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ABSTRACT In integrative distributional, demographic and coalescent (iDDC) modelling, a critical component is the statistical relationship between habitat suitability and local population sizes. This study explores this relationship in two Enyalius lizard species from the Brazilian Atlantic Forest: the high‐elevation E. iheringii and low‐elevation E. catenatus and how this transformation affects spatiotemporal demographic inference. Most previous iDDC studies assumed a linear relationship, but this study hypothesises that the relationship may be nonlinear, especially for high‐elevation species with broader environmental tolerances. We test two key hypotheses: (1) The habitat suitability to population size relationship is nonlinear for E. iheringii (high‐elevation) and linear for E. catenatus (low‐elevation); and (2) E. iheringii exhibits higher effective migration across populations than E. catenatus. Our findings provide clear support for hypothesis (2), but mixed support for hypothesis (1), with strong model support for a nonlinear transformation in the high‐elevation E. iheringii and some (albeit weak) support for a nonlinear transformation also in E. catenatus. The iDDC models allow us to generate landscape‐wide maps of predicted genetic diversity for both species, revealing that genetic diversity predictions for the high‐elevation E. iheringii align with estimated patterns of historical range stability, whereas predictions for low‐elevation E. catenatus are distinct from range‐wide stability predictions. This research highlights the importance of accurately modelling the habitat suitability to population size relationship in iDDC studies, contributing to our understanding of species' demographic responses to environmental changes. [ABSTRACT FROM AUTHOR]

Neotropical forest ecosystems harbour significant biodiversity. To develop effective insect conservation practices, it is important to understand the factors that influence the diversity and population structure of the species.Dispersal, a key determinant of population structure, is well studied in termites nesting in wood, for which it can be influenced by wood transport, or in termites living in urban environments. However, understanding the dispersal of termites whose mobility remains unaffected by wood transport remains understudied.We investigated the dispersal of Embiratermes neotenicus, a soil‐feeding species with short dispersal distance, in the Neotropical region, where both intact and degraded forests exist. Using mitochondrial and nuclear data, we analysed genetic diversity, structure and factors contributing to population differentiation in Suriname and French Guiana at multiple scales for 70 colonies.The population in French Guiana is the ancestral population in the region that subsequently expanded.Significant genetic differentiation between populations was observed, with distinct patterns identified in Suriname and French Guiana. The Suriname population showed higher genetic diversity and no subpopulation differentiation, whereas the French Guiana population showed substructure into distinct genetic clusters.Analyses at the scale of all colonies suggest the influence of landscape features, such as the Maroni River, on genetic differentiation. At the local scale, genetic differentiation between colonies increases with forest alteration, even when this does not include major changes in forest cover.Our results highlight the sensitivity of soil‐feeding termite populations to habitat change. We argue that multi‐scale studies are needed for a comprehensive understanding of genetic patterns, especially for species with short dispersal distances. [ABSTRACT FROM AUTHOR]

Modelling population connectivity is central to biodiversity conservation and often relies on resistance surfaces reflecting multi‐generational gene flow. ResistanceGA (RGA) is a common optimization framework for parameterizing these surfaces by maximizing the fit between genetic distances and cost distances using maximum likelihood population effect models. As the reliability of this framework has rarely been studied, we investigated the conditions maximizing its accuracy for both prediction and interpretation of landscape features' permeability. We ran demo‐genetic simulations in contrasted landscapes for species with distinct dispersal capacities and specialization levels, using corresponding reference cost scenarios. We then optimized resistance surfaces from the simulated genetic distances using RGA. First, we evaluated whether RGA identified the drivers of the genetic patterns, that is, distinguished Isolation‐by‐Resistance (IBR) patterns from either Isolation‐by‐Distance or patterns unrelated to ecological distances. We then assessed RGA predictive performance using a cross‐validation method, and its ability to recover the reference cost scenarios shaping genetic structure in simulations. IBR patterns were well detected and genetic distances were predicted with great accuracy. This performance depended on the strength of the genetic structuring, sampling design and landscape structure. Matching the scale of the genetic pattern by focusing on population pairs connected through gene flow and limiting overfitting through cross‐validation further enhanced inference reliability. Yet, the optimized cost values often departed from the reference values, making their interpretation and extrapolation potentially dubious. While demonstrating the value of RGA for predictive modelling, we call for caution and provide additional guidance for its optimal use. [ABSTRACT FROM AUTHOR]

Between 1925 and 1930, 11 or 12 non‐native mountain goats (Oreamnos americanus) were translocated from Alaska and British Columbia to the foothills of the Olympic Range. By 1970, descendants of these goats had colonized the entire range and concerns about the management of this introduced species developed as damage to alpine soil and vegetation occurred. A series of removals reduced the population from 1175 in 1983 to 389 by 1990, eventually growing to 584 in 2016. We used demographic and genetic data to parameterize a population genetics individual‐based simulation model of the Olympic Range mountain goats. We calibrated the model to replicate the population trajectory for Olympic mountain goats from establishment in the 1920s through the 1983 first census. As expected, modeled population dynamics from 1928 to 1983 mimicked parameter initialization from expanding populations. However, simulated heterozygosity did not align with observations, suggesting a process not accounted for within the simulation model, such as a bottleneck or founder effect. Sensitivity analyses showed changes in annual reproductive rate, juvenile mortality, and adult female mortality influencing population trajectories, but variation in male mortality revealed no changes. Evaluating the population dynamics of the model after removals showed that approximately 80% of the total animals removed during the 1980s needed to be female in order for the observed population estimates to occur. This model has the potential to be used more widely with established or introduced mountain goat populations, as well as to provide an approach for studying other introduced species and their population dynamics. [ABSTRACT FROM AUTHOR]

Climate change is altering the geographical distribution and abundance of species. Abundant genetic variation generally indicates a stronger adaptability and evolutionary potentiality, especially in case of sharply changing climates or environments. With the past global climate fluctuations, especially the climate oscillation since the Quaternary, the global temperature changes related to glaciation, many relict plant species have formed possible refugia in humid subtropical/warm temperate forests, thus retaining a high level of genetic diversity patterns. Based on the contraction and expansion of the geographical distribution of Taxus wallichiana Zucc. in the past driven by climate change, combined with the contemporary genetic diversity modeling, the distribution performance of Taxus wallichiana Zucc. in future climate change was predicted. The areas of highly suitable habitat will increase with climate change in the future. There were continuous and stable high suitable areas of T. wallichiana in the southeastern Tibet and northwestern Yunnan as long-term stable climate refugia. We made the genetic landscape surface of T. wallichiana complex and discovered geographical barriers against gene flow. Genetic barriers spatially isolated the center of genetic diversity into three regions: west (east Himalaya), middle (Yunnan plateau, Sichuan basin, Shennongjia, and the junction of Guizhou and Guangxi provinces), and east (Mt. Huangshan and Fujian). Southern Tibet was isolated from other populations. The central and western Yunnan, the Sichuan basin, and surrounding mountains were isolated from the southern China populations. We found that the positive correlationships between the present species genetic diversity and suitability index during LGM, MH, and 2070. This infers that T. wallichiana has provisioned certain genetic diversity and has strong evolutionary potential under conditions of climate change. [ABSTRACT FROM AUTHOR]

The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco‐evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016–2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen–microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies. [ABSTRACT FROM AUTHOR]

Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes. [ABSTRACT FROM AUTHOR]

Abstract Background White forsythia (Abeliophyllum distichum) is an endangered Korean Peninsula endemic that has been subjected to recent population genomics studies using SNPs via RAD sequencing. Here, we primarily employed the often underutilized haplotype information from RAD loci to further describe the species’ previously uninvestigated haplotype-based genomic variation and structure, and genetic-geographic characteristics and gene flow patterns among its five earlier identified genetic groups. We also inferred the time of past events that may have impacted the effective population size of these groups, as well as the species’ potential future distribution amidst the warming climate and anthropogenic threats. Results Our findings emphasized the recognition of the species’ regional patterns of genetic structure, and the role of topography and its associated gene flow patterns as some of the possible factors that may have influenced the species’ present-day fragmented population distribution. The inferred bottleneck events during the Anthropocene, some of which aligned with the time of historical catastrophic events on the Peninsula (e.g., the Korean War), were revealed to have contributed to the generally low effective population size of its five lineages, particularly those with marginal distributional range. Future distribution under both optimistic and pessimistic climatic scenarios suggests unlikely suitable habitats for these populations to expand from their current range limits, at least in the next 80 years. Conclusions The small effective population size and landscape-driven limited gene flow among white forsythia populations will remain a big challenge for the conservation management of the species’ already fragmented population distribution. To help mitigate these impacts, the merging of various research approaches and the use of genomic data to their full potential is recommended to provide the optimized knowledge-based tools for the conservation of this endangered species, and other similar plants under pressure.

