Ecological metrics predict connectivity better than geographic distance

We use microsatellite loci to examine genetic structure of the Florida scrub lizard (Sceloporus woodi) and test for the effects of landscape variables at the scale of neighboring patches. We evaluate ecological metrics of connectivity with genetics data, which to our knowledge is the first application of these particular metrics to landscape-level genetics studies in Florida scrub. Florida scrub is a highly threatened ecosystem in which habitat patches are remnants of a previously widespread xeric landscape. Analysis of mitochondrial DNA (mtDNA) has shown that landscape structure influenced the evolutionary history of the Florida scrub lizard (S. woodi) across its range. Our results concur with these mtDNA studies in documenting divergence between xeric ridge systems and also demonstrate divergence at very local scales. Both least-cost distance and pairwise isolation (a metric used in ecological studies that includes patch size, quality and a modified isolation index) were better predictors of genetic distance than Euclidean distance, indicating that mesic and hydric habitat influence spatial patterns in genetic variation. Our results support the need for focusing on spatial distribution of scrub habitat at the scale of neighboring patches, as well as regionally, in conservation management and restoration. Also, our study points to the value of integrating landscape ecology metrics into landscape genetics.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

Fire alters patterns of genetic diversity among 3 lizard species in Florida Scrub habitat

The Florida Sand Skink (Plestiodon reynoldsi), the Florida Scrub Lizard (Sceloporus woodi), and the Six-lined Racerunner (Aspidoscelis sexlineata) occur in the threatened and fire-maintained Florida scrub habitat. Fire may have different consequences to local genetic diversity of these species because they each have different microhabitat preference. We collected tissue samples of each species from 3 sites with different time-since-fire: Florida Sand Skink n = 73, Florida Scrub Lizard n = 70, and Six-lined Racerunner n = 66. We compared the effect of fire on genetic diversity at microsatellite loci for each species. We screened 8 loci for the Florida Sand Skink, 6 loci for the Florida Scrub Lizard, and 6 loci for the Six-lined Racerunner. We also tested 2 potential driving mechanisms for the observed change in genetic diversity, a metapopulation source/sink model and a local demographic model. Genetic diversity varied with fire history, and significant genetic differentiation occurred among sites. The Florida Scrub Lizard had highest genetic variation at more recently burned sites, whereas the Florida Sand Skink and the Six-lined Racerunner had highest genetic variation at less recently burned sites. Habitat preferences of the Florida Sand Skink and the Florida Scrub Lizard may explain their discordant results, and the Six-lined Racerunner may have a more complicated genetic response to fire or is acted on at a different geographic scale than we have investigated. Our results indicate that these species may respond to fire in a more complicated manner than predicted by our metapopulation model or local demographic model. Our results show that the population-level responses in genetic diversity to fire are species-specific mandating conservation management of habitat diversity through a mosaic of burn frequencies.     

Fragmented landscapes, habitat specificity, and conservation genetics of three lizards in Florida scrub

Dry, sandy scrub habitats of the Floridapeninsula represent naturally fragmentedremnants of xeric ecosystems that werewidespread during the Pliocene and earlyPleistocene. This habitat is characterized byhigh endemism, and distribution of genetic andevolutionary diversity among scrub ``islands' isof compelling interest because Florida scrub israpidly disappearing under human development. We compare range-wide diversity inmitochondrial cytochrome b sequences forthree scrub-associated lizards with contrastinglevels of habitat specificity. All speciesshow strong geographic partitioning of geneticdiversity, supporting the hypothesis that scrubfauna is highly restricted by vicariantseparations. The mole skink (Eumecesegregius), the least habitat specific, has thelowest phylogeographic structure among thelizards (_st = 0.631). The mtDNAgeneology for E. egregius is not entirelyconcordant with the five recognized subspeciesand supports a link between populations incentral Florida (E. e. lividus) and theFlorida Keys (E.e. egregius) rather thana previously proposed affiliation betweennorthern and southern populations. The Floridascrub lizard (Sceloporus woodi) is themost habitat specific of the lizards and hasthe strongest phylogeographic structure (_st = 0.876). The sand skink (Neosepsreynoldsi) falls between the moleskink and scrub lizard in terms of habitatspecificity and phylogeographic structure (_st = 0.667). For all three species,networks of mtDNA haplotypes coalesce on twocentral ridges that contain the oldest scrub. The geographic structure and deep evolutionarylineages observed in these species have strongimplications for conservation, includingstrategies for translocation, reserve design,and management of landscape connectivity.     

