Effects of Culling on Mesopredator Population Dynamics

Anthropogenic changes in land use and the extirpation of apex predators have facilitated explosive growth of mesopredator populations. Consequently, many species have been subjected to extensive control throughout portions of their range due to their integral role as generalist predators and reservoirs of zoonotic disease. Yet, few studies have monitored the effects of landscape composition or configuration on the demographic or behavioral response of mesopredators to population manipulation. During 2007 we removed 382 raccoons (Procyon lotor) from 30 forest patches throughout a fragmented agricultural ecosystem to test hypotheses regarding the effects of habitat isolation on population recovery and role of range expansion and dispersal in patch colonization of mesopredators in heterogeneous landscapes. Patches were allowed to recolonize naturally and demographic restructuring of patches was monitored from 2008–2010 using mark-recapture. An additional 25 control patches were monitored as a baseline measure of demography. After 3 years only 40% of experimental patches had returned to pre-removal densities. This stagnant recovery was driven by low colonization rates of females, resulting in little to no within-patch recruitment. Colonizing raccoons were predominantly young males, suggesting that dispersal, rather than range expansion, was the primary mechanism driving population recovery. Contrary to our prediction, neither landscape connectivity nor measured local habitat attributes influenced colonization rates, likely due to the high dispersal capability of raccoons and limited role of range expansion in patch colonization. Although culling is commonly used to control local populations of many mesopredators, we demonstrate that such practices create severe disruptions in population demography that may be counterproductive to disease management in fragmented landscapes due to an influx of dispersing males into depopulated areas. However, given the slow repopulation rates observed in our study, localized depopulation may be effective at reducing negative ecological impacts of mesopredators in fragmented landscapes at limited spatial and temporal scales.     

Population Dynamics of the Andean Lizard Anolis heterodermus: Fast‐slow Demographic Strategies in Fragmented Scrubland Landscapes

Habitat fragmentation and loss affect population stability and demographic processes, increasing the extinction risk of species. We studied Anolis heterodermus populations inhabiting large and small Andean scrubland patches in three fragmented landscapes in the Sabana de Bogotá (Colombia) to determine the effect of habitat fragmentation and loss on population dynamics. We used the capture‐mark‐recapture method and multistate models to estimate vital rates for each population. We estimated growth population rate and the most important processes that affect λ by elasticity analysis of vital rates. We tested the effects of habitat fragmentation and loss on vital rates of lizard populations. All six isolated populations showed a positive or an equilibrium growth rate (λ = 1), and the most important demographic process affecting λ was the growth to first reproduction. Populations from landscapes with less scrubland natural cover showed higher stasis of young adults. Populations in highly fragmented landscapes showed highest juvenile survival and growth population rates. Independent of the landscape's habitat configuration and connectivity, populations from larger scrubland patches showed low adult survivorship, but high transition rates. Populations varied from a slow strategy with low growth and delayed maturation in smaller patches to a fast strategy with high growth and early maturation in large patches. This variation was congruent with the fast‐slow continuum hypothesis and has serious implications for Andean lizard conservation and management strategies. We suggest that more stable lizard populations will be maintained if different management strategies are adopted according to patch area and habitat structure.     

Unexpected persistence on habitat islands: genetic signatures reveal dispersal of a eucalypt-dependent marsupial through a hostile pine matrix

Several factors contribute to the extinction of populations in fragmented habitat but key ones include habitat loss and disruptions to connectivity. Aspects of the ecology of greater gliders (Petauroides volans), along with observations of their response to native forest clearance at a site in southeastern Australia, lead to the prediction in the 1960s that the species would not persist in the replacement exotic pine plantation. However, 35 years later, the species was observed in many remnant native vegetation patches retained within the plantation boundary, albeit at a lower occupancy rate than at matched continuous forest control sites. To determine the role of patch connectivity in persistence of P. volans in remnants, we employed 12 microsatellite markers to genotype individuals from 11 remnants, three contemporary nearby continuous native eucalypt forest sites and a sample collected during native vegetation clearance at the site in the 1960s. Patch samples retained substantially more genetic diversity than expected under an isolation model, suggesting that patches have experienced some immigration. Five putative patch immigrants--two from sampled sites 1- and 7-km distant, and three from unresolved or unsampled localities--were identified via genetic parentage and population assignment analyses. Patch populations displayed varying levels of admixture in Bayesian genetic structure analyses, with the oldest and most geographically isolated ones showing the least admixture, suggesting they have experienced relatively little immigration. Evidence of at least some immigration into patches may explain why P. volans has persisted contrary to expectation in heavily fragmented habitat.     

