Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards.

The opposing forces of gene flow and isolation are two major processes shaping genetic diversity. Understanding how these vary across space and time is necessary to identify the environmental features that promote diversification. The detection of considerable geographic structure in taxa from the arid Nearctic has prompted research into the drivers of isolation in the region. Several geographic features have been proposed as barriers to gene flow, including the Colorado River, Western Continental Divide (WCD), and a hypothetical Mid-Peninsular Seaway in Baja California. However, recent studies suggest that the role of barriers in genetic differentiation may have been overestimated when compared to other mechanisms of divergence. In this study, we infer historical and spatial patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus magister) and Baja Spiny Lizards (Sceloporus zosteromus), which together form a species complex composed of parapatric lineages with wide distributions in arid western North America. Our analyses incorporate mitochondrial sequences, genomic-scale data, and past and present climatic data to evaluate the nature and strength of barriers to gene flow in the region. Our approach relies on estimates of migration under the multispecies coalescent to understand the history of lineage divergence in the face of gene flow. Results show that the S. magister complex is geographically structured, but we also detect instances of gene flow. The WCD is a strong barrier to gene flow, while the Colorado River is more permeable. Analyses yield conflicting results for the catalyst of differentiation of peninsular lineages in S. zosteromus. Our study shows how large-scale genomic data for thoroughly sampled species can shed new light on biogeography. Furthermore, our approach highlights the need for the combined analysis of multiple sources of evidence to adequately characterize the drivers of divergence.

Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China.

BACKGROUND: The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China. RESULTS: We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region. CONCLUSION: Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene-Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China's secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems.

Temperate Zone Isolation by Climate: An Extension of Janzen's 1967 Hypothesis.

AbstractOne of the most stunning patterns of the distribution of life on Earth is the latitudinal biodiversity gradient. In an influential article, Janzen (1967) predicted that tropical mountains are more effective migration barriers than temperate mountains of the same elevation, because annual temperature variation in the tropics is lower. A great deal of research has demonstrated that the mechanism envisioned by Janzen operates at broad latitudinal scales. However, the extent that the mechanism mediates biodiversity generally, and at smaller scales, is far less understood. We investigated whether climate overlap is associated with genetic similarity between populations within temperate regions using lizards in the Sierra Nevada mountain range of California as a study system. By comparing genetic differentiation between high- and low-elevation populations, we found that in addition to the expected strong pattern of isolation by distance, high climate overlap was negatively associated with genetic differentiation, indicating that population pairs that inhabit climatically similar environments are less genetically differentiated. Moreover, while climate overlap between high- and low-elevation sites is predicted to increase from the equator to temperate regions, we find that in adjacent mountain ranges at the same latitude in temperate regions, climate overlap values can vary widely. This study suggests that in addition to the well-studied main effect of latitude on climate overlap and population differentiation, local climate factors within bioclimatic regions can also influence genetic differentiation between populations and do so by the same general mechanism that operates at larger geographic scales.

Landscape genetics across the Andes mountains: Environmental variation drives genetic divergence in the leaf-cutting ant Atta cephalotes.

Distinguishing among the mechanisms underlying the spatial distribution of genetic variation resulting from the environmental or physical barriers from those arising due to simple geographic distance is challenging in complex landscapes. The Andean uplift represents one of the most heterogeneous habitats where multiple mechanisms may interact, confounding their relative roles. We explore this broad question in the leaf-cutting ant Atta cephalotes, a species that is distributed across the Andes mountains, using nuclear microsatellite markers and mtCOI gene sequences. We investigate spatial genetic divergence across the western range of the northern Andes in Colombia by testing the relative role of alternative scenarios of population divergence, including isolation by geographic distance (IBD), climatic conditions (IBE), and the physical barriers presented by the Andes mountains (IBB). Our results reveal substantial genetic differentiation among A. cephalotes populations for both types of markers, but only nuclear divergence followed a hierarchical pattern with multiple models of genetic divergence imposed by the western range. Model selection showed that the IBD, IBE (temperature and precipitation), and IBB (Andes mountains) models, often proposed as individual drivers of genetic divergence, interact, and explain up to 33% of the genetic divergence in A. cephalotes. The IBE model remained significant after accounting for IBD, suggesting that environmental factors play a more prominent role than IBB. These factors, in combination with the idiosyncratic dispersal patterns of ants, appear to determine the hierarchical patterns of gene flow. This study enriches our understanding of the forces shaping population divergence in complex habitat landscapes.

