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.     

Genetic variability and the effect of habitat fragmentation in spotted suslik Spermophilus suslicus populations from two different regions

Endangered species worldwide exist in remnant populations, often within fragmented landscapes. Although assessment of genetic diversity in fragmented habitats is very important for conservation purposes, it is usually impossible to evaluate the amount of diversity that has actually been lost. Here, we compared population structure and levels of genetic diversity within populations of spotted suslik Spermophilus suslicus, inhabiting two different parts of the species range characterized by different levels of habitat connectivity. We used microsatellites to analyze 10 critically endangered populations located at the western part of the range, where suslik habitat have been severely devastated due to agriculture industrialization. Their genetic composition was compared with four populations from the eastern part of the range where the species still occupies habitat with reasonable levels of connectivity. In the western region, we detected extreme population structure (F _ST = 0.20) and levels of genetic diversity (Allelic richness ranged from 1.45 to 3.07) characteristic for highly endangered populations. Alternatively, in the eastern region we found significantly higher allelic richness (from 5.09 to 5.81) and insignificant population structure (F _ST = 0.03). As we identified a strong correlation between genetic and geographic distance and a lack of private alleles in the western region, we conclude that extreme population structure and lower genetic diversity is due to recent habitat loss. Results from this study provide guidelines for conservation and management of this highly endangered species.     

大叶藻居群微卫星遗传多样性研究

采用4对微卫星引物对大叶藻的7个地理居群进行了遗传多样性与遗传结构分析。扩增148株大叶藻得到57个等位基因, 每个位点平均等位基因数为6, 大叶藻居群的平均期望杂合度(He)为0.687, 平均观测杂合度(Ho)为0.417。青岛湾居群的遗传多样性最高(A=7.750, AR=7.043), 俚岛居群最低(A=4.750, AR=4.543)。从F_st值来看, 7个大叶藻居群间属于中度分化。UPGMA系统发育树显示, 中国4个大叶藻居群聚类到一起, 其遗传分化可能是由于历史大海草场的遗留小片段居群产生, 而中国、韩国、日本和爱尔兰居群间的遗传分化则主要是由于地理隔离造成的。自由交配估计结果支持海草的东亚起源说。青岛湾居群遗传多样性较高, 可优先作为大叶藻移植修复的材料和基因库, 并进行重点保护。     

Conservation genetics of an ex situ population of <Emphasis Type="Italic">Primula reinii</Emphasis> var. <Emphasis Type="Italic">rhodotricha</Emphasis>, an endangered primrose endemic to Japan on a limestone mountain

Primula reinii var. rhodotricha is a perennial herb endemic to the limestone slope of Mt. Buko, located approximately 50 km northwest of central Tokyo, Japan. In recent years, its natural population size has decreased markedly due to limestone mining, and this species has been assigned to the ‘Critically Endangered (CR)’ category on the latest Japanese Red List. Although a remnant population of this species has been protected by a mining company outside their historical distribution range on Mt. Buko, the ex situ conservation of this endangered plant has been difficult because of insufficient low seed production. The genetic status of ex situ P. reinii var. rhodotricha and related species were investigated to develop an effective conservation plan for this species. Microsatellite analysis indicated that the ex situ population harbors lower genetic diversity than sister taxa, providing molecular evidence for the recent critical status designation of the ex situ population, whereas the presence of rare alleles may imply further potential for seed reproduction by outcrossing. Therefore, an appropriate propagation strategy that considers genetic diversity is needed for restoration and recovery of this critically endangered ex situ primrose population.     

A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes

Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600 km in the northwest Mediterranean Sea and focused on a 50‐km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free‐living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.     

Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense

Background and Aims

Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species.

Methods

Population differentiation at five quantitative traits (Q_ST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (F_ST) in seven populations of P. sinense. Q_ST estimates were derived using a Bayesian hierarchical variance component method.

Key Results

Trait-specific Q_ST values were equal to or lower than F_ST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense.

Conclusions

Despite the prevalent empirical evidence for Q_ST > F_ST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower Q_ST relative to F_ST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, Q_ST estimates were of the same magnitude as F_ST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers.     

Geographic range and structure of cryptic genetic diversity among Pacific North American populations of the non-native amphipod Grandidierella japonica

Reconstructing the invasion history of aquatic invasive species can enhance understanding of invasion risks by recognizing areas most susceptible to invasion and forecasting future spread based on past patterns of population expansion. Here we reconstruct the invasion history of the Japanese amphipod Grandidierella japonica Stephensen 1938 combining information from historical collection data with molecular genetic data to better understand post-invasion range expansion and anthropogenic connectivity across the Pacific coast of North America. Compilation of collection data from bays and estuaries of the Pacific North American coast show many new localities have been colonized in the last two decades, moving outward from harbors and bays with high commercial traffic into smaller coastal locations dominated by local recreational traffic. DNA barcode sequence data for G. japonica reveals two distinct clades: one found in San Francisco Bay and sites to the north, and one also found in San Francisco Bay and sites to the south. The two clades differ by an average 7.28 % genetic distance, large enough to consider these invasive amphipods two separate species. Both northern and southern clades exhibit low levels of genetic diversity, suggesting a single introduction event for each. The presence of cryptic diversity within this invasive amphipod highlights the need for more extensive study of the invasive and native populations of aquatic invasive invertebrates to address questions of taxonomy, diversity, and invasion history.     