Delayed genetic effects of habitat fragmentation on the ecologically specialized Florida sand skink (Plestiodon reynoldsi)

Populations rarely show immediate genetic responses to habitat fragmentation, even in taxa that possess suites of traits known to increase their vulnerability to extinction. Thus conservation geneticists must consider the time scale over which contemporary evolutionary processes operate to accurately portray the effects of habitat isolation. Here, we examine the genetic impacts of fragmentation on the Florida sand skink Plestiodon reynoldsi, a sand swimming lizard that is highly adapted to the upland scrub habitat of central Florida. We studied fragments located on the southern Lake Wales Ridge, where human activity in the latter half of the 20th century has modified the natural patchiness of the landscape. Based on a relaxed molecular clock method, we estimate that sand skinks have persisted in this region for approximately 1.5 million years and that the time frame of human disturbance is equivalent to fewer than 30 skink generations. Using genotypes from eight microsatellite loci, we screened for molecular signatures of this disturbance by assessing congruence between population structure, as inferred from spatially-informed Bayesian assignment tests, and the current geography of scrub fragments. We also tested for potential intrapopulation genetic effects of inbreeding in isolated populations by comparing the average pairwise relatedness of individuals within fragments of different areas and isolation. Our results indicate that although some patches show a higher degree of relatedness than expected under random mating, the genetic effects of recent isolation are not evident in this part of the species’ range. We argue that this result is an artefact of a time-lag in the response to disturbance, and that species-typical demographic features may explain the genetic inertia observed in these populations.     

Landscape configuration determines gene flow and phenotype in a flightless forest-edge ground-dwelling bush-cricket, Pholidoptera griseoaptera

Spatial configuration of habitats influences genetic structure and population fitness whereas it affects mainly species with limited dispersal ability. To reveal how habitat fragmentation determines dispersal and dispersal-related morphology in a ground-dispersing insect species we used a bush-cricket (Pholidoptera griseoaptera) which is associated with forest-edge habitat. We analysed spatial genetic patterns together with variability of the phenotype in two forested landscapes with different levels of fragmentation. While spatial configuration of forest habitats did not negatively affect genetic characteristics related to the fitness of sampled populations, genetic differentiation was found higher among populations from an extensive forest. Compared to an agricultural matrix between forest patches, the matrix of extensive forest had lower permeability and posed barriers for the dispersal of this species. Landscape configuration significantly affected also morphological traits that are supposed to account for species dispersal potential; individuals from fragmented forest patches had longer hind femurs and a higher femur to pronotum ratio. This result suggests that selection pressure act differently on populations from both landscape types since dispersal-related morphology was related to the level of habitat fragmentation. Thus observed patterns may be explained as plastic according to the level of landscape configuration; while anthropogenic fragmentation of habitats for this species can lead to homogenization of spatial genetic structure.     