More opportunities more species: Pleistocene differentiation and northward expansion of an evergreen broad-leaved tree species Machilus thunbergii (Lauraceae) in Southeast China.

BACKGROUND: The broad continuum between tropical and temperate floras in Eastern Asia (EAS) are thought to be one of the main factors responsible for a prominent species diversity anomaly of temperate plants between EAS and eastern North America (ENS). However, how the broad continuum and niche evolution between tropical and temperate floras in EAS contributes to lineage divergence and species diversity remains largely unknown. RESULTS: Population genetic structure, demography, and determinants of genetic structure [i.e., isolation-by-distance (IBD), isolation-by-resistance (IBR), and isolation-by-environment (IBE)] of Machilus thunbergii Sieb. et Zucc. (Lauraceae) were evaluated by examining sequence variation of ten low-copy nuclear genes across 43 populations in southeast China. Climatic niche difference and potential distributions across four periods (Current, mid-Holocene, the last glacial maximum, the last interglacial) of two genetic clusters were determined by niche modelling. North and south clusters of populations in M. thunbergii were revealed and their demarcation line corresponds well with the northern boundary of tropical zone in China of Zhu & Wan. The divergence time between the clusters and demographic expansion of M. thunbergii occurred after the mid-Pleistocene climate transition (MPT, 0.8-1.2 Ma). Migration rates between clusters were asymmetrical, being much greater from north to south than the reverse. Significant effects of IBE, but non-significant effects of IBD and IBR on population genetic divergence were detected. The two clusters have different ecological niches and require different temperature regimes. CONCLUSIONS: The north-south genetic differentiation may be common across the temperate-tropical boundary in southeast China. Divergent selection under different temperature regimes (possibly above and below freezing temperature in winter) could account for this divergence pattern. The broad continuum between tropical and temperate floras in EAS may have provided ample opportunities for tropical plant lineages to acquire freezing tolerance and to colonize the temperate regions during the late-Cenozoic global cooling. Our findings shed deeper insights into the high temperate plant species diversity in EAS.

Tracking population genetic signatures of local extinction with herbarium specimens.

BACKGROUND AND AIMS: Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. METHODS: We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. KEY RESULTS: Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. CONCLUSIONS: Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.

Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant.

Landscape heterogeneity can shape genetic structure and functional connectivity of populations. When this heterogeneity imposes variable costs of moving across the landscape, populations can be structured according to a pattern of "isolation by resistance" (IBR). At the same time, divergent local environmental filters can limit gene flow, creating an alternative pattern of "isolation by environment" (IBE). Here, we evaluate IBR and IBE in the insect-pollinated, biennial plant Sabatia angularis (L.) Pursh (Gentianaceae) across serpentine grasslands in the fragmented landscape of SE Pennsylvania, USA using ~4500 neutral SNP loci. Specifically, we test the extent to which radical alteration of the landscape matrix by humans has fundamentally altered the cost of movement, imprinting a pattern of IBR dictated by land use type and intensity, and the potential for IBE in relation to a gradient of heavy metal concentrations found in serpentine soil. We reveal a strong signal of IBR and a weak signal of IBE across sites, indicating the greater importance of the landscape matrix in shaping genetic structure of S. angularis populations in the study region. Based on Circuitscape and least cost path approaches, we find that both low- and high-intensity urbanization resist gene flow by orders of magnitude greater than "natural" habitats, although resistance to low-intensity urbanization weakens at larger spatial scales. While cropland presents a substantially lower barrier than urban development, cumulative human land use surrounding populations predicts within-population genetic diversity and inbreeding in S. angularis. Our results emphasize the role of forest buffers and corridors in facilitating gene flow between serpentine grassland patches and averting local extinction of plant populations.

