Demographic and spatially-explicit landscape genomic analyses in a tropical oak reveal the impacts of late Quaternary climate change on Andean montane forests

Tropical Andes are one of the most important biodiversity hotspots on earth, yet our understanding on how their biotas have responded to Quaternary climatic oscillations is extraordinarily limited and the alternative models proposed to explain their demographic dynamics have been seldom formally evaluated. Here, we test the hypothesis that the interplay between the spatial configuration of geographical barriers to dispersal and elevational displacements driven by Quaternary cooling-warming cycles have shaped the demographic trajectories of montane oak forests (Quercus humboldtii) from the Colombian Andes. Specifically, we integrate genomic data and environmental niche modelling at fine temporal resolution to test competing spatially-explicit demographic and coalescent models, including scenarios considering (i) isotropic gene flow through the landscape, (ii) the hypothetical impact of contemporary barriers to dispersal (i.e., inter-Andean valleys), and (ii) distributional shifts of montane oak forests from the Last Glacial Maximum to present. Although our data revealed a marked genetic fragmentation of montane oak forests, statistical support for isolation-with-migration models indicate that geographically separated populations from the different Andean Cordilleras regularly exchange gene flow. Accordingly, spatiotemporally-explicit demographic analyses supported a model of flickering connectivity, with scenarios considering isotropic gene flow or currently unsuitable habitats as persistent barriers to dispersal providing a comparatively worse fit to empirical genomic data. Overall, these results emphasize the role of landscape heterogeneity on shaping spatial patterns of genomic variation in montane oak forests, rejecting the hypothesis of genetic continuity and supporting a significant impact of Quaternary climatic oscillations on their demographic trajectories.

Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur

Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.

Inferring population connectivity in eastern massasauga rattlesnakes (Sistrurus catenatus) using landscape genetics

Assessing the environmental factors that influence the ability of a threatened species to move through a landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited, making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the eastern massasauga rattlesnake (Sistrurus catenatus). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity was impacted by both contemporary land-cover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and least-cost paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for S. catenatus movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmented landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.

Estimating resistance surfaces using gradient forest and allelic frequencies

Understanding landscape connectivity has become a global priority for mitigating the impact of landscape fragmentation on biodiversity. Connectivity methods that use link-based methods traditionally rely on relating pairwise genetic distance between individuals or demes to their landscape distance (e.g., geographic distance, cost distance). In this study, we present an alternative to conventional statistical approaches to refine cost surfaces by adapting the gradient forest approach to produce a resistance surface. Used in community ecology, gradient forest is an extension of random forest, and has been implemented in genomic studies to model species genetic offset under future climatic scenarios. By design, this adapted method, resGF, has the ability to handle multiple environmental predicators and is not subjected to traditional assumptions of linear models such as independence, normality and linearity. Using genetic simulations, resistance Gradient Forest (resGF) performance was compared to other published methods (maximum likelihood population effects model, random forest-based least-cost transect analysis and species distribution model). In univariate scenarios, resGF was able to distinguish the true surface contributing to genetic diversity among competing surfaces better than the compared methods. In multivariate scenarios, the gradient forest approach performed similarly to the other random forest-based approach using least-cost transect analysis but outperformed MLPE-based methods. Additionally, two worked examples are provided using two previously published data sets. This machine learning algorithm has the potential to improve our understanding of landscape connectivity and inform long-term biodiversity conservation strategies.

Pilot Study on the Geographical Mapping of Genetic Diversity among European Chestnut (Castanea sativa Mill.) Cultivars in Southern Italy

Knowledge of the spatial distribution of European chestnut (Castanea sativa Mill.) cultivar diversity is essential for managing and conserving the genetic resources of this fruit tree species in Southern Italy. To this goal, the present work investigated the feasibility of mapping, through spatial representation, the distribution of genetic diversity of traditional chestnut varieties in the area of the Roccamonfina Regional Park in the Campania Region. After Principal Coordinates Analysis (PCoA) of molecular-genetic data, chestnuts formed varietal groups in a leopard spot on PCoA plots with a relatively high degree of genetic diversity. Successively, a Geographic Information System (GIS) tool utilized these molecular-genetic data to create a genetic divergence surface by geospatial interpolation on the geographic map of the Regional Park corresponding to each chestnut variety. The regions containing more biodiversity richness resulted in differentially colored from those containing cultivars less genetically distant from each other; thus, the area in study was consistently colored according to the allelic richness as evaluated by molecular-genetic markers. The combined use of tools for molecular and spatial analysis allowed for drafting genetic landscapes with the aim of extracting useful information for the safeguarding of the chestnut biodiversity at risk.