Genetic diversity of Astragalus nitidiflorus, a critically endangered endemic of SE Spain,and implications for its conservation

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in five populations of Astragalus nitidiflorus, a critically endangered species endemic to southeast Spain. Eight primers amplified 78 bands with 40 (51.3%) being polymorphic. Statistical results indicated a low genetic diversity at the population and species level, with percentages of polymorphic bands (PPB) ranging from 28.2 to 37.2% (an average of 31.8%), and means of gene diversity (H_E) of 0.129 and 0.171 respectively. The Shannon’s index (SI) ranged from 0.160 to 0.214 at the population level and was 0.260 at the species level. A low level of genetic differentiation among populations was detected, based on the Shannon’s information index (0.297), the coefficient of genetic differentiation between populations (G_ST = 0.2418) and AMOVA analysis (Φ_ST = 0.255). The estimated gene flow (Nm) was 0.789. The high genetic connectivity found among populations of A. nitidiflorus is an evidence of a recent habitat fragmentation. In addition, a bottleneck event in the past has been revealed, with a subsequent reduction of population size and a loss of genetic variation. Based on these results, the conservation strategy of A. nitidiflorus was proposed.     

Genetic diversity and structure of Pinus dabeshanensis revealed by expressed sequence tag-simple sequence repeat (EST-SSR) markers

Assessing patterns of genetic variation in rare endangered species is critical for developing both in situ and ex situ conservation strategies. Pinus dabeshanensis Cheng et Law is an endangered species endemic to the Dabieshan Mountains of eastern China. To obtain fundamental information of genetic diversity, population history, effective population size, and gene flow in this species, we explored patterns of genetic variation of natural populations, in addition to an ex situ conserved population, using expressed sequence tag-simple sequence repeats (EST-SSR) markers. Our results revealed moderate levels of genetic diversity (e.g., H_E = 0.458 vs. H_E = 0.423) and a low level of genetic differentiation (F_ST = 0.028) among natural and conserved populations relative to other conifers. Both contemporary and historical migration rates among populations were high. Bayesian coalescent-based analyses suggested that 3 populations underwent reductions in population size ca. 10,000 yr ago, and that two populations may have experienced recent genetic bottlenecks under the TPM. Bayesian clustering revealed that individuals from the ex situ population were largely assigned to the ‘red’ cluster. Additionally, our results identified private alleles in the natural populations but not in the ex situ population, suggesting that the ex situ conserved population insufficiently represents the genetic diversity present in the species. Past decline in population size is likely to be due to Holocene climate change. Based on the genetic information obtained for P. dabeshanensis, we propose some suggestions for the conservation and efficient management of this endangered species.     

Molecular characterization and population genetic diversity of Limonium sinense based on nuclear ribosomal DNA and ISSR

The single nucleotide polymorphism (SNP) and amplification refractory mutation system (ARMS) have been applied to authenticate Limonium species and their corresponding herb samples. One species specific primer was designed and the amplification product is 200 bp (Limonium sinense) by using this primer. No band was observed with other Limonium species. The phylogenetic relationship of Limonium species were studied using ribosomal DNA ITS and the adulterants (L. bicolor, L. aureum and L. wrightii) were clustered with L. sinense in NJ tree. Inter simple sequence repeat (ISSR) was used to assess genetic diversity and population structure of L. sinense and a high level of genetic diversity was detected (H _E = 0.2573, PPB = 85.71%) with POPGENE. Based on AMOVA analysis, there was moderate variation between pairs of populations with Φ_ST from 0.1744 to 0.5131 and on average 28.81% of the genetic variation occurred among populations. Five main clusters were shown in UPGMA dendrogram using TFPGA. The results showed that SNP and ARMS could be used to authenticate not only Limonium species but related herbs on rDNA internal transcribed spacer region. Possible strategies should be implemented for conservation of this endemic herb.     