Genetic structure among remnant populations of a migratory passerine,the Northern Wheatear Oenanthe oenanthe

Continuous animal populations often become fragmented due to anthropogenic habitat alterations. These small, fragmented populations are fragile due to demographic and genetic factors, whereas immigration can enhance their long‐term viability. Previously, we showed that high philopatry affected the local dynamics of three small and remnant subpopulations of Northern Wheatears in The Netherlands. Here, we show that these three populations together with an additional larger population in the European lowlands are highly genetically differentiated based on 22 microsatellite markers. In contrast, we found no evidence for differentiation using two mitochondrial DNA markers. An IMa2 analysis indicates that gene flow has occurred regularly among our sampled populations. As immigration of colour‐ringed birds among our sampled populations is rare at best, our results suggest that the populations have recently become isolated from one another. Low dispersal rates in highly mobile birds may occur when suitable habitat becomes highly fragmented, and will accentuate stochastic demographic processes and inbreeding, both reducing population viability. As dispersal rates are low among populations of Northern Wheatears in The Netherlands, there is only a small probability of recolonization of habitat patches where populations have become locally extinct.     

Forest Fragmentation Alters the Population Dynamics of a Late‐successional Tropical Tree

Tropical late‐successional tree species are at high risk of local extinction due to habitat loss and fragmentation. Population‐growth rates in fragmented populations are predicted to decline as a result of reduced fecundity, survival and growth. We examined the demographic effects of habitat fragmentation by comparing the population dynamics of the late‐successional tree Poulsenia armata (Moraceae) in southern Mexico between a continuous forest and several forest fragments using integral projection models (IPMs) during 2010–2012. Forest fragmentation did not lead to differences in population density and even resulted in a higher population‐growth rate (λ) in fragments compared to continuous forests. Habitat fragmentation had drastic effects on the dynamics of P. armata, causing the population structure to shift toward smaller sizes. Fragmented populations experienced a significant decrease in juvenile survival and growth compared to unaltered populations. Adult survival and growth made the greatest relative contributions to λ in both habitat types during 2011–2012. However, the relative importance of juvenile survival and growth to λ was highest in the fragmented forest in 2010–2011. Our Life Table Response Experiment analysis revealed that positive contributions of adult fecundity explained most of the variation of λ between both habitats and annual periods. Finally, P. armata has a relatively slow speed of recovery after disturbances, compromising persistence of fragmented populations. Developing a mechanistic understanding of how forest fragmentation affects plant population dynamics, as done here, will prove essential for the preservation of natural areas.     

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

Although habitat loss and fragmentation threaten species throughout the world and are a major threat to biodiversity, it is apparent that some species are at greater risk of extinction in fragmented landscapes than others. Identification of these species and the characteristics that make them sensitive to habitat fragmentation has important implications for conservation management. Here, we present a comparative study of the population genetic structure of two arboreal gecko species (Oedura reticulata and Gehyra variegata) in fragmented and continuous woodlands. The species differ in their level of persistence in remnant vegetation patches (the former exhibiting a higher extinction rate than the latter). Previous demographic and modelling studies of these two species have suggested that their difference in persistence levels may be due, in part, to differences in dispersal abilities with G. variegata expected to have higher dispersal rates than O. reticulata. We tested this hypothesis and genotyped a total of 345 O. reticulata from 12 sites and 353 G. variegata from 13 sites at nine microsatellite loci. We showed that O. reticulata exhibits elevated levels of structure (FST=0.102 vs. 0.044), lower levels of genetic diversity (HE=0.79 vs. 0.88), and fewer misassignments (20% vs. 30%) than similarly fragmented populations of G. variegata, while all these parameters were fairly similar for the two species in the continuous forest populations (FST=0.003 vs. 0.004, HE=0.89 vs. 0.89, misassignments: 58% vs. 53%, respectively). For both species, genetic structure was higher and genetic diversity was lower among fragmented populations than among those in the nature reserves. In addition, assignment tests and spatial autocorrelation revealed that small distances of about 500 m through fragmented landscapes are a barrier to O. reticulata but not for G. variegata. These data support our hypothesis that G. variegata disperse more readily and more frequently than O. reticulata and that dispersal and habitat specialization are critical factors in the persistence of species in habitat remnants.     