Linking life history to landscape for threatened species conservation in a multiuse region

Landscape-scale conservation that considers metapopulation dynamics will be essential for preventing declines of species facing multiple threats to their survival. Toward this end, we developed a novel approach that combines occurrence records, spatial-environmental data, and genetic information to model habitat, connectivity, and patterns of genetic structure and link spatial attributes to underlying ecological mechanisms. Using the threatened northern quoll (Dasyurus hallucatus) as a case study, we applied this approach to address the need for conservation decision-making tools that promote resilient metapopulations of this threatened species in the Pilbara, Western Australia, a multiuse landscape that is a hotspot for biodiversity and mining. Habitat and connectivity were predicted by different landscape characteristics. Whereas habitat suitability was overwhelmingly driven by terrain ruggedness, dispersal was facilitated by proximity to watercourses. Although there is limited evidence for major physical barriers in the Pilbara, areas with high silt and clay content (i.e., alluvial and hardpan plains) showed high resistance to dispersal. Climate subtlety shaped distributions and patterns of genetic turnover, suggesting the potential for local adaptation. By understanding these spatial-environmental associations and linking them to life-history and metapopulation dynamics, we highlight opportunities to provide targeted species management. To support this, we have created habitat, connectivity, and genetic uniqueness maps for conservation decision-making in the region. These tools have the potential to provide a more holistic approach to conservation in multiuse landscapes globally.

Validating graph-based connectivity models with independent presence-absence and genetic data sets

Habitat connectivity is a key objective of current conservation policies and is commonly modeled by landscape graphs (i.e., sets of habitat patches [nodes] connected by potential dispersal paths [links]). These graphs are often built based on expert opinion or species distribution models (SDMs) and therefore lack empirical validation from data more closely reflecting functional connectivity. Accordingly, we tested whether landscape graphs reflect how habitat connectivity influences gene flow, which is one of the main ecoevolutionary processes. To that purpose, we modeled the habitat network of a forest bird (plumbeous warbler [Setophaga plumbea]) on Guadeloupe with graphs based on expert opinion, Jacobs' specialization indices, and an SDM. We used genetic data (712 birds from 27 populations) to compute local genetic indices and pairwise genetic distances. Finally, we assessed the relationships between genetic distances or indices and cost distances or connectivity metrics with maximum-likelihood population-effects distance models and Spearman correlations between metrics. Overall, the landscape graphs reliably reflected the influence of connectivity on population genetic structure; validation R² was up to 0.30 and correlation coefficients were up to 0.71. Yet, the relationship among graph ecological relevance, data requirements, and construction and analysis methods was not straightforward because the graph based on the most complex construction method (species distribution modeling) sometimes had less ecological relevance than the others. Cross-validation methods and sensitivity analyzes allowed us to make the advantages and limitations of each construction method spatially explicit. We confirmed the relevance of landscape graphs for conservation modeling but recommend a case-specific consideration of the cost-effectiveness of their construction methods. We hope the replication of independent validation approaches across species and landscapes will strengthen the ecological relevance of connectivity models.

How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree

Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas such as the Loky-Manambato region (north) raise questions regarding the causes and age of forest fragmentation. The Loky-Manambato region also harbours a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamics in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction-associated DNA sequencing data and chloroplast microsatellites. Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across these antique mosaic habitats, calling for the study of organismal interactions that promote gene flow.

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

Genetic diversity pattern reveals the primary determinant of burcucumber (Sicyos angulatus L.) invasion in Korea

Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.

