The genetic basis of the plumage polymorphism in red-footed boobies (Sula sula): a melanocortin-1 receptor (MC1R) analysis

The red-footed booby (Sula sula) is considered one of the most polymorphic seabirds, with 3 recognized major adult plumage types: 1) white, 2) white-tailed brown, and 3) brown and several degrees of intermediates. Here we show that the white/melanic polymorphism observed in this species is perfectly associated with 2 point substitutions, Val85Met and His207Arg, at the melanocortin-1 receptor (MC1R) gene. Among the melanic plumage variants, we also found a strong association between the degree of melanism and the number of copies of variant MC1R alleles. Furthermore, the Val85Met point substitution has been previously shown to be associated with melanic phenotypes in the lesser snow goose (Anser c. caerulescens), suggesting parallel evolution of the melanic allele, and hence, melanism, between these 2 distantly related species. We also compared the MC1R locus in red-footed boobies with a nonpolymorphic congener, the Nazca booby (Sula granti), in which all adults are white. We found that Nazca boobies present the same genotype at sites 85 and 207 as white morph red-footed boobies.     

Phylogeography of Sula: the role of physical barriers to gene flow in the diversification of tropical seabirds

We examined mitochondrial cytochrome b sequence variation in masked Sula dactylatra , red-footed S. sula , and brown S. leucogaster boobies sampled from islands in the central and eastern Pacific Ocean and in the Caribbean Sea. Each species showed a different phylogeographic pattern. Whereas haplotypes in masked and red-footed boobies were shared across the central and eastern Pacific (i.e., across the Eastern Pacific Basin), brown booby haplotypes were not shared across the Eastern Pacific Basin. Although most masked booby haplotypes from the Pacific were distinct from those in the Caribbean, one haplotype was shared across the Isthmus of Panama. Red-footed and brown boobies, however, did not share haplotypes across the Isthmus of Panama. We estimate that divergence of these regional populations occurred within the last 560,000 years. Thus, the Isthmus of Panama and the Eastern Pacific Basin (albeit to a lesser degree) appear to have played a role in the diversification of these species.     

Population genetic structure in Atlantic and Pacific Ocean common murres (Uria aalge): natural replicate tests of post‐Pleistocene evolution

Understanding the factors that influence population differentiation in temperate taxa can be difficult because the signatures of both historic and contemporary demographics are often reflected in population genetic patterns. Fortunately, analyses based on coalescent theory can help untangle the relative influence of these historic and contemporary factors. Common murres (Uria aalge) are vagile seabirds that breed in the boreal and low arctic waters of the Northern Hemisphere. Previous analyses revealed that Atlantic and Pacific populations are genetically distinct; however, less is known about population genetic structure within ocean basins. We employed the mitochondrial control region, four microsatellite loci and four intron loci to investigate population genetic structure throughout the range of common murres. As in previous studies, we found that Atlantic and Pacific populations diverged during the Pleistocene and do not currently exchange migrants. Therefore, Atlantic and Pacific murre populations can be used as natural replicates to test mechanisms of population differentiation. While we found little population genetic structure within the Pacific, we detected significant east–west structuring among Atlantic colonies. The degree that population genetic structure reflected contemporary population demographics also differed between ocean basins. Specifically, while the low levels of population differentiation in the Pacific are at least partially due to high levels of contemporary gene flow, the east–west structuring of populations within the Atlantic appears to be the result of historic fragmentation of populations rather than restricted contemporary gene flow. The contrasting results in the Atlantic and Pacific Oceans highlight the necessity of carefully considering multilocus nonequilibrium population genetic approaches when reconstructing the demographic history of temperate Northern Hemisphere taxa.     

