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Understanding the ecological, behavioural and evolutionary response of organisms to changing environments is of primary importance in a human-altered world. It is crucial to elucidate how human activities alter gene flow and what are the consequences for the genetic structure of a species. We studied two lineages of the Egyptian fruit bat (Rousettus aegyptiacus) throughout the contact zone between mesic and arid Ecozones in the Middle East to evaluate the species' response to the growing proportion of human-altered habitats in the desert. We integrated population genetics, morphometrics and movement ecology to analyse population structure, morphological variation and habitat use from GPS- or radio-tagged individuals from both desert and Mediterranean areas. We classified the spatial distribution and environmental stratification by describing physical–geographical conditions and land cover. We analysed this information to estimate patch occupancy and used an isolation-by-resistance approach to model gene flow patterns. Our results suggest that lineages from desert and Mediterranean habitats, despite their admixture, are isolated by environment and by adaptation supporting their classification as ecotypes. We found a positive effect of human-altered habitats on patch occupancy and habitat use of fruit bats by increasing the availability of roosting and foraging areas. While this commensalism promotes the distribution of fruit bats throughout the Middle East, gene flow between colonies has not been altered by human activities. This discrepancy between habitat use and gene flow patterns may, therefore, be explained by the breeding system of the species and modifications of natal dispersal patterns., This work was funded by the Israel Science Foundation (ISF) Grants ISF‐FIRST 1316/05 and ISF 1259/09, the Grant Agency of the Academy of Sciences of the Czech Republic (IAA 601110905) and the Institutional Research Support grant No. SVV 260 313/2016, the Adelina and Massimo Della Pergolla Chair of Life Sciences and the Minerva Center for Movement Ecology (R.N.), the President of Israel Doctoral Award (D.S.), the Lady Davis Fellowship Trust and the University Pablo de Olavide (A.C‐C).

Understanding the processes underlying spatial patterns of genetic diversity and structure of natural populations is a central topic in evolutionary biogeography. In this study, we combine data on ancient and contemporary landscape composition to get a comprehensive view of the factors shaping genetic variation across the populations of the scrub-legume grasshopper (Chorthippus binotatus binotatus) from the biogeographically complex region of southeast Iberia. First, we examined geographical patterns of genetic structure and employed an approximate Bayesian computation (ABC) approach to compare different plausible scenarios of population divergence. Second, we used a landscape genetic framework to test for the effects of (1) Late Miocene paleogeography, (2) Pleistocene climate fluctuations, and (3) contemporary topographic complexity on the spatial patterns of population genetic differentiation. Genetic structure and ABC analyses supported the presence of three genetic clusters and a sequential west-to-east splitting model that predated the last glacial maximum (LGM, c. 21 Kya). Landscape genetic analyses revealed that population genetic differentiation was primarily shaped by contemporary topographic complexity, but was not explained by any paleogeographic scenario or resistance distances based on climate suitability in the present or during the LGM. Overall, this study emphasizes the need of integrating information on ancient and contemporary landscape composition to get a comprehensive view of their relative importance to explain spatial patterns of genetic variation in organisms inhabiting regions with complex biogeographical histories., VN was supported by a FPI predoctoral fellowship (BES‐2012‐053741) from Ministerio de Economía y Competitividad. JO was supported by Severo Ochoa (SEV‐2012‐0262) and Ramón y Cajal (RYC‐2013‐12501) research fellowships. This work received financial support from research grants CGL2011‐25053 and CGL2014‐54671‐P (Ministerio de Economía y Competitividad and European Social Fund), POII10‐0197‐0167 and PEII‐2014023‐P (Junta de Comunidades de Castilla‐La Mancha and European Social Fund) and UNCM08‐1E‐018 (European Regional Development Fund).