Pleistocene-Holocene vicariance, not Anthropocene landscape change, explains the genetic structure of American black bear (Ursus americanus) populations in the American Southwest and northern Mexico

The phylogeography of the American black bear (Ursus americanus) is characterized by isolation into glacial refugia, followed by population expansion and genetic admixture. Anthropogenic activities, including overharvest, habitat loss, and transportation infrastructure, have also influenced their landscape genetic structure. We describe the genetic structure of the American black bear in the American Southwest and northern Mexico and investigate how prehistoric and contemporary forces shaped genetic structure and influenced gene flow. Using a suite of microsatellites and a sample of 550 bears, we identified 14 subpopulations organized hierarchically following the distribution of ecoregions and mountain ranges containing black bear habitat. The pattern of subdivision we observed is more likely a product of postglacial habitat fragmentation during the Pleistocene and Holocene, rather than a consequence of contemporary anthropogenic barriers to movement during the Anthropocene. We used linear mixed‐effects models to quantify the relationship between landscape resistance and genetic distance among individuals, which indicated that both isolation by resistance and geographic distance govern gene flow. Gene flow was highest among subpopulations occupying large tracts of contiguous habitat, was reduced among subpopulations in the Madrean Sky Island Archipelago, where montane habitat exists within a lowland matrix of arid lands, and was essentially nonexistent between two isolated subpopulations. We found significant asymmetric gene flow supporting the hypothesis that bears expanded northward from a Pleistocene refugium located in the American Southwest and northern Mexico and that major highways were not yet affecting gene flow. The potential vulnerability of the species to climate change, transportation infrastructure, and the US–Mexico border wall highlights conservation challenges and opportunities for binational collaboration.

Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata

Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of Triodanis perfoliata, a widespread mix‐mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between a breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R² = .63, p = .01, n = 9 populations), and we found significant population structuring (F_ST = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environments appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that T. perfoliata experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that the breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of T. perfoliata in the US.

Natural and anthropogenic landscape factors shape functional connectivity of an ecological specialist in urban Southern California

Identifying how natural (i.e., unaltered by human activity) and anthropogenic landscape variables influence contemporary functional connectivity in terrestrial organisms can elucidate the genetic consequences of environmental change. We examine population genetic structure and functional connectivity among populations of a declining species, the Blainville's horned lizard (Phrynosoma blainvillii), in the urbanized landscape of the Greater Los Angeles Area in Southern California, USA. Using single nucleotide polymorphism data, we assessed genetic structure among populations occurring at the interface of two abutting evolutionary lineages, and at a fine scale among habitat fragments within the heavily urbanized area. Based on the ecology of P. blainvillii, we predicted which environmental variables influence population structure and gene flow and used gravity models to distinguish among hypotheses to best explain population connectivity. Our results show evidence of admixture between two evolutionary lineages and strong population genetic structure across small habitat fragments. We also show that topography, microclimate, and soil and vegetation types are important predictors of functional connectivity, and that anthropogenic disturbance, including recent fire history and urban development, are key factors impacting contemporary population dynamics. Examining how natural and anthropogenic sources of landscape variation affect contemporary population genetics is critical to understanding how to best manage sensitive species in a rapidly changing landscape.

Seizing the Moment: The opportunity and relevance of the California Conservation Genomics Project to state and federal conservation policy

Conservation science and environmental regulation are sibling constructs of the latter half of the 20th century, part of a more general awakening to humanity's effect on the natural world in the wake of two world wars. Efforts to understand the evolution of biodiversity using the models of population genetics and the data derived from DNA sequencing, paired with legal and political mandates to protect biodiversity through novel laws, regulations, and conventions arose concurrently. The extremely rapid rate of development of new molecular tools to document and compare genetic identities, and the global goal of prioritizing species and habitats for protection are separate enterprises that have benefited from each other, ultimately leading to improved outcomes for each. In this article, we explore how the California Conservation Genomics Project has, and should, contribute to ongoing and future conservation implementation, and how it serves as a model for other geopolitical regions and taxon-oriented conservation efforts. One of our primary conclusions is that conservation genomics can now be applied, at scale, to inform decision-makers and identify regions and their contained species that are most resilient, and most in need of conservation interventions.

