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As primarily sessile organisms, plants often show a non-random spatial distribution of genotypes over distance. This process known as fine-scale spatial genetic structure (FSGS) has been suggested through systematic reviews to depend on life form, mating system, and pollen and seed dispersal vectors, while there is no consensus on its behaviour due to external factors, such as anthropogenic habitat changes. By conducting a systematic review and global meta-analysis of empirical FSGS studies, we aimed to evaluate how anthropogenic habitat fragmentation and degradation influence the strength of FSGS in plant populations by means of the Sp statistic. Moreover, we tested how pollination and seed dispersal vectors contribute to the variation of the Sp statistic. We retrieved 243 FSGS studies from 1960 to 2020 of which only 65 were informative for the systematic review. Most empirical studies comprised outcrossers (84%) and trees (67%), with few herbs (23%) and scarce annual species (2%). In weighted meta-analyses for 116 plant populations (31 studies), we did not detect significant effects in the magnitude of effect sizes for the Sp statistic among undisturbed, degraded and fragmented habitats. Results showed significant effects for seed dispersal vectors, but not for pollination. Overall, we observed high variation among the effect sizes (not related to the goodness-of-fit of mixed models) of habitat status, pollination and seed dispersal categories, which precludes identifying biological trends on the Sp statistic. More empirical studies are needed that contrast multiple plant populations in disturbed versus undisturbed habitats, and by increasing the taxonomic groups, such as herbs and annual plants.

El jaguar, bestia majestuosa reverenciada por nuestros antepasados e icono de las selvas tropicales, es un animal con una historia fascinante. Los estudios científicos nos ayudan a develar los detalles de su épica travesía a través del tiempo y la geografía del continente americano.

The free-tailed bat (Tadarida brasiliensis) likely migrates from the southwestern USA and northern Mexico to the south of Mexico to spend the winter in the Cueva San Francisco (CSF), which is the southernmost known roost of the species. In this study, we examined colony size and composition of the free-tailed bats at the CSF for two annual cycles to know if these parameters fluctuate throughout the year and whether these fluctuations indicate that the CSF is a winter roost. From February 2018 to November 2019, we conducted monthly observations and captured bats with a mist net of 12 × 2.6 m to determine sex, age, reproductive status, and relative abundance. The duration of the emergence flight (DEF) was also recorded. We detected significant fluctuations in colony size that were caused by the movement of pregnant females in spring, lactating and post-lactating females and males in summer, and by females and males in autumn and winter. The CSF was occupied all year-round by females and males. Our results indicate that the cave is a winter roost for females and males, a transitional roost for pregnant females that form their maternity colony elsewhere in summer, and a temporary roost for males in summer. We suggest that the CSF is crucial for the conservation of the free-tailed bat.

Functional connectivity of semiaquatic species is poorly studied despite that freshwater ecosystems are amongst the most threatened worldwide due to habitat deterioration. The Neotropical otter, Lontra longicaudis, is a threatened species that represents a good model to evaluate the effect of landscape-riverscape features on genetic structure and gene flow of freshwater species. We aimed to assess the spatial genetic structure of L. longicaudis and to evaluate the landscape-riverscape attributes that shape its genetic structure and gene flow at local sites (habitat patches) and between sites (landscape matrix). We conducted the study in three basins located in Veracruz, Mexico, which have a high degree of ecosystem deterioration. We used a non-invasive genetic sampling and a landscape genetics individual-based approach to test the effect stream hierarchical structure, isolation-by-distance, and isolation-by-resistance on genetic structure and gene flow. We found genetic structure that corresponded to the latitudinal and altitudinal heterogeneity of the landscape and riverscape, as well as to the hierarchical structure of the streams. Open areas and steep slopes were the variables affecting genetic structure at local sites, whereas areas with suitable habitat conditions, higher ecosystem integrity and larger streams enhanced gene flow between sites. The landscape-riverscape characteristics that maintain functional connectivity of L. longicaudis differed between the upper, middle, and lower basins. Our results have important implications for the conservation of the species, including the maintenance of larger suitable areas in Actopan and the necessity to improve connectivity in Jamapa, through the establishment of biological corridors.

