The tales of two geckos: does dispersal prevent extinction in recently fragmented populations?

Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction

Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406-0.134 and nucleotide diversity 0.0812-0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (Fis - 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.

Differential effects of habitat loss on occupancy patterns of the eastern green lizard Lacerta viridis at the core and periphery of its distribution range

The effects of habitat loss on the distribution of populations are often linked with species specialization degree. Specialist species can be more affected by changes in landscape structure and local patch characteristics compared to generalist species. Moreover, the spatial scale at which different land covers (eg. habitat, cropland, urban areas) affect specialist species can be smaller. Specialization is usually assumed as a constant trait along the distribution range of species. However, for several taxa, there is evidence of higher specialization degree in peripheral populations compared with populations in the core. Hence, peripheral populations should have a higher sensitivity to habitat loss, and strongest effects should be found at a smaller spatial scale. To test these expectations, we implemented a patch-landscape approach at different spatial scales, and compared effects of landscape structure and patch characteristics on occupancy probability among northern peripheral, more specialized populations (Czech Republic) and core populations (Bulgaria) of the eastern green lizard Lacerta viridis. We found that landscape structure and patch characteristics affect differently the occupancy probability of Lacerta viridis in each region. Strongest effects of habitat loss were found at a spatial scale of 150m around patches in the periphery, but at a scale of 500m in the core. In the periphery occupancy probability of populations was principally affected by landscape composition, and the effect of habitat quality was stronger compared to core populations. In the core, persistence of populations was mainly explained by characteristics of the spatial configuration of habitat patches. We discuss possible ecological mechanisms behind the relationship between sensitivity to habitat loss, populations' specialization degree and position in the distribution range, and suggest conservation measures for L. viridis.

Town and Country Reptiles: A Review of Reptilian Responses to Urbanization

The majority of the world population is now inhabiting urban areas, and with staggering population growth, urbanization is also increasing. While the work studying the effects of changing landscapes and specific urban pressures on wildlife is beginning to amass, the majority of this work focuses on avian or mammalian species. However, the effects of urbanization likely vary substantially across taxonomic groups due to differences in habitat requirements and life history. The current article aims first to broaden the review of urban effects across reptilian species; second, to summarize the responses of reptilian fauna to specific urban features; and third, to assess the directionality of individual and population level responses to urbanization in reptile species. Based on our findings, urban research in reptilian taxa is lacking in the following areas: (1) investigating interactive or additive urban factors, (2) measuring multiple morphological, behavioral, and physiological endpoints within an animal, (3) linking individual to population-level responses, and (4) testing genetic/genomic differences across an urban environment as evidence for selective pressures.

Historical demography of four gecko species specializing in boulder cave habitat: Implications in the evolutionary dead end hypothesis and conservation

Specialization in narrow ecological niches may not only help species to survive in competitive or unique environments but also contribute to their extermination over evolutionary time. Although the "evolutionary dead end" hypothesis has long been debated, empirical evidence from species with detailed information on niche specialization and evolutionary history remains rare. Here we use a group of four closely related Cnemaspis gecko species that depend highly on granite boulder caves in the Mekong Delta to investigate the potential impact of ecological specialization on their evolution and population dynamics. Isolated by unsuitable floodplain habitats, these boulder-dwelling geckos are among the most narrowly distributed Squamata in the world. We applied several coalescence-based approaches combined with the RAD-seq technique to estimate their divergence times, gene flow and demographic fluctuations during the speciation and population differentiation processes. Our results reveal long-term population shrinkage in the four geckos and limited gene flow during their divergence. The results suggest that the erosion and fragmentation of the granite boulder hills have greatly impacted population divergence and declines. The habitat specialization of these geckos has led to fine-scaled speciation in these granite rocky hills; in contrast, specialization might also have pushed these species toward the edge of extinction. Our study also emphasizes the conservation urgency of these vulnerable, cave-dependent geckos.