Habitat degradation and climate change are currently threatening wild pollinators, compromising their ability to provide pollination services to wild and cultivated plants. Landscape genomics offers powerful tools to assess the influence of landscape modifications on genetic diversity and functional connectivity, and to identify adaptations to local environmental conditions that could facilitate future bee survival. Here, we assessed range‐wide patterns of genetic structure, genetic diversity, gene flow, and local adaptation in the stingless bee Melipona subnitida, a tropical pollinator of key biological and economic importance inhabiting one of the driest and hottest regions of South America. Our results reveal four genetic clusters across the species’ full distribution range. All populations were found to be under a mutation–drift equilibrium, and genetic diversity was not influenced by the amount of reminiscent natural habitats. However, genetic relatedness was spatially autocorrelated and isolation by landscape resistance explained range‐wide relatedness patterns better than isolation by geographic distance, contradicting earlier findings for stingless bees. Specifically, gene flow was enhanced by increased thermal stability, higher forest cover, lower elevations, and less corrugated terrains. Finally, we detected genomic signatures of adaptation to temperature, precipitation, and forest cover, spatially distributed in latitudinal and altitudinal patterns. Taken together, our findings shed important light on the life history of M. subnitida and highlight the role of regions with large thermal fluctuations, deforested areas, and mountain ranges as dispersal barriers. Conservation actions such as restricting long‐distance colony transportation, preserving local adaptations, and improving the connectivity between highlands and lowlands are likely to assure future pollination services.

The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.

The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.

Made available in DSpace on 2018-12-11T17:37:19Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-08-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Habitat fragmentation threatens tropical rainforests, which can significantly hinder dispersal in species such as arboreal primates. For conservation actions to be effective there must be an understanding of how landscape structure and biological traits shape dispersal. We assessed the effects of landscape, sex and population management (reintroductions and translocations) on gene flow of Leontopithecus rosalia, an endangered arboreal primate living in highly fragmented forests of Brazil. We genotyped 201 individuals using 14 microsatellite loci to answer three questions: (1) How far does L. rosalia disperse? (2) Is dispersal sex-biased? (3) What are the relative contributions of population management, distance, roads and landscape resistance to genetic kinship? We hypothesized that (1) gene flow decrease between more distant sites; (2) males disperse more than females; and (3) management and land-cover resistance (i.e. landscape resistance) are the variables that most influence genetic kinship. We found positive spatial population-structure up to 8 km. The spatial structure was similar between females and males suggesting that they equally contribute to gene flow. Management and landscape resistance best explained genetic kinship, showing that different land-cover types affect the dispersal at different degrees of landscape permeability. We advocate that maintaining more permeable landscapes is essential to ensure dispersal and gene flow of arboreal mammals. Conservation measures in tropical rainforests must take into account not only the habitat amount, but also the degree at which each land use – roads, urban areas, agriculture, pasture, isolated trees, and stepping stones – facilitates or impedes the species dispersal. Programa de Pós-graduação em Ecologia e Recursos Naturais Instituto de Biociências e Biotecnologia Universidade Estadual do Norte Fluminense Laboratório de Biodiversidade Molecular e Conservação Departamento de Genética e Evolução Universidade Federal de São Carlos Laboratório de Ecologia Espacial e Conservação (LEEC) Instituto de Biociências Universidade Estadual Paulista (UNESP) Programa de Pós-graduação em Ecologia Departamento de Ecologia Instituto de Biologia Universidade Federal do Rio de Janeiro Laboratório de Ecologia Espacial e Conservação (LEEC) Instituto de Biociências Universidade Estadual Paulista (UNESP) FAPESP: 2013/50421-2 FAPESP: 2015/17739-4 CNPq: 312045/2013-1 CNPq: 312292/2016-3

