapes the genetic structure of the common cuckoo in China

Amid coevolutionary arms races between brood parasitic birds and their diverse host species, the formation of host-specific races, or gentes, has drawn significant research focus. Nevertheless, numerous questions about gentes evolutionary patterns persist. Here, we investigated the potential for gentes evolution across multiple common cuckoo (Cuculus canorus) populations parasitizing diverse host species in China. Using maternal (mitochondrial and W-linked DNA) and biparental (autosomal and Z-linked DNA) markers, we found consistent clustering of cuckoo gentes (rather than geographical populations) into distinct clades in matrilineal gene trees, indicating robust differentiation. In contrast, biparental markers indicated intermixing of all gentes, suggesting asymmetric gene flow regardless of geography. Unlike the mitonuclear discordance commonly resulting from incomplete lineage sorting, adaptive introgression, or demographic disparities, the observed pattern in brood parasitic cuckoos might reflect biased host preferences between sexes. We hereby present the "Isolation by Gentes with Asymmetric Migration" model. According to this model, the maternal line differentiation of the common cuckoo in China is potentially driven by host preferences in females, whereas males maintained the integrity of the cuckoo species through random mating. To achieve this, cuckoo males could perform flexible migration among gentes or engage in early copulation with females before reaching the breeding sites, allowing female cuckoos to store sperm from various gentes. Future studies collecting additional samples from diverse cuckoo gentes with overlapping distribution and investigating the migratory and copulation patterns of each sex would enhance our understanding of sex-biased differentiation among cuckoo populations in China.

Effective dispersal patterns in prairie plant species across human-modified landscapes

Effective dispersal among plant populations is dependent on vector behaviour, landscape features and availability of adequate habitats. To capture landscape feature effects on dispersal, studies must be conducted at scales reflecting single-generation dispersal events (mesoscale). Many studies are conducted at large scales where genetic differentiation is due to dispersal occurring over multiple generations, making it difficult to interpret the effects of specific landscape features on vector behaviour. Genetic structure at the mesoscale may be determined by ecological and evolutionary processes, such as the consequences of vector behaviour on patterns of gene flow. We used chloroplast haplotypes and nuclear genome SNP surveys to identify landscape features influencing seed and pollen dispersal at a mesoscale within the Rogue River Valley in southern Oregon. We evaluated biotic and abiotic vector behaviour by contrasting two annual species with differing dispersal mechanisms; Achyrachaena mollis (Asteraceae) is a self-pollinating and anemochoric species, and Plectritis congesta (Caprifoliaceae) is biotically pollinated with barochoric seeds. Using landscape genetics methods, we identified features of the study region that conduct or restrict dispersal. We found chloroplast haplotypes were indicative of historic patterns of gene flow prior to human modification of landscapes. Seed dispersal of A. mollis was best supported by models of isolation by distance, while seed-driven gene flow of P. congesta was determined by the distribution of preserved natural spaces and quality habitat. Nuclear genetic structure was driven by both pollen and seed dispersal, and both species responded to contemporary landscape changes, such as urban and agricultural conversion, and habitat availability.

The effect of terrain on the fine-scale genetic diversity of sub-Antarctic Collembola: A landscape genetics approach

Biodiversity patterns are shaped by the interplay between geodiversity and organismal characteristics. Superimposing genetic structure onto landscape heterogeneity (i.e., landscape genetics) can help to disentangle their interactions and better understand population dynamics. Previous studies on the sub-Antarctic Prince Edward Islands (located midway between Antarctica and Africa) have highlighted the importance of landscape and climatic barriers in shaping spatial genetic patterns and have drawn attention to the value of these islands as natural laboratories for studying fundamental concepts in biology. Here, we assessed the fine-scale spatial genetic structure of the springtail, Cryptopygus antarcticus travei, which is endemic to Marion Island, in tandem with high-resolution geological data. Using a species-specific suite of microsatellite markers, a fine-scale sampling design incorporating landscape complexity and generalised linear models (GLMs), we examined genetic patterns overlaid onto high-resolution digital surface models and surface geology data across two 1-km sampling transects. The GLMs revealed that genetic patterns across the landscape closely track landscape resistance data in concert with landscape discontinuities and barriers to gene flow identified at a scale of a few metres. These results show that the island's geodiversity plays an important role in shaping biodiversity patterns and intraspecific genetic diversity. This study illustrates that fine-scale genetic patterns in soil arthropods are markedly more structured than anticipated, given that previous studies have reported high levels of genetic diversity and evidence of genetic structing linked to landscape changes for springtail species and considering the homogeneity of the vegetation complexes characteristic of the island at the scale of tens to hundreds of metres. By incorporating fine-scale and high-resolution landscape features into our study, we were able to explain much of the observed spatial genetic patterns. Our study highlights geodiversity as a driver of spatial complexity. More widely, it holds important implications for the conservation and management of the sub-Antarctic islands.