Abundance and survival rates of three leaf-litter frog species in fragments and continuous forest of the Mata Atlântica, Brazil

Habitat destruction and fragmentation alter the quality of habitats and put populations under the risk of extinction. Changes in population parameters can provide early warning signs of negative impacts. In tropical forests, where habitat loss and fragmentation are vast, such indicators are of high relevance for directing conservation efforts before effects are irreversible. Most of our knowledge from tropical ecosystems originates from community level surveys, whereas our understanding of the influence of habitat conversion on vital rates of species is limited. This study focused on the influence of anthropogenic habitat fragmentation on the survival probability and abundance of three leaf-litter frog species (Rhinellaornata, Ischnocnemaguentheri and I.parva) in forest patches of the Atlantic rainforest of South-east Brazil compared to a continuous forest. The species differ in their matrix tolerance: high for R.ornata and low for I.guentheri and I.parva and, thus, we examined whether their survival and abundance correspond to this classification. Ischnocnemaguentheri showed highest abundances in all study sites and low mortality in the forest patches compared to the continuous forest; I.parva was encountered only in isolated fragments, with very low mortality in one isolated fragment; and the matrix tolerant species had generally low abundance and showed no clear pattern in terms of mortality in the different sites. Our counter-intuitive results show that even matrix sensitive amphibian species may show high abundance and low mortality in small forest patches. Therefore, these patches can be of high value for amphibian conservation regardless of their degree of matrix aversion. Landscape level conservation planning should not abandon small habitat patches, especially in highly fragmented tropical environments.

Barking up the right tree: comparative use of arboreal and terrestrial artificial refuges to survey reptiles in temperate eucalypt woodlands

Context Artificial refuges (cover boards) are a popular method to survey and monitor herpetofauna worldwide. However, one limitation of using artificial refuges in terrestrial environments is the low detection rates of arboreal species. Furthermore, destructive search techniques can damage critical microhabitat such as exfoliating rock or flaking bark of mature trees. Aim We tested a non-destructive, passive method of sampling arboreal reptiles in fragmented agricultural landscapes in south-eastern Australia. Methods We installed 84 artificial bark refuges consisting of strips of non-toxic, closed-cell foam attached to eucalypt trees in 13 patches of remnant vegetation. We used Bayesian statistics to compare differences in detection rates among artificial bark refuges, terrestrial artificial refuges and active searches of natural habitat over a 4-year period. Key results Active searches combined with terrestrial artificial refuges detected the highest number of reptile species, including several cryptic fossorial species. Artificial bark refuges detected, on average, 132 times more individuals of the arboreal southern marbled gecko, Christinus marmoratus, than did terrestrial refuges. Gecko abundance patterns were related to tree characteristics such as tree size, bark thickness and stand basal area, as well as survey year. Conclusions Traditional survey methods such as terrestrial cover boards, in combination with active searches of natural habitat, may significantly underestimate counts for arboreal gecko species. Implications Artificial bark refuges provide a cost-effective, non-destructive and durable method for surveying and monitoring arboreal reptiles in woodland environments over short to medium time frames. Foil-backed, closed-cell foam has broad application for use in spatial capture–recapture studies and long-term monitoring of arboreal reptiles. This method also may be effective for procuring records of threatened arboreal geckos or as a solution for providing temporary habitat in ecological restoration projects.

Genetic diversity and spatial structure of the Rufous-throated Antbird (Gymnopithys rufigula), an Amazonian obligate army-ant follower

Amazonian understory antbirds are thought to be relatively sedentary and to have limited dispersal ability; they avoid crossing forest gaps, and even narrow roads through a forest may limit their territories. However, most evidence for sedentariness in antbirds comes from field observations and plot‐based recapture of adult individuals, which do not provide evidence for lack of genetic dispersal, as this often occurs through juveniles. In this study, we used microsatellite markers and mitochondrial control‐region sequences to investigate contemporary and infer historical patterns of genetic diversity and structure of the Rufous‐throated Antbird (Gymnopithys rufigula) within and between two large reserves in central Amazonia. Analyses based on microsatellites suggested two genetically distinct populations and asymmetrical gene flow between them. Within a population, we found a lack of genetic spatial autocorrelation, suggesting that genotypes are randomly distributed and that G. rufigula may disperse longer distances than expected for antbirds. Analyses based on mitochondrial sequences did not recover two clear genetic clusters corresponding to the two reserves and indicated the whole population of the Rufous‐throated Antbird in the region has been expanding over the last 50,000 years. Historical migration rates were low and symmetrical between the two reserves, but we found evidence for a recent unilateral increase in gene flow. Recent differentiation between individuals of the two reserves and a unilateral increase in gene flow suggest that recent urban expansion and habitat loss may be driving changes and threatening populations of Rufous‐throated Antbird in central Amazonia. As ecological traits and behavioral characteristics affect patterns of gene flow, comparative studies of other species with different behavior and ecological requirements will be necessary to better understand patterns of genetic dispersal and effects of urban expansion on Amazonian understory antbirds.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity inN. stellatus Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics.

