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Human activity continues to impact global ecosystems, often by altering the habitat suitability, persistence, and movement of native species. It is thus critical to examine the population genetic structure of key ecosystemservice providers across human‐altered landscapes to provide insight into the forces that limit wildlife persistence and movement across multiple spatial scales. While some studies have documented declines of bee pollinators as a result of human‐mediated habitat alteration, others suggest that some bee species may benefit from altered land use due to increased food or nesting resource availability; however, detailed population and dispersal studies have been lacking. We investigated the population genetic structure of the Eastern carpenter bee, Xylocopa virginica, across 14 sites spanning more than 450 km, including dense urban areas and intensive agricultural habitat. X. virginica is a large bee which constructs nests in natural and human‐associated wooden substrates, and is hypothesized to disperse broadly across urbanizing areas. Using 10 microsatellite loci, we detected significant genetic isolation by geographic distance and significant isolation by land use, where urban and cultivated landscapes were most conducive to gene flow. This is one of the first population genetic analyses to provide evidence of enhanced insect dispersal in human‐altered areas as compared to semi‐natural landscapes. We found moderate levels of regional‐scale population structure across the study system (GʹST = 0.146) and substantial co‐ancestry between the sampling regions, where co‐ancestry patterns align with major human transportation corridors, suggesting that human‐mediated movement may be influencing regional dispersal processes. Additionally, we found a signature of strong site‐level philopatry where our analyses revealed significant levels of high genetic relatedness at very fine scales (

Made available in DSpace on 2020-12-10T20:10:47Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-08-31 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Neotropical Grassland Conservancy Aim: Effective conservation policies rely on information about population genetic structure and the connectivity of remnants of suitable habitats. The interaction between natural and anthropogenic discontinuities across landscapes can uncover the relative contributions of different barriers to gene flow, with direct consequences for decision-making in conservation. We aimed to quantify the relative roles of land cover and topographic variables on the population genetic differentiation and diversity of a stream-breeding savanna tree frog (Bokermannohyla ibitiguara) across its range. Location: Serra da Canastra mountain range, Cerrado of Minas Gerais State, Brazil. Methods: We collected samples and extracted DNA samples from 12 populations within and outside a strictly protected park, and used 17 microsatellite markers to assess genetic structure, among-population differentiation and within-population diversity measures. We incorporated landscape data derived from digital models and satellite images to create connectivity matrices to correlate with genetic differentiation using Mantel tests. We used generalized linear models and path analyses to assess the roles of each landscape variable in shaping genetic diversity in this species. Results: Populations within and outside the park boundaries belonged to four genetic clusters. Most populations showed evidence of limited gene flow, with significant genetic differentiation, except for those within the park, which also had higher levels of allelic richness and heterozygosity. However, genetic differentiation among populations in this landscape was primarily explained by topographic complexity. Likewise, within-population measures of genetic diversity were best explained by models including elevation and topographic complexity, and not the amount of natural habitat or gallery forests. Main conclusions: Our results underscore that topography may be a strong historical factor shaping genetic structure among amphibian populations. Therefore, effective conservation strategies for endangered amphibians should avoid focusing exclusively on habitat suitability, and incorporate topographic complexity, which seems to be a key factor for the fauna of the extremely threatened Brazilian savanna. Univ Estadual Paulista, Inst Biociencias, Programa Posgrad Ciencias Biol Zool, Rio Claro, SP, Brazil Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY USA Univ Alabama, Dept Biol Sci, Tuscaloosa, AL USA Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Morfol & Fisiol Anim, Jaboticabal, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Programa Posgrad Ciencias Biol Zool, Rio Claro, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Morfol & Fisiol Anim, Jaboticabal, SP, Brazil FAPESP: 2010/036566 FAPESP: 2012/06228-0 FAPESP: 2013/04023-5 FAPESP: 2014/04394-6 FAPESP: 2009/12013-4