Spatial explicit demography: The effects habitat patch isolation have on vole matrilines

Populations of many species are spatially structured in matrilines, and their dynamics may be determined by matriline specific demographic processes. We examined whether the isolation of habitat patches (i.e. interpatch distance) affected the demography of matrilines in 14 experimentally fragmented populations of the root vole. Matrilines inhabiting the most isolated patches decreased in size over the breeding season, while matrilines in less isolated patches increased. The survival rate of adult females was the main factor underlying the variation in growth rates among matrilines. Low survival when patches were isolated seemed to be due to long-distance interpatch movements exposing females to increased predation rate.
The differential success of matrilines in patchy populations with variable interpatch distances acted to decrease the matrilineal diversity at the population level. Furthermore, isolated patches may function as sinks. Thus spatially explicit landscape features may affect both population demography and genetics.     

Life history of the Glanville fritillary butterfly in fragmented versus continuous landscapes

Habitat loss and fragmentation threaten the long‐term viability of innumerable species of plants and animals. At the same time, habitat fragmentation may impose strong natural selection and lead to evolution of life histories with possible consequences for demographic dynamics. The Baltic populations of the Glanville fritillary butterfly (Melitaea cinxia) inhabit regions with highly fragmented habitat (networks of small dry meadows) as well as regions with extensive continuous habitat (calcareous alvar grasslands). Here, we report the results of common garden studies on butterflies originating from two highly fragmented landscapes (FL) in Finland and Sweden and from two continuous landscapes (CL) in Sweden and Estonia, conducted in a large outdoor cage (32 by 26 m) and in the laboratory. We investigated a comprehensive set of 51 life‐history traits, including measures of larval growth and development, flight performance, and adult reproductive behavior. Seventeen of the 51 traits showed a significant difference between fragmented versus CL. Most notably, the growth rate of postdiapause larvae and several measures of flight capacity, including flight metabolic rate, were higher in butterflies from fragmented than CL. Females from CL had shorter intervals between consecutive egg clutches and somewhat higher life‐time egg production, but shorter longevity, than females from FL. These results are likely to reflect the constant opportunities for oviposition in females living in continuous habitats, while the more dispersive females from FL allocate more resources to dispersal capacity at the cost of egg maturation rate. This study supports theoretical predictions about small population sizes and high rate of population turnover in fragmented habitats selecting for increased rate of dispersal, but the results also indicate that many other life‐history traits apart from dispersal are affected by the degree of habitat fragmentation.     

Demographic response of plant populations to habitat fragmentation and temporal environmental variability

Many plant species currently exist in fragmented populations of different sizes, while they also experience unpredictable climatic fluctuation over time. However, we still understand little about how plant demography responds to such spatial and temporal environmental variability. We studied population dynamics of an understory perennial herb Trillium camschatcense in the Tokachi plain of Hokkaido, Japan, where a significant effect of forest fragmentation on seedling recruitment was previously reported. Four populations across a range of fragment sizes were studied for 6 years, and the data were analyzed using matrix population models. Per capita fecundity (the number of recruits per plant) varied greatly among populations, but the variation in population growth rates (λ) was mainly driven by the variation in stasis and growth rates, suggesting that the general trend of reduced fecundity in fragmented populations may not be readily translated into subsequent dynamics. Temporal variation in λ among years was more than 2 times larger than spatial variation among populations, and this result was likely attributable to the contrasting response of correlation structures among demographic rates. The among-population variation in λ was dampened by negative covariation between matrix elements possibly due to density-dependent regulation as well as an inherent constraint that some elements are not independent, whereas positive covariation between matrix elements resulted in large temporal variation in λ. Our results show that population dynamics responded differently to habitat fragmentation and temporal variability of the environment, emphasizing the need to discriminate these spatial and temporal variations in demographic models. Although no populations were projected to be declining in stochastic simulations, correlation between current habitat size and plant density implies historical λ is positively related to habitat size.     