Habitat specialization predicts genetic response to fragmentation in tropical birds

Habitat fragmentation is one of the most severe threats to biodiversity as it may lead to changes in population genetic structure, with ultimate modifications of species evolutionary potential and local extinctions. Nonetheless, fragmentation does not equally affect all species and identifying which ecological traits are related to species sensitivity to habitat fragmentation could help prioritization of conservation efforts. Despite the theoretical link between species ecology and extinction proneness, comparative studies explicitly testing the hypothesis that particular ecological traits underlies species-specific population structure are rare. Here, we used a comparative approach on eight bird species, co-occurring across the same fragmented landscape. For each species, we quantified relative levels of forest specialization and genetic differentiation among populations. To test the link between forest specialization and susceptibility to forest fragmentation, we assessed species responses to fragmentation by comparing levels of genetic differentiation between continuous and fragmented forest landscapes. Our results revealed a significant and substantial population structure at a very small spatial scale for mobile organisms such as birds. More importantly, we found that specialist species are more affected by forest fragmentation than generalist ones. Finally, our results suggest that even a simple habitat specialization index can be a satisfying predictor of genetic and demographic consequences of habitat fragmentation, providing a reliable practical and quantitative tool for conservation biology.

Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

Physiological vagility and its relationship to dispersal and neutral genetic heterogeneity in vertebrates

Vagility is the inherent power of movement by individuals. Vagility and the available duration of movement determine the dispersal distance individuals can move to interbreed, which affects the fine-scale genetic structure of vertebrate populations. Vagility and variation in population genetic structure are normally explained by geographic variation and not by the inherent power of movement by individuals. We present a new, quantitative definition for physiological vagility that incorporates aerobic capacity, body size, body temperature and the metabolic cost of transport, variables that are independent of the physical environment. Physiological vagility is the speed at which an animal can move sustainably based on these parameters. This meta-analysis tests whether this definition of physiological vagility correlates with empirical data for maximal dispersal distances and measured microsatellite genetic differentiation with distance {[F(ST)/[1-F(ST))]/ln distance} for amphibians, reptiles, birds and mammals utilizing three locomotor modes (running, flying, swimming). Maximal dispersal distance and physiological vagility increased with body mass for amphibians, reptiles and mammals utilizing terrestrial movement. The relative slopes of these relationships indicate that larger individuals require longer movement durations to achieve maximal dispersal distances. Both physiological vagility and maximal dispersal distance were independent of body mass for flying vertebrates. Genetic differentiation with distance was greatest for terrestrial locomotion, with amphibians showing the greatest mean and variance in differentiation. Flying birds, flying mammals and swimming marine mammals showed the least differentiation. Mean physiological vagility of different groups (class and locomotor mode) accounted for 98% of the mean variation in genetic differentiation with distance in each group. Genetic differentiation with distance was not related to body mass. The physiological capacity for movement (physiological vagility) quantitatively predicts genetic isolation by distance in the vertebrates examined.

Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus) in China

The Chinese crocodile lizard Shinisaurus crocodilurus is a critically endangered species, listed in Appendix II of CITES. Its populations and habitat in China have undergone significant changes in recent years. Understanding the genetic variability and phylogeography of this species is very important for successful conservation. In this study, samples were taken from 11 wild ponds and two captive populations in China. We sequenced mitochondrial CYTB, partial ND6, and partial tRNA-Glu and genotyped 10 microsatellite loci. Our analyses of these data showed low genetic variability, no strong isolation caused by distance, and a lack of a phylogeographic structure in this species. Based on our results, the basal divergence between two clades of S. crocodilurus in China may have been caused by the formation of the Pearl River system. We found a population expansion in one of these clades. Microsatellite analysis indicated the presence of three clusters, separated by significant genetic differences. We found that most individuals in the two captive populations were from the Luokeng (Guangdong) and Guangxi wild source populations, respectively.

Fine-scale genetic response to landscape change in a gliding mammal

Understanding how populations respond to habitat loss is central to conserving biodiversity. Population genetic approaches enable the identification of the symptoms of population disruption in advance of population collapse. However, the spatio-temporal scales at which population disruption occurs are still too poorly known to effectively conserve biodiversity in the face of human-induced landscape change. We employed microsatellite analysis to examine genetic structure and diversity over small spatial (mostly 1-50 km) and temporal scales (20-50 years) in the squirrel glider (Petaurus norfolcensis), a gliding mammal that is commonly subjected to a loss of habitat connectivity. We identified genetically differentiated local populations over distances as little as 3 km and within 30 years of landscape change. Genetically isolated local populations experienced the loss of genetic diversity, and significantly increased mean relatedness, which suggests increased inbreeding. Where tree cover remained, genetic differentiation was less evident. This pattern was repeated in two landscapes located 750 km apart. These results lend support to other recent studies that suggest the loss of habitat connectivity can produce fine-scale population genetic change in a range of taxa. This gives rise to the prediction that many other vertebrates will experience similar genetic changes. Our results suggest the future collapse of local populations of this gliding mammal is likely unless habitat connectivity is maintained or restored. Landscape management must occur on a fine-scale to avert the erosion of biodiversity.

Sex-biased dispersal at different geographical scales in a cooperative breeder from fragmented rainforest

Dispersal affects both social behavior and population structure and is therefore a key determinant of long-term population persistence. However, dispersal strategies and responses to spatial habitat alteration may differ between sexes. Here we analyzed spatial and temporal variation in ten polymorphic microsatellite DNA loci of male and female Cabanis's greenbuls (Phyllastrephuscabanisi), a cooperative breeder of Afrotropical rainforest, to quantify rates of gene flow and fine-grained genetic structuring within and among fragmented populations. We found genetic evidence for female-biased dispersal at small spatial scales, but not at the landscape level. Local autocorrelation analysis provided evidence of positive genetic structure within 300 m distance ranges, which is consistent with behavioral observations of short-distance natal dispersal. At a landscape scale, individual-based autocorrelation values decreased over time while levels of admixture increased, possibly indicating increased gene flow over the past decade.

Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico

Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.

Can genetic estimators provide robust estimates of the effective number of breeders in small populations?

The effective population size (N(e)) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of N(e). Because geckos have overlapping generations, our goal was to demographically estimate N(bI), the inbreeding effective number of breeders and to calculate the N(bI)/N(a) ratio (N(a) =number of adults) for four populations. Demographically estimated N(bI) ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (N(bI)/N(a)) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders N(bI(gen)) and the variance effective populations size N(eV(gen)) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14-55 and 24-48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate N(bI) for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.

Phylogeography and population genetic structure of the Ornate Dragon Lizard, Ctenophorus ornatus

Species inhabiting ancient, geologically stable landscapes that have been impacted by agriculture and urbanisation are expected to have complex patterns of genetic subdivision due to the influence of both historical and contemporary gene flow. Here, we investigate genetic differences among populations of the granite outcrop-dwelling lizard Ctenophorus ornatus, a phenotypically variable species with a wide geographical distribution across the south-west of Western Australia. Phylogenetic analysis of mitochondrial DNA sequence data revealed two distinct evolutionary lineages that have been isolated for more than four million years within the C. ornatus complex. This evolutionary split is associated with a change in dorsal colouration of the lizards from deep brown or black to reddish-pink. In addition, analysis of microsatellite data revealed high levels of genetic structuring within each lineage, as well as strong isolation by distance at multiple spatial scales. Among the 50 outcrop populations’ analysed, non-hierarchical Bayesian clustering analysis revealed the presence of 23 distinct genetic groups, with outcrop populations less than 4 km apart usually forming a single genetic group. When a hierarchical analysis was carried out, almost every outcrop was assigned to a different genetic group. Our results show there are multiple levels of genetic structuring in C. ornatus, reflecting the influence of both historical and contemporary evolutionary processes. They also highlight the need to recognise the presence of two evolutionarily distinct lineages when making conservation management decisions on this species.