As most ecosystems around the world are threatened by anthropogenic degradation and climate change, there is an increasing urgency to implement restoration strategies aiming at ensuring ecosystem self-sustainability and resilience. An initial step towards that goal relies on selecting the most suitable seed sources for a successful revegetation, which can be extremely challenging in highly degraded landscapes. The most common seed sourcing strategy is to select local seeds because it is assumed that plants experience strong adaptations to their natal sites. An alternative strategy is the selection of climate-adapted genotypes to future conditions. While considering future climatic projections is important to account for spatial shifts in climate to inform assisted gene flow and translocations, to restore highly degraded landscapes we need a comprehensive approach that first accounts for species adaptations to current at-site environmental conditions. In this issue of Molecular Ecology Resources, Carvalho et al. present a novel landscape genomics framework to identify the most appropriate seed sourcing strategy for moderately and highly degraded sites by integrating genotype, phenotype and environmental data in a spatially explicit context for two native plant species with potential to help restore iron-rich Amazonian savannas. This framework is amenable to be applicable and adapted to a broad range of restoration initiatives, as the dichotomy between focusing on the current or future climatic conditions should depend on the goals and environmental circumstances of each restoration site.

Habitat deterioration and fragmentation increase the risk of wildlife extirpation as they have strong impacts on population size, genetic diversity and gene flow. Small populations are more susceptible to these factors because the loss of genetic diversity by drift and inbreeding occurs at faster rates. Therefore, estimates of genetic diversity and population sizes of threatened and small wildlife populations in deteriorated landscapes are critical for managing and conservation. Here, we used a non-invasive sampling approach in combination with eleven microsatellite loci to evaluate genetic diversity, genetic structure, and demographic parameters of the Neotropical otter (Lontra longicaudis) in three river basins (Actopan, La Antigua and Jamapa), which are priority conservation areas for Veracruz, Mexico. Our results revealed moderate genetic diversity and genetic structure among river basins. However, we detected first-generation migrants among basins, suggesting current gene flow. Effective population size for each basin was considerably lower than the value (Ne

The Peromyscus maniculatus species complex is one of the most widespread group of small mammals in North America. However, the taxonomy and phylogenetic relationships among its constituent taxa remain unclear. As part of a revision of Peromyscus specimens from the highlands of the Trans-Mexican Volcanic Belt in central Mexico, we identified five individuals collected in 1968 that differed externally from other Peromyscus specimens, although morphologically similar to P. labecula and P. melanotis, both latter in the P. maniculatus species complex. Based on cranial measurements and mitochondrial DNA sequences, we aimed to more accurately determine the phylogenetic relationships and the taxonomic status of these individuals. Molecular phylogenetic analyses showed that the specimens formed a monophyletic clade sister to the P. maniculatus species complex. Pairwise genetic distances between those specimens and other species within the P. maniculatus species complex were greater than 7.91%. In addition, morphological analyses clearly distinguished the test specimens from P. melanotis and P. labecula. Based on the results of our molecular and morphological analyses, we conclude that these specimens represent an undescribed species of the P. maniculatus species complex, which we describe herein.

Non-invasive DNA sampling to identify and enumerate species is critical to population monitoring and for developing effective management strategies. However, individual DNA identification is often limited by degraded and low template DNA (LT-DNA) that routinely yields partial profiles prone to technical artifacts, thus limiting their utility/reliability. Massively parallel, genotyping-by-sequencing (GBS) assays present an opportunity to amplify not only a large suite of molecular markers simultaneously, providing higher resolution to identify individuals, but also higher levels of sequence redundancy to enable quality metric evaluations of profiles from LT-DNA. Taxidea taxus jacksoni is an endangered badger subspecies in Canada, with low levels of genetic diversity, complicating individual identifications from closely related DNA sequences. Challenges arise from the small number of hairs collected from snag traps set in badger burrows that rarely provide full profiles. We designed a GBS assay to obtain microsatellite profiles compatible with pre-existing databases generated with conventional capillary electrophoresis (CE) genotyping. We assessed the assay’s reproducibility via a dilution series to mimic LT-DNA and tested if the assay produced similar CE-generated results. While GBS offers the potential to genotype large numbers of individuals and markers at the same time, we found low concordance between GBS- and CE-based genotypes from DNA templates