Philopatry drives genetic differentiation in an island archipelago: comparative population genetics of Galapagos Nazca boobies (Sula granti) and great frigatebirds (Fregata minor)

Seabirds are considered highly mobile, able to fly great distances with few apparent barriers to dispersal. However, it is often the case that seabird populations exhibit strong population genetic structure despite their potential vagility. Here we show that Galapagos Nazca booby (Sula granti) populations are substantially differentiated, even within the small geographic scale of this archipelago. On the other hand, Galapagos great frigatebird (Fregata minor) populations do not show any genetic structure. We characterized the genetic differentiation by sampling five colonies of both species in the Galapagos archipelago and analyzing eight microsatellite loci and three mitochondrial genes. Using an F‐statistic approach on the multilocus data, we found significant differentiation between nearly all island pairs of Nazca booby populations and a Bayesian clustering analysis provided support for three distinct genetic clusters. Mitochondrial DNA showed less differentiation of Nazca booby colonies; only Nazca boobies from the island of Darwin were significantly differentiated from individuals throughout the rest of the archipelago. Great frigatebird populations showed little to no evidence for genetic differentiation at the same scale. Only two island pairs (Darwin – Wolf, N. Seymour – Wolf) were significantly differentiated using the multilocus data, and only two island pairs had statistically significant φ_ST values (N. Seymour – Darwin, N. Seymour – Wolf) according to the mitochondrial data. There was no significant pattern of isolation by distance for either species calculated using both markers. Seven of the ten Nazca booby migration rates calculated between island pairs were in the south or southeast to north or northwest direction. The population differentiation found among Galapagos Nazca booby colonies, but not great frigatebird colonies, is most likely due to differences in natal and breeding philopatry.     

Mechanisms of global diversification in the brown booby (Sula leucogaster) revealed by uniting statistical phylogeographic and multilocus phylogenetic methods

Recent theoretical and empirical research suggests that statistical models based on coalescent theory can improve both phylogeographic and phylogenetic inference. An approach that involves elements of both statistical phylogeography (e.g. Isolation with Migration analyses) and multilocus phylogenetic inference (e.g. *beast) may be particularly useful when applied to populations with relatively old divergence times. Here, we use such an approach in the globally distributed brown booby (Sula leucogaster). We sampled 215 individuals from all major breeding areas and genotyped them at eight microsatellite and three nuclear intron loci. We found that brown booby populations were highly differentiated and that colonies can be grouped into four major genetic populations (Caribbean Sea, Central Atlantic Ocean, Indo-Central Pacific and Eastern Pacific). These populations apparently diverged in the absence of gene flow and, with one exception, currently exchange few to no migrants. The Eastern Pacific population diverged from all other populations approximately one million years ago [90% highest posterior density: 330,000-2,000,000 years ago] and exhibits a distinct male plumage, relative to other populations. However, recent gene flow from the Indo-Central Pacific into the Eastern Pacific appears to have occurred, suggesting that approximately one million years of genetic isolation and divergence in male plumage colour are not sufficient to prevent interbreeding. Gene flow following secondary contact of the Indo-Central Pacific and Eastern Pacific populations was not detected in previous mitochondrial DNA (mtDNA) studies, and the contrast between the mtDNA results and our current results highlights the advantage of a multilocus phylogeographic approach.     

A role for nonphysical barriers to gene flow in the diversification of a highly vagile seabird, the masked booby (Sula dactylatra)

To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low-latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies (Sula dactylatra). In accord with previous studies, we found that Indo-Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo-Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher-level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher-level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo-Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo-Pacific populations. We estimate that Indo-Pacific masked boobies experienced rapid population growth approximately 180,000 years ago and that the majority of Indo-Pacific and Atlantic populations diverged within the last approximately 115,000 years. These combined data suggest that the predominant pattern between Indo-Pacific and Atlantic populations is long-term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.     

Could specialization to cold‐water upwelling systems influence gene flow and population differentiation in marine organisms? A case study using the blue‐footed booby,Sula nebouxii