Population genetic structure of male black grouse (Tetrao tetrix L.) in fragmented vs. continuous landscapes

We investigated the association of habitat fragmentation with genetic structure of male black grouse Tetrao tetrix. Using 14 microsatellites, we compared the genetic differentiation of males among nine localities in continuous lowland habitats in Finland to the genetic differentiation among 14 localities in fragmented habitats in the Alps (France, Switzerland and Italy). In both areas, we found significant genetic differentiation. However, the average differentiation, measured as theta, was more than three times higher in the Alps than in Finland. The greater differentiation found in the Alps is probably due to the presence of mountain ridges rising above natural habitats of the species, which form barriers to gene flow, and to a higher influence of genetic drift resulting from lower effective sizes in highly fragmented habitats. The detection of isolation by distance in the Alps suggests that gene flow among populations does occur. The genetic variability measured as gene diversity HE and allelic richness A was lower in the Alps than in Finland. This could result from the higher fragmentation and/or from the fact that populations in the Alps are isolated from the main species range and have a lower effective size than in Finland. This study suggests that habitat fragmentation can affect genetic structure of avian species with relatively high dispersal propensities.     

The effects of habitat fragmentation via forestry plantation establishment on spatial genotypic structure in the small marsupial carnivore, Antechinus agilis

Dispersal is an important influence on species' distributions, patch colonization and population persistence in fragmented habitat. We studied the impacts of habitat fragmentation resulting from establishment of an exotic pine plantation on dispersal of the marsupial carnivore, Antechinus agilis. We applied spatial analyses of individual multilocus microsatellite genotypes and mitochondrial haplotypes to study patterns of gene flow in fragmented habitat and natural habitat 'control' areas, and how this is affected by the spatial dispersion of habitat patches, the presence of corridors and a 'mainland' source of migrants. Spatial analysis of molecular variance and partial Mantel tests confirmed the absence of cryptic barriers to gene flow in continuous habitat, which if present would confound the comparison of genetic structures in fragmented vs. unfragmented habitats. Spatial genotypic structure suggested that although dispersal was male-biased in both habitat types, fragmentation restricted dispersal of males more than that of females and the degree of restriction of male dispersal was dependent on the geographical isolation of the patch. The scale of positive genotypic structure in fragmented habitat was restricted to the two closest patches for females and the three closest patches for males. Our results provide evidence for significantly increased gene flow through habitat corridors relative to that across the matrix and for significantly lower gene flow between 'mainland' unfragmented habitat and habitat patches relative to that within either habitat type, suggesting a behavioural barrier to crossing habitat interfaces.     

Impacts of Restored Patch Density and Distance from Natural Forests on Colonization Success

Abstract The reduction and fragmentation of forest habitats is expected to have profound effects on plant species diversity as a consequence of the decreased area and increased isolation of the remnant patches. To stop the ongoing process of forest fragmentation, much attention has been given recently to the restoration of forest habitat. The present study investigates restoration possibilities of recently established patches with respect to their geographical isolation. Because seed dispersal events over 100 m are considered to be of long distance, a threshold value of 100 m between recent and old woodland was chosen to define isolation. Total species richness, individual patch species richness, frequency distributions in species occurrences, and patch occupancy patterns of individual species were significantly different among isolated and nonisolated stands. In the short term no high species richness is to be expected in isolated stands. Establishing new forests adjacent to existing woodland ensures higher survival probabilities of existing populations. In the long term, however, the importance of long‐distance seed dispersal should not be underestimated because most species showed occasional long‐distance seed dispersal. A clear distinction should be made between populations colonizing adjacent patches and patches isolated from old woodland. The colonization of isolated stands may have important effects on the dynamics and diversity of forest networks, and more attention should be directed toward the genetic traits and viability of founding populations in isolated stands.     

Isolation of microsatellite loci in the Florida Scrub‐Jay Aphelocoma coerulescens

The Florida Scrub‐Jay (Aphelocoma coerulescens), a habitat specialist listed as Threatened by the U.S. Fish and Wildlife Service, exhibits extremely limited natal dispersal. We hypothesize that this behaviour results in a correlation of genetic and geographical distance. To test this, we are sampling intensively along the north–south orientated Lake Wales Ridge of central Florida. We describe the isolation and characterization of 31 microsatellite loci developed to determine the minimum distance at which genetic structure can be detected, and to test for isolation by distance. There are 3–15 alleles per locus, with expected heterozygosities from 0.16 to 0.86.     