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.

Genetic analysis of harvest samples reveals population structure in a highly mobile generalist carnivore

Delineating wildlife population boundaries is important for effective population monitoring and management. The bobcat (Lynx rufus) is a highly mobile generalist carnivore that is ecologically and economically important. We sampled 1225 bobcats harvested in South Dakota, USA (2014-2019), of which 878 were retained to assess genetic diversity and infer population genetic structure using 17 microsatellite loci. We assigned individuals to genetic clusters (K) using spatial and nonspatial Bayesian clustering algorithms and quantified differentiation (F ST and G ST ″ ) among clusters. We found support for population genetic structure at K = 2 and K = 4, with pairwise F ST and G ST ″ values indicating weak to moderate differentiation, respectively, among clusters. For K = 2, eastern and western clusters aligned closely with historical bobcat management units and were consistent with a longitudinal suture zone for bobcats previously identified in the Great Plains. We did not observe patterns of population genetic structure aligning with major rivers or highways. Genetic divergence observed at K = 4 aligned roughly with ecoregion breaks and may be associated with environmental gradients, but additional sampling with more precise locational data may be necessary to validate these patterns. Our findings reveal that cryptic population structure may occur in highly mobile and broadly distributed generalist carnivores, highlighting the importance of considering population structure when establishing population monitoring programs or harvest regulations. Our study further demonstrates that for elusive furbearers, harvest can provide an efficient, broad-scale sampling approach for genetic population assessments.

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.

Considerable genetic diversity and structure despite narrow endemism and limited ecological specialization in the Hayden's ringlet, Coenonympha haydenii

Understanding the processes that underlie the development of population genetic structure is central to the study of evolution. Patterns of genetic structure, in turn, can reveal signatures of isolation by distance (IBD), barriers to gene flow, or even the genesis of speciation. However, it is unclear how severe range restriction might impact the processes that dominate the development of genetic structure. In narrow endemic species, is population structure likely to be adaptive in nature, or rather the result of genetic drift? In this study, we investigated patterns of genetic diversity and structure in the narrow endemic Hayden's ringlet butterfly. Specifically, we asked to what degree genetic structure in the Hayden's ringlet can be explained by IBD, isolation by resistance (IBR) (in the form of geographic or ecological barriers to migration between populations), and isolation by environment (in the form of differences in host plant availability and preference). We employed a genotyping-by-sequencing (GBS) approach coupled with host preference assays, Bayesian modelling, and population genomic analyses to answer these questions. Our results suggest that despite their restricted range, levels of genetic diversity in the Hayden's ringlet are comparable to those seen in more widespread butterfly species. Hayden's ringlets showed a strong preference for feeding on grasses relative to sedges, but neither larval preference nor potential host availability at sampling sites correlated with genetic structure. We conclude that geography, in the form of IBR and simple IBD, was the major driver of contemporary patterns of differentiation in this narrow endemic species.

Ecological characteristics explain neutral genetic variation of three coastal sparrow species

Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.

Transcriptome data analysis provides insights into the conservation of Michelia lacei, a plant species with extremely small populations distributed in Yunnan province, China

BACKGROUND

Michelia lacei W.W.Smith (Magnoliaceae), was classified as a Plant Species with Extremely Small Populations (PSESP) by the Yunnan Provincial Government in both action plans of 2012 and 2021. This evergreen tree is known for its high ornamental and scientific value, but it faces significant threats due to its extremely small population size and narrow geographical distribution. The study aims to understand the genetic structure, diversity, and demographic history of this species to inform its conservation strategies.