The genusBursera, includes ~100 shrub and trees species in tropical dry forests with its center of diversification and endemism in Mexico. Morphologically intermediate individuals have commonly been observed in MexicanBurserain areas where closely related species coexist. These individuals are assumed to result from interspecific hybridization, but no molecular evidence has supported their hybrid origins. This study aimed to investigate the existence of interspecific hybridization among three MexicanBurseraspecies (Bullockiasection:B.cuneata,B.palmeriandB.bipinnata) from nine populations based on DNA sequences (three nuclear and four chloroplast regions) and ecological niche modeling for three past and two future scenario projections. Results from the only two polymorphic nuclear regions (PEPC, ETS) supported the hybrid origin of morphologically intermediate individuals and revealed thatB.cuneataandB.bipinnataare the parental species that are genetically closer to the putative hybrids. Ecological niche modeling accurately predicted the occurrence of putative hybrid populations and showed a potential hybrid zone extending in a larger area (74,000 km2) than previously thought. Paleo-reconstructions showed a potential hybrid zone existing from the Last Glacial Maximum (~ 21 kya) that has increased since the late Holocene to the present. Future ecological niche projections show an increment of suitability of the potential hybrid zone for 2050 and 2070 relative to the present. Hybrid zone changes responded mostly to an increase in elevational ranges. Our study provides the first insight of an extensive hybrid zone among three MexicanBurseraspecies based on molecular data and ecological niche modeling.

Antecedentes y Objetivos: Hedeoma piperita es una especie popularmente conocida como quiensabe con importantes usos tradicionales entre los purépechas de San Francisco Pichátaro en Michoacán, México. A pesar de su importancia cultural, las poblaciones de H. piperita han sido reducidas drásticamente debido a la sobreexplotación. Este trabajo se realizó para evaluar el conocimiento tradicional acerca de la biología, ecología y manejo de H. piperita en la comunidad indígena de San Francisco Pichátaro. Además, se evaluó su desarrollo fenológico y las relaciones entre fases fenológicas y variables ambientales locales. Métodos: Se realizaron 75 encuestas semiestructuradas en hombres y mujeres en tres grupos de edades de la comunidad. El análisis fenológico se realizó en 31 plantas en estado silvestre y se registró la altura, el número total de hojas, ramas, flores, frutos y retoños cada 15 días entre marzo de 2014 y marzo de 2015. Las correlaciones entre las variables fenológicas y ambientales se calcularon utilizando el coeficiente de correlación de Spearman. Resultados clave: Sesenta por ciento de los entrevistados reconocieron y han usado a H. piperita, siendo la mayoría mujeres (71%). Los usos alimenticios (té en el desayuno) fueron reconocidos como el principal uso por niños y jóvenes, mientras que los adultos la usan principalmente como medicinal. Sin embargo, entre los entrevistados muy pocos conocen detalles de la biología y ecología de la especie. Encontramos que las etapas de floración y fructificación coinciden con la temporada de recolección. Conclusiones: Es urgente diseñar estrategias de manejo que permitan recuperar las poblaciones silvestres para seguir manteniendo a la especie dentro del complejo cosmos-corpus-praxis purépecha.

The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.