Abstract Background Sassafras tzumu, an elegant deciduous arboreal species, belongs to the esteemed genus Sassafras within the distinguished family Lauraceae. With its immense commercial value, escalating market demands and unforeseen human activities within its natural habitat have emerged as new threats to S. tzumu in recent decades, so it is necessary to study its genetic diversity and influencing factors, to propose correlative conservation strategies. Results By utilizing genotyping-by-sequence (GBS) technology, we acquired a comprehensive database of single nucleotide polymorphisms (SNPs) from a cohort of 106 individuals sourced from 13 diverse Sassafras tzumu natural populations, scattered across various Chinese mountainous regions. Through our meticulous analysis, we aimed to unravel the intricate genetic diversity and structure within these S. tzumu populations, while simultaneously investigating the various factors that potentially shape genetic distance. Our preliminary findings unveiled a moderate level of genetic differentiation (F ST = 0.103, p

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

Tick‐borne encephalitis (TBE) virus is considered the medically most important arthropod‐borne virus in Europe. Although TBE is endemic throughout central Europe, ticks and rodents determine its maintenance in small, difficult‐to‐assess, natural foci. We investigated the interrelation between the population genetics of the main TBE virus (TBEV) vector tick (Ixodes ricinus), the most important reservoir host (Myodes glareolus, syn. Clethrionomys glareolus), and TBEV. Rodents and ticks were sampled on 15 sites within an exploratory study area, which has been screened regularly for TBEV occurrence in ticks for more than 10 years. On all 15 sites, ticks and bank voles were sampled, screened for TBEV presence via serology and RT‐PCR, and genetically examined. Moreover, TBEV isolates derived from these analyses were sequenced. In long‐term TBEV foci bank vole populations show extraordinary genetic constitutions, leading to a particular population structure, whereas ticks revealed a panmictic genetic structure overall sampling sites. Landscape genetics and habitat connectivity modeling (analysis of isolation by resistance) showed no landscape‐related barriers explaining the genetic structure of the bank vole populations. The results suggest that bank voles do not simply serve as TBEV reservoirs, but their genetic composition appears to have a significant influence on establishing and maintaining long‐term natural TBEV foci, whereas the genetic structure of TBEV's main vector I. ricinus does not play an important role in the sustainability of long‐term TBEV foci. A thorough investigation of how and to which extent TBEV and M. glareolus genetics are associated is needed to further unravel the underlying mechanisms. [ABSTRACT FROM AUTHOR]

Understanding how past and current environmental conditions shape the demographic and genetic distributions of organisms facilitates our predictions of how future environmental patterns may affect populations. The Canyon Rubyspot damselfly (Odonata: Zygoptera: Hetaerina vulnerata) is an insect with a range distribution from Colombia to the arid southwestern United States, where it inhabits shaded mountain streams in the arid southwestern United States. Past spatial fragmentation of habitat and limited dispersal capacity of H. vulnerata may cause population isolation and genetic differentiation, and projected climate change may exacerbate isolation by further restricting the species' distribution. We constructed species distribution models (SDMs) based on occurrences of H. vulnerata and environmental variables characterizing the species' niche. We inferred seven current potential population clusters isolated by unsuitable habitat. Paleoclimate models indicated habitat contiguity in past conditions; projected models indicated some habitat fragmentation in future scenarios. Seventy‐eight H. vulnerata individuals from six of the current clusters were sequenced via ddRADseq and processed with Stacks. Principal components and phylogeographic analyses resolved three subpopulations; Structure resolved four subpopulations. FST values were low (<0.05) for nearby populations and >0.15 for populations separated by expanses of unsuitable habitat. Isolation by distance was an existing but weak factor in determining genomic structure; isolation by environment and the intervening landscape explained a significant proportion of genetic distance. Hetaerina vulnerata populations were shown to be isolated by a lack of tree canopy coverage, an important habitat predictor for oviposition and territoriality. Thus, H. vulnerata populations are likely separated and are genetically isolated. Integrating SDMs with landscape genetics allowed us to identify populations separated by distance and unsuitable habitat, explaining population genetic patterns and probable fates for populations under future climate scenarios. [ABSTRACT FROM AUTHOR]

Aim: The factors that influence the diversity of Yungas Andean forest remain unexplored. Our study seeks to investigate the impact of key isolating factors on the genetic structure of multiple taxa, testing for four hypotheses: isolation by distance (IBD), isolation by resistance due to topography (IBRtopo), isolation by resistance due to habitat suitability (IBRsuit) and isolation by environmental dissimilarity (IBE). Location: Yungas Andean forest. Taxon: Tetrapoda. Methods: We analysed a dataset consisting of 477 Cyt‐b sequences from 138 localities, encompassing 13 species. Through multiple matrix regression, Moran Spectral Randomization of Mantel and GDM analyses, we tested the impact of each extrinsic predictor on observed genetic variation and determined the effect size of environmental variation on genetic divergence. Additionally, we investigated the spatial distribution of lineages within the study species. Results: The genetic variation within the Yungas exhibited varied responses that correspond to the regional landscape heterogeneity. We identified different isolating factors as the main predictor for specific species: IBD for Akodon spegazzinii; IBRtopo for certain small mammals' species; IBE for Thylamys cinderella and Oligoryzomys brendae; and IBRsuit for Calomys fecundus, Oreobates barituensis and Melanophryniscus rubriventris with some considerations. Furthermore, our results support the presence of a latitudinal pattern in the distribution of genetic lineages. Main Conclusions: The heterogeneous landscape of the Yungas Andean forest posed varied effects on genetic variation. The effect of topography and continuity of suitable habitats over vertebrate dispersal shapes the genetic diversity, in particular topography acts either as a barrier or as corridor, while habitat suitability resistance mainly shapes endemism genetic structure; local climate represents a strong genetic promoter in transition zones; and the effect of geographic distance is less evident when considering other landscape promoter of genetic divergence. This reinforces the understanding that the complex interplay of environmental and historical factors contributes to the observed patterns of genetic diversity in this region. [ABSTRACT FROM AUTHOR]

Humans and wildlife experience complex interactions in urban ecosystems, favoring the presence of commensal species, among which invasive species are particularly successful. Rodents are the main vertebrate group introduced to oceanic islands, where the invasion process and dispersal patterns strongly influence their evolutionary and genetic patterns. We evaluated the house mouse Mus musculus and the black rat Rattus rattus on Cozumel Island, Mexico. We assessed genetic diversity and structure, connectivity, gene flow, relatedness and bottleneck signals based on microsatellite loci. Our genetic findings suggest that introduction of individuals of different geographic sources to the island promotes high allelic diversity and the effective establishment of migrants. We identified a clear genetic structure and low connectivity for the two species, tightly linked with anthropogenic and urban features. Notably, we found that the genetic structure of the house mouse sampled within the city of San Miguel Cozumel is associated with the historical human population growth pulses accompanying the urbanization of the city. At the fine-scale genetic level, the main urban drivers of connectivity of the house mouse were both the impervious land surfaces, i.e. the urban landscape, and the informal commerce across the city (a proxy of resources availability). Chances of a secondary invasion to natural environments have been relatively low, which is crucial for the endemic taxa of the island. Nonetheless, improving urban planning to regulate future expansions of San Miguel Cozumel is of the outmost importance to prevent these invasive species to disperse further. [ABSTRACT FROM AUTHOR]