Aim We assessed population differentiation and gene flow across the range of the blue‐footed booby (Sula nebouxii) (1) to test the generality of the hypothesis that tropical seabirds exhibit higher levels of population genetic differentiation than their northern temperate counterparts, and (2) to determine if specialization to cold‐water upwelling systems increases dispersal, and thus gene flow, in blue‐footed boobies compared with other tropical sulids. Location Work was carried out on islands in the eastern tropical Pacific Ocean from Mexico to northern Peru. Methods We collected samples from 173 juvenile blue‐footed boobies from nine colonies spanning their breeding distribution and used molecular markers (540 base pairs of the mitochondrial control region and seven microsatellite loci) to estimate population genetic differentiation and gene flow. Our analyses included classic population genetic estimation of pairwise population differentiation, population growth, isolation by distance, associations between haplotypes and geographic locations, and analysis of molecular variance, as well as Bayesian analyses of gene flow and population differentiation. We compared our results with those for other tropical seabirds that are not specialized to cold‐water upwellings, including brown (Sula leucogaster), red‐footed (S. sula) and masked (S. dactylatra) boobies. Results Blue‐footed boobies exhibited weak global population differentiation at both mitochondrial and nuclear loci compared with all other tropical sulids. We found evidence of high levels of gene flow between colonies within Mexico and between colonies within the southern portion of the range, but reduced gene flow between these regions. We also found evidence for population growth, isolation by distance and weak phylogeographic structure. Main conclusions Tropical seabirds can exhibit weak genetic differentiation across large geographic distances, and blue‐footed boobies exhibit the weakest population differentiation of any tropical sulid studied thus far. The weak population genetic structure that we detected in blue‐footed boobies may be caused by increased dispersal, and subsequently increased gene flow, compared with other sulids. Increased dispersal by blue‐footed boobies may be the result of the selective pressures associated with cold‐water upwelling systems, to which blue‐footed boobies appear specialized. Consideration of foraging environment may be particularly important in future studies of marine biogeography.     

Amplicon sequencing of 42 nuclear loci supports directional gene flow between South Pacific populations of a hydrothermal vent limpet

In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity and population demography in marine environments. Studies of deep‐sea hydrothermal vent populations have identified barriers to gene flow, hybrid zones, and demographic events, such as historical population expansions and contractions. These deep‐sea studies, however, used few loci, which limit the amount of information they provided for coalescent analysis and thus our ability to confidently test complex population dynamics scenarios. In this study, we investigated population structure, demographic history, and gene flow directionality among four Western Pacific hydrothermal vent populations of the vent limpet Lepetodrilus aff. schrolli. These vent sites are located in the Manus and Lau back‐arc basins, currently of great interest for deep‐sea mineral extraction. A total of 42 loci were sequenced from each individual using high‐throughput amplicon sequencing. Amplicon sequences were analyzed using both genetic variant clustering methods and evolutionary coalescent approaches. Like most previously investigated vent species in the South Pacific, L. aff. schrolli showed no genetic structure within basins but significant differentiation between basins. We inferred significant directional gene flow from Manus Basin to Lau Basin, with low to no gene flow in the opposite direction. This study is one of the very few marine population studies using >10 loci for coalescent analysis and serves as a guide for future marine population studies.     

Global population genetic structure and male-mediated gene flow in the green sea turtle (Chelonia mydas): analysis of microsatellite loci

We assessed the degree of population subdivision among global populations of green sea turtles, Chelonia mydas, using four microsatellite loci. Previously, a single-copy nuclear DNA study indicated significant male-mediated gene flow among populations alternately fixed for different mitochondrial DNA haplotypes and that genetic divergence between populations in the Atlantic and Pacific Oceans was more common than subdivisions among populations within ocean basins. Even so, overall levels of variation at single-copy loci were low and inferences were limited. Here, the markedly more variable microsatellite loci confirm the presence of male-mediated gene flow among populations within ocean basins. This analysis generally confirms the genetic divergence between the Atlantic and Pacific. As with the previous study, phylogenetic analyses of genetic distances based on the microsatellite loci indicate a close genetic relationship among eastern Atlantic and Indian Ocean populations. Unlike the single-copy study, however, the results here cannot be attributed to an artifact of general low variability and likely represent recent or ongoing migration between ocean basins. Sequence analyses of regions flanking the microsatellite repeat reveal considerable amounts of cryptic variation and homoplasy and significantly aid in our understanding of population connectivity. Assessment of the allele frequency distributions indicates that at least some of the loci may not be evolving by the stepwise mutation model.     