Gene flow in an endangered willow <Emphasis Type="Italic">Salix hukaoana</Emphasis> (Salicaceae) in natural and fragmented riparian landscapes

Salix hukaoana is an endangered riparian pioneer tree that is distributed within a restricted area of Japan. Microsatellite genetic variations and genetic structures were investigated in 80 subpopulations patchily distributed within five river basins with varying degrees of habitat fragmentation. The correlation between geographic distance and genetic distance based on the Bayesian assignment test was significant across relatively intact riparian habitats, with steeper slopes of regression for more densely grouped subpopulations, suggesting restricted gene flow. However, the correlation became less apparent with increasing spacing of the habitat patches. These contradictory results are attributed to the increased chance of long-distance dispersal of sexual propagules among more isolated habitat patches. The observed accumulation of genetic diversity with increasing distance downstream along a few, but not all, of the rivers and the results of assignment tests suggested a downstream directionality of gene flow. The results of this study illustrate the patterns of genetic diversity and contemporary dispersal of S. hukaoana, and provide important insights into understanding the gene dispersal of riparian trees and into the conservation of genetic resources for this species.     

Dispersal and habitat cuing of Eurasian red squirrels in fragmented habitats

Animal dispersal and subsequent settlement is a key process in the life history of many organisms, when individuals use demographic and environmental cues to target post-dispersal habitats where fitness will be highest. To investigate the hypothesis that environmental disturbance (habitat fragmentation) may alter these cues, we compared dispersal patterns of 60 red squirrels (Sciurus vulgaris) in three study sites that differ in habitat composition and fragmentation. We determined dispersal distances, pre- and post-dispersal habitat types and survival using a combination of capture–mark–recapture, radio-tracking and genetic parentage assignment. Most (75%) squirrels emigrated from the natal home range with mean dispersal distance of 1,014 ± 925 m (range 51–4,118 m). There were no sex-related differences in dispersal patterns and no differences in average dispersal distance, and the proportion of dispersers did not differ between sites. In one of the sites, dispersers settled in patches where density was lower than in the natal patch. In the least fragmented site, 90% of animals settled in the natal habitat type (habitat cuing) against 44–54% in the more strongly fragmented sites. Overall, more squirrels settled in the natal habitat type than expected based on habitat availability, but this was mainly due to individuals remaining within the natal wood. In the highly fragmented landscape, habitat cuing among emigrants did not occur more frequently than expected. We concluded that increased habitat fragmentation seemed to reduce reliable cues for habitat choice, but that dispersing squirrels settled in patches with lower densities of same-sex animals than at the natal home range or patch, independent of degree of fragmentation.     

Mapping scrub vegetation cover from photogrammetric point clouds: A useful tool in reserve management

Scrub vegetation is a valuable habitat and resource for wildlife, but if unmanaged can encroach and dominate adjacent habitats, reducing biodiversity value. A primary task in the management of terrestrial nature reserves in the UK is monitoring and controlling scrub. The methods used to monitor and assess scrub cover are often basic, relying on qualitative assessment. Inaccurate assessments may fail to inform appropriate management of the habitats and lead to loss or degradation of important ecological features. Scrub can be monitored using UAV or satellite‐derived imagery, but it can be difficult to distinguish between other vegetation types without using high‐cost hyperspectral sensors. An alternative method using high‐resolution surface models from photogrammetric point clouds enables the isolation of vegetation types based on height. Scrub can be isolated from woodland, hedgerows, and tall ground vegetation. In this study, we calculate scrub cover using a photogrammetric point cloud modeling approach using UAVs.We illustrate the method with two case studies from the UK. The scrub cover at Daneway Banks, a calcareous grassland site in Gloucestershire, was calculated at 21.8% of the site. The scrub cover at Flat Holm Island, a maritime grassland in the Severn Estuary, was calculated at 7%. This approach enabled the scrub layer to be readily measured and if required, modeled to provide a visual guide of what a projected management objective would look like. This approach provides a new tool in reserve management, enabling habitat management strategies to be informed, and progress toward objectives monitored.     