The phylogeny of California, and how it informs setting multi-species conservation priorities

Incorporating measures of taxonomic diversity into research and management plans has long been a tenet of conservation science. Increasingly, active conservation programs are turning towards multi-species landscape and regional conservation actions, and away from single species approaches. This is both a reflection of changing trends in conservation science and advances in foundational technologies, including genomics and geospatial science. Multi-species approaches may provide more fundamental insights into evolutionary processes and equip managers with a more holistic understanding of the landscapes under their jurisdiction. Central to this approach are data generation and analyses which embrace and reflect a broad range of taxonomic diversity. Here we examine the family-level phylogenetic breadth of the California Conservation Genomics Project (CCGP) based on family-level phylogenetic diversity, family-level phylogenetic distinctness, and family richness. We place this in the context of the diversity present in California and compare it to the 35-plus years of genetic research compiled in the CaliPopGen Database. We found that the family-level phylogenetic diversity in the CCGP reflected that of California very well, slightly over-representing chordates and under-representing arthropods, and that 42% of CCGP phylogenetic diversity represented new contributions to genetic data for the state. In one focused effort, the CCGP was able to achieve roughly half the family-level phylogenetic diversity studied over the last several decades. To maximize studied phylogenetic diversity, future work should focus on arthropods, a conclusion that likely reflects the overall lack of attention to this hyper diverse clade.

Elevated inbreeding in Heliconia tortuosa is determined by tropical forest stand age, isolation, and loss of hummingbird functional diversity

Forest conversion and habitat loss are major threats to biological diversity. Forest regeneration can mitigate the negative effects of old growth forest loss on species diversity, but less is known about the extent to which forest loss reduces genetic diversity in remnant populations and whether secondary forests play a role in the maintenance of genetic diversity. We quantified genetic diversity in a tropical hummingbird-pollinated understory herb, Heliconia tortuosa, across a landscape mosaic of primary and secondary forest regrowth. Using microsatellite genotypes from >850 adult and juvenile plants within 33 forest patches and extensive bird surveys, we examined the effect of contemporary and historical landscape features including forest age (primary vs. secondary forest), stand isolation, and pollinator assemblages on genetic diversity and levels of inbreeding in H. tortuosa. We found that inbreeding was up to 3x higher in secondary forest, and this effect was amplified with reductions in primary forest in the surrounding landscape through reduced observed heterozygosity in isolated fragments. Inbreeding in forest patches was negatively correlated with the local frequency of specialist long-distance foraging traplining hummingbirds. Traplining hummingbirds therefore appear to facilitate mating among unrelated plants - an inference we tested using empirically parameterized simulations. Higher levels of inbreeding in H. tortuosa are therefore associated with reduced functional diversity of hummingbirds in secondary forests and forest patches isolated from primary forests. Our findings suggest a cryptic consequence of primary forest loss and secondary forest regeneration through the disruption of mutualistic interactions resulting in the erosion of genetic diversity in a common understory plant.

Population demography maintains biogeographic boundaries

Global biodiversity is organised into biogeographic regions that comprise distinct biotas. The contemporary factors maintaining differences in species composition between regions are poorly understood. Given evidence that populations with sufficient genetic variation can adapt to fill new habitats, it is surprising that more homogenisation of species assemblages across regions has not occurred. Theory suggests that expansion across biogeographic regions could be limited by reduced adaptive capacity due to demographic variation along environmental gradients, but this possibility has not been empirically explored. Using three independently curated data sets describing continental patterns of mammalian demography and population genetics, we show that populations near biogeographic boundaries have lower effective population sizes and genetic diversity, and are more genetically differentiated. These patterns are consistent with reduced adaptive capacity in areas where one biogeographic region transitions into the next. That these patterns are replicated across mammals suggests they are stable and generalisable in their contribution to long-term limits on biodiversity homogenisation. Understanding the contemporary processes that maintain compositional differences among regional biotas is crucial for our understanding of the current and future organisation of global biodiversity.

Scale-dependent influence of the sagebrush community on genetic connectivity of the sagebrush obligate Gunnison sage-grouse