Multimodal dispersal during the range expansion of the tropical house gecko Hemidactylus mabouia

Dispersal influences both the ecological and evolutionary dynamics of range expansion. While some studies have demonstrated a role for human-mediated dispersal during invasion, the genetic effects of such dispersal remain to be understood, particularly in terrestrial range expansions. In this study, we investigated multimodal dispersal during the range expansion of the invasive gecko Hemidactylus mabouia in Florida using 12 microsatellite loci. We investigated dispersal patterns at the regional scale (metropolitan areas), statewide scale (state of Florida), and global scale (including samples from the native range). Dispersal was limited at the smallest, regional scale, within metropolitan areas, as reflected by the presence of genetic structure at this scale, which is in agreement with a previous study in this same invasion at even smaller spatial scales. Surprisingly, there was no detectable genetic structure at the intermediate statewide scale, which suggests dispersal is not limited across the state of Florida. There was evidence of genetic differentiation between Florida and other areas where H. mabouia occurs, so we concluded that at the largest scale, dispersal was limited. Humans likely contributed to patterns of dispersal at all three scales but in different ways. Infrequent low-volume dispersal has occurred within regions, frequent high-volume dispersal has occurred across the state, and infrequent long-distance dispersal has occurred among continents at the global scale. This study highlights the importance of considering different modes of dispersal at multiple spatial scales to understand the dynamics of invasion and range expansion.

A comparative analysis of fine-scale genetic structure in three closely related syntopic species of the grasshopper genus Calliptamus

Landscape analysis and genetics can allow a better understanding of grasshoppers for which ecology is not very well known. We analysed landscape changes between 1990 and 2006 at two areas from southern France where three grasshopper species ( Calliptamus italicus (L., 1758), Calliptamus wattenwylianus Pantel, 1896, and Calliptamus barbarus (Costa, 1836)) occur. We then applied microsatellite markers to the study of 1200 georeferenced samples collected over both areas. We used a recent Bayesian clustering method with correlated allele frequencies to detect weak population genetic structure. We found evidence of breaks in gene flow only in C. wattenwylianus, thought to be sedentary relative to its congenerics. By using different allele frequency models and prior information to different levels of genetic differentiation for our six real data sets, our study also informs on the ability of the newly available Bayesian clustering methods model to detect weak genetic structure in natural field populations.

High gene flow across large geographic scales reduces extinction risk for a highly specialised coral feeding butterflyfish

The vulnerability of ecologically specialised species to environmental fluctuations has been well documented. However, population genetic structure can influence vulnerability to environmental change and recent studies have indicated that specialised species may have lower genetic diversity and greater population structuring compared to their generalist counterparts. To examine whether there were differences in population genetic structure between a dietary specialist (Chaetodon trifascialis) and a dietary generalist (Chaetodon lunulatus) we compared the demographic history and levels of gene flow of two related coral-feeding butterflyfishes. Using allele frequencies of ≥11 microsatellite loci and >350 bases of mitochondrial control region sequence our analyses of C. trifascialis and C. lunulatus from five locations across the Pacific Ocean revealed contrasting demographic histories and levels of genetic structure. Heterozygosity excess tests, neutrality tests and mismatch distributions were all highly significant in the dietary specialist C. trifascialis (all P < 0.01), suggesting genetic bottlenecks have occurred in all locations. In contrast, we found little evidence of genetic bottlenecks for the dietary generalist C. lunulatus. High gene flow and low genetic structuring was detected among locations for C. trifascialis (amova: R(ST) = 0.0027, P = 0.371; Φ(ST) = 0.068, P < 0.0001). Contrary to our expectations, a greater level of genetic structuring between locations was detected for C. lunulatus (amova: R(ST) = 0.0277, Φ(ST) = 0.166, both P < 0.0001). These results suggest that dietary specialisation may affect demographic history through reductions in population size following resource declines, without affecting population structure through reductions in gene flow in the same way that habitat specialisation appears to. Although C. trifascialis is highly vulnerable to coral loss, the high gene flow detected here suggests populations will be able to recover from local declines through the migration of individuals.