Contrasting genetic responses to population fragmentation in a coevolving fig and fig wasp across a mainland–island archipelago

Interacting species of pollinator–host systems, especially the obligate ones, are sensitive to habitat fragmentation, due to the nature of mutual dependence. Comparative studies of genetic structure can provide insights into how habitat fragmentation contributes to patterns of genetic divergence among populations of the interacting species. In this study, we used microsatellites to analyse genetic variation in Chinese populations of a typical mutualistic system – Ficus pumila and its obligate pollinator Wiebesia sp. 1 – in a naturally fragmented landscape. The plants and wasps showed discordant patterns of genetic variation and geographical divergence. There was no significant positive relationship in genetic diversity between the two species. Significant isolation‐by‐distance (IBD) patterns occurred across the populations of F. pumila and Wiebesia sp. 1 as whole, and IBD also occurred among island populations of the wasps, but not the plants. However, there was no significant positive relationship in genetic differentiation between them. The pollinator populations had significantly lower genetic variation in small habitat patches than in larger patches, and three island pollinator populations showed evidence of a recent bottleneck event. No effects of patch size or genetic bottlenecks were evident in the plant populations. Collectively, the results indicate that, in more fragmented habitats, the pollinators, but not the plants, have experienced reduced genetic variation. The contrasting patterns have multiple potential causes, including differences in longevity and hence number of generations experiencing fragmentation; different dispersal patterns, with the host's genes dispersed as seeds as well as a result of pollen dispersal via the pollinator; asymmetrical responses to fluctuations in partner populations; and co‐existence of a rare second pollinating wasp on some islands. These results indicate that strongly interdependent species may respond in markedly different ways to habitat fragmentation.     

Contrasting genetic structures in sister species of North American scrub-jays

Threatened Florida scrub-jays (Aphelocoma coerulescens breed communally, are restricted to xeric sandy scrub habitat, generally disperse fewer than three territory diameters. Closely related Western scrub-jays (A. californica) do not breed communally, have a broader habitat range, disperse greater distances, and are not threatened. We compared the genetic structure of 445 individuals in 11 populations in Florida with 157 individuals in eight populations of Western scrub-jays. At ten microsatellite loci, Florida had 24 out of 47 total alleles, while Western scrub-jays had 44. The Florida populations were more differentiated (G_ST = 0.048) than were a set of five California populations (G_ST = 0.015). A randomization extension of a Mantel test showed a stronger correlation between geographic and Cavalli-Sforza genetic distances among Western than Florida populations. Neighbour-joining trees clustered Florida populations from the same sandy ridge systems, suggesting that habitat continuity is more important than geographic proximity in allowing gene flow and preventing differentiation. For Western populations, isolation by distance appears to be the major determinant of genetic structure. Our results suggest that contrasting genetic structures may arise between closely related species, as a result of differences in ecology and social system. Conserving extant genetic variation in Florida jays will require maintaining viable populations in each of the major sandy ridge systems.     

Dynamic landscapes shape post‐wildfire recolonisation and genetic structure of the endangered Hermes copper (Lycaena hermes) butterfly