Hedeoma piperita Benth. is a perennial herb from the Lamiaceae family, which is highly valued for its medicinal and culinary properties by the Purepecha ethnic group in Michoacan, Mexico. The species presents populations of two morphotypes (white and purple corollas) that have not been formally studied. In this work, we aimed to evaluate the morphological and genetic variation between the two morphotypes. We sampled individuals from 15 populations within the Purepecha Plateau in western Mexico to measure 33 quantitative and qualitative morphological variable characters (vegetative and reproductive) and to estimate genetic diversity and structure using six nuclear microsatellite markers. Principal Component Analysis showed a clear separation between populations of the two morphotypes, which differences were statistically significant for all vegetative (n = 11) and reproductive (n = 22) characters. Similarly, Bayesian and multivariate cluster analyses based on the microsatellite data supported the distinction of the two morphotypes, except for one population of the white corolla that was genetically closer to the purple corolla group. Genetic diversity was moderate to low across populations of the two morphotypes, and inbreeding (FIS) was significantly higher in populations of the purple corolla. Our morphological and genetic data support the presence of two divergent morphotypes in H. piperita. This species is of high importance within the Purepecha culture, but unfortunately is declining in the region due to its high extraction rates. Thus, our results are valuable to delineate germplasm zones for future breeding programs and for informing in situ conservation strategies.

Los copales y cuajiotes, pertenecientes a la familia Burseraceae y del genero Bursera , son arboles cuya diversidad de especies se concentra en Mexico y son dominantes de los bosques tropicales secos. Tienen un alto valor cultural, economico y ecologico, ya que de ellos se extraen resinas aromaticas como el incienso, esencias naturales y madera para la elaboracion de artesanias como alebrijes, mascaras y figurillas religiosas. A pesar de su importancia, el conocimiento de relaciones biologicas con especies asociadas a las burseras, como son sus polinizadores y dispersores de semillas, es aun limitado. En este trabajo se tratara la relacion entre las aves y la burseras, al enfocarnos en como ocurre el proceso de la dispersion de semillas, la importancia que tiene para su supervivencia y las acciones concretas necesarias para la conservacion de esta vital interaccion.

The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk,rpl32-trnL,trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico:Magnolia pedrazae(north-region),M. schiedeana(central-region), andM. schiedeanapopulation Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High‐throughput sequencing (HTS) technologies, such as genotype‐by‐sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization‐based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300‐kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on‐target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer‐read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune‐related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

The fungus that causes bat white-nose syndrome (WNS) recently leaped from eastern North America to the Pacific Coast. The pathogen’s spread is associated with the genetic population structure of a host ( Myotis lucifugus). To understand the fine-scale neutral and immunogenetic variation among northern populations of M. lucifugus, we sampled 1142 individuals across the species’ northern range. We used genotypes at 11 microsatellite loci to reveal the genetic structure of, and directional gene flow among, populations to predict the likely future spread of the pathogen in the northwest and to estimate effective population size ( Ne). We also pyrosequenced the DRB1-like exon 2 of the class II major histocompatibility complex (MHC) in 160 individuals to explore immunogenetic selection by WNS. We identified three major neutral genetic clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and Haida Gwaii, with admixture at intermediate areas and significant substructure west of the prairies. Estimates of Newere unexpectedly low (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the western mountain ranges are not barriers to its dispersal in M. lucifugus and are unlikely to slow its spread. Our major histocompatibility complex (MHC) data suggest potential selection by WNS on the MHC, but gene duplication limited the immunogenetic analyses.

Quantifying spatial genetic structure is key to inform forest management and restoration strategies. Reliable evaluations of genetic structure require sound sampling schemes because inappropriate sampling may over- and under-estimate spatial patterns of genetic structure. Sampling bias has been investigated through computer simulations mostly for animal species with continuous distributions. For tree species that have different life history traits, results from such studies may not apply. Here, I used spatially explicit landscape genetic simulations to assess the effects of spatial sampling scheme (random, systematic, and cluster), sampling intensity (35, 50, 65, and 80%), and the number of microsatellite loci (8, 14, and 20) on inferences of genetic structure under isolation by distance (IBD) in two forest tree species with varying dispersal distances and patchy distributions. Results showed that random sampling with 20 loci was the best performing sampling scheme, irrespective of sampling intensity and the strength of IBD. In contrast, the cluster and systematic sampling were sensitive to sample size. For the three sampling schemes, the number of loci had a large effect because with 8 loci there was an increasing chance of underestimating IBD. Increasing the number of samples over the number of loci, did not improve the performance of sampling schemes. Hence, researchers should put more effort on increasing the number of loci over increasing sample size. Results also showed that sampling error rates varied between species, and sampling bias appeared stronger for the species with a more aggregated spatial distribution.