Evidence for Asymmetrical Divergence-Gene Flow of Nuclear Loci,but Not Mitochondrial Loci,between Seabird Sister Species: Blue-Footed (Sula nebouxii) and Peruvian (S. variegata) Boobies

Understanding the process of speciation requires understanding how gene flow influences divergence. Recent analyses indicate that divergence can take place despite gene flow and that the sex chromosomes can exhibit different levels of gene flow than autosomes and mitochondrial DNA. Using an eight marker dataset including autosomal, z-linked, and mitochondrial loci we tested the hypothesis that blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies diverged from their common ancestor with gene flow, paying specific attention to the differences in gene flow estimates from nuclear and mitochondrial markers. We found no gene flow at mitochondrial markers, but found evidence from the combined autosomal and z-linked dataset that blue-footed and Peruvian boobies experienced asymmetrical gene flow during or after their initial divergence, predominantly from Peruvian boobies into blue-footed boobies. This gene exchange may have occurred either sporadically between periods of allopatry, or regularly throughout the divergence process. Our results add to growing evidence that diverging species can remain distinct but exchange genes.     

Connectivity and gene flow among Eastern Tiger Salamander (Ambystoma tigrinum) populations in highly modified anthropogenic landscapes

Fragmented landscapes resulting from anthropogenic habitat modification can have significant impacts on dispersal, gene flow, and persistence of wildlife populations. Therefore, quantifying population connectivity across a mosaic of habitats in highly modified landscapes is critical for the development of conservation management plans for threatened populations. Endangered populations of the eastern tiger salamander (Ambystoma tigrinum) in New York and New Jersey are at the northern edge of the species’ range and remaining populations persist in highly developed landscapes in both states. We used landscape genetic approaches to examine regional genetic population structure and potential barriers to migration among remaining populations. Despite the post-glacial demographic processes that have shaped genetic diversity in tiger salamander populations at the northern extent of their range, we found that populations in each state belong to distinct genetic clusters, consistent with the large geographic distance that separates them. We detected overall low genetic diversity and high relatedness within populations, likely due to recent range expansion, isolation, and relatively small population sizes. Nonetheless, landscape connectivity analyses reveal habitat corridors among remaining breeding ponds. Furthermore, molecular estimates of population connectivity among ponds indicate that gene flow still occurs at regional scales. Further fragmentation of remaining habitat will potentially restrict dispersal among breeding ponds, cause the erosion of genetic diversity, and exacerbate already high levels of inbreeding. We recommend the continued management and maintenance of habitat corridors to ensure long-term viability of these endangered populations.     

Population structure of the dusky pipefish (Syngnathus floridae) from the Atlantic and Gulf of Mexico,as revealed by mitochondrial DNA and microsatellite analyses

Aim To elucidate the historical phylogeography of the dusky pipefish (Syngnathus floridae) in the North American Atlantic and Gulf of Mexico ocean basins. Location Southern Atlantic Ocean and northern Gulf of Mexico within the continental United States. Methods A 394‐bp fragment of the mitochondrial cytochrome b gene and a 235‐bp fragment of the mitochondrial control region were analysed from individuals from 10 locations. Phylogenetic reconstruction, haplotype network, mismatch distributions and analysis of molecular variance were used to infer population structure between ocean basins and time from population expansion within ocean basins. Six microsatellite loci were also analysed to estimate population structure and gene flow among five populations using genetic distance methods (F_ST, Nei’s genetic distance), isolation by distance (Mantel’s test), coalescent‐based estimates of genetic diversity and migration patterns, Bayesian cluster analysis and bottleneck simulations. Results Mitochondrial analyses revealed significant structuring between ocean basins in both cytochrome b (Φ_ST = 0.361, P < 0.0001; Φ_CT = 0.312, P < 0.02) and control region (Φ_ST = 0.166, P < 0.0001; Φ_CT = 0.128, P < 0.03) sequences. However, phylogenetic reconstructions failed to show reciprocal monophyly in populations between ocean basins. Microsatellite analyses revealed significant population substructuring between all locations sampled except for the two locations that were in closest proximity to each other (global F_ST value = 0.026). Bayesian analysis of microsatellite data also revealed significant population structuring between ocean basins. Coalescent‐based analyses of microsatellite data revealed low migration rates among all sites. Mismatch distribution analysis of mitochondrial loci supports a sudden population expansion in both ocean basins in the late Pleistocene, with the expansion of Atlantic populations occurring more recently. Main conclusions Present‐day populations of S. floridae do not bear the mitochondrial DNA signature of the strong phylogenetic discontinuity between the Atlantic and Gulf coasts of North America commonly observed in other species. Rather, our results suggest that Atlantic and Gulf of Mexico populations of S. floridae are closely related but nevertheless exhibit local and regional population structure. We conclude that the present‐day phylogeographic pattern is the result of a recent population expansion into the Atlantic in the late Pleistocene, and that life‐history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.     