Heterogenous landscape features of the Himalayan region shape the genetic structure of animal populations by delimiting spatial patterns of dispersal and reproduction. Integrating population genetic analysis with landscape features could yield results that shed light on the evolutionary diversity of the taxa therein. This study assessed the population genetic structure of the Nepal Himalayan langurs (Semnopithecus spp.) across almost their entire distribution range in the complex landscape of the Nepal Himalaya using the mitochondrial cytochrome b (CYTB, 1140 bp), cytochrome c oxidase I (COI, 676 bp), and control region (1088 bp) sequences. Sequences were successfully retrieved from 52 samples belonging to 17 troops of wild Himalayan langurs in Nepal. The concatenated alignment of the three loci (2904 bp) defined 35 unique haplotypes with haplotype and nucleotide diversities of 0.961 ± 0.017 and 0.0204 ± 0.004, respectively. The results of a median joining haplotype network and of inter-haplotypic phylogenetic analyses revealed five major clades across the country: one from the eastern, two from the central, and two from the western region of Nepal. No haplotypes were shared among the regions. The Mantel test results indicated that the landscape heterogeneity of the Himalaya has shaped the population genetic structure of the Himalayan langurs due to the combined effects of isolation by resistance and isolation by distance phenomena. The strong population genetic structure and deep mtDNA divergence warrants a detailed taxonomic assessment of the Himalayan langurs across their entire range.

International audience; In forest-specialist mammals, forest loss may induce resistance to animal movement and reduce gene flow between populations, and thereby increase genetic erosion and extinction risks for populations. Understanding how landscape features affect gene flow is of critical importance for conservation. Using landscape genetic tools at multiple spatial scales, we assessed the effects of landscape heterogeneity (in particular the presence of wide open or rural habitats) on gene flow in an endangered forest-specialist species – the Barbary macaque (Macaca sylvanus) –, in its major forest site in Morocco. We genotyped 248 individuals from 23 macaque groups using 11 microsatellite loci. We modelled different scenarios of isolation by landscape resistance. We further tested the relationships between genetic distance and isolation by resistance, after controlling for the effect of isolation by distance. Our results revealed a significant genetic structure and a disruption of gene flow even in geographic proximity. Whatever the spatial scale, remoteness from the forest edge beyond 1km acted as a barrier to macaque movements. In addition, at a fine scale, human-dominated areas were also detected as a barrier. The detection of private alleles in each population suggests an ongoing process of isolation. The preservation of the Barbary macaque implies 1) strictly avoiding all silvicultural practices (in particular clear-cutting of holm oak forests) that could contribute to increase distances between forest patches, 2) restoring corridors between forests, 3) and preserving key small forest patches as potential stepping stones facilitating macaque dispersal.

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.

In modern wildlife ecology, spatial population genetic methods are becoming increasingly applied. Especially for animal species in fragmented landscapes, preservation of gene flow becomes a high priority target in order to restore genetic diversity and prevent local extinction. Within Central Europe, the Alps represent the core distribution area of the black grouse, Lyrurus tetrix. At its easternmost Alpine range, events of subpopulation extinction have already been documented in the past decades. Molecular data combined with spatial analyses can help to assess landscape effects on genetic variation and therefore can be informative for conservation management. Here, we addressed whether the genetic pattern of the easternmost Alpine black grouse metapopulation system is driven by isolation by distance or isolation by resistance. Correlative ecological niche modeling was used to assess geographic distances and landscape resistances. We then applied regression‐based approaches combined with population genetic analyses based on microsatellite data to disentangle effects of isolation by distance and isolation by resistance among individuals and subpopulations. Although population genetic analyses revealed overall low levels of genetic differentiation, the ecological niche modeling showed subpopulations to be clearly delimited by habitat structures. Spatial genetic variation could be attributed to effects of isolation by distance among individuals and isolation by resistance among subpopulations, yet unknown effects might factor in. The easternmost subpopulation was the most differentiated, and at the same time, immigration was not detected; hence, its long‐term survival might be threatened. Our study provides valuable insights into the spatial genetic variation of this small‐scale metapopulation system of Alpine black grouse., By using correlative niche modeling and population genetic methods, we found the spatial genetic structure of Alpine black grouse to be driven by effects of isolation by distance and isolation by resistance.

[Aim]: Coastal plants are terrestrial organisms for which ocean surface currents often act as long‐distance dispersal vectors (thalassochorous species) favouring broad distributions and connecting distant populations. However, few studies have statistically assessed the role of currents in modulating gene flow and species distributions of terrestrial organisms. Here we evaluate the hypothesis that some thalassochorous plants exhibit population connectivity, presumably due to effective seed dispersal driven by sea currents. Location Galápagos Islands (Ecuador). Taxon Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm. Methods Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance. Results Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal., [Location]: Galápagos Islands (Ecuador)., [Taxon]: Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm., [Methods]: Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance., [Results]: Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal., This study is framed within a project also financed by the Ministerio de Economía y Competitividad (CGL2012‐C02‐01).