The rich biodiversity of Mexico is threatened due to habitat fragmentation and climate change. Landscape genetics provides an excellent framework that integrates genetic, geographic, and ecological landscape data to inform conservation strategies. To discuss the value of landscape genetics for the study of the Mexican biota, a literature review of landscape genetics studies in Mexico was conducted to highlight trends of taxonomic groups, habitats, and research objectives. A total of 20 studies were identified: 65% in plants and 35% in animals. A large proportion of studies focused on temperate ecosystems and tropical forests, whereas marine and urban environments were lacking. Detection of linear barriers and landscape features on gene flow were the most popular objectives, while two objectives were exclusive to plants: spatial adaptive variation and estimates of contemporary gene flow with parentage analyses to evaluate effects of habitat fragmentation. Potential areas of research for landscape genetics studies in Mexico and recommendations are discussed

Strong spatial genetic structure in plant populations can increase homozygosity, reducing genetic diversity and adaptive potential. The strength of spatial genetic structure largely depends on rates of seed dispersal and pollen flow. Seeds without dispersal adaptations are likely to be dispersed over short distances within the vicinity of the mother plant, resulting in spatial clustering of related genotypes (fine-scale spatial genetic structure, hereafter spatial genetic structure (SGS)). However, primary seed dispersal by zoochory can promote effective dispersal, increasing the mixing of seeds and influencing SGS within plant populations. In this study, we investigated the effects of seed dispersal by rotational sheep grazing on the strength of SGS and genetic diversity using 11 nuclear microsatellites for 49 populations of the calcareous grassland forb Dianthus carthusianorum. Populations connected by rotational sheep grazing showed significantly weaker SGS and higher genetic diversity than populations in ungrazed grasslands. Independent of grazing treatment, small populations showed significantly stronger SGS and lower genetic diversity than larger populations, likely due to genetic drift. A lack of significant differences in the strength of SGS and genetic diversity between populations that were recently colonized and pre-existing populations suggested that populations colonized after the reintroduction of rotational sheep grazing were likely founded by colonists from diverse source populations. We conclude that dispersal by rotational sheep grazing has the potential to considerably reduce SGS within D. carthusianorum populations. Our study highlights the effectiveness of landscape management by rotational sheep grazing to importantly reduce genetic structure at local scales within restored plant populations.

Plant functional connectivity integrates species-environment interactions, dispersal vectors, and landscape structure variables to understand species’ spatial responses to habitat fragmentation. Functional connectivity is still poorly understood for aquatic plants despite the promise it holds for informing wetland conservation across landscapes. Through a landscape genetics approach, we quantified plant functional connectivity among geographically isolated wetlands by genotyping seven nuclear microsatellite loci in 18 populations of Nymphoides fallax, a tetraploid aquatic plant endemic to Mexican and Guatemalan highland wetlands. We tested if wetland connectivity, quantified with three connectivity indices, translated to high genetic diversity within populations and if geographical distance per se explained gene flow among wetlands. We also tested if landscape features such as vegetation and surface water cover explained gene flow among N. fallax populations. Our results show that wetland connectivity is positively associated with genetic diversity over threshold distances up to 5 km. The Si Hanski connectivity index, with wetland area incorporated, was the best predictor explaining the effective number of alleles, allelic richness, and expected heterozygosity. Population-specific FST, as a proxy for gene flow, was better explained by a model including forest cover than by geographical distance or water cover. Our findings highlight the importance of forest conservation to maintain gene flow at the landscape scale for N. fallax and allows the detection of key populations to maintain genetic diversity and connectivity. Understanding wetland connectivity is critical to address wetland loss in human-impacted landscapes.