RESULTS

The analysis of transcriptome data from 64 individuals across seven populations of M. lacei identified three distinct genetic clusters and generated 104,616 single-nucleotide polymorphisms (SNPs). The KM ex-situ population, originating from Longling County, exhibited unique genetic features, suggesting limited gene flow. The genetic diversity was substantial, with significant differences between populations, particularly between the KM lineage and the OTHER lineage. Demographic history inferred from the data indicated population experienced three significant population declines during glaciations, followed by periods of recovery. We estimated the effective population size (Ne) of the KM and OTHER lineages 1,000 years ago were 85,851 and 416,622, respectively. Gene flow analysis suggested past gene flow between populations, but the KM ex-situ population showed no recent gene flow. A total of 805 outlier SNPs, associated with four environmental factors, suggest potential local adaptation and showcase the species' adaptive potential. Particularly, the BZ displayed 515 adaptive loci, highlighting its strong potential for adaptation within this group.

CONCLUSIONS

The comprehensive genomic analysis of M. lacei provides valuable insights into its genetic background and highlights the urgent need for conservation efforts. The study underscores the importance of ex-situ conservation methods, such as seed collection and vegetative propagation, to safeguard genetic diversity and promote population restoration. The preservation of populations like MC and BZ is crucial for maintaining the species' genetic diversity. In-situ conservation measures, including the establishment of in-situ conservation sites and community engagement, are essential to enhance protection awareness and ensure the long-term survival of this threatened plant species.

The role of biogeographical barriers on the historical dynamics of passerine birds with a circum-Amazonian distribution

Common distributional patterns have provided the foundations of our knowledge of Neotropical biogeography. A distinctive pattern is the "circum-Amazonian distribution", which surrounds Amazonia across the forested lowlands south and east of the basin, the Andean foothills, the Venezuelan Coastal Range, and the Tepuis. The underlying evolutionary and biogeographical mechanisms responsible for this widespread pattern of avian distribution have yet to be elucidated. Here, we test the effects of biogeographical barriers in four species in the passerine family Thamnophilidae by performing comparative demographic analyses of genome-scale data. Specifically, we used flanking regions of ultraconserved regions to estimate population historical parameters and genealogical trees and tested demographic models reflecting contrasting biogeographical scenarios explaining the circum-Amazonian distribution. We found that taxa with circum-Amazonian distribution have at least two main phylogeographical clusters: (1) Andes, often extending into Central America and the Tepuis; and (2) the remaining of their distribution. These clusters are connected through corridors along the Chaco-Cerrado and southeastern Amazonia, allowing gene flow between Andean and eastern South American populations. Demographic histories are consistent with Pleistocene climatic fluctuations having a strong influence on the diversification history of circum-Amazonian taxa, Refugia played a crucial role, enabling both phenotypic and genetic differentiation, yet maintaining substantial interconnectedness to keep considerable levels of gene flow during different dry/cool and warm/humid periods. Additionally, steep environmental gradients appear to play a critical role in maintaining both genetic and phenotypic structure.

Lizard host abundances and climatic factors explain phylogenetic diversity and prevalence of blood parasites on an oceanic island

Host abundance might favour the maintenance of a high phylogenetic diversity of some parasites via rapid transmission rates. Blood parasites of insular lizards represent a good model to test this hypothesis because these parasites can be particularly prevalent in islands and host lizards highly abundant. We applied deep amplicon sequencing and analysed environmental predictors of blood parasite prevalence and phylogenetic diversity in the endemic lizard Gallotia galloti across 24 localities on Tenerife, an island in the Canary archipelago that has experienced increasing warming and drought in recent years. Parasite prevalence assessed by microscopy was over 94%, and a higher proportion of infected lizards was found in warmer and drier locations. A total of 33 different 18s rRNA parasite haplotypes were identified, and the phylogenetic analyses indicated that they belong to two genera of Adeleorina (Apicomplexa: Coccidia), with Karyolysus as the dominant genus. The most important predictor of between-locality variation in parasite phylogenetic diversity was the abundance of lizard hosts. We conclude that a combination of climatic and host demographic factors associated with an insular syndrome may be favouring a rapid transmission of blood parasites among lizards on Tenerife, which may favour the maintenance of a high phylogenetic diversity of parasites.