Broken barriers: human-induced changes to gene flow and introgression in animals: an examination of the ways in which humans increase genetic exchange among populations and species and the consequences for biodiversity

We identify two processes by which humans increase genetic exchange among groups of individuals: by affecting the distribution of groups and dispersal patterns across a landscape, and by affecting interbreeding among sympatric or parapatric groups. Each of these processes might then have two different effects on biodiversity: changes in the number of taxa through merging or splitting of groups, and the extinction/extirpation of taxa through effects on fitness. We review the various ways in which humans are affecting genetic exchange, and highlight the difficulties in predicting the impacts on biodiversity. Gene flow and hybridization are crucially important evolutionary forces influencing biodiversity. Humans alter natural patterns of genetic exchange in myriad ways, and these anthropogenic effects are likely to influence the genetic integrity of populations and species. We argue that taking a gene-centric view towards conservation will help resolve issues pertaining to conservation and management. Editor's suggested further reading in BioEssays A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture Abstract.

Levels of dispersal and tail loss in an Australian gecko (Gehyra variegata) are associated with differences in forest structure

Corridors of natural habitat are often sought to maintain dispersal and gene flow among habitat patches. However, structural changes in natural habitat over space and time may influence connectivity. Here we investigate whether differences in forest structure and the frequency of potential retreat sites is associated with the genetic structure of a tree-dwelling Australian gecko (Gehyra variegata). We sampled 113 adult geckos from multiple state forest and adjacent reserve locations within the Pilliga forest, New South Wales, Australia. Individuals were genotyped at 14 microsatellite loci and levels of dispersal were inferred by the degree of genetic structuring observed in state forest and reserve. A greater proportion of dead trees and tree debris (features that are used as retreat sites by G. variegata) were present within the state forests than in the reserve locations (P < 0.05). This reduction in frequency of retreat sites in reserves was associated with significantly less genetic structuring of G. variegata, implying higher levels of dispersal. Tail loss was also significantly higher in G. variegata sampled in reserves than in the state forests. We conclude that dispersal characteristics in G. variegata are associated with structural changes to natural habitat and that this may influence rates of predation.

Differential threshold effects of habitat fragmentation on gene flow in two widespread species of bush crickets

Effects of habitat fragmentation on genetic diversity vary among species. This may be attributed to the interacting effects of species traits and landscape structure. While widely distributed and abundant species are often considered less susceptible to fragmentation, this may be different if they are small sized and show limited dispersal. Under intensive land use, habitat fragmentation may reach thresholds at which gene flow among populations of small-sized and dispersal-limited species becomes disrupted. Here, we studied the genetic diversity of two abundant and widespread bush crickets along a gradient of habitat fragmentation in an agricultural landscape. We applied traditional (G(ST), θ) and recently developed (G'ST', D) estimators of genetic differentiation on microsatellite data from each of twelve populations of the grassland species Metrioptera roeselii and the forest-edge species Pholidoptera griseoaptera to identify thresholds of habitat fragmentation below which genetic population structure is affected. Whereas the grassland species exhibited a uniform genetic structuring (G(ST) = 0.020-0.033; D = 0.085-0.149) along the whole fragmentation gradient, the forest-edge species' genetic differentiation increased significantly from D < 0.063 (G(ST) < 0.018) to D = 0.166 (G(ST) = 0.074), once the amount of suitable habitat dropped below a threshold of 20% and its proximity decreased substantially at the landscape scale. The influence of fragmentation on genetic differentiation was qualitatively unaffected by the choice of estimators of genetic differentiation but quantitatively underestimated by the traditional estimators. These results indicate that even for widespread species in modern agricultural landscapes fragmentation thresholds exist at which gene flow among suitable habitat patches becomes restricted.