Many studies suggest that aside from environmental variables, such as topography and climate, species‐specific ecological traits are relevant to explain the geographic distribution of intraspecific genetic lineages. Here, we investigated whether and to what extent incorporating such traits systematically improves the accuracy of random forest models in predicting genetic differentiation among pairs of localities. We leveraged available ecological datasets for birds and tested the inclusion of two categories of ecological traits: dispersal‐related traits (i.e. morphology and foraging ecology) and demographic traits (such as species survival rate and generation length). We estimated genetic differentiation from published mitochondrial DNA sequences for 28 species of birds (1578 total genetic samples, 391 localities) in the Atlantic Forest of South America. Aside from the aforementioned ecological traits, we included geographic, topographic and climatic distances between localities as environmental predictors. We then created models using all available data to evaluate model uncertainty both across space and across the different categories of predictors. Finally, we investigated model uncertainty in predicting genetic differentiation individually for each species (a common challenge in conservation biology). Our results show that while environmental conditions are the most important predictors of genetic differentiation, model accuracy largely increases with the addition of ecological traits. Additionally, the inclusion of dispersal traits improves model accuracy to a larger extent than the inclusion of demographic traits. Similar results are observed in models for individual species, although model accuracy is highly variable. We conclude that ecological traits improve predictive models of genetic differentiation, refining our ability to predict phylogeographic patterns from existing data. Additionally, demographic traits may not be as informative as previously hypothesized. Finally, prediction of genetic differentiation for species with conservation concerns may require further careful assessment of the environmental and ecological variation within the species range. [ABSTRACT FROM AUTHOR]

Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non‐urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote (Canis latrans) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities. [ABSTRACT FROM AUTHOR]

Spatially isolated plant populations in agricultural landscapes exhibit genetic responses not only to habitat fragmentation per se but also to the composition of the landscape matrix between habitat patches. These responses can only be understood by examining how the landscape matrix influences among‐habitat movements of pollinators and seed vectors, which act as genetic linkers among populations. We studied the forest herb Polygonatum multiflorum and its associated pollinator and genetic linker, the bumblebee Bombus pascuorum, in three European agricultural landscapes. We aimed to identify which landscape features affect the movement activity of B. pascuorum between forest patches and to assess the relative importance of these features in explaining the forest herb's population genetic structure. We applied microsatellite markers to estimate the movement activity of the bumblebee as well as the population genetic structure of the forest herb. We modelled the movement activity as a function of various landscape metrics. Those metrics found to explain the movement activity best were then used to explain the population genetic structure of the forest herb. The bumblebee movement activity was affected by the cover of maize fields and semi‐natural grasslands on a larger spatial scale and by landscape heterogeneity on a smaller spatial scale. For some measures of the forest herb's population genetic structure, that is, allelic richness, observed heterozygosity and the F‐value, the combinations of landscape metrics, which explained the linker movement activity best, yielded lower AICc values than 95% of the models including all possible combinations of landscape metrics. Synthesis: The genetic linker, B. pascuorum, mediates landscape effects on the population genetic structure of the forest herb P. multiflorum. Our study indicates, that the movement of the genetic linker among forest patches, and thus the pollen driven gene flow of the herb, depends on the relative value of floral resources in the specific landscape setting. Noteworthy, the population genetic structure of the long‐lived, clonal forest herb species correlated with recent land‐use types such as maize, which have been existing for not more than a few decades within these landscapes. This underscores the short time in which land‐use changes can influence the evolutionary potential of long‐lived wild plants. [ABSTRACT FROM AUTHOR]

Characterizing spatial patterns in allele frequencies is fundamental to evolutionary biology because these patterns contain evidence of underlying processes. However, the spatial scales at which gene flow, changing selection, and drift act are often unknown. Many of these processes can operate inconsistently across space, causing nonstationary patterns. We present a wavelet approach to characterize spatial pattern in allele frequency that helps solve these problems. We show how our approach can characterize spatial patterns in relatedness at multiple spatial scales, i.e. a multilocus wavelet genetic dissimilarity. We also develop wavelet tests of spatial differentiation in allele frequency and quantitative trait loci (QTL). With simulation, we illustrate these methods under different scenarios. We also apply our approach to natural populations of Arabidopsis thaliana to characterize population structure and identify locally adapted loci across scales. We find, for example, that Arabidopsis flowering time QTL show significantly elevated genetic differentiation at 300–1,300 km scales. Wavelet transforms of allele frequencies offer a flexible way to reveal geographic patterns and underlying evolutionary processes. [ABSTRACT FROM AUTHOR]

Population genetics is a valuable tool for assessing the impact of human‐altered landscapes on genetic connectivity in various species. However, when applied to insects, challenges arise due to potentially large effective population sizes (Ne), high dispersal capacities and the recency of anthropogenic impacts.This study assessed the population genetic structure of two pollinators across a human‐altered landscape in Luxembourg. Samples from the ashy mining bee (Andrena cineraria, N = 201) and the greater bee fly (Bombylius major, N = 637) were genotyped at 25 microsatellite loci, including a genotyping‐by‐amplicon‐sequencing approach for A. cineraria.Despite high statistical power of FST > 0.002 in B. major and FST > 0.0025 in A. cineraria, no deviations from genetic homogeneity were detected. For both species, there was no evidence for isolation‐by‐distance or genetic clustering. Genetic homogeneity was most likely the result of high levels of gene flow that compensate for the effects of genetic drift.Estimates of Ne ranged between several thousand to tens of thousands, although precision was low. Simulations highlighted that genetic lag times can substantially affect our ability to detect recent (<50 generations) population differentiation when Ne is very large. Lag times were shorter with data from 25,000 simulated di‐allelic loci, but only when sample sizes remained high.Insect genetic studies should consider lag times due to large Ne and ensure sample size and markers offer adequate power to reject the null hypothesis of no landscape effect on genetic connectivity. [ABSTRACT FROM AUTHOR]

Dispersal is an important process that is widely studied across species, and it can be influenced by intrinsic and extrinsic factors. Intrinsic factors commonly assessed include the sex and age of individuals, while landscape features are frequently-tested extrinsic factors. Here, we investigated the effects of both sex and landscape composition and configuration on genetic distances among bare-nosed wombats (Vombatus ursinus)—one of the largest fossorial mammals in the world and subject to habitat fragmentation, threats from disease, and human persecution including culling as an agricultural pest. We analyzed a data set comprising 74 Tasmanian individuals (30 males and 44 females), genotyped for 9,064 single-nucleotide polymorphisms. We tested for sex-biased dispersal and the influence of landscape features on genetic distances including land use, water, vegetation, elevation, and topographic ruggedness. We detected significant female-biased dispersal, which may be related to females donating burrows to their offspring due to the energetic cost of excavation, given their large body sizes. Land use, waterbodies, and elevation appeared to be significant landscape predictors of genetic distance. Land use potentially reflects land clearing and persecution over the last 200 years. If our findings based on a limited sample size are valid, retention and restoration of nonanthropogenic landscapes in which wombats can move and burrow may be important for gene flow and maintenance of genetic diversity. [ABSTRACT FROM AUTHOR]