Landscape Heterogeneity Explains the Genetic Differentiation of a Forest Bird across the Sino-Himalayan Mountains

Mountains are the world's most important centers of biodiversity. The Sino-Himalayan Mountains are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the Sino-Himalayan Mountains. However, little is known about the role of landscape heterogeneity and other environmental features in driving diversification in this region. We utilized whole genomes and phenotypic data in combination with landscape genetic approaches to investigate population structure, demography, and genetic diversity in a forest songbird species native to the Sino-Himalayan Mountains, the red-billed leiothrix (Leiothrix lutea). We identified 5 phylogeographic clades, including 1 in the East of China, 1 in Yunnan, and 3 in Tibet, roughly consistent with differences in song and plumage coloration but incongruent with traditional subspecies boundaries. Isolation-by-resistance model best explained population differentiation within L. lutea, with extensive secondary contact after allopatric isolation leading to admixture among clades. Ecological niche modeling indicated relative stability in the extent of suitable distribution areas of the species across Quaternary glacial cycles. Our results underscore the importance of mountains in the diversification of this species, given that most of the distinct genetic clades are concentrated in a relatively small area in the Sino-Himalayan Mountain region, while a single shallow clade populates vast lower-lying areas to the east. This study highlights the crucial role of landscape heterogeneity in promoting differentiation and provides a deep genomic perspective on the mechanisms through which diversity hotspots form.

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.

RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna

Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.

The natural and human-mediated expansion of a human-commensal lizard into the fringes of Southeast Asia

BACKGROUND

Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E. multifasciata for the mitochondrial ND2 gene and reanalyzed a previous RADseq population genetic dataset in a phylogenetic framework.

RESULTS

Nuclear and mitochondrial trees are concordant and show that E. multifasciata has retained high levels of genetic structure across Southeast Asia despite being frequently moved by humans. Lineage boundaries in the native range roughly correspond to several major biogeographic barriers, including Wallace's Line and the Isthmus of Kra. Islands at the outer fringe of the range show evidence of founder-effects and multiple introductions.

CONCLUSIONS

Most of enormous range of E. multifasciata across Southeast Asia is native and it only displays signs of human-introduction or recent expansion along the eastern and northern fringe of its range. There were at least three events of human-introductions to Taiwan and offshore islands, and several oceanic islands in eastern Indonesia show a similar pattern. In Myanmar and Hainan, there is a founder-effect consistent with post-warming expansion after the last glacial maxima or human introduction.

Climatic and soil characteristics account for the genetic structure of the invasive cactus moth Cactoblastis cactorum, in its native range in Argentina

Background

Knowledge of the physical and environmental conditions that may limit the migration of invasive species is crucial to assess the potential for expansion outside their native ranges. The cactus moth, Cactoblastis cactorum, is native to South America (Argentina, Paraguay, Uruguay and Brazil) and has been introduced and invaded the Caribbean and southern United States, among other regions. In North America there is an ongoing process of range expansion threatening cacti biodiversity of the genus Opuntia and the commercial profits of domesticated Opuntia ficus-indica.

Methods

To further understand what influences the distribution and genetic structure of this otherwise important threat to native and managed ecosystems, in the present study we combined ecological niche modeling and population genetic analyses to identify potential environmental barriers in the native region of Argentina. Samples were collected on the host with the wider distribution range, O. ficus-indica.

Results

Significant genetic structure was detected using 10 nuclear microsatellites and 24 sampling sites. At least six genetic groups delimited by mountain ranges, salt flats and wetlands were mainly located to the west of the Dry Chaco ecoregion. Niche modeling supports that this region has high environmental suitability where the upper soil temperature and humidity, soil carbon content and precipitation were the main environmental factors that explain the presence of the moth. Environmental filters such as the upper soil layer may be critical for pupal survival and consequently for the establishment of populations in new habitats, whereas the presence of available hosts is a necessary conditions for insect survival, upper soil and climatic characteristics will determine the opportunities for a successful establishment.