Background and Aims: The genus Bursera (~100 species) has its center of diversification and endemism in Mexico. Interspecific hybridization is a frequent phenomenon in Bursera in areas where related species coexist. Hybridization on the one hand can reinforce reproductive barriers, increase genetic variation, generate novel ecotypes and new lineages, and on the other hand, can lead to maladaptation. However, the ecological and evolutionary consequences of natural hybridization critically depend on hybrid fitness. In this study, within a putative hybrid population in the tropical dry forest of the Bajío region in Mexico and as a proxy of hybrid fitness, we investigated pollen viability among Bursera cuneata, B. bipinnata, and their putative hybrid.Methods: We used two techniques: a pollen staining test with tetrazolium chloride 1% and an in vitro germination test to observe the formation of pollen tubes. Viability percentages were calculated for each group; statistical tests were conducted with general linear models. Key results: Results demonstrated that the putative hybrid is not sterile and exhibited higher germination rates relative to the parental species. Conclusions: Our results imply that gene flow between the parental species and the putative hybrid is likely to occur. Future genetic studies should confirm the genetic identity and ploidy levels of hybrids and evaluate whether genetic introgression has occurred. Our study demonstrates that Bursera hybrids can be fertile and contributes towards understanding the role of hybridization and reproductive isolation in Mexican Bursera species.

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.

Magnolias are characteristic tree species of the Tropical Montane Cloud Forest (TMCF) in Mexico, an ecosystem that is highly threatened by habitat fragmentation and climate change. In this study, based on DNA sequences from five regions (chloroplast: trnT-trnL, trnK5-matK, trnS-trnG, rpl32-trnL, nuclear: ITS) and seven nuclear microsatellite markers, we aimed to delineate species boundaries between two-endemic species of the TMCF, Magnolia pedrazae and Magnolia schiedeana, and to estimate levels of genetic structure and diversity among populations. Phylogenetic and haplotype network analyses for the chloroplast and ITS regions did not support genetic differentiation as two distinctive species. Results from Bayesian and multivariate cluster analyses based on microsatellite loci showed high genetic differentiation across most populations, which was consistent with a strong and significant pattern of isolation by geographical distance. We found moderate to high levels of population genetic diversity, but it was lower in small populations relative to large populations. Our results suggest a contemporary decrease of genetic connectivity among populations, likely as a consequence of the current decline of suitable TMCF habitat. Managing landscape connectivity among remnant Magnolia populations within protected natural parks and surroundings, and with emphasis of small populations, would be key for the species conservation.

Distance, environmental heterogeneity and local adaptation can strongly influence population structure and connectivity. Understanding how these factors shape the genomic landscape of threatened species is a major goal in conservation genomics and wildlife management. Herein, we use thousands (6,859) of single nucleotide polymorphism markers and spatial data from hundreds of individuals (n = 646) to re-evaluate the population structure of Agassiz’s desert tortoise (Gopherus agassizii). Analyses resolve from 4 to 8 spatially well-defined clusters across the range. Western, central, and southern populations within the Western Mojave recovery unit are consistent throughout, while analyses sometimes merge other recovery units depending on the level of clustering. Causal modeling consistently associates genetic connectivity with least-cost distance, based on multiple landscape features associated with tortoise habitat, better than geographic distance. Some features include elevation, soil depth, rock volume, precipitation, and vegetation coverage, suggesting that physical, climatic, and biotic landscape features have played a strong evolutionary role restricting gene flow between populations. Further, 12 highly differentiated outlier loci have associated functions that may be involved with neurogenesis, wound healing, lipid metabolism, and possibly vitellogenesis. Together, these findings have important implications for recovery programs, such as translocations, population augmentation, reproduction in captivity and the identification of ecologically important genes, opening new venues for conservation genomics in desert tortoises.