Genetic characterization of brown meagre (Sciaena umbra) and Shi Drum (Umbrina cirrosa) populations

This study analyzed population structure of fish, brown meagre (Sciaena umbra) and Shi drum (Umbrina cirrosa) from the Black Sea, the Aegean Sea, and the Mediterranean Sea. The Cytb and 16S rRNA genes of Shi drum and brown meagre fish were sequenced. In brown meagre and Shi drum, 25 and 20 haplotypes, respectively, of Cytb gene were identified; while for 16S rRNA, 4 and 8 haplotypes were identified. Nucleotide diversities of 16S rRNA and Cytb gene sites were found to be 83.8% and 52.6%, respectively, for brown meagre; while that for Shi drum were of 80.5% and 73.6%, respectively. There was a significant relationship between geographic distance and the genetic distance of the fish. Since Shi drum and brown meagre are migratory species, they can migrate between the seas. The lack of barriers among different populations facilitates the gene flow among the populations belonging to different regions. Since there is no information available on Shi drum and brown meagre population genetics, this study may be useful to understand the genetic diversity of these species to assist fishery managers for the management of these resources in terms of conservation and sustainability.     

Genetic structure of brown trout, salmo trutta l., at the southern limit of the distribution range of the anadromous form

Genetic variation at 33 protein loci was investigated in 41 wild brown trout populations from four river basins in Galicia (northwest Spain) to analyse the amount and distribution of genetic diversity in a marginal area, located in the distribution limit of the anadromous form of this species. The genetic diversity detected within populations (H between 0 and 6%) lies within the range quoted for this species in previous reports. The Mino, the most southern river basin analysed, showed a significantly lower genetic diversity and the highest genetic differentiation among the river basins studied. The hierarchical gene diversity analysis showed high population differentiation in a restricted area (GST = 27%), mostly due to differences among populations within basins (GSC = 22%). The reduction of GST observed when the isolated samples were excluded from the analysis (GST = 17%) showed the importance of habitat fragmentation on the heterogeneity detected. Gene flow among populations was comparatively evaluated by three indirect methods, which in general revealed low figures of absolute number of migrants per generation, slightly higher than 1. The gene flow among basins reflected a positive relationship with geographical distance. This trend was confirmed by the significant correlation observed between geographical and genetic distances, including all population pairs, which suggests a component of isolation by distance in brown trout genetic structure. Nevertheless, the nonsignificant intrabasin correlation demonstrates the complexity of genetic relationships among populations in this species. The model of genetic structure in brown trout is discussed in the light of the results obtained.     

The Isthmus of Panama: a major physical barrier to gene flow in a highly mobile pantropical seabird

To further test the hypothesis that the Isthmus of Panama is a major barrier to gene flow in pantropical seabirds, we applied phylogeographic methods to mitochondrial control sequence variation in masked booby (Sula dactylatra) populations on either side of the Isthmus of Panama and the southern tip of Africa. In accord with Steeves et al. (2003), we found that all Caribbean masked boobies with the 'secondary contact' cytochrome b haplotype (m-B) shared a control region haplotype (Sd_100), which grouped with Indian-Pacific haplotypes and not Caribbean-Atlantic haplotypes. In addition, Sd_100 was more closely related to control region haplotypes in the Indian Ocean than in the Pacific. We also found that the 'secondary contact' birds diverged more recently from extant populations in the Indian Ocean than in the Pacific. Thus, it appears that these masked boobies did not breach the Isthmus of Panama. Rather, birds likely dispersed around the southern tip of Africa during favourable oceanographic conditions in the Pleistocene.     