Genomic architecture controls multivariate adaptation to climate change

As climate change advances, environmental gradients may decouple, generating novel multivariate environments that stress wild populations. A commonly invoked mechanism of evolutionary rescue is adaptive gene flow tracking climate shifts, but gene flow from populations inhabiting similar conditions on one environmental axis could cause maladaptive introgression when populations are adapted to different environmental variables that do not shift together. Genomic architecture can play an important role in determining the effectiveness and relative magnitudes of adaptive gene flow and in situ adaptation. This may have direct consequences for how species respond to climate change but is often overlooked. Here, we simulated microevolutionary responses to environmental change under scenarios defined by variation in the polygenicity, linkage, and genetic redundancy of two independent traits, one of which is adapted to a gradient that shifts under climate change. We used these simulations to examine how genomic architecture influences evolutionary outcomes under climate change. We found that climate-tracking (up-gradient) gene flow, though present in all scenarios, was strongly constrained under scenarios of lower linkage and higher polygenicity and redundancy, suggesting in situ adaptation as the predominant mechanism of evolutionary rescue under these conditions. We also found that high polygenicity caused increased maladaptation and demographic decline, a concerning result given that many climate-adapted traits may be polygenic. Finally, in scenarios with high redundancy, we observed increased adaptive capacity. This finding adds to the growing recognition of the importance of redundancy in mediating in situ adaptive capacity and suggests opportunities for better understanding the climatic vulnerability of real populations.

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.

Disease-driven top predator decline affects mesopredator population genomic structure

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

Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil

Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.

Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii)

The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the species' designation as critically endangered. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS is unknown. To address these uncertainties, we sequenced and analyzed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Genetic divergence between sites is minimal, and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Despite this, however, demographic inference confirms a severe population bottleneck beginning around the time of WS onset, highlighting the temporal offset that may occur between a population collapse and its potential impact on genetic diversity. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of genetic structure, uniform diversity, and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.

Patterns of Leaf and Fruit Morphological Variation in Marginal Populations of Acer tataricum L. subsp. tataricum

Marginal populations are usually smaller and more isolated and grow in less favourable conditions than those at the distribution centre. The variability of these populations is of high importance, as it can support the adaptations needed for the conditions that they grow in. In this research, the morphological variability of eight Tatar maple (Acer tataricum L. subsp. tataricum) populations was analysed. Tatar maple is an insect-pollinated and wind-dispersed shrub/tree, whose northwestern distribution edge is in southeastern Europe. Morphometric methods were used to analyse the variability of the populations using leaf and fruit morphology. The research revealed significant differences between and within populations. Furthermore, differences in the distribution of the total variability were noted, which suggest that different evolutionarily factors affect different plant traits. Correlation analysis confirmed a weak dependency between the vegetative and generative traits. In addition, no evidence was found for the presence of isolation by environment (IBE). However, the Mantel test for isolation by distance (IBD) was significant for the leaf morphometric traits and non-significant for the fruit morphometric traits. Being the marginal leading-edge populations, they are younger and were less likely to have had time for adaptation to local environments, which would have resulted in the development of IBE. Overall, edge populations of Tatar maple were characterised by great morphological variability, which helps these populations in their response to the intensive selective pressures they face in their environment.

Continent-island boundary and environment-shaped evolution in the marine amphipod Ampithoe marcuzzii complex (Crustacea: Eumalacostraca: Ampithoidae)

Marine amphipods are crustaceans that lack a larval phase and consequently have low dispersion rates. Despite that, these crustaceans present a remarkable ability to be transported by rafting on natural floating substrata, especially macroalgae, where they find shelter, food and a mating ground. The species Ampithoe marcuzzii is widely distributed throughout the western Atlantic Ocean. Here, it was used as a model to study seascape genomics and phylogeography in invertebrates with low dispersion capacities. We anticipated that the lineages would present isolation-by-distance patterns. However, surface currents and other abiotic variables could facilitate connectivity among distant sites. Based on mitochondrial and nuclear genes, SNPs, and environmental associations, we observed the presence of a species complex within A. marcuzzii, separating mainland and insular populations. Each species showed an independent evolutionary history, with a strong latitudinal population structure and evidence of isolation-by-distance and isolation-by-environment, characterizing the 'continent' species. Historical expansion and environmental variables were observed associated with the southeastern population, and ecological niche modeling corroborated the region as a paleorefuge. Conversely, populations from 'islands' presented complicated evolutionary histories, with closer localities genetically isolated and distant localities connected. These findings indicate that insular populations with low dispersion capacity might be more susceptible to spatial connectivity by floating substrata and to changes in surface currents. In contrast, mainland populations might be more vulnerable to local climate changes due to lack of gene flow.

Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual-based genetic distance metric

Estimates of gene flow resulting from landscape resistance inferences frequently inform conservation management decision-making processes. Therefore, results must be robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 32 individual-based genetic distance metrics on the robustness and accuracy of landscape resistance modelling results. We analysed three empirical microsatellite datasets and 36 simulated datasets that varied in landscape resistance and genetic spatial autocorrelation. We used ResistanceGA to generate optimised multi-feature resistance surfaces for each of these datasets using 32 different genetic distance metrics. Results of the empirical dataset demonstrated that the choice of genetic distance metric can have strong impacts on inferred optimised resistance surfaces. Simulations showed accurate parametrisation of resistance surfaces across most genetic distance metrics only when a small number of environmental features was impacting gene flow. Landscape scenarios with many features impacting gene flow led to a generally poor recovery of true resistance surfaces. Simulation results also emphasise that choosing a genetic distance metric should not be based on marginal R2 -based model fit. Until more robust methods are available, resistance surfaces can be optimised with different genetic distance metrics and the convergence of results needs to be assessed via pairwise matrix correlations. Based on the results presented here, high correlation coefficients across different genetic distance categories likely indicate accurate inference of true landscape resistance. Most importantly, empirical results should be interpreted with great caution, especially when they appear counter-intuitive in light of the ecology of a species.

Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype

Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long-term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of "structure" versus "species" when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species-delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

Genomic signals of local adaptation across climatically heterogenous habitats in an invasive tropical fruit fly (Bactrocera tryoni)

Local adaptation plays a key role in the successful establishment of pest populations in new environments by enabling them to tolerate novel biotic and abiotic conditions experienced outside their native range. However, the genomic underpinnings of such adaptive responses remain unclear, especially for agriculturally important pests. We investigated population genomic signatures in the tropical/subtropical Queensland fruit fly, Bactrocera tryoni, which has an expanded range encompassing temperate and arid zones in Australia, and tropical zones in the Pacific Islands. Using reduced representation sequencing data from 28 populations, we detected allele frequency shifts associated with the native/invasive status of populations and identified environmental factors that have likely driven population differentiation. We also determined that precipitation, temperature, and geographic variables explain allelic shifts across the distribution range of B. tryoni. We found spatial heterogeneity in signatures of local adaptation across various climatic conditions in invaded areas. Specifically, disjunct invasive populations in the tropical Pacific Islands and arid zones of Australia were characterised by multiple significantly differentiated single nucleotide polymorphisms (SNPs), some of which were associated with genes with well-understood function in environmental stress (e.g., heat and desiccation) response. However, invasive populations in southeast Australian temperate zones showed higher gene flow with the native range and lacked a strong local adaptive signal. These results suggest that population connectivity with the native range has differentially affected local adaptive patterns in different invasive populations. Overall, our findings provide insights into the evolutionary underpinnings of invasion success of an important horticultural pest in climatically distinct environments.

Riverscape community genomics: A comparative analytical approach to identify common drivers of spatial structure

Genetic differentiation among local groups of individuals, that is, genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how this riverscape community genomics approach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N = 24) were partitioned into discrete subpopulations (K = 2-7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x̄ = 62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the stream hierarchy model. We discuss our conclusions regarding conservation and management and identify the 8-digit hydrologic unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.

Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms

The natural products (NPs) biosynthetic gene clusters (BGCs) represent the adapting biochemical toolkit for microorganisms to thrive different microenvironments. Despite their high diversity, particularly at the genomic level, detecting them in a shake-flask is challenging and remains the primary obstacle limiting our access to valuable chemicals. Studying the molecular mechanisms that regulate BGC expression is crucial to design of artificial conditions that derive on their expression. Here, we propose a phylogenetic analysis of regulatory elements linked to biosynthesis gene clusters, to classify BGCs to regulatory mechanisms based on protein domain information. We utilized Hidden Markov Models from the Pfam database to retrieve regulatory elements, such as histidine kinases and transcription factors, from BGCs in the MIBiG database, focusing on actinobacterial strains from three distinct environments: oligotrophic basins, rainforests, and marine environments. Despite the environmental variations, our isolated microorganisms share similar regulatory mechanisms, suggesting the potential to activate new BGCs using activators known to affect previously characterized BGCs.