Ecological connectivity networks have been proposed as an efficient way to reconnect communities in fragmented landscapes. Yet few studies have evaluated if they are successful at enhancing actual functional connectivity (i.e. realized dispersal or gene flow) of focal species, or if this enhanced connectivity is enough to maintain genetic diversity and fitness of plant populations. Here we test the efficacy of an ecological connectivity network implemented in southern Germany since 1989 to reconnect calcareous grassland fragments through rotational shepherding. We genotyped 1449 individuals from 57 populations and measured fitness-related traits in 10 populations of Puisatilla vulgaris, a flagship species of calcareous grasslands in Europe. We tested if the shepherding network explained functional connectivity in P. vulgaris and if higher connectivity translated to higher genetic diversity and fitness of populations. We found that population-specific F-st was lowest in populations that had high connectivity within the shepherding network, and that well-connected populations within the network had significantly higher genetic diversity than ungrazed and more isolated grazed populations. Moreover, genetic diversity was significantly positively correlated with both seed set and seed mass. Together our results suggest that the implementation of an ecological shepherding network is an effective management measure to maintain functional connectivity and genetic diversity at the landscape scale for a calcareous grassland specialist. Populations with reduced genetic diversity would likely benefit from inclusion, or better integration into the ecological connectivity network. Our study demonstrates the often postulated but rarely tested sequence of positive associations between connectivity, genetic diversity, and fitness at the landscape scale, and provides a framework for testing the efficacy of ecological connectivity networks for focal species using molecular genetic tools.

Directed dispersal by animal vectors has been found to have large effects on the structure and dynamics of plant populations adapted to frugivory. Yet, empirical data are lacking on the potential of directed dispersal by rotational grazing of domestic animals to mediate gene flow across the landscape. Here, we investigated the potential effect of large-flock shepherding on landscape-scale genetic structure in the calcareous grassland plant Dianthus carthusianorum, whose seeds lack morphological adaptations to dispersal to animals or wind. We found a significant pattern of genetic structure differentiating population within grazed patches of three nonoverlapping shepherding systems and populations of ungrazed patches. Among ungrazed patches, we found a strong and significant effect of isolation by distance (r = 0.56). In contrast, genetic distance between grazed patches within the same herding system was unrelated to geographical distance but significantly related to distance along shepherding routes (r = 0.44). This latter effect of connectivity along shepherding routes suggests that gene flow is spatially restricted occurring mostly between adjacent populations. While this study used nuclear markers that integrate gene flow by pollen and seed, the significant difference in the genetic structure between ungrazed patches and patches connected by large-flock shepherding indicates the potential of directed seed dispersal by sheep across the landscape.

Response to habitat fragmentation may not be generalized among species, in particular for plant communities with a variety of dispersal traits. Calcareous grasslands are one of the most species-rich habitats in Central Europe, but abandonment of traditional management has caused a dramatic decline of calcareous grassland species. In the Southern Franconian Alb in Germany, reintroduction of rotational shepherding in previously abandoned grasslands has restored species diversity, and it has been suggested that sheep support seed dispersal among grasslands. We tested the effect of rotational shepherding on demographic and genetic connectivity of calcareous grassland specialist plants and whether the response of plant populations to shepherding was limited to species dispersed by animals (zoochory). Specifically, we tested competing dispersal models and source and focal patch properties to explain landscape connectivity with patch-occupancy data of 31 species. We fitted the same connectivity models to patch occupancy and nuclear microsatellite data for the herb Dianthus carthusianorum (Carthusian pink). For 27 species, patch connectivity was explained by dispersal by rotational shepherding regardless of adaptations to zoochory, whereas population size (16% species) and patch area (0% species) of source patches were not important predictors of patch occupancy in most species. [Correction made after online publication, February 25, 2014: Population size and patch area percentages were mistakenly inverted, and have now been fixed.] Microsite diversity of focal patches significantly increased the model variance explained by patch occupancy in 90% of the species. For D. carthusianorum, patch connectivity through rotational shepherding explained both patch occupancy and population genetic diversity. Our results suggest shepherding provides dispersal for multiple plant species regardless of their dispersal adaptations and thus offers a useful approach to restore plant diversity in fragmented calcareous grasslands.