A rapid, strong, and convergent genetic response to urban habitat fragmentation in four divergent and widespread vertebrates

BACKGROUND

Urbanization is a major cause of habitat fragmentation worldwide. Ecological and conservation theory predicts many potential impacts of habitat fragmentation on natural populations, including genetic impacts. Habitat fragmentation by urbanization causes populations of animals and plants to be isolated in patches of suitable habitat that are surrounded by non-native vegetation or severely altered vegetation, asphalt, concrete, and human structures. This can lead to genetic divergence between patches and in turn to decreased genetic diversity within patches through genetic drift and inbreeding.

METHODOLOGY/PRINCIPAL FINDINGS

We examined population genetic patterns using microsatellites in four common vertebrate species, three lizards and one bird, in highly fragmented urban southern California. Despite significant phylogenetic, ecological, and mobility differences between these species, all four showed similar and significant reductions in gene flow over relatively short geographic and temporal scales. For all four species, the greatest genetic divergence was found where development was oldest and most intensive. All four animals also showed significant reduction in gene flow associated with intervening roads and freeways, the degree of patch isolation, and the time since isolation.

CONCLUSIONS/SIGNIFICANCE

Despite wide acceptance of the idea in principle, evidence of significant population genetic changes associated with fragmentation at small spatial and temporal scales has been rare, even in smaller terrestrial vertebrates, and especially for birds. Given the striking pattern of similar and rapid effects across four common and widespread species, including a volant bird, intense urbanization may represent the most severe form of fragmentation, with minimal effective movement through the urban matrix.

Land clearing reduces gene flow in the granite outcrop-dwelling lizard, Ctenophorus ornatus

An important question for the conservation of species dwelling in fragmented habitats is whether changes to the intervening landscape create a barrier to gene flow. Here, we make use of the spatial distribution of the granite outcrop-dwelling lizard, Ctenophorus ornatus, to compare inferred levels of gene flow between outcrops in a nature reserve with that between outcrops in the adjacent agricultural land. Genetic variation, relatedness and subdivision were compared within groups of individuals from different outcrops similar in size and distance apart at each site. In the agricultural land, we found significantly lower genetic variation within outcrops and greater genetic differentiation between outcrops than in the reserve. Further, the rate at which genetic divergence between outcrops increased over geographical distance was significantly greater in the agricultural land than in the reserve. We also found that individuals were more closely related within outcrops but more distantly related between outcrops in the cleared land. These effects occur over a small spatial scale with an average distance between outcrops of less than five kilometres. Thus, even though land clearing around the outcrops leaves outcrop size unchanged, it restricts gene flow, reducing genetic variation and increasing population structure, with potentially negative consequences for the long-term persistence of the lizards on these outcrops.

Effects of habitat fragmentation on effective dispersal of Florida scrub-jays

Studies comparing dispersal in fragmented versus unfragmented landscapes show that habitat fragmentation alters the dispersal behavior of many species. We used two complementary approaches to explore Florida Scrub-Jay (Aphelocoma coerulescens) dispersal in relation to landscape fragmentation. First, we compared dispersal distances of color-marked individuals in intensively monitored continuous and fragmented landscapes. Second, we estimated effective dispersal relative to the degree of fragmentation (as inferred from two landscape indexes: proportion of study site covered with Florida Scrub-Jay habitat and mean distance to nearest habitat patch within each study site) by comparing genetic isolation-by-distance regressions among 13 study sites having a range of landscape structures. Among color-banded individuals, dispersal distances were greater in fragmented versus continuous landscapes, a result consistent with other studies. Nevertheless, genetic analyses revealed that effective dispersal decreases as the proportion of habitat in the landscape decreases. These results suggest that although individual Florida Scrub-Jays may disperse farther as fragmentation increases, those that do so are less successful as breeders than those that disperse short distances. Our study highlights the importance of combining observational data with genetic inferences when evaluating the complex biological and life-history implications of dispersal.