Distribution, stand characteristics and habitat of a critically endangered plant Euryodendron excelsum H. T. Chang (Theaceae): implications for conservation

In the present study, the distribution, population size and structure, habitat and stand disturbance of a critically endangered plant Euryodendron excelsum H. T. Chang were examined using field investigations. A total of 179 individual plants, including 23 adult trees, were found. The population was distributed in 10 highly isolated and fragmented patches. Half of the 10 patches had less than 10 individual plants and two patches had only one remnant adult; there were no adult plants in two of the patches. Although the overall population structure trends to a reversed 'J' shape, two fragile stages of E. excelsum limit its natural recruitment and regeneration: seed germination and seedling growth toward adulthood. The major threats for the survival of this species are its specific small population size and the high frequency of anthropogenic destruction. Based on the results, some strategies were put forward for the conservation of E. excelsum populations.     

Transcriptome Analysis Reveals Signature of Adaptation to Landscape Fragmentation

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic rate and dispersal rate in the field, and higher larval growth rate, than butterflies from continuous landscapes. In fragmented landscapes, local populations are small and have a high risk of local extinction, and hence the long-term persistence at the landscape level is based on frequent re-colonization of vacant habitat patches, which is predicted to select for increased dispersal rate. Using RNA-seq data and a common garden experiment, we found that a large number of genes (1,841) were differentially expressed between the landscape types. Hexamerin genes, the expression of which has previously been shown to have high heritability and which correlate strongly with larval development time in the Glanville fritillary, had higher expression in fragmented than continuous landscapes. Genes that were more highly expressed in butterflies from newly-established than old local populations within a fragmented landscape were also more highly expressed, at the landscape level, in fragmented than continuous landscapes. This result suggests that recurrent extinctions and re-colonizations in fragmented landscapes select a for specific expression profile. Genes that were significantly up-regulated following an experimental flight treatment had higher basal expression in fragmented landscapes, indicating that these butterflies are genetically primed for frequent flight. Active flight causes oxidative stress, but butterflies from fragmented landscapes were more tolerant of hypoxia. We conclude that differences in gene expression between the landscape types reflect genomic adaptations to landscape fragmentation.     

Population genetics of chamois in the contact zone between the Alps and the Dinaric Mountains: uncovering the role of habitat fragmentation and past management

The chamois is a habitat specialist ungulate occupying “continental archipelagos” of fragmented rocky habitats which are frequently restricted to high altitudes. It is not clear whether forest habitats separating such population fragments act as barriers to gene flow. We studied the genetic makeup of the chamois in a topographically diverse landscape at the contact zone of two mountain ranges in Slovenia. Based on sequences of mitochondrial DNA, all Slovenian populations belong to a Northern chamois (Rupicapra r. rupicapra) subspecies. The range of chamois in Slovenia encompasses three different regions, each with unique topography, habitat connectivity and abundance of chamois: the Alps, the Dinaric Mts., and the Pohorje Mts. The habitat of the chamois is extensive and more or less continuous in the Alps, but suboptimal and fragmented in the remaining regions. In agreement with neutral genetic theory, large Northern chamois populations tended to have higher allelic richness and observed heterozygosity. Spatial clustering bears the differentiation into four geographically associated clusters within Slovenia and also revealed a strong substructure within all mountain ranges with suboptimal chamois habitat. Surprisingly, some small Dinaric populations have stayed genetically isolated in restricted habitat patches, even if they are geographically very close to each other. The four clusters, each having a unique demographic history, should be regarded as independent units for management purposes.     

Metapopulation Persistence in Random Fragmented Landscapes

Habitat destruction and land use change are making the world in which natural populations live increasingly fragmented, often leading to local extinctions. Although local populations might undergo extinction, a metapopulation may still be viable as long as patches of suitable habitat are connected by dispersal, so that empty patches can be recolonized. Thus far, metapopulations models have either taken a mean-field approach, or have modeled empirically-based, realistic landscapes. Here we show that an intermediate level of complexity between these two extremes is to consider random landscapes, in which the patches of suitable habitat are randomly arranged in an area (or volume). Using methods borrowed from the mathematics of Random Geometric Graphs and Euclidean Random Matrices, we derive a simple, analytic criterion for the persistence of the metapopulation in random fragmented landscapes. Our results show how the density of patches, the variability in their value, the shape of the dispersal kernel, and the dimensionality of the landscape all contribute to determining the fate of the metapopulation. Using this framework, we derive sufficient conditions for the population to be spatially localized, such that spatially confined clusters of patches act as a source of dispersal for the whole landscape. Finally, we show that a regular arrangement of the patches is always detrimental for persistence, compared to the random arrangement of the patches. Given the strong parallel between metapopulation models and contact processes, our results are also applicable to models of disease spread on spatial networks.     