Habitat fragmentation and degradation impacts an organism's ability to navigate the landscape, ultimately resulting in decreased gene flow and increased extinction risk. Understanding how landscape composition impacts gene flow (i.e., connectivity) and interacts with scale is essential to conservation decision‐making. We used a landscape genetics approach implementing a recently developed statistical model based on the generalized Wishart probability distribution to identify the primary landscape features affecting gene flow and estimate the degree to which each component influences connectivity for Gunnison sage‐grouse (Centrocercus minimus). We were interested in two spatial scales: among distinct populations rangewide and among leks (i.e., breeding grounds) within the largest population, Gunnison Basin. Populations and leks are nested within a landscape fragmented by rough terrain and anthropogenic features, although requisite sagebrush habitat is more contiguous within populations. Our best fit models for each scale confirm the importance of sagebrush habitat in connectivity, although the important sagebrush characteristics differ. For Gunnison Basin, taller shrubs and higher quality nesting habitat were the primary drivers of connectivity, while more sagebrush cover and less conifer cover facilitated connectivity rangewide. Our findings support previous assumptions that Gunnison sage‐grouse range contraction is largely the result of habitat loss and degradation. Importantly, we report direct estimates of resistance for landscape components that can be used to create resistance surfaces for prioritization of specific locations for conservation or management (i.e., habitat preservation, restoration, or development) or as we demonstrated, can be combined with simulation techniques to predict impacts to connectivity from potential management actions.

Main roads and land cover shaped the genetic structure of a Mediterranean island wild boar population

Patterns of genetic differentiation within and among animal populations might vary due to the simple effect of distance or landscape features hindering gene flow. An assessment of how landscape connectivity affects gene flow can help guide management, especially in fragmented landscapes. Our objective was to analyze population genetic structure and landscape genetics of the native wild boar (Sus scrofa meridionalis) population inhabiting the island of Sardinia (Italy), and test for the existence of Isolation-by-Distance (IBD), Isolation-by-Barrier (IBB), and Isolation-by-Resistance (IBR). A total of 393 Sardinian wild boar samples were analyzed using a set of 16 microsatellite loci. Signals of genetic introgression from introduced non-native wild boars or from domestic pigs were revealed by a Bayesian cluster analysis including 250 reference individuals belonging to European wild populations and domestic breeds. After removal of introgressed individuals, genetic structure in the population was investigated by different statistical approaches, supporting a partition into five discrete subpopulations, corresponding to five geographic areas on the island: north-west (NW), central west (CW), south-west (SW), north-central east (NCE), and south-east (SE). To test the IBD, IBB, and IBR hypotheses, we optimized resistance surfaces using genetic algorithms and linear mixed-effects models with a maximum likelihood population effects parameterization. Landscape genetics analyses revealed that genetic discontinuities between subpopulations can be explained by landscape elements, suggesting that main roads, urban settings, and intensively cultivated areas are hampering gene flow (and thus individual movements) within the Sardinian wild boar population. Our results reveal how human-transformed landscapes can affect genetic connectivity even in a large-sized and highly mobile mammal such as the wild boar, and provide crucial information to manage the spread of pathogens, including the African Swine Fever virus, endemic in Sardinia.

Remote sensing of cytotype and its consequences for canopy damage in quaking aspen

Mapping geographic mosaics of genetic variation and their consequences via genotype x environment interactions at large extents and high resolution has been limited by the scalability of DNA sequencing. Here, we address this challenge for cytotype (chromosome copy number) variation in quaking aspen, a drought-impacted foundation tree species. We integrate airborne imaging spectroscopy data with ground-based DNA sequencing data and canopy damage data in 391 km² of southwestern Colorado. We show that (1) aspen cover and cytotype can be remotely sensed at 1 m spatial resolution, (2) the geographic mosaic of cytotypes is heterogeneous and interdigitated, (3) triploids have higher leaf nitrogen, canopy water content, and carbon isotope shifts (δ¹³ C) than diploids, and (4) canopy damage varies among cytotypes and depends on interactions with topography, canopy height, and trait variables. Triploids are at higher risk in hotter and drier conditions.

Species-landscape interactions drive divergent population trajectories in four forest-dependent Afromontane forest songbird species within a biodiversity hotspot in South Africa

Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest-dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest-dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost-distances along least-cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest-thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors- where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land-cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest-dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.

Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction

Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.

Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails

The environment plays an important role in the movement of individuals and their associated genes among populations, which facilitates gene flow. Gene flow can help maintain the genetic diversity both within and between populations and counter the negative impact of genetic drift, which can decrease the fitness of individuals. Sympatric species can have different habitat preferences, and thus can exhibit different patterns of genetic variability and population structure. The specialist-generalist variation hypothesis (SGVH) predicts that specialists will have lower genetic diversity, lower effective population sizes (Ne), and less gene flow among populations. In this study, we used spatially explicit, individual-based comparative approaches to test SGVH predictions in two sympatric cottontail species and identify environmental variables that influence their gene flow. New England cottontail (Sylvilagus transitionalis) is the only native cottontail in the Northeast US, an early successional habitat specialist, and a species of conservation concern. Eastern cottontail (S. floridanus) is an invasive species in the Northeast US and a habitat generalist. We characterized each species' genomic variation by developing double-digest Restriction-site Associated DNA sequence single nucleotide polymorphism markers, quantified their habitat with Geographic Information System environmental variables, and conducted our analyses at multiple scales. Surprisingly, both species had similar levels of genetic diversity and eastern cottontail's Ne was only higher than New England cottontail in one of three subregions. At a regional level, the population clusters of New England cottontail were more distinct than eastern cottontail, but the subregional levels showed more geographic areas of restricted gene flow for eastern cottontail than New England cottontail. In general, the environmental variables had the predicted effect on each species' gene flow. However, the most important environmental variable varied by subregion and species, which shows that location and species matter. Our results provide partial support for the SGVH and the identification of environmental variables that facilitate or impede gene flow can be used to help inform management decisions to conserve New England cottontail.

Strip spraying delays pyrethroid resistance in the redlegged earth mite, Halotydeus destructor: a novel refuge strategy

BACKGROUND

Pesticide resistance has seen control options for the redlegged earth mite (RLEM), Halotydeus destructor, dwindle for Australian grain farmers. The recent discovery of high recessiveness for pyrethroid resistance in RLEM provided an opportunity to examine the feasibility of a refuge strategy to slow the evolution of resistance. Unlike lepidopterous pests in Bt crops, where refuge strategies are routinely practiced, RLEM is a slow-moving pest, which will impact the design of susceptible refuges.

RESULTS

Firstly, we confirmed the pyrethroid resistant allele is recessive to the susceptible (wildtype) allele (in terms of resistance) across spatially separated Australian populations. Secondly, we demonstrated that a small, localized resistant mite population can revert to susceptibility at field relevant scales and conditions. Next, we used a simulation modelling approach to design a practical refuge strategy to maintain susceptibility to pyrethroids in populations with a low incidence of resistance. Certain configurations (e.g. a pesticide strip width of 50 m and refuge spacing of 10 m) maintained low levels of resistance across a 10-year time horizon, with lower mite abundance and minimal yield loss. A larger refuge proportion did not always delay resistance, and, under certain conditions, increased resistance frequency.

CONCLUSION

Strip spraying to maintain refuges can be readily incorporated into RLEM management programs where sprayer widths in commercial cropping contexts are typically between 20-40 m. A refuge approach to RLEM management that uses strip spraying may enhance long term control options in the absence of new chemical registrations but will now require field validation. © 2021 Society of Chemical Industry.

Dispersal behaviour and riverine network connectivity shape the genetic diversity of freshwater amphipod metapopulations

Theory predicts that the distribution of genetic diversity in a landscape is strongly dependent on the connectivity of the metapopulation and the dispersal of individuals between patches. However, the influence of explicit spatial configurations such as dendritic landscapes on the genetic diversity of metapopulations is still understudied, and theoretical corroborations of empirical patterns are largely lacking. Here, we used microsatellite data and stochastic simulations of two metapopulations of freshwater amphipods in a 28,000 km² riverine network to study the influence of spatial connectivity and dispersal strategies on the spatial distribution of their genetic diversity. We found a significant imprint of the effects of riverine network connectivity on the local and global genetic diversity of both amphipod species. Data from 95 sites showed that allelic richness significantly increased towards more central nodes of the network. This was also seen for observed heterozygosity, yet not for expected heterozygosity. Genetic differentiation increased with instream distance. In simulation models, depending on the mutational model assumed, upstream movement probability and dispersal rate, respectively, emerged as key factors explaining the empirically observed distribution of local genetic diversity and genetic differentiation. Surprisingly, the role of site‐specific carrying capacities, for example by assuming a direct dependency of population size on local river size, was less clear cut: while our best fitting model scenario included this feature, over all simulations, scaling of carrying capacities did not increase data‐model fit. This highlights the importance of dispersal behaviour along spatial networks in shaping population genetic diversity.