Climate oscillations have left a significant impact on the patterns of genetic diversity observed in numerous taxa. In this study, we examine the effect of Quaternary climate instability on population genetic variability of a bumble bee pollinator species, Bombus huntii in western North America. Pleistocene and contemporary B. huntii habitat suitability (HS) was estimated with an environmental niche model (ENM) by associating 1,035 locality records with 10 bioclimatic variables. To estimate genetic variability, we genotyped 380 individuals from 33 localities at 13 microsatellite loci. Bayesian inference was used to examine population structure with and without a priori specification of geographic locality. We compared isolation by distance (IBD) and isolation by resistance (IBR) models to examine population differentiation within and among the Bayesian inferred genetic clusters. Furthermore, we tested for the effect of environmental niche stability (ENS) on population genetic diversity with linear regression. As predicted, high‐latitude B. huntii habitats exhibit low ENS when compared to low‐latitude habitats. Two major genetic clusters of B. huntii inhabit western North America: (a) a north genetic cluster predominantly distributed north of 28°N and (b) a south genetic cluster distributed south of 28°N. In the south genetic cluser, both IBD and IBR models are significant. However, in the north genetic cluster, IBD is significant but not IBR. Furthermore, the IBR models suggest that low‐latitude montane populations are surrounded by habitat with low HS, possibly limiting dispersal, and ultimately gene flow between populations. Finally, we detected high genetic diversity across populations in regions that have been climatically unstable since the last glacial maximum (LGM), and low genetic diversity across populations in regions that have been climatically stable since the LGM. Understanding how species have responded to climate change has the potential to inform management and conservation decisions of both ecological and economic concerns.

Functional connectivity, quantified using landscape genetics, can inform conservation through the identification of factors linking genetic structure to landscape mechanisms. We used breeding habitat metrics, landscape attributes, and indices of grouse abundance, to compare fit between structural connectivity and genetic differentiation within five long‐established Sage‐Grouse Management Zones (MZ) I‐V using microsatellite genotypes from 6,844 greater sage‐grouse (Centrocercus urophasianus) collected across their 10.7 million‐km2 range. We estimated structural connectivity using a circuit theory‐based approach where we built resistance surfaces using thresholds dividing the landscape into “habitat” and “nonhabitat” and nodes were clusters of sage‐grouse leks (where feather samples were collected using noninvasive techniques). As hypothesized, MZ‐specific habitat metrics were the best predictors of differentiation. To our surprise, inclusion of grouse abundance‐corrected indices did not greatly improve model fit in most MZs. Functional connectivity of breeding habitat was reduced when probability of lek occurrence dropped below 0.25 (MZs I, IV) and 0.5 (II), thresholds lower than those previously identified as required for the formation of breeding leks, which suggests that individuals are willing to travel through undesirable habitat. The individual MZ landscape results suggested terrain roughness and steepness shaped functional connectivity across all MZs. Across respective MZs, sagebrush availability (10%; I, II, IV), and cultivation (>25%; I, II, IV, V) each reduced movement beyond their respective thresholds. Model validations confirmed variation in predictive ability across MZs with top resistance surfaces better predicting gene flow than geographic distance alone, especially in cases of low and high differentiation among lek groups. The resultant resistance maps we produced spatially depict the strength and redundancy of range‐wide gene flow and can help direct conservation actions to maintain and restore functional connectivity for sage‐grouse.

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).