1. The coastal sage scrub vegetation community experiences frequent fires, so the long‐term survival of species depends on the rate of recolonisations exceeding the rate of local extinctions. Recolonisation of these post‐wildfire habitats probably requires long‐distance dispersal events. These movements can also counter detrimental impacts associated with inbreeding. 2. The Hermes copper (Lycaena hermes) is an extremely rare butterfly inhabiting coastal sage scrub adjacent to San Diego, California, USA. Habitat loss due to urbanisation and impacts of recent wildfires has greatly restricted its range, prompting the United States Fish and Wildlife Service to list the Hermes copper as a Candidate Species in 2011. 3. Surveys for Hermes copper butterflies in 2010–2013 documented only two recolonisation events following wildfires in 2003 and 2007. Larger populations were readily detected each year, but detection of smaller populations was inconsistent. 4. Amplified fragment length polymorphism was used to identify potential genetic discontinuities within this species across the landscape. Results indicated that movements across much of the landscape were possible historically. However, individuals from three peripheral populations exhibited a higher degree of differentiation, suggesting more restricted dispersal in these regions. 5. From the results, it can be concluded that historically Hermes copper butterflies were able to move among habitat patches prior to recent changes in the landscape. However, low post‐fire recolonisation rates suggest limited contemporary dispersal, probably due to recent habitat fragmentation. This fragmentation is a relatively new event, as the human population in San Diego County experienced substantial growth in the late 20th Century.     

Effects of forest-dune ecotone management on the endangered heath grasshopper, Chorthippus vagans (Orthoptera: Acrididae)

Dry, oligotrophic ecosystems are highly threatened in Europe due to massive changes in land use and eutrophication. The conservation of these xeric habitats has received much attention, whereas the ecotones between xeric habitats and other habitat types are often disregarded. One species which mainly inhabits the transition zone between pine forests and adjacent xeric habitats is the heath grasshopper, Chorthippus vagans. This species is endangered in large parts of Europe. One of the largest populations in northern Germany is found on a degraded inland dune near Hanover. This population is threatened by dense growth of deciduous trees and litter accumulation. We analyzed changes in the distribution of this population after the implementation of conservation measures (thinning out the forest and removal of leaf litter). Moreover, we examined dispersal distances of the species in order to assess its colonization potential. We also studied the microhabitat preferences of C. vagans to assess key factors influencing its local distribution. Our data show a substantial growth in population size, which might be a consequence of the conservation measures. New patches on the dune were colonized, promoting dispersal between the subpopulations. We propose that restoration of forest-dune ecotones should be considered more often in landscape planning and conservation management.     

Pervasive effects of dispersal limitation on within- and among-community species richness in agricultural landscapes

Aim To determine whether the effect of habitat fragmentation and habitat heterogeneity on species richness at different spatial scales depends on the dispersal ability of the species assemblages and if this results in nested species assemblages. Location Agricultural landscapes distributed over seven temperate Europe countries covering a range from France to Estonia. Methods We sampled 16 local communities in each of 24 agricultural landscapes (16 km²) that differ in the amount and heterogeneity of semi‐natural habitat patches. Carabid beetles were used as model organisms as dispersal ability can easily be assessed on morphological traits. The proximity and heterogeneity of semi‐natural patches within the landscape were related to average local (alpha), between local (beta) and landscape (gamma) species richness and compared among four guilds that differ in dispersal ability. Results For species assemblages with low dispersal ability, local diversity increased as the proximity of semi‐natural habitat increased, while mobile species showed an opposite trend. Beta diversity decreased equally for all dispersal classes in relation to proximity, suggesting a homogenizing effect of increased patch isolation. In contrast, habitat diversity of the semi‐natural patches affected beta diversity positively only for less mobile species, probably due to the low dispersal ability of specialist species. Species with low mobility that persisted in highly fragmented landscapes were consistently present in less fragmented ones, resulting in nested assemblages for this mobility class only. Main conclusions The incorporation of dispersal ability reveals that only local species assemblages with low dispersal ability show a decrease of richness as a result of fragmentation. This local species loss is compensated at least in part by an increase in species with high dispersal ability, which obscures the effect of fragmentation when investigated across dispersal groups. Conversely, fragmentation homogenizes the landscape fauna for all dispersal groups, which indicates the invasion of non‐crop habitats by similar good dispersers across the whole landscape. Given that recolonization of low dispersers is unlikely, depletion of these species in modern agricultural landscapes appears temporally pervasive.     