Using environmental and geographic data to optimize ex situ collections and preserve evolutionary potential.

Maintenance of biodiversity through seed banks and botanical gardens, where the wealth of species' genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections if trade-offs exist among cost, effort, and conserving species evolutionary potential, particularly when genetic data are not available. We evaluated the genetic consequences of population preservation informed by geographic (isolation by distance [IBD]) and environmental (isolation by environment [IBE]) distance for ex situ collections for which population provenance is available. We used 19 genetic and genomic data sets from 15 plant species to assess the proportion of population genetic differentiation explained by geographic and environmental factors and to simulate ex situ collections prioritizing source populations based on pairwise geographic distance, environmental distance, or both. Specifically, we tested the impact prioritizing sampling based on these distances may have on the capture of neutral, functional, or putatively adaptive genetic diversity and differentiation. Individually, IBD and IBE explained limited population genetic differences across all 3 genetic marker classes (IBD, 10-16%; IBE, 1-5.5%). Together, they explained a substantial proportion of population genetic differences for functional (45%) and adaptive (71%) variation. Simulated ex situ collections revealed that inclusion of IBD, IBE, or both increased allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections based on environmental and geographic distance data can optimize genetic variation captured ex situ. For the vast majority of plant species for which there is no genetic information, these data are invaluable to conservation because they can guide preservation of genetic variation needed to maintain evolutionary potential within collections.

Uso de Datos Ambientales y Geográficos para Optimizar las Colecciones Ex Situ y Preservar el Potencial Evolutivo Resumen El mantenimiento de la biodiversidad por medio de bancos de semillas y jardines botánicos, en donde la riqueza de la variación genética de las especies puede preservarse ex situ, es una de las principales metas de la conservación. Sin embargo, los obstáculos para la optimización de las colecciones ex situ pueden persistir si existen compensaciones entre el costo, el esfuerzo y la conservación del potencial evolutivo de la especie, particularmente cuando no están disponibles los datos genéticos. Evaluamos las consecuencias genéticas que tiene la preservación de una población fundamentada en la distancia geográfica (aislamiento por distancia [APD]) y ambiental (aislamiento por entorno [APE]) para las colecciones ex situ cuyo origen poblacional está disponible. Usamos 19 conjuntos de datos genéticos y genómicos de 15 especies de plantas para evaluar la proporción de la diferenciación genética de la población explicada por los factores geográficos y ambientales y para simular las colecciones ex situ que priorizan a las poblaciones de origen con base en la distancia geográfica por pares, la distancia ambiental, o ambas. Específicamente, comprobamos el impacto que puede tener la priorización de muestreos basados en estas distancias sobre la captura de la diferenciación y la diversidad genética neutral, funcional o putativamente adaptativa. De manera individual, el APD y el APE explicaron las diferencias limitadas en la genética poblacional en todas las clases de marcadores genéticos (APD, 10-16%; APE, 1-5.5%). En conjunto, ambos tipos de aislamiento explicaron una proporción sustancial de las diferencias en la genética poblacional para la variación funcional (45%) y adaptativa (71%). La simulación de colecciones ex situ reveló que la inclusión del APD, APE o ambos incrementó la diversidad de alelos y la diferenciación genética capturada entre las poblaciones, particularmente para los loci que pueden ser importantes para la adaptación. Por lo tanto, la priorización de las colecciones poblacionales basadas en los datos de distancia geográfica o ambiental pueden optimizar la variación genética capturada ex situ. Para la mayoría de las especies de plantas para las cuales no hay información genética, estos datos son indispensables para la conservación porque pueden dirigir la preservación de la variación genética necesaria para mantener el potencial evolutivo dentro de las colecciones.

Seascape Genetics of the Atlantic Spotted Dolphin (Stenella frontalis) Based on Mitochondrial DNA.