Temporal genetic dynamics of reintroduced and translocated populations of the endangered golden lion tamarin (<Emphasis Type="Italic">Leontopithecus rosalia</Emphasis>)

Reintroductions—captive-born animals introduced into the species’ original distribution area—and translocations—free-living animals transferred to another location within the historical distribution area—are important conservation strategies for endangered species. Genetic analyses of 239 individuals from unmanaged, translocated and reintroduced populations of Leontopithecus rosalia were performed using 14 microsatellites. These samples were collected during two periods: (a) 1996–1997 (historic), when individuals were translocated and reintroduced into forest fragments in the lowland Atlantic Forest, and (b) 2007–09 (recent). We hypothesized that effective population size and genetic diversity would increase over time and that these management strategies would affect the resulting population genetic structure. We found trends indicating that the effective population size at the translocation site increased while that at the reintroduction sites diminished over time. The inbreeding coefficient of the translocated population diminished over time (from 0.38 to 0.03) and was much lower than that of the native (0.29) and reintroduced (0.13) recent populations. We observed a greater genetic admixture among the reintroduced sites on the historic sampling, as well as a strong genetic structure at the translocation site. In the recent sampling, the population structuring became more site-related suggesting low or inconsistent gene flow between sampling sites. This research highlights how conservation management decisions have an important influence on the genetic outcome of translocations and reintroductions. Future conservation planning should consider population genetic monitoring before and after management measures and maintain population connectivity thereafter to avoid the negative effects of a population size reduction.     

Population Genomics of the Euryhaline Teleost Poecilia latipinna

Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative F_ST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant F_ST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive F_ST values that could indicate adaptive divergence.     

Population structure of an endangered species living in contrasted habitats: Parnassia palustris (Saxifragaceae)

In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within-population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.     

A complex history of introgression and vicariance in a threatened montane skink (<Emphasis Type="Italic">Pseudemoia cryodroma</Emphasis>) across an Australian sky island system

Species endemic to sky island systems are isolated to mountain peaks and high elevation plateaux both geographically and ecologically, making them particularly vulnerable to the effects of climate change. Pressures associated with climate change have already been linked to local extinctions of montane species, emphasizing the importance of understanding the genetic diversity and population connectivity within sky islands systems for the conservation management of remaining populations. Our study focuses on the endangered alpine skink Pseudemoia cryodroma, which is endemic to the Victorian Alps in south-eastern Australia, and has a disjunct distribution in montane habitats above 1100 m a.s.l. Using mitochondrial DNA (mtDNA) and microsatellite loci, we investigated species delimitation, genetic connectivity and population genetic structure across the geographic range of this species. We found discordance between genetic markers, indicating historical mtDNA introgression at one of the study sites between P. cryodroma and the closely related, syntopic P. entrecasteauxii. Molecular diversity was positively associated with site elevation and extent of suitable habitat, with inbreeding detected in three of the five populations. These results demonstrate the complex interaction between geography and habitat in shaping the population structure and genetic diversity of P. cryodroma, and highlight the importance of minimising future habitat loss and fragmentation for the long-term persistence of this species.     

Conservation genetics of the yellow-bellied toad (Bombina variegata): population structure,genetic diversity and landscape effects in an endangered amphibian

Revealing patterns of genetic diversity and barriers for gene flow are key points for successful conservation in endangered species. Methods based on molecular markers are also often used to delineate conservation units such as evolutionary significant units and management units. Here we combine phylo-geographic analyses (based on mtDNA) with population and landscape genetic analyses (based on microsatellites) for the endangered yellow-bellied toad Bombina variegata over a wide distribution range in Germany. Our analyses show that two genetic clusters are present in the study area, a northern and a southern/central one, but that these clusters are not deeply divergent. The genetic data suggest high fragmentation among toad occurrences and consequently low genetic diversity. Genetic diversity and genetic connectivity showed a negative relationship with road densities and urban areas surrounding toad occurrences, indicating that these landscape features act as barriers to gene flow. To preserve a maximum of genetic diversity, we recommend considering both genetic clusters as management units, and to increase gene flow among toad occurrences with the aim of restoring and protecting functional meta-populations within each of the clusters. Several isolated populations with especially low genetic diversity and signs of inbreeding need particular short-term conservation attention to avoid extinction. We also recommend to allow natural gene flow between both clusters but not to use individuals from one cluster for translocation or reintroduction into the other. Our results underscore the utility of molecular tools for species conservation, highlight outcomes of habitat fragmentation onto the genetic structure of an endangered amphibian and reveal particularly threatened populations in need for urgent conservation efforts.

     

Genetic structure of Japanese Chattonella marina (Raphidophyceae) populations revealed using microsatellite markers

Chattonella marina var. antiqua and C. marina var. marina (Raphidophyceae) are red tide‐forming, harmful phytoplankton species. We investigated the genetic diversity and genetic relationship among the populations using microsatellite markers to identify putative sources of C. marina var. antiqua and C. marina var. marina in Japanese coastal populations. A positive correlation between genetic divergence and geographical distance (isolation by distance) was recognized for C. marina var. antiqua. The C. marina var. antiqua populations were established throughout a geological time scale, and genetic divergence had progressed in each population with gene flow depending on geographic distances. In contrast, isolation by distance was not observed for C. marina var. marina populations, and the genetic divergence among populations was extremely high. The Tokyo Bay population of C. marina var. marina, which was first recognized in 2008, had many private alleles but was related to the Kagoshima Bay population. The Tokyo Bay population may have been established by several invasions from the Kagoshima Bay population and other regions.     