Fine-scale spatial genetic structure within continuous and fragmented populations of Trillium camschatcense

Spatial genetic structure (SGS) within populations was analyzed for the ling-lived understory perennial herb Trillium camschatcense using allozyme loci. We used Sp statistics to compare SGS between 2 life-history stages, juveniles (J) and reproductives (R), as well as between 2 populations, continuous and fragmented, with different habitat conditions. In the continuous population, significant SGS was detected in both stages but the extent was greatly reduced with the progress of the stage (J, Sp = 0.0475; R, Sp = 0.0053). We inferred that limited seed dispersal and subsequent random loss of individuals from the family patches are responsible for the J and R stage structures, respectively. The fragmented population differed in the patterns of SGS; significant structure was detected in the R stage, but not in the J stage (J, Sp = 0.0021; R, Sp = 0.0165) despite significant positive inbreeding coefficients (J, F(IS) = 0.251). The observed differences in the J-stage structures between populations may be explained by habitat fragmentation effects because reduced recruitment in the fragmented population prevents the development of maternal sibling cohort. Such comparative analysis between populations and life-history stages can be useful to understand the different underlying causes of SGS.     

生境片断化对植物种群遗传结构的影响及植物遗传多样性保护

生境片断化是指大而连续的生境变成空间隔离的小种群的现象。生境片断化对植物种群遗传效应包括生境片断化过程中的取样效应及其后的小种群效应（遗传漂变、近交等）。理论研究表明,生境片断化后,植物种群的遗传变异程度将降低,而残留的小种群间的遗传分化程度将升高。然而对一些植物的研究表明,生境片断化对植物种群的遗传效应要受其他一些因素的影响,如世代长度、片断化时间、片断种群的大小、基因流的改变等。最后,针对生境     

Habitat quality of source patches and connectivity in fragmented landscapes

Because spatial connectivity is critical to dispersal success and persistence of species in highly fragmented landscapes, the way that we envision and measure connectivity is consequential for biodiversity conservation. Connectivity metrics used for predictive modeling of spatial turnover and patch occupancy for metapopulations, such as with Incidence Function Models (IFM), incorporate distances to and sizes of possible source populations. Here, our focus is on whether habitat quality of source patches also is considered in these connectivity metrics. We propose that effective areas (weighted by habitat quality) of source patches should be better surrogates for population size and dispersal potential compared to unadjusted patch areas. Our review of a representative sample of the literature revealed that only 12.5% of studies incorporated habitat quality of source patches into IFM-type connectivity metrics. Quality of source patches generally was not taken into account in studies even if habitat quality of focal patches was included in analyses. We provide an empirical example for a metapopulation of a rare wetland species, the round-tailed muskrat (Neofiber alleni), demonstrating that a connectivity metric based on effective areas of source patches better predicts patch colonization and occupancy than a metric that used simple patch areas. The ongoing integration of landscape ecology and metapopulation dynamics could be hastened by incorporating habitat quality of source patches into spatial connectivity metrics applied to species conservation in fragmented landscapes.     

The effect of habitat fragmentation on dispersal patterns, mating behavior, and genetic variation in a pika (Ochotona princeps) metapopulation

 Habitat fragmentation is becoming increasingly common, yet, the effect of habitat spatial structure on population dynamics remains undetermined for most species. Populations of a single species found in fragmented and nonfragmented habitat present a rare opportunity to examine the effect of habitat spatial structure on population dynamics. This study investigates the impact of highly fragmented habitat on dispersal patterns, mating behavior, and genetic variation in a pika (Ochotona princeps) population with a mainland-island spatial structure. Juvenile dispersal patterns in fragmented habitat revealed that individuals tended to disperse to neighboring habitat patches. However, within-patch band-sharing scores from multilocus DNA fingerprints did not differ from what would be expected if individuals were assorting randomly among habitat patches each year. Multiple, short-distance dispersal targets for juveniles and occasional long-distance dispersal events suggest that habitat fragmentation on this scale has not resulted in restricted dispersal and a genetically subdivided population. Although pikas tended to mate with the closest available partner, DNA fingerprinting band-sharing scores between mated pairs were consistent with a random mating hypothesis. Random mating in this population appears to be an incidental effect of dispersal in a fragmented habitat. This pattern is distinct from that found in nonfragmented habitat (large talus patches) where mating was non-random and consistent with mating between individuals of intermediate relatedness. DNA fingerprinting data revealed within-species variation in the mating habits of the pika directly attributable to habitat spatial structure. Received: 4 November 1996 / Accepted: 30 June 1997     