The Atlantic spotted dolphin (Stenella frontalis) is endemic to tropical, subtropical, and warm temperate waters of the Atlantic Ocean. Throughout its distribution, both geographic distance and environmental variation may contribute to population structure of the species. In this study, we follow a seascape genetics approach to investigate population differentiation of Atlantic spotted dolphins based on a large worldwide dataset and the relationship with marine environmental variables. The results revealed that the Atlantic spotted dolphin exhibits population genetic structure across its distribution based on mitochondrial DNA control region (mtDNA-CR) data. Analyses based on the contemporary landscape suggested, at both the individual and population level, that the population genetic structure is consistent with the isolation-by-distance model. However, because geography and environmental matrices were correlated, and because in some, but not all analyses, we found a significant effect for the environment, we cannot rule out the addition contribution of environmental factors in structuring genetic variation. Future analyses based on nuclear data are needed to evaluate whether local processes, such as social structure and some level of philopatry within populations, may be contributing to the associations among genetic structure, geographic, and environmental distance.

Limited divergent adaptation despite a substantial environmental cline in wild pea.

Isolation by environment (IBE) is a widespread phenomenon in nature. It is commonly expected that the degree of difference among environments is proportional to the level of divergence between populations in their respective environments. It is therefore assumed that a species' genetic diversity displays a pattern of IBE in the presence of a strong environmental cline if gene flow does not mitigate isolation. We tested this common assumption by analysing the genetic diversity and demographic history of Pisum fulvum, which inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, making it an ideal test case. Ecogeographical and subpopulation structure were analysed and compared. The correlation of genetic with environmental distances was calculated to test the effect of isolation by distance and IBE and detect the main drivers of these effects. Historical effective population size was estimated using stairway plot. Limited overlap of ecogeographical and genetic clustering was observed, and correlation between genetic and environmental distances was statistically significant but small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to a past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive gene flow.

Gene flow and climate-associated genetic variation in a vagile habitat specialist.

Previous work in landscape genetics suggests that geographic isolation is of greater importance to genetic divergence than variation in environmental conditions. This is intuitive when configurations of suitable habitat are a dominant factor limiting dispersal and gene flow, but has not been thoroughly examined for habitat specialists with strong dispersal capability. Here, we evaluate the effects of geographic and environmental isolation on genetic divergence for a vagile invertebrate with high habitat specificity and a discrete dispersal life stage: Dod's Old World swallowtail butterfly, Papilio machaon dodi. In Canada, P. m. dodi are generally restricted to eroding habitat along major river valleys where their larval host plant occurs. A series of causal and linear mixed effects models indicate that divergence of genome-wide single nucleotide polymorphisms is best explained by a combination of environmental isolation (variation in summer temperatures) and geographic isolation (Euclidean distance). Interestingly, least-cost path and circuit distances through a resistance surface parameterized as the inverse of habitat suitability were not supported. This suggests that, although habitat associations of many butterflies are specific due to reproductive requirements, habitat suitability and landscape permeability are not equivalent concepts due to considerable adult vagility. We infer that divergent selection related to variation in summer temperatures has produced two genetic clusters within P. m. dodi, differing in voltinism and diapause propensity. Within the next century, temperatures are predicted to rise by amounts greater than the present-day difference between regions of the genetic clusters, potentially affecting the persistence of the northern cluster under continued climate change.

Fragmented and isolated: limited gene flow coupled with weak isolation by environment in the paleoendemic giant sequoia (Sequoiadendron giganteum).

PREMISE: Patterns of genetic structure across a species' range reflect the long-term interplay between genetic drift, gene flow, and selection. Given the importance of gene flow in preventing the loss of diversity through genetic drift among spatially isolated populations, understanding the dynamics of gene flow and the factors that influence connectivity across a species' range is a major goal for conservation of genetic diversity. Here we present a detailed look at gene flow dynamics of Sequoiadendron giganteum, a paleoendemic tree species that will likely face numerous threats due to climate change. METHODS: We used microsatellite markers to examine nineteen populations of S. giganteum for patterns of genetic structure and to estimate admixture and rates of gene flow between eight population pairs. Also, we used Generalized Dissimilarity Models to elucidate landscape factors that shape genetic differentiation among populations. RESULTS: We found minimal gene flow between adjacent groves in the northern disjunct range. In most of the southern portion of the range, groves showed a signal of connectivity which degrades to isolation in the extreme south. Geographic distance was the most important predictor of genetic dissimilarity across the range, with environmental conditions related to precipitation and temperature explaining a small, but significant, portion of the genetic variance. CONCLUSIONS: Due to their isolation and unique genetic composition, northern populations of S. giganteum should be considered a high conservation priority. In this region, we suggest germplasm conservation as well as restoration planting to enhance genetic diversity.