Summary 1.Dispersal is essential for species to survive the threats of habitat destruction and climate change. Combining descriptions of dispersal ability with those of landscape structure, the concept of functional connectivity has been popular for understanding and predicting species’ spatial responses to environmental change. 2.Following recent advances, the functional connectivity concept is now able to move beyond landscape structure to consider more explicitly how other external factors such as climate and resources affect species movement. We argue that these factors, in addition to a consideration of the complete dispersal process, are critical for an accurate understanding of functional connectivity for plant species in response to environmental change. 3.We use recent advances in dispersal, landscape and molecular ecology to describe how a range of external factors can influence effective dispersal in plant species, and how the resulting functional connectivity can be assessed. 4.Synthesis. We define plant functional connectivity as the effective dispersal of propagules or pollen among habitat patches in a landscape. Plant functional connectivity is determined by a combination of landscape structure, interactions between plant, environment and dispersal vectors, and the successful establishment of individuals. We hope that this consolidation of recent research will help focus future connectivity research and conservation. This article is protected by copyright. All rights reserved.

Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species’ range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well‐connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.

Understanding processes and landscape features governing connectivity among individuals and populations is fundamental to many ecological, evolutionary, and conservation questions. Network analyses based on graph theory are emerging as a prominent approach to quantify patterns of connectivity with more recent applications in landscape genetics aimed at understanding the influence of landscape features on gene flow. Despite the strong conceptual framework of graph theory, the effect of incomplete networks resulting from missing nodes (i.e. populations) and their genetic connectivity network interactions on landscape genetic inferences remains unknown. We tested the violation of this assumption by subsampling from a known complete network of breeding ponds of the Columbia Spotted Frog (Rana luteiventris) in the Bighorn Crags (Idaho, USA). Variation in the proportion of missing nodes strongly influenced node-level centrality indices, whereas indices describing network-level properties were more robust. Overall incomplete networks combined with network algorithm types used to link nodes appears to be critical to the rank-order sensitivity of centrality indices and to the Mantel-based inferences made regarding the role of landscape features on gene flow. Our findings stress the importance of sampling effort and topological network structure as they both affect the estimation of genetic connectivity. Given that failing to account for uncertainty on network outcomes can lead to quantitatively different conclusions, we recommend the routine application of sensitivity analyses to network inputs and assumptions.

This paper evaluates the long-term effect of an ecological network of calcareous grasslands, a habitat type that experienced dramatic habitat loss and fragmentation during the 20th century, on species richness of habitat specialist plants. Calcareous grasslands are of special conservation concern as the habitat type with the highest diversity in plant and invertebrate species in central Europe. A baseline survey in 1989 established complete vascular plant species lists for all 62 previously abandoned calcareous grassland patches in the study area and assessed the presence of 48 habitat specialist plant species. An ecological network was initiated in 1989 to reconnect these patches with existing grazed pastures (core areas) through large flock sheep herding where feasible, as sheep are thought to be the primary dispersal vectors for calcareous grassland plants. An evaluation survey in 2009 showed significant increase in species richness of habitat specialist plants in patches reconnected by sheep herding, indicating successful colonizations by habitat specialist plants, while ungrazed patches showed no significant change. Observed increase in species richness between 1989 and 2009 was related to connectivity by sheep herding and the presence of a diversity of structural elements providing microsites for establishment. Baseline species richness of the patches, which had been abandoned since at least 1960, was associated with patch area, supporting the effect of ecological drift, and with vegetation type, which suggests that delays in extinction may be related to site factors governing the strength of competition with later seral species. The implementation of this ecological network represents a long-term ‘natural experiment’ with baseline data, manipulation, and evaluation of hypothesized effects on a clearly defined target variable. It thus provides much needed empirical evidence that species loss in fragmented calcareous grassland communities can be counteracted by restoring functional connectivity among remnant patches.