Anthropogenic landscape change promotes asymmetric dispersal and limits regional patch occupancy in a spatially structured bird population

1. Local extinctions in habitat patches and asymmetric dispersal between patches are key processes structuring animal populations in heterogeneous environments. Effective landscape conservation requires an understanding of how habitat loss and fragmentation influence demographic processes within populations and movement between populations. 2. We used patch occupancy surveys and molecular data for a rainforest bird, the logrunner (Orthonyx temminckii), to determine (i) the effects of landscape change and patch structure on local extinction; (ii) the asymmetry of emigration and immigration rates; (iii) the relative influence of local and between-population landscapes on asymmetric emigration and immigration; and (iv) the relative contributions of habitat loss and habitat fragmentation to asymmetric emigration and immigration. 3. Whether or not a patch was occupied by logrunners was primarily determined by the isolation of that patch. After controlling for patch isolation, patch occupancy declined in landscapes experiencing high levels of rainforest loss over the last 100 years. Habitat loss and fragmentation over the last century was more important than the current pattern of patch isolation alone, which suggested that immigration from neighbouring patches was unable to prevent local extinction in highly modified landscapes. 4. We discovered that dispersal between logrunner populations is highly asymmetric. Emigration rates were 39% lower when local landscapes were fragmented, but emigration was not limited by the structure of the between-population landscapes. In contrast, immigration was 37% greater when local landscapes were fragmented and was lower when the between-population landscapes were fragmented. Rainforest fragmentation influenced asymmetric dispersal to a greater extent than did rainforest loss, and a 60% reduction in mean patch area was capable of switching a population from being a net exporter to a net importer of dispersing logrunners. 5. The synergistic effects of landscape change on species occurrence and asymmetric dispersal have important implications for conservation. Conservation measures that maintain large patch sizes in the landscape may promote asymmetric dispersal from intact to fragmented landscapes and allow rainforest bird populations to persist in fragmented and degraded landscapes. These sink populations could form the kernel of source populations given sufficient habitat restoration. However, the success of this rescue effect will depend on the quality of the between-population landscapes.     

From individual behavior to metapopulation dynamics: unifying the patchy population and classic metapopulation models

Spatially structured populations in patchy habitats show much variation in migration rate, from patchy populations in which individuals move repeatedly among habitat patches to classic metapopulations with infrequent migration among discrete populations. To establish a common framework for population dynamics in patchy habitats, we describe an individual-based model (IBM) involving a diffusion approximation of correlated random walk of individual movements. As an example, we apply the model to the Glanville fritillary butterfly (Melitaea cinxia) inhabiting a highly fragmented landscape. We derive stochastic patch occupancy model (SPOM) approximations for the IBMs assuming pure demographic stochasticity, uncorrelated environmental stochasticity, or completely correlated environmental stochasticity in local dynamics. Using realistic parameter values for the Glanville fritillary, we show that the SPOMs mimic the behavior of the IBMs well. The SPOMs derived from IBMs have parameters that relate directly to the life history and behavior of individuals, which is an advantage for model interpretation and parameter estimation. The modeling approach that we describe here provides a unified framework for patchy populations with much movements among habitat patches and classic metapopulations with infrequent movements.     

Genetic structure,diversity and distribution of a threatened lizard affected by widespread habitat fragmentation

Understanding the demographic consequences of habitat loss on populations is essential for the conservation of threatened species. The threatened swamp skink (Lissolepis coventryi) is restricted to fragmented wetland habitats in Victoria and southeast South Australia. It has experienced significant habitat loss in the last 150 years, particularly around the Melbourne metropolitan area, where several small and isolated populations remain. Using mtDNA and nuDNA SNPs, we examined distribution patterns and population structure to infer evolutionary history and genetic distinctiveness of populations throughout the species’ range. For populations in the Melbourne metropolitan area, we examined genetic diversity. We found the species to be highly divergent, separating into two distinct lineages to the east and west of Melbourne, likely due to geological and climate influences causing isolation of populations. Species’ detectability was low, particularly in the far east despite relatively intact habitat and presumed higher abundance. Melbourne populations showed signs of limited genetic diversity. We suggest that translocations to promote gene diversity amongst these populations, together with habitat restoration and protection, present an important management strategy for L. coventryi.