Influence of environmental factors on the genetic variation of the aquatic macrophyte Ranunculus subrigidus on the Qinghai-Tibetan Plateau.

BACKGROUND: Due to the environmental heterogeneity along elevation gradients, alpine ecosystems are ideal study objects for investigating how ecological variables shape the genetic patterns of natural species. The highest region in the world, the Qinghai-Tibetan Plateau, is a hotspot for the studies of evolutionary processes in plants. Many large rivers spring from the plateau, providing abundant habitats for aquatic and amphibious organisms. In the present study, we examined the genetic diversity of 13 Ranunculus subrigidus populations distributed throughout the plateau in order to elucidate the relative contribution of geographic distance and environmental dissimilarity to the spatial genetic pattern. RESULTS: A relatively low level of genetic diversity within populations was found. No spatial genetic structure was suggested by the analyses of molecular variance, Bayesian clustering analysis and Mantel tests. Partial Mantel tests and multiple matrix regression analysis showed a significant influence of the environment on the genetic divergence of the species. Both climatic and water quality variables contribute to the habitat heterogeneity of R. subrigidus populations. CONCLUSIONS: Our results suggest that historical processes involving long-distance dispersal and local adaptation may account for the genetic patterns of R. subrigidus and current environmental factors play an important role in the genetic differentiation and local adaptation of aquatic plants in alpine landscapes.

Phylogeography of a widespread lizard complex reflects patterns of both geographic and ecological isolation.

A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction site-associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.

Rarity does not limit genetic variation or preclude subpopulation structure in the geographically restricted desert forb Astragalus lentiginosus var. piscinensis.

PREMISE OF THE STUDY: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in rarity. Here, we compare genetic variation among varieties of Astragalus lentiginosus differing in range size. Additionally, we ask if genetic structure exists in A. lentiginosus var. piscinensis, a rare taxon consisting of several thousand individuals that persist on ~8 km2 of alkaline soil. METHODS: We compared genetic variation among 11 varieties of A. lentiginosus differing in range size using a genotyping by sequencing (GBS) approach, which generated 11,475 single nucleotide polymorphisms (SNPs). We characterized genetic structure among subpopulations of A. lentiginosus var. piscinensis using a second GBS data set of 7274 SNPs and explored associations between genetic structure and environmental variation. KEY RESULTS: We found no association between genetic variation and range size among varieties of A. lentiginosus. Additionally, despite the extremely small range of A. lentiginosus var. piscinensis, we report a well-defined genetic structure among subpopulations associated with microhabitat variation in soil composition. CONCLUSIONS: Our results suggest that fine scale genetic structure may exist within other rare Astragalus taxa and that rarity does not preclude the maintenance of genetic diversity in this genus.

Disjunct distribution and distinct intraspecific diversification of Eothenomys melanogaster in South China.