Subterranean rodents of the genus Ctenomys typically occupy fragmented habitats, many currently altered by anthropogenic development. These changes affect functional connectivity among individuals, reducing gene flow levels. This study assessed the functional connectivity of two sympatric species of subterranean rodents, Ctenomys australis and Ctenomys talarum, examining the impact of landscape changes on their population genetic structure at a fine spatial scale. We conducted a spatially continuous sampling over 12 km of coastline in Southeastern Buenos Aires Province, Argentina, genotyping 91 and 106 individuals of C. australis and C. talarum, respectively, using 10-12 microsatellite loci. We applied various spatial layers characterizing both species' habitats to evaluate the landscape configuration's effect on individual gene flow. We employed Bayesian genetic clustering methods to infer population structure levels. Ctenomys talarum showed greater structure than C. australis. NDVI temporal variation was the main factor influencing C. australis' genetic structure, whereas suitable habitat, linked to the current landscape configuration, was the most significant factor in shaping C. talarum's genetic structure. Differences in dispersal capacity and habitat specificity appear to have influenced the population genetic structures of these species. The results indicated varying sensitivities to landscape changes; temporal landscape variations primarily impacted C. australis' genetic connectivity, whereas for C. talarum, the current landscape configuration was more influential. [ABSTRACT FROM AUTHOR]

We present a framework for identifying when conditions are favourable for transmission of vector‐borne diseases between communities by incorporating predicted disease prevalence mapping with landscape analysis of sociological, environmental and host/parasite genetic data. We explored the relationship between environmental features and gene flow of a filarial parasite of humans, Onchocerca volvulus, and its vector, blackflies in the genus Simulium. We generated a baseline microfilarial prevalence map from point estimates from 47 locations in the ecological transition separating the savannah and forest in Ghana, where transmission of O. volvulus persists despite onchocerciasis control efforts. We generated movement suitability maps based on environmental correlates with mitochondrial population structure of 164 parasites from 15 communities and 93 vectors from only four sampling sites, and compared these to the baseline prevalence map. Parasite genetic distance between sampling locations was significantly associated with elevation (r =.793, p =.005) and soil moisture (r =.507, p =.002), while vector genetic distance was associated with soil moisture (r =.788, p =.0417) and precipitation (r =.835, p =.0417). The correlation between baseline prevalence and parasite resistance surface maps was stronger than that between prevalence and vector resistance surface maps. The centre of the study area had high prevalence and suitability for parasite and vector gene flow, potentially contributing to persistent transmission and suggesting the importance of re‐evaluating transmission zone boundaries. With suitably dense sampling, this framework can help delineate transmission zones for onchocerciasis and would be translatable to other vector‐borne diseases. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Comparative landscape genetics studies provide insights on the impact of landscape elements on gene flow patterns of different species inhabiting the same geographic area. We investigated the population genetic structure of two sympatric ungulates, roe deer Capreolus capreolus and Northern chamois Rupicapra rupicapra, in a mountain area of the central Italian Alps (Trentino, northern Italy). A total of 122 chamois and 72 roe deer samples were genotyped by two species-specific panels of 11 polymorphic microsatellite loci and analyzed by aspatial and spatially explicit analyses. While the roe deer population resulted unstructured, a clear population structure was detected in chamois, with two main groups, one inhabiting the eastern and the other spread in the western part of the study area. Landscape genetics analysis confirmed these scenarios and revealed a different effect of landscape on gene flow. An IBD (Isolation-By-Distance) model best explained genetic variation in roe deer, while IBR (Isolation-By-Resistance) was found as the process underlying genetic variation patterns in chamois, suggesting arable lands, coniferous forests, watercourses, and main roads as potential barriers. Species distribution and landscape use might explain these results: roe deer mostly occupy valley floors relatively connected to each other, and their spatial behavior may promote gene flow across areas. On the other hand, chamois prefer higher elevations and their movements may be hindered by valleys, rivers, and road networks. This study highlights the different impacts of natural and anthropic landscape elements on gene flow in two sympatric species, resulting from their different ecological requirements. [ABSTRACT FROM AUTHOR]

This study employs landscape genetics to investigate the environmental drivers of a deadly vector-borne disease, malaria caused by Plasmodium falciparum, in a more spatially comprehensive manner than any previous work. With 1804 samples from 44 sites collected in western Kenya in 2012 and 2013, we performed resistance surface analysis to show that Lake Victoria acts as a barrier to transmission between areas north and south of the Winam Gulf. In addition, Mantel correlograms clearly showed significant correlations between genetic and geographic distance over short distances (less than 70 km). In both cases, we used an identity-by-state measure of relatedness tailored to find highly related individual parasites in order to focus on recent gene flow that is more relevant to disease transmission. To supplement these results, we performed conventional population genetics analyses, including Bayesian clustering methods and spatial ordination techniques. These analyses revealed some differentiation on the basis of geography and elevation and a cluster of genetic similarity in the lowlands north of the Winam Gulf of Lake Victoria. Taken as a whole, these results indicate low overall genetic differentiation in the Lake Victoria region, but with some separation of parasite populations north and south of the Winam Gulf that is explained by the presence of the lake as a geographic barrier to gene flow. We recommend similar landscape genetics analyses in future molecular epidemiology studies of vector-borne diseases to extend and contextualize the results of traditional population genetics.

Dispersal of individuals and gene flow are crucial aspects to maintain genetic diversity and viability of populations, especially in the case of threatened species. Landscape composition and structure may facilitate or limit individual movement within and among populations. We used a landscape genetics approach to assess the connectivity patterns of the threatened Dupont's lark (Chersophilus duponti subsp. duponti), considering their genetic patterns and the landscape features associated with its gene flow in Spain. We analysed the genetic relatedness based on 11 species‐specific polymorphic microsatellites on 416 Dupont's lark individuals sampled across peninsular Spain between 2017 and 2019, covering most of the European distribution of the species. To assess the relationship between the landscape composition and the species gene flow, we estimated genetic distance at the individual level (Dps). Next, we built a set of environmental surfaces from two time periods (years 1990 and 2018), based on factors such as land use and topography, influencing individuals' movement. We then obtained resistance surfaces from an optimization process on landscape variables. Landscape genetics analyses were done for single and composite surface models for each year separately. Our findings from both time points show that scatter or mosaic‐structured vegetation composed by low agricultural and tree cover and high presence of sclerophyllous shrubs favoured Dupont's lark dispersal, while dense and continuous tree cover, as well as areas of intensive agriculture, were limiting factors. Our results suggest the importance of steppe habitat patches for the species' establishment and dispersal. In addition, our results provide key information to develop conservation measures, including conserving and restoring steppe habitats as scattered and/or mosaic‐structured vegetation that could warrant the connectivity and persistence of Dupont's lark populations. [ABSTRACT FROM AUTHOR]

The mapmixture R package and interactive web app are tools to aid visualisation of admixture and population structure in geographic space. The purpose of mapmixture is to enable and encourage molecular ecologists, and in particular population geneticists and phylogeneticists, to plot their admixture, ancestry or assignment results on a map when location information is available. mapmixture accepts data in the format typically generated by admixture analyses and visualises proportions to each genetic cluster per site as pie charts on a projected (optional) map. Combining this site‐based map presentation approach with the routine individual‐based presentation of admixture (structure) barplots will enhance interpretation of genetic‐geographic patterns. Additionally, in the context of science communication, this enables clearer transfer of spatial genetic information to readers or listeners, and especially to audiences that do not have a background in genetics but who are able to use the genetic information as evidence in conservation management. The latest version of mapmixture is available on GitHub (https://github.com/tom‐jenkins/mapmixture), which details installation instructions and examples of how to use the package and interactive web app. [ABSTRACT FROM AUTHOR]