Amphibians are often considered excellent environmental indicator species. Natural and man‐made landscape features are known to form effective genetic barriers to amphibian populations; however, amphibians with different characteristics may have different species–landscape interaction patterns. We conducted a comparative landscape genetic analysis of two closely related syntopic frog species from central China, Pelophylax nigromaculatus (PN) and Fejervarya limnocharis (FL). These two species differ in several key life history traits; PN has a larger body size and larger clutch size, and reaches sexual maturity later than FL. Microsatellite DNA data were collected and analyzed using conventional (F ST, isolation by distance (IBD), AMOVA) and recently developed (Bayesian assignment test, isolation by resistance) landscape genetic methods. As predicted, a higher level of population structure in FL (F ST′ = 0.401) than in PN (F ST′ = 0.354) was detected, in addition to FL displaying strong IBD patterns (r = .861) unlike PN (r = .073). A general north–south break in FL populations was detected, consistent with the IBD pattern, while PN exhibited clustering of northern‐ and southern‐most populations, suggestive of altered dispersal patterns. Species‐specific resistant landscape features were also identified, with roads and land cover the main cause of resistance to FL, and elevation the main influence on PN. These different species–landscape interactions can be explained mostly by their life history traits, revealing that closely related and ecologically similar species have different responses to the same landscape features. Comparative landscape genetic studies are important in detecting such differences and refining generalizations about amphibians in monitoring environmental changes.

Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km(2) in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.

En contraste con la visión tradicional de que el levantamiento de los Andes impulsó la diversificación biótica causando vicarianza en varios grupos con distribuciones que antes eran continuas, investigaciones recientes sugieren que eventos de dispersión a través de los Andes sucedidos después de los principales episodios de levantamiento fueron catalizadores principales de la especiación en aves neotropicales, y que la habilidad de los linajes para persistir y dispersarse en el paisaje predice fuertemente los patrones de especiación. Sin embargo, se desconoce cuándo y dónde sucedieron dichos eventos de dispersión, y el papel de las fluctuaciones climáticas y el consecuente desplazamiento de la vegetación como promotores de la dispersión a través de los Andes en distintos momentos no ha sido estudiado. Empleamos modelos de la distribución potencial de especies basados en datos de clima actual e histórico para examinar escenarios de dispersión a través de los Andes en 41 especies de aves neotropicales de tierras bajas con diferentes afinidades de hábitat. Nuestros resultados indican que la conectividad ecológica que favorecería la dispersión a través de los Andes en el presente es mayor en pasos bajos de la cordillera del sur de Ecuador y el norte de Perú que en pasos bajos de Colombia, y este patrón espacial parece haberse mantenido en cuatro momentos diferentes de los últimos 130,000 años. También encontramos que aunque algunas áreas actualmente no serían propicias para la dispersión de las aves a través de los Andes, bajo condiciones climáticas del pasado (i.e. durante períodos más fríos y secos) presentaron condiciones climáticas sustancialmente más idóneas para permitir la conectividad ecológica de poblaciones a través de la cordillera. No encontramos diferencias consistentes en la conectividad ecológica presente y pasada a través de los Andes entre especies de diferentes tipos de hábitat. Sugerimos que los valles andinos impulsan la diversificación evolutiva no solo porque aíslan las poblaciones de especies de montaña, sino porque permiten la dispersión episódica de especies de las tierras bajas. Nuestros modelos permiten hacer predicciones sobre flujo genético que pueden ser evaluadas en estudios futuros que examinen patrones de intercambio genético a escala fina usando herramientas de genética del paisaje. Contrary to the long-held view that the uplift of the Andes spurred biotic diversification by causing vicariance across multiple lineages with formerly continuous distributions, recent work suggests that dispersal across the Andes occurring after major uplift episodes was a major driver of speciation in Neotropical birds, with the ability of lineages to persist and disperse in the landscape being strong predictors of speciation. However, where and when dispersal events across the Andes occurred is unknown, and the role of climatic fluctuations and associated shifts in vegetation in promoting cross-Andes dispersal at different moments remains to be studied. We used models of species potential distributions based on contemporary and historical climatic data to examine scenarios of cross-Andes dispersal by 41 species of Neotropical lowland birds with varying habitat affinities. Our results indicate that ecological connectivity favoring cross-Andes dispersal at the present is higher in low-lying passes across the Andes of southern Ecuador and northern Peru than in passes in Colombia, and this spatial pattern appears to have been consistent at four different moments over the past 130,000 years. We also found that although some areas may be presently unsuitable for the dispersal of birds across the Andes, under past climatic conditions (i.e. during cooler and drier periods) they were substantially more likely to allow for ecological connectivity of populations across the cordillera. No consistent differences were found in ecological connectivity across the Andes in the present nor in the past for species occupying different habitat types. We suggest that valleys in the Andes are major drivers of evolutionary diversification not only by isolating populations of montane species, but also by allowing episodic dispersal of lowland species. Our models allow us to make predictions about gene flow which may be assessed in future studies examining fine-grain patterns of genetic exchange with landscape genetics tools.