BACKGROUND: South China encompasses complex and diverse landforms, giving rise to high biological diversity and endemism from the Hengduan Mountains to Taiwan Island. Many species are widely distributed across South China with similar disjunct distribution patterns. To explore the causes of these disjunct distribution patterns and their genetic consequences, we investigated the endemic species Père David's Chinese Vole (Eothenomys melanogaster) by integrating geological and ecological factors. We analysed the genetic structure and divergence time of E. melanogaster based on fast-evolving mitochondrial and nuclear markers using Bayesian trees and coalescent species tree approaches. Historical scenarios of distribution range and demography were reconstructed based on spatial interpolations of genetic diversity and distance, extended Bayesian skyline plots, phylogeographic diffusion analysis, and ecological niche modelling (ENM) during different periods. We also assessed the relationships between geographical distance/ecological vicariance and genetic distance (isolation by distance, IBD; isolation by environment, IBE). RESULTS: The genetic analysis revealed three deeply divergent clades-Southeast, Southwest and Central clades, centred on the Wuyi Mountains, the Yunnan-Guizhou Plateau (YGP) and the mountains around the Sichuan Basin, respectively-that have mostly developed since the Pleistocene. IBD played an important role in early divergence, and geological events (sedimentation of plains and linking of palaeo-rivers) and IBE further reinforced genetic differentiation. ENM shows the importance of suitable habitats and elevations. CONCLUSIONS: Our results suggest that the primary cause of the disjunct distribution in E. melanogaster is the high dependence on middle-high-altitude habitat in the current period. Mountains in the occurence range have served as "sky islands" for E. melanogaster and hindered gene flow. Pleistocene climatic cycles facilitated genetic admixture in cold periods and genetic diversification in warm periods for inland clades. During cold periods, these cycles led to multiple colonization events between the mainland and Taiwan and erased genetic differentiation.

Rapid divergence of mussel populations despite incomplete barriers to dispersal.

Striking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation-by-distance, isolation-by-environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000-10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double-digest restriction-site-associated DNA sequencing), we show strong genetic structuring across populations (range FST : 0.07-0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation-by-distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often-neglected role of (evolution-mediated) priority effects in shaping population divergence.

Inferring spatial patterns and drivers of population divergence of Neolitsea sericea (Lauraceae), based on molecular phylogeography and landscape genomics.

The relative roles of geography, climate and ecology in driving population divergence and (incipient) speciation has so far been largely neglected in studies addressing the evolution of East Asia's island flora. Here, we employed chloroplast and ribosomal DNA sequences and restriction site-associated DNA sequencing (RADseq) loci to investigate the phylogeography and drivers of population divergence of Neolitsea sericea. These data sets support the subdivision of N. sericea populations into the Southern and Northern lineages across the 'Tokara gap'. Two distinct sublineages were further identified for the Northern lineage of N. sericea from the RADseq data. RADseq was also used along with approximate Bayesian computation to show that the current distribution and differentiation of N. sericea populations resulted from a combination of relatively ancient migration and successive vicariant events that likely occurred during the mid to late Pleistocene. Landscape genomic analyses showed that, apart from geographic barriers, barrier, potentially local adaptation to different climatic conditions appears to be one of the major drivers for lineage diversification of N. sericea.

Population genetic structure is shaped by historical, geographic, and environmental factors in the leguminous shrub Caragana microphylla on the Inner Mongolia Plateau of China.

BACKGROUND: Understanding how landscape factors, including suites of geographic and environmental variables, and both historical and contemporary ecological and evolutionary processes shape the distribution of genetic diversity is a primary goal of landscape and conservation genetics and may be particularly consequential for species involved in ecological restoration. In this study, we examine the factors that shape the distribution of genetic variation in a leguminous shrub (Caragana microphylla) important for restoration efforts on the Mongolian Plateau in China. This region houses several major bioclimatic gradients, and C. microphylla is an important restoration species because it stabilizes soils and prevents advancing desertification on the Inner Mongolia Plateau caused by ongoing climate change. RESULTS: We assembled an expansive genomic dataset, consisting of 22 microsatellite loci, four cpDNA regions, and 5788 genome-wide SNPs from ten populations of C. microphylla. We then applied ecological niche modelling and linear and non-linear regression techniques to investigate the historical and contemporary forces that explain patterns of genetic diversity and population structure in C. microphylla on the Inner Mongolia Plateau. We found strong evidence that both geographic and environmental heterogeneity contribute to genetic differentiation and that the spatial distribution of genetic diversity in C. microphylla appears to result partly from the presence of a glacial refugium at the southwestern edge of its current range. CONCLUSIONS: These results suggest that geographic, environmental, and historical factors have all contributed to spatial genetic variation in this ecologically important species. These results should guide restoration plans to sustain genetic diversity during plant translocations.

Habitat use, but not gene flow, is influenced by human activities in two ecotypes of Egyptian fruit bat (Rousettus aegyptiacus).

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.