In alpine ecosystems, elevation broadly functions as a steep thermal gradient, with plant communities exposed to regular fluctuations in hot and cold temperatures. These conditions lead to selective filtering, potentially contributing to species-level variation in thermal tolerance and population-level genetic divergence. Few studies have explored the breadth of alpine plant thermal tolerances across a thermal gradient or the underlying genetic variation thereof. We measured photosystem heat (Tcrit-hot) and cold (Tcrit-cold) thresholds of ten Australian alpine species across elevation gradients and characterised their neutral genetic variation. To reveal the biogeographical drivers of present-day genetic signatures, we also reconstructed temporal changes in habitat suitability across potential distributional ranges. We found intraspecific variation in thermal thresholds, but this was not associated with elevation, nor underpinned by genetic differentiation on a local scale. Instead, regional population differentiation and considerable homozygosity within populations may, in part, be driven by distributional contractions, long-term persistence, and migrations following habitat suitability. Our habitat suitability models suggest that cool-climate-distributed alpine plants may be threatened by a warming climate. Yet, the observed wide thermal tolerances did not reflect this vulnerability. Conservation efforts should seek to understand variations in species-level thermal tolerance across alpine microclimates. [ABSTRACT FROM AUTHOR]

Context: Elucidating how demography and contemporary landscape features regulate functional connectivity is crucial to implementing effective conservation strategies. We assessed the impacts of landscape features on the genetic variation of a locally endangered carnivore, the leopard cat (Prionailurus bengalensis) in Taiwan. Objectives: We aim to evaluate the association between genetic structure and landscape features. We further predicted the changes in genetic diversity and suitable habitats in the future. Methods: We genotyped 184 leopard cats in western Taiwan using 12 nuclear microsatellites and a mitochondrial marker. We applied a landscape optimization procedure with two genetic distances to identify major genetic barriers and employed ecological niche modeling to predict the future distribution of the leopard cat. Results: Bayesian demographic inferences revealed a dramatic population decline for all leopard cat populations in Taiwan. Genetic clustering and resistance surface modeling supported that the population connectivity was influenced by highways and high elevation. Niche modeling indicated low temperature was one of the primary factors limiting the occurrence of leopard cats that may inhibit their movement in high elevations. We predicted the suitable habitats of leopard cats would shrink northward and towards higher altitudes with rugged topography in response to global warming. Conclusions: Our study provided genetic evidence that leopard cats in Taiwan had undergone a dramatic population decline that may be associated with anthropogenic impacts. We also inferred the anthropogenic linear feature compromised the connectivity and persistence of leopard cats in human-mediated landscapes. Our finding serves as a model for landscape genetic studies of island carnivores in subtropical regions. [ABSTRACT FROM AUTHOR]

Context: Habitat fragmentation is expected to erode genetic diversity, which instead needs to be preserved for promoting species adaptation to a changing climate. As this expectation has found mixed support in forest trees, consistent results on the genetic consequences of fragmentation requires adequately replicated experimental designs, as well as an explicit assessment of which landscape features, if any, could mitigate its detrimental effects. Objective: Evaluating the role of several landscape attributes in buffering the detrimental effects of fragmentation in two metapopulations of silver fir. Methods: We genotyped 904 silver fir (Abies alba Mill.) trees from 18 local populations forming two metapopulations comparable for size and extension in the Apennines, a Mediterranean mountain range. We identified the signatures left by the fragmentation process on the genetic features of silver fir local populations. After removing potentially confounding effects due to different evolutionary histories, we used a multivariate approach for testing the relative effect of demographic, geographic, environmental and topographic factors on genetic features of both metapopulations. Results: We found comparable signals of the habitat fragmentation impact on the genetic diversity and structure of both investigated metapopulations. Fragmentation effects were less pronounced in the largest local populations (but not the least isolated), located on gentler slopes with higher soil water availability and lower heat exposure. Conclusions: Our results suggest the existence of a set of demographic and environmental factors that could have coherently buffered the detrimental genetic effects of fragmentation in both metapopulations. These findings could be useful to plan landscape restoration for the evolutionary rescue of mixed forests that once characterized Mediterranean mountain ecosystems. [ABSTRACT FROM AUTHOR]

Hoverflies (Syrphidae) are essential pollinators, and their severe decline jeopardizes their invaluable contribution to plant diversity and agricultural production. However, we know little about the dispersal abilities of hoverflies in urbanized landscapes, limiting our understanding of the spatiotemporal dynamics of plant–pollinator systems and reducing our ability to preserve biodiversity in the context of global change. Previous work has not addressed how urbanization affects the functional connectivity of hoverflies and whether dispersal is a limiting factor in their population dynamics. In this study, we investigated the spatial genetic structure of two nonmigratory species of hoverflies in two urban areas. We collected more than a thousand specimens of each Syritta pipiens and Myathropa florea, each, by hand netting in two western European urbanized study areas of 490 and 460 km2 in 2021, and we genotyped them at 14 and 24 microsatellite loci, respectively. Based on spatial and nonspatial Bayesian clustering methods, we failed to reject the null hypothesis of panmixia, suggesting that both species exhibited high genetic connectivity despite urbanization. The distribution of allele frequencies was not correlated with geographic distance, implying that isolation‐by‐distance was negligible at the investigated spatial scale in both species. Although anthropogenic land cover changes generally have dramatic consequences on biodiversity, these hoverfly species retain high connectivity, which suggests that dispersal is not a strong limiting factor in their metapopulational dynamics. However, high effective population size and its confounding effect on signals of genetic drift may limit our ability to conclude confidently about landscape effects on gene flow in those two species. Provided we maintain or restore habitat, recolonization may be prompt even in urban areas. [ABSTRACT FROM AUTHOR]

Due to their limited dispersal ability, fossorial species with predominantly belowground activity usually show increased levels of population subdivision across relatively small spatial scales. This may be exacerbated in harsh mountain ecosystems, where landscape geomorphology limits species' dispersal ability and leads to small effective population sizes, making species relatively vulnerable to environmental change. To better understand the environmental drivers of species' population subdivision in remote mountain ecosystems, particularly in understudied high‐elevation systems in Africa, we studied the giant root‐rat (Tachyoryctes macrocephalus), a fossorial rodent confined to the afro‐alpine ecosystem of the Bale Mountains in Ethiopia. Using mitochondrial and low‐coverage nuclear genomes, we investigated 77 giant root‐rat individuals sampled from nine localities across its entire ~1000 km2 range. Our data revealed a distinct division into a northern and southern group, with no signs of gene flow, and higher nuclear genetic diversity in the south. Landscape genetic analyses of the mitochondrial and nuclear genomes indicated that population subdivision was driven by slope and elevation differences of up to 500 m across escarpments separating the north and south, potentially reinforced by glaciation of the south during the Late Pleistocene (~42,000–16,000 years ago). Despite this landscape‐scale subdivision between the north and south, weak geographic structuring of sampling localities within regions indicated gene flow across distances of at least 16 km at the local scale, suggesting high, aboveground mobility for relatively long distances. Our study highlights that despite the potential for local‐scale gene flow in fossorial species, topographic barriers can result in pronounced genetic subdivision. These factors can reduce genetic variability, which should be considered when developing conservation strategies. [ABSTRACT FROM AUTHOR]