[Background]: Understanding the underlying processes shaping spatial patterns of genetic structure in free-ranging organisms is a central topic in evolutionary biology. Here, we aim to disentangle the relative importance of neutral (i.e. genetic drift) and local adaptation (i.e. ecological divergence) processes in the evolution of spatial genetic structure of the Morales grasshopper (Chorthippus saulcyi moralesi), a narrow-endemic taxon restricted to the Central Pyrenees. More specifically, we analysed range-wide patterns of genetic structure and tested whether they were shaped by geography (isolation-by-distance, IBD), topographic complexity and present and past habitat suitability models (isolation-byresistance, IBR), and environmental dissimilarity (isolation-by-environment, IBE)., [Results]: Different clustering analyses revealed a deep genetic structure that was best explained by IBR based on topographic complexity. Our analyses did not reveal a significant role of IBE, a fact that may be due to low environmental variation among populations and/or consequence of other ecological factors not considered in this study are involved in local adaptation processes. IBR scenarios informed by current and past climate distribution models did not show either a significant impact on genetic differentiation after controlling for the effects of topographic complexity, which may indicate that they are not capturing well microhabitat structure in the present or the genetic signal left by dispersal routes defined by habitat corridors in the past., [Conclusions]: Overall, these results indicate that spatial patterns of genetic variation in our study system are primarily explained by neutral divergence and migration-drift equilibrium due to limited dispersal across abrupt reliefs, whereas environmental variation or spatial heterogeneity in habitat suitability associated with the complex topography of the region had no significant effect on genetic discontinuities after controlling for geography. Our study highlights the importance of considering a comprehensive suite of potential isolating mechanisms and analytical approaches in order to get robust inferences on the processes promoting genetic divergence of natural populations., VN was supported by a FPI pre-doctoral scholarship (BES-2012-053741) from Ministerio de Economía y Competitividad. JO was supported by Severo Ochoa (SEV-2012-0262) and Ramón y Cajal (RYC-2013-12501) research fellowships. This work received financial support from research grants CGL2011-25053 (Ministerio de Ciencia e Innovación and European Social Fund), POII10-0197-0167, PEII-2014-023-P (Junta de Comunidades de Castilla-La Mancha and European Social Fund) and UNCM08-1E-018 (European Regional Development Fund)., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad-leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, DC) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoDb). Mantel tests between distance matrices highlighted how the Log-DC in PEF populations was related to log-transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log-EcoD, and particularly by the Log-EcoDb, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when population are strongly structured.

1. The simple and partialMantel tests are routinely used in many areas of evolutionary biology to assess the significance of the association between two ormorematrices of distances relative to the same pairs of individuals or demes. Partial Mantel tests rather than simple Mantel tests are widely used to assess the relationship between two variables displaying some form of structure.2. We show that contrary to a widely shared belief, partialMantel tests are not valid in this case, and their bias remains close to that of the simpleMantel test.3. We confirm that strong biases are expected under a sampling design and spatial correlation parameter drawn from an actual study.4. TheMantel tests should not be used in case autocorrelation is suspected in both variables compared under the null hypothesis.We outline alternative strategies. The R code used for our computer simulations is distributed as supportingmaterial.