Although habitat loss has large, consistently negative effects on biodiversity, its genetic consequences are not yet fully understood. This is because measuring the genetic consequences of habitat loss requires accounting for major methodological limitations like the confounding effect of habitat fragmentation, historical processes underpinning genetic differentiation, time-lags between the onset of disturbances and genetic outcomes, and the need for large numbers of samples, genetic markers, and replicated landscapes to ensure sufficient statistical power. In this paper we overcame all these challenges to assess the genetic consequences of extreme habitat loss driven by mining in two herbs endemic to Amazonian savannas. Relying on genotyping-by-sequencing of hundreds of individuals collected across two mining landscapes, we identified thousands of neutral and independent single-nucleotide polymorphisms (SNPs) in each species and used these to evaluate population structure, genetic diversity, and gene flow. Since open-pit mining in our study region rarely involves habitat fragmentation, we were able to assess the independent effect of habitat loss. We also accounted for the underlying population structure when assessing landscape effects on genetic diversity and gene flow, examined the sensitivity of our analyses to the resolution of spatial data, and used annual species and cross-year analyses to minimize and quantify possible time-lag effects. We found that both species are remarkably resilient, as genetic diversity and gene flow patterns were unaffected by habitat loss. Whereas historical habitat amount was found to influence inbreeding; heterozygosity and inbreeding were not affected by habitat loss in either species, and gene flow was mainly influenced by geographic distance, pre-mining land cover, and local climate. Our study demonstrates that it is not possible to generalize about the genetic consequences of habitat loss, and implies that future conservation efforts need to consider species-specific genetic information.

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 study of the drivers that shape spatial genetic structure across heterogeneous landscapes is one of the main approaches used to understand population dynamics and responses in changing environments. While the Isolation-by-Distance model (IBD) assumes that genetic differentiation increases among populations with geographical distance, the Isolation-by-Resistance model (IBR) also considers geographical barriers and other landscape features that impede gen flow. On the other hand, the Isolation-by-Environment model (IBE) explains genetic differentiation through environmental differences between populations. Although spatial genetic studies have increased significantly in recent years, plants from alpine ecosystems are highly underrepresented, even though they are great suitable systems to disentangle the role of the different factors that structure genetic variation across environmental gradients. Here, we studied the spatial genetic structure of the Mediterranean alpine specialist Silene ciliata across its southernmost distribution limit. We sampled three populations across an altitudinal gradient from 1850 m to 2400 m, and we replicated this sample over three mountain ranges aligned across an E-W axis in the central part of the Iberian Peninsula. We genotyped 20 individuals per population based on eight microsatellite markers and used different landscape genetic tools to infer the role of topographic and environmental factors in shaping observed patterns along the altitudinal gradient. We found a significant genetic structure among the studied Silene ciliata populations which was related to the orography and E-W configuration of the mountain ranges. IBD pattern arose as the main factor shaping population genetic differentiation. Geographical barriers between mountain ranges also affected the spatial genetic structure (IBR pattern). Although environmental variables had a significant effect on population genetic diversity parameters, no IBE pattern was found on genetic structure. Our study reveals that IBD was the driver that best explained the genetic structure, whereas environmental factors also played a role in determining genetic diversity values of this dominant plant of Mediterranean alpine environments.

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.

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

Although genetic diversity ultimately determines the ability of organisms to adapt to environmental changes, conservation assessments like the widely used International Union for Conservation of Nature (IUCN) Red List Criteria do not explicitly consider genetic information. Including a genetic dimension into the IUCN Red List Criteria would greatly enhance conservation efforts, because the demographic parameters traditionally considered are poor predictors of the evolutionary resilience of natural populations to global change. Here we perform the first genomic assessment of genetic diversity, gene flow, and patterns of local adaptation in tropical plant species belonging to different IUCN Red List Categories. Employing RAD-sequencing we identified tens of thousands of single-nucleotide polymorphisms in an endangered narrow-endemic and a least concern widespread morning glory (Convolvulaceae) from Amazonian savannas, a highly threatened and under-protected tropical ecosystem. Our results reveal greater genetic diversity and less spatial genetic structure in the endangered species. Whereas terrain roughness affected gene flow in both species, forested and mining areas were found to hinder gene flow in the endangered plant. Finally we implemented environmental association tests and genome scans for selection, and identified a higher proportion of candidate adaptive loci in the widespread species. These mainly contained genes related to pathogen resistance and physiological adaptations to life in nutrient-limited environments. Our study emphasizes that IUCN Red List Criteria do not always prioritize species with low genetic diversity or whose genetic variation is being affected by habitat loss and fragmentation, and calls for the inclusion of genetic information into conservation assessments. More generally, our study exemplifies how landscape genomic tools can be employed to assess the status, threats and adaptive responses of imperiled biodiversity.

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.