Aim: As climate change accelerates, assessing how climate shapes gene flow and neutral and adaptive genetic differentiation on landscapes is increasingly important. Aardvarks (Orycteropus afer) are ecologically important in sub‐Saharan Africa but are sensitive to human pressures and increasing aridity. We used individual, population and landscape genetic approaches to infer the influence of landscape, climate and potential adaptive differences on gene flow. Location: We surveyed 8 protected and 4 privately owned areas in South Africa, 2 protected areas in Eswatini and one location in Kenya during 2016–2018. Methods: We developed microsatellite markers and methods for DNA extraction from faeces, collected and genotyped faecal samples from focal areas and estimated genetic structure. We inferred space use from individual redetections, tested for close relatives and estimated genetic neighbourhood distance. We applied individual‐based landscape genetic analyses at multiple scales to test hypotheses about genetic differentiation by landscape resistance and potential adaptive differences. Results: We developed 19 variable microsatellite loci and collected 253 faecal samples from 13 focal areas. We genotyped 104 samples successfully at ≥8 loci as needed for individual identification. The genetic structure suggested 3 regional divisions in South Africa. We detected individuals at locations ≤7.3 km distant and closely related individuals at ≤44 km; genetic neighbourhood distance was <55 km. Lower precipitation increased landscape resistance and strongly predicted genetic differentiation at most spatial scales. Temperature differences at sampling sites also influenced structure, suggesting climate‐associated adaptive differences. Main Conclusions: The genetic structure of aardvarks is strongly shaped by climate, with arid areas limiting gene flow and reflects apparent isolation by adaptation associated with temperature. Dispersal distances likely are <55 km. The markers we developed will facilitate studies of space use, dispersal, population density or survival. Aridification will increase fragmentation and we recommend monitoring aardvark presence as an indicator of ecosystem change associated with aridification. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract Tick‐borne encephalitis (TBE) virus is considered the medically most important arthropod‐borne virus in Europe. Although TBE is endemic throughout central Europe, ticks and rodents determine its maintenance in small, difficult‐to‐assess, natural foci. We investigated the interrelation between the population genetics of the main TBE virus (TBEV) vector tick (Ixodes ricinus), the most important reservoir host (Myodes glareolus, syn. Clethrionomys glareolus), and TBEV. Rodents and ticks were sampled on 15 sites within an exploratory study area, which has been screened regularly for TBEV occurrence in ticks for more than 10 years. On all 15 sites, ticks and bank voles were sampled, screened for TBEV presence via serology and RT‐PCR, and genetically examined. Moreover, TBEV isolates derived from these analyses were sequenced. In long‐term TBEV foci bank vole populations show extraordinary genetic constitutions, leading to a particular population structure, whereas ticks revealed a panmictic genetic structure overall sampling sites. Landscape genetics and habitat connectivity modeling (analysis of isolation by resistance) showed no landscape‐related barriers explaining the genetic structure of the bank vole populations. The results suggest that bank voles do not simply serve as TBEV reservoirs, but their genetic composition appears to have a significant influence on establishing and maintaining long‐term natural TBEV foci, whereas the genetic structure of TBEV's main vector I. ricinus does not play an important role in the sustainability of long‐term TBEV foci. A thorough investigation of how and to which extent TBEV and M. glareolus genetics are associated is needed to further unravel the underlying mechanisms.

Abstract Understanding how past and current environmental conditions shape the demographic and genetic distributions of organisms facilitates our predictions of how future environmental patterns may affect populations. The Canyon Rubyspot damselfly (Odonata: Zygoptera: Hetaerina vulnerata) is an insect with a range distribution from Colombia to the arid southwestern United States, where it inhabits shaded mountain streams in the arid southwestern United States. Past spatial fragmentation of habitat and limited dispersal capacity of H. vulnerata may cause population isolation and genetic differentiation, and projected climate change may exacerbate isolation by further restricting the species' distribution. We constructed species distribution models (SDMs) based on occurrences of H. vulnerata and environmental variables characterizing the species' niche. We inferred seven current potential population clusters isolated by unsuitable habitat. Paleoclimate models indicated habitat contiguity in past conditions; projected models indicated some habitat fragmentation in future scenarios. Seventy‐eight H. vulnerata individuals from six of the current clusters were sequenced via ddRADseq and processed with Stacks. Principal components and phylogeographic analyses resolved three subpopulations; Structure resolved four subpopulations. FST values were low (0.15 for populations separated by expanses of unsuitable habitat. Isolation by distance was an existing but weak factor in determining genomic structure; isolation by environment and the intervening landscape explained a significant proportion of genetic distance. Hetaerina vulnerata populations were shown to be isolated by a lack of tree canopy coverage, an important habitat predictor for oviposition and territoriality. Thus, H. vulnerata populations are likely separated and are genetically isolated. Integrating SDMs with landscape genetics allowed us to identify populations separated by distance and unsuitable habitat, explaining population genetic patterns and probable fates for populations under future climate scenarios.

Increased access to genetic data has substantially improved how we manage threatened species. The Tasmanian devil (Sarcophilus harrisii) is listed as endangered due to the ongoing threat of a highly contagious cancer, devil facial tumour disease (DFTD), causing more than 80% population reductions. To assist future management interventions (e.g. releases into wild sites) we expanded upon previous studies of gene flow for the devil by assessing more recent and broad-scale patterns. We use genome-wide single nucleotide polymorphisms generated via DArTSeq across 21 devil sites to delineate source-sink dynamics across the species’ range. Our findings revealed gene flow is stronger on the northeast and central regions of Tasmania, with high rates of bidirectional gene flow among central sites. The northwest exhibits weaker connectivity relative to other regions of Tasmania, while gene flow appears to be non-existent between the southwest and other areas. Northeast coastal sites tend to serve as ‘sources’ for inland central sites, whereas gene flow appears restricted to the coastline in the northwest. These results are consistent with genetic structure of devil sites and spatial spread of DFTD, which has yet to arrive in the southwest region of Tasmania. Southwest isolation is probably due to mountain ranges and lack of roadways. Interestingly, some waterbodies did not appear to restrict devil movement among sites. Conversely, areas of high elevation act as apparent barriers, as evidenced by limited gene flow observed between eastern and western sites. Integrating source-sink dynamics into conservation management planning will be crucial in developing effective strategies to safeguard the Tasmanian devil and other threatened species facing similar threats (i.e. disease, habitat loss).

Abstract Spatially isolated plant populations in agricultural landscapes exhibit genetic responses not only to habitat fragmentation per se but also to the composition of the landscape matrix between habitat patches. These responses can only be understood by examining how the landscape matrix influences among‐habitat movements of pollinators and seed vectors, which act as genetic linkers among populations. We studied the forest herb Polygonatum multiflorum and its associated pollinator and genetic linker, the bumblebee Bombus pascuorum, in three European agricultural landscapes. We aimed to identify which landscape features affect the movement activity of B. pascuorum between forest patches and to assess the relative importance of these features in explaining the forest herb's population genetic structure. We applied microsatellite markers to estimate the movement activity of the bumblebee as well as the population genetic structure of the forest herb. We modelled the movement activity as a function of various landscape metrics. Those metrics found to explain the movement activity best were then used to explain the population genetic structure of the forest herb. The bumblebee movement activity was affected by the cover of maize fields and semi‐natural grasslands on a larger spatial scale and by landscape heterogeneity on a smaller spatial scale. For some measures of the forest herb's population genetic structure, that is, allelic richness, observed heterozygosity and the F‐value, the combinations of landscape metrics, which explained the linker movement activity best, yielded lower AICc values than 95% of the models including all possible combinations of landscape metrics. Synthesis: The genetic linker, B. pascuorum, mediates landscape effects on the population genetic structure of the forest herb P. multiflorum. Our study indicates, that the movement of the genetic linker among forest patches, and thus the pollen driven gene flow of the herb, depends on the relative value of floral resources in the specific landscape setting. Noteworthy, the population genetic structure of the long‐lived, clonal forest herb species correlated with recent land‐use types such as maize, which have been existing for not more than a few decades within these landscapes. This underscores the short time in which land‐use changes can influence the evolutionary potential of long‐lived wild plants.

Species resilience to diversified environments largely depends on their genetic diversity. Disentangling the respective roles of multiple landscape factors on population genetic variation could help us interpret the adaptive mechanism of species to environments, which is a central issue in evolutionary biology and biodiversity conservation. Herein, a typical Tibetan loach Triplophysa stenura was selected as study object to perform landscape genetics analyses inferred from mitochondrial cytochrome b gene sequences. Based on extensive sample collection, a total of 377 individuals from 20 sites in the Yarlung Tsangpo River were included in the analyses and results of genetic diversity assessment demonstrated relatively high haplotype diversity and low nucleotide diversity for most geographic populations. Genetic diversity pattern analysis proved that both haplotype and nucleotide diversity were greater in higher, colder and drier areas, which was consistent with the central-marginal hypothesis for this plateau hinterland-originated species. Degree of genetic differentiation among geographic populations varied from low level to extremely high level, with genetic variation coming mainly from within populations. Elevational and climatic divergences were detected to be principally responsible for the formation of population genetic structure of this species, coinciding with the isolation-by-environment model. On this basis, we put forward some applicable proposals that the marginal populations with relatively low elevations deserved more attentions in designing conservation scheme and those genetically differentiated populations should be treated as separate conservation units. In the context of global climate change and intensifying human activity, a sound genetic resources monitoring along elevational or climatic gradient is pivotal to develop future conservation interventions.