The legacy of ice ages in mountain species: post‐glacial colonization of mountain tops rather than current range fragmentation determines mitochondrial genetic diversity in an endemic Pyrenean rock lizard

Aim The genetic impact of Quaternary climatic fluctuations on mountain endemic species has rarely been investigated. The Pyrenean rock lizard (Iberolacerta bonnali) is restricted to alpine habitats in the Pyrenees where it exhibits a highly fragmented distribution between massifs and between habitats within massifs. Using mitochondrial DNA markers, we set out: (1) to test whether several evolutionary units exist within the species; (2) to understand how the species persisted through the Last Glacial Maximum and whether the current range fragmentation originates from distribution shifts after the Last Glacial Maximum or from more ancient events; and (3) to investigate whether current mitochondrial diversity reflects past population history or current habitat fragmentation. Location The Pyrenees in south‐western France and northern Spain. Methods We used variation in the hypervariable left domain of the mitochondrial control region of 146 lizards collected in 15 localities, supplemented by cytochrome b sequences downloaded from GenBank to cover most of the species’ distribution range. Measures of population genetic diversity were contrasted with population isolation inferred from topography. Classical (F‐statistics) and coalescence‐based methods were used to assess the level of gene flow and estimate divergence time between populations. We used coalescence‐based simulations to test the congruence of our genetic data with a scenario of simultaneous divergence of current populations. Results Coalescence‐based analyses suggested that these peripheral populations diverged simultaneously at the end of the last glacial episode when their habitats became isolated on mountain summits. High mitochondrial diversity was found in peripheral, isolated populations, while the populations from the core of the species’ range were genetically impoverished. Where mitochondrial diversity has been retained, populations within the same massif exhibited high levels of genetic differentiation. Main conclusions As suggested for many other mountain species, the Pyrenean rock lizard survived glacial maxima through short‐distance range shifts instead of migration or contraction in distant southern refugia. Most of the main Pyrenean range has apparently been re‐colonized from a single or a few source populations, resulting in a loss of genetic diversity in re‐colonized areas. As a result, current levels of intra‐population mitochondrial diversity are better explained by post‐glacial population history than by current habitat fragmentation. Genetic population differentiation within massifs implies severe reduction in female‐mediated gene flow between patches of habitats.     

The effects of habitat fragmentation on the social kin structure and mating system of the agile antechinus, Antechinus agilis

Habitat fragmentation is one of the major contributors to the loss of biodiversity worldwide. However, relatively little is known about its more immediate impacts on within-patch population processes such as social structure and mating systems, whose alteration may play an important role in extinction risk. We investigated the impacts of habitat fragmentation due to the establishment of an exotic softwood plantation on the social kin structure and breeding system of the Australian marsupial carnivore, Antechinus agilis. Restricted dispersal by males in fragmented habitat resulted in elevated relatedness among potential mates in populations in fragments, potentially increasing the risk of inbreeding. Antechinus agilis nests communally in tree hollows; these nests are important points for social contact between males and females in the mating season. In response to elevated relatedness among potential mates in fragmented habitat, A. agilis significantly avoided sharing nests with opposite-sex relatives in large fragment sites (but not in small ones, possibly due to limited nest locations and small population sizes). Because opposite-sex individuals shared nests randomly with respect to relatedness in unfragmented habitat, we interpreted the phenomenon in fragmented habitat as a precursor to inbreeding avoidance via mate choice. Despite evidence that female A. agilis at high inbreeding risk selected relatively unrelated mates, there was no overall increased avoidance of related mates by females in fragmented habitats compared to unfragmented habitats. Simulations indicated that only dispersal, and not nonrandom mating, contributed to inbreeding avoidance in either habitat context. However, habitat fragmentation did influence the mating system in that the degree of multiple paternity was reduced due to the reduction in population sizes and population connectivity. This, in turn, reduced the number of males available to females in the breeding season. This suggests that in addition to the obvious impacts of reduced recruitment, patch recolonization and increased genetic drift, the isolation of populations in habitat patches may cause changes in breeding behaviour that contribute to the negative impacts of habitat fragmentation.