Nests of the brown booby (Sula leucogaster) as a potential indicator of tropical ocean pollution by marine debris

Seabirds collect debris primarily nearby breeding sites, and thus they may be used to monitor these pollutants in the ocean. This study aimed to investigate the prevalence of marine debris used as nesting materials by the brown booby (Sula leucogaster) and to test the species selectivity to debris type and color in two coastal islands of Brazil. We found marine debris in 61% of the brown booby nests on both islands. Fishing gear and hard plastic were the most frequent types of debris. Higher prevalence of fishing gear was found on the island with greater fishery activity. Similarly, hard plastic was the most frequent type of debris in nests and adjacent beach environment. The frequency of debris in brown booby nests can be a potential indicator of the abundance of specific items in surrounding marine waters. Monitoring debris in brown booby nests in a long-term may provide a better understanding of the species⿿ selectivity for specific debris. Furthermore, the impacts of debris in seabird nests at population level remain an overlooked threat that may reduce the quality of nesting habitats. We showed that brown booby nests are widely impacted by marine debris and that these organisms are exposed to this form of pollution from the beginning of their life.     

Genetic diversity of trout (genus Salmo) from its most eastern native range based on mitochondrial DNA and nuclear gene variation

Russia and western Asia harbour trout populations that have been classified as distinct species and subspecies, most often on the basis of morphological and ecological variation. In order to assess their origins and to verify whether traditional taxonomy reflects their evolutionary distinctiveness, we documented their genetic relationships on the basis of mitochondrial DNA (mtDNA) RFLP, mtDNA sequence analysis, and allozyme variation. Both mtDNA and nuclear gene variation defined two ancient phylogenetic assemblages of populations distributed among northern (Baltic, White, Barents), and southern (Black, Caspian, Aral) sea basins, between which gene flow has been possible but limited in postglacial times. These results supported the traditional taxonomic differentiation between populations of these two regions. They provided weak support for the taxonomic distinction of southern brown trout (Salmo trutta) populations based on their basin of origin. They also refuted the hypothesis that L. Sevan trout (Salmo ischchan) diverged from a primitive brown trout ancestor. Nevertheless, all trout populations from southern sea basins possessed private alleles or mtDNA genotypes and were genetically distinct Therefore, they represent unique gene pools that warrant individual recognition for conservation and management.     

Landscape heterogeneity predicts gene flow in a widespread polymorphic bumble bee, Bombus bifarius (Hymenoptera: Apidae)

Bombus bifarius is a widespread bumble bee that occurs in montane regions of western North America. This species has several major color pattern polymorphisms and shows evidence of genetic structuring among regional populations, and the taxonomic status of regional populations has repeatedly been debated. We test whether observed structure is evidence for discrete gene flow barriers that might indicate isolation or instead reflects clinal variation associated with spatially limited dispersal in a complex landscape. We first consider color pattern variation and identify geographical patterns of B. bifarius color variation using cluster analysis. We then use climate data and a comprehensive set of B. bifarius natural history records with an existing genetic data set to model the distribution of environmentally suitable habitat in western North America and predict pathways of potential gene flow using circuit theory. Resistance distances among populations that incorporate environmental suitability information predict patterns of genetic structure much better than geographic distance or Bayesian clustering alone. Results suggest that there may not be barriers to gene flow warranting further taxonomic considerations, but rather that the arrangement of suitable habitat at broad scales limits dispersal sufficiently to explain observed levels of population differentiation in B. bifarius.     

Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species’ range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and significant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale ( <10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining ‘connected’8 brush-tailed rock-wallaby colonies in the northern parts of the species’8 range and the remnant endangered populations in the south.