Aim: The poleward range expansion of tropical species, and range contraction of temperate species (known as tropicalisation) has mainly been studied from an ecological perspective, with little research on its genetic consequences. Here, we used distributional and genetic data to document the consequences of tropicalisation in rocky shore gastropods and assess more broadly the future implications of tropicalisation on phylogeographic patterns. Location: Nineteen sampling sites along >3000 km of the eastern Pacific rocky intertidal zone, from the tip of the Baja California Peninsula to southern California. Taxon: Temperate gastropods: Lottia conus, L. strigatella, Fissurella volcano and Tegula gallina. Tropical gastropods: Fissurella rubropicta, Nerita funiculata and N. scabricosta. Methods: We determine historical and modern distributions of tropical and temperate species by combining historical records with current field surveys. Using a section of the cytochrome oxidase subunit I gene, we utilised comparative phylogeography, analysis of molecular variance, FST pairwise comparison, mismatch distributions of haplotype differences and neutrality tests to detect genetic signatures of tropicalisation and to better understand its consequences. Results: We identified range contractions in two temperate species and range expansion in all three tropical species. We detected genetic signatures of range expansion in the tropical species through unimodal distributions of pairwise haplotype differences and strongly negative values for the Fu and Li D and F* statistics. We found population subdivision and phylogeographic breaks in three temperate species, although the geographic location of the breaks differed among species. Main Conclusions: Genetic signatures and field surveys indicate recent range expansions in tropical species, supporting tropicalisation along the studied coastline. Conversely, we found phylogeographic breaks in temperate species, suggesting that tropicalisation may cause genetic erosion of evolutionary distinct lineages with range‐contraction. The different locations of the phylogeographic breaks among temperate species suggests that some barriers are species specific. [ABSTRACT FROM AUTHOR]

In the early 1980s, the observation that Drosophila melanogaster larvae differed in their foraging behaviour laid the foundation for the work that would later lead to the discovery of the foraging gene (for) and its associated foraging phenotypes, rover and sitter. Since then, the molecular characterization of the for gene and our understanding of the mechanisms that maintain its phenotypic variants in the laboratory have progressed enormously. However, the significance and dynamics of such variation are yet to be investigated in nature. With the advent of next-generation sequencing, it is now possible to identify loci underlying the adaptation of populations in response to environmental variation. Here, I present the results of a genotype–environment association analysis that quantifies variation at the for gene among samples of D. melanogaster structured across space and time. These samples consist of published genomes of adult flies collected worldwide, and at least twice per site of collection (during spring and fall). Both an analysis of genetic differentiation based on F s ⁢ t values and an analysis of population structure revealed an east–west gradient in allele frequency. This gradient may be the result of spatially varying selection driven by the seasonality of precipitation. These results support the hypothesis that different patterns of gene flow as expected under models of isolation by distance and potentially isolation by environment are driving genetic differentiation among populations. Overall, this study is essential for understanding the mechanisms underlying the evolution of foraging behaviour in D. melanogaster. [ABSTRACT FROM AUTHOR]

Premise: Snow is an important environmental factor affecting plant distribution. Past changes in snowfall regimes may have controlled the demographies of snow‐dependent plants. However, our knowledge of changes in the distribution and demographies of such plants is limited because of the lack of fossil records. Methods: Population genetic and landscape genetic analyses were used to investigate the response of population dynamics of Arnica mallotopus (Asteraceae)—a plant confined to heavy‐snow areas of Japan—to changes in snowfall regimes from the Last Glacial Period to the Holocene. Results: The population genetic analysis suggested that the four geographic lineages diverged during the Last Glacial Period. The interaction between reduced snowfall and lower temperatures during this period likely triggered population isolation in separate refugia. Subpopulation differentiation in the northern group was lower than in the southern group. Our ecological niche model predicted that the current distribution was patchy in the southern region; that is, the populations were isolated by topologically flat and climatically unsuitable lowlands. The landscape genetic analysis suggested that areas with little snowfall acted as barriers to the Holocene expansion of species distribution and continued limiting gene flow between local populations. Conclusions: These findings indicate that postglacial population responses vary among regions and are controlled by environmental and geographic factors. Thus, changes in snowfall regime played a major role in shaping the distribution and genetic structure of the snow‐dependent plant. [ABSTRACT FROM AUTHOR]

Forest fragmentation studies are now urgent due to increased rates of deforestation and forest fires worldwide. In South America, the bee-pollinated Cariniana estrellensis is one of the largest trees, and a paradigm for the health and sustainability of forest biomes. For a large-yet-fragmented population (four subpopulations) in the transition zone between Brazilian Savannah and Atlantic Forest, we carried out a study of pollen flow, mating system and spatial genetic structure using nine microsatellite loci. This revealed that the subpopulations are not reproductively isolated because of pollen flow from outside the study area (18.3%) and between subpopulations (16.1–31.3%). Pollen dispersal reached long distances (3.5 km), but mating occurred predominantly between larger-diameter trees located close to mother-trees. We found that C. estrellensis is self-compatible with reproduction mediated mainly by outcrossing (> 0.95), but matings were not random due to biparental inbreeding (tr: 0.048–0.124) and correlated-paternity (rp: 0.16–0.28), which was higher within (rpw: 0.524–0.95) than among fruits (rpa: 0.048–0.052). Inbreeding decreased from seedlings (0.088) to adults, indicating inbreeding depression between the seedling and adult stages. Subpopulations exhibited spatial genetic structure (50–200 m), revealing a pattern of genetic dispersion of isolation-by-distance. Seeds should be harvested from trees that are > 200 m apart for successful ex-situ conservation and populations should not be isolated by more than the maximum pollen-dispersion distance observed (3.5 km) for in-situ conservation. The findings are consistent with the maximum distance that bees can disperse pollen and thereby maintain genetic connectivity between populations and resilience to population fragmentation into forest remnants. [ABSTRACT FROM AUTHOR]

Context: Processes that shape genomic and ecological divergence can reveal important evolutionary dynamics to inform the conservation of threatened species. Fontainea is a genus of rainforest shrubs and small trees including critically endangered and threatened species restricted to narrow, but complex geographic and ecological regions. Several species of Fontainea are subject to spatially explicit conditions and experience limited intra-specific gene flow, likely generating genetic differentiation and local adaptation. Objectives: Here, we explored the genetic and ecological mechanisms underlying patterns of diversification in two, closely related threatened Fontainea species. Our aim was to compare spatial patterns of genetic variation between the vulnerable Fontainea australis (Southern Fontainea) and critically endangered F. oraria (Coastal Fontainea), endemic to the heterogeneous subtropical region of central, eastern Australia, where large-scale clearing has severely reduced rainforest habitat to a fraction (< 1%) of its pre-European settlement extent. Methods: We used a set of 10,000 reduced-representation markers to infer genetic relationships and the drivers of spatial genetic variation across the two species. In addition, we employed a combination of univariate and multivariate genome-environment association analysis using a set of topo-climatic variables to explore potential patterns of local adaptation as a factor impacting genomic divergence. Results: Our study revealed that Coastal Fontainea have a close genetic relationship with Southern Fontainea. We showed that isolation by distance has played a key role in their genetic variation, indicating that vicariance can explain the spatial genetic distribution of the two species. Genotype-environment analyses showed a strong association with temperature and topographic features, suggesting adaptation to localised thermal environments. We used a multivariate redundancy analysis to identify a range of putatively adapted loci associated with local environmental conditions. Conclusions: Divergent selection at the local-habitat scale as a result of dispersal limitations and environmental heterogeneity (including physical barriers) are likely contributors to adaptive divergence between the two Fontainea species. Our findings have presented evidence to indicate that Southern and Coastal Fontainea were comprised of distinct genetic groups and ecotypes, that together may form a single species continuum, with further phenotype research suggested to confirm the current species boundaries. Proactive conservation actions, including assisted migration to enhance the resilience of populations lacking stress-tolerant single nucleotide polymorphisms (SNPs) may be required to secure the long-term future of both taxa. This is especially vital for the critically endangered Coastal Fontainea given projections of habitat decline for the species under future climate scenarios. [ABSTRACT FROM AUTHOR]

Biological invasions are a major threat to biodiversity and have particularly devastating impacts on island ecosystems. The New Caledonia archipelago is considered a biodiversity hotspot due to its diverse native flora. Javan rusa deer (Rusa timorensis) were introduced to New Caledonia in 1870 and the population consists of several hundred thousand individuals today. They directly threaten rare endemic species and affect the composition and structure of the vegetation. While a rusa deer management plan has identified ten priority areas for deer control operations, removing deer could be offset by the dispersal of animals back into the control areas. Here, we genotyped 628 rusa deer using 16 microsatellite markers to analyse the genetic structure of the animals in New Caledonia. We aimed to assess fine-scale genetic structure, to identify natural barriers to deer movement and to assess functional connectivity by optimising individual-based landscape resistance models. Our results suggested that rusa deer formed a single genetic population on the main New Caledonian island. The isolation-by-distance pattern suggested that female dispersal was limited, whereas males had larger dispersal distances. We assessed functional connectivity using different genetic distance metrics and all models performed poorly (mR2 ≤ 0.0043). Landscape features thus hardly affected deer movement. The characteristics of our results suggested that they were not an artefact of the colonisation history of the species. Achieving an effective reduction of deer population sizes in specific management areas will be difficult because of the deer's high dispersal capabilities and impossible without very substantial financial investment. [ABSTRACT FROM AUTHOR]

Anthropogenically driven environmental changes over recent centuries have led to severe declines of wildlife populations. Better tools are needed to assess the magnitude and consequences of these declines. Anecdotal evidence suggests European bat populations have suffered substantial declines in the past centuries. However, there is little empirical evidence of these declines that can be used to put more recent population trends into historic context.This study is a collaboration between academics and conservation practitioners to develop molecular approaches capable of providing evidence of historic population changes that can inform conservation status assessments and management. We generated a genomic dataset of 46,872 SNPs for the Western barbastelle, Barbastella barbastellus, a regionally Vulnerable bat species, including colonies from across the species' British and Iberian ranges. We used a combination of landscape genetics and model‐based inference of demographic history to identify both evidence of population size changes and possible drivers of these changes.Levels of genetic diversity increased and inbreeding decreased with increasing broadleaf woodland cover around the colony. Genetic connectivity was impeded by artificial lights and facilitated by rivers and broadleaf woodland cover.The demographic history analysis showed that both the northern and southern British barbastelle populations have declined by 99% over the past 330–548 years. These declines may be linked to the loss of large oak trees and native woodlands due to shipbuilding during the early colonial period.Synthesis and applications. Genomic approaches can provide a better understanding of the conservation status of threatened species, within historic and contemporary contexts, and inform their conservation management. Our findings of will directly influence the definition of the Favourable Conservation Status of the barbastelle, in turn influencing considerations of the conservation of the species in development plans. Knowledge gained will also help set species recovery targets. Policymakers are interested in using our approach for other species. This study shows how we can bridge the implementation gap between genomic research and direct conservation applications. There is an urgent need to carry out such collaborative studies for other priority species to enable informed species recovery interventions via policy mechanisms and project delivery. [ABSTRACT FROM AUTHOR]

Maintaining habitat connectivity is crucial for maintaining genetic diversity and reducing the risk of inbreeding depression in numerous species. Human-modified habitats pose a threat to population persistence, particularly for amphibians that require both aquatic and terrestrial habitats and often exhibit low dispersal capacity. In this study, we investigated the genetic structure and variation of two sympatric newt species, Triturus cristatus and Lissotriton vulgaris, in an urbanized and agricultural landscape. Using a multiscale resistance modeling approach, we evaluated how landscape features affect gene flow in both species. Our results confirmed that the less abundant T. cristatus exhibited more genetically distinct demes than the more common L. vulgaris, which showed a more subtle structure. Additionally, levels of genetic variation were lower in T. cristatus than in L. vulgaris, but with a similar spatial distribution pattern across shared ponds. We found that the proportion of managed grassland in the study area played a major role in reducing the level of connectivity in both species. Furthermore, considering multiple spatial scales proved to be effective in improving the fit of the landscape resistance models, with the largest scale (900 m) providing the best fit. In T. cristatus, areas with low proportions of trees or high proportions of crop fields negatively affected genetic connectivity. Notably, resistance surfaces optimized for each species were highly correlated. The intensively managed grassland lacked the structural heterogeneity necessary for newts. Therefore, switching to a more traditional management approach in the landscape to increase spatial patchiness at the scale of dispersal would benefit both species. [ABSTRACT FROM AUTHOR]

Context: Tropical dry forests (TDFs) are one of the richest and also one of the most threatened ecosystems in the world due to anthropization. In Mexico, only a minimal proportion of TDF is conserved in protected areas, typically surrounded by human-modified landscapes. Habitat modification can impact gene flow, affecting the populations' genetic structure, and ultimately, the long-term persistence of natural populations. Objectives: We examined the influence of landscape features on the genetic connectivity of Thryophilus sinaloa, a common and highly territorial TDF-associated bird species. We conducted our study in a Mexican landscape along the Pacific coast characterized by a protected area surrounded by a heterogenous human-modified landscape. Methods: We genotyped 90 individuals from 20 localities at 24,549 SNPs derived from 3RADseq and de novo assembling techniques to examine the relationship between population genetic patterns and landscape features using a resistance surface optimization framework. Results: Populations were genetically structured in two groups across the landscape. An open-areas resistance surface, along with geographic distance, reduced genetic connectivity. This finding suggests that protected areas are partially isolated from TDF fragments and other non-protected areas. Conclusions: Our research highlights the impact of TDF landscape modification by human-induced activities on the genetic connectivity of a common bird. Our study reveals that the only TDF reserve in the region is mostly disconnected from other remnants of non-protected areas of continuous TDF. The increasing deterioration of the habitat could eventually cause a decrease in genetic diversity and effective population size. Moreover, genetic differentiation could be enhanced as habitat patches are more isolated, increasing the likelihood of local extinctions. [ABSTRACT FROM AUTHOR]

Assessing the value of ecosystem services (ESV) can promote coordinated economic and ecological development. This study aimed to systematically review ecosystem services (ES) research history and research methodology and used the CiteSpace software to analyze 4063 papers in the field of service value in the ecosystem and visually analyze the developments in ES assessment; a conceptual framework combined with landscape genetics for evaluating ES was then constructed. The results showed that, first, the number of articles in the Web of Science (WoS) and China National Knowledge Infrastructure (CNKI) databases has been increasing annually. Moreover, Ecosystem Services, Sustainability, Ecological Indicators, Science of The Total Environment and Journal of Cleaner Production are the top five journals publishing the greatest number of studies. Second, ES research has seeped into life cycles and landscapes. Lastly, valuation of ES under the impacts of climate change and land use is the current research hotspot. The landscape genetics conceptual framework proposed in this study is a classification system based on the nature of ecological processes and can provide new ideas and methods for ES assessment. [ABSTRACT FROM AUTHOR]