High genetic diversity and differentiation of an extremely narrowly distributed and critically endangered decaploid rose (<Emphasis Type="Italic">Rosa praelucens</Emphasis>): implications for its conservation

Rosa praelucens is a critically endangered decaploid alpine rose with an extremely narrow geographic distribution in Northwestern Yunnan, China. We sampled almost all the extant individuals (527 individuals in 31 natural locations and 56 individuals preserved in three local living collections) to assess the genetic variation and to probe the genetic connectivity among the individuals and populations based on three cpDNA intergenic spacers and six fluorescent amplified fragment length polymorphism (AFLP) markers. The morphological traits from seven populations were also measured. R. praelucens exhibited high levels of morphological variation, genetic diversity, and differentiation. The extant individuals were clustered into eight groups in neighbor-net networks, and subsequent Bayesian analysis assigned them into three larger gene pools, both in accordance with their morphological traits, especially flower color. The living collections embraced two private cpDNA haplotypes and included three out of the species’ total eight AFLP genotypes. Rhizome clonal growth, decaploid, and mixed breeding system may largely contribute to high genetic diversity and differentiation in R. praelucens. We concluded that the endangered status of R. praelucens may mainly be due to habitat fragmentation and loss and inherent reproductive difficulties, rather than low genetic diversity. The populations contributing higher cpDNA genetic diversity, representing more AFLP genotypes, and encompassing private cpDNA haplotypes should be given conservation priority by creating plant-micro reserves. The living collections should also be targeted for further ex situ conservation, population recovery, and reintroduction of R. praelucens plants.     

Analysis of genetic variability and population structure of the endemic medicinal Limonium sinense using molecular markers

Limonium sinense is an endemic medicinal herb used to treat fever, hemorrhage and other disorders. In the present study, population genetic diversity was elucidated using random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) primers. Percentage of polymorphic bands, Nei's gene diversity and Shannon's information index revealed a high level of genetic diversity at species level. The analysis of molecular variance revealed that 69.88% (RAPD), 71.19% (ISSR) and 70.97% (AFLP) of variability were partitioned among individuals within populations, which indicated the coherent trend by Gst (0.3849/0.3577/0.3670). Gene flow number (Nm) was 0.581/0.618/0.612, which indicated that there was a limited gene exchange between populations. The UPGMA clustering results showed that the genetic distance had no significant correlation with geographic distance. These results indicate that these markers were reliable tools for the differentiation and determination of the genetic diversity among the populations of L. sinense and the conservation of existing natural population is necessary.     

Genetic diversity and differentiation of the Korean starry flounder (Platichthys stellatus) between and within cultured stocks and wild populations inferred from microsatellite DNA analysis

The Korean starry flounder, Platichthys stellatus, is economically valuable coastal resident fish species. However, the annual catch of this fish has fluctuated and suffered major declines in Korea. We examined the genetic diversity and population structure for four wild populations and three hatchery stocks of Korean starry flounder to protect its genetic integrity using nine microsatellites. A group of 339 genotypes belonging to seven populations were screened. High degrees of polymorphism at the microsatellite loci were observed within both the wild and hatchery populations. Compared to the wild populations, genetic changes, including reduced genetic diversity and highly significant differentiation, have occurred in cultured stocks. Significant population differentiation was also observed in wild starry flounder populations. Similar degrees of inbreeding and significant Hardy–Weinberg equilibrium deviations were detected in both the wild and the hatchery populations. The genetic connectivity pattern identified four distinct metapopulations of starry flounder in Korea by clustering in the phylogenetic tree, Bayesian analyses, molecular variance analysis, PCA and multidimensional scaling analysis. A pattern of isolation-by-distance was not significant. This genetic differentiation may be the result of the co-effects of various factors, such as historic dispersal, local environment or anthropogenic activities. These results provide useful information for the genetic monitoring of P. stellatus hatchery stocks, for the genetic improvement of this species by selective breeding and for designing suitable management guidelines for the conservation of this species.     

Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins

Gene flow among small fragmented populations is critical for maintaining genetic diversity, and therefore the evolutionary potential of a species. Concern for two New Zealand endemic subspecies, the Hector’s (Cephalorhynchus hectori hectori) and Maui’s (C. h. maui) dolphins, arises from their low abundance, slow rate of reproduction, and susceptibility to fisheries-related mortality. Our work examined genetic differentiation and migration between the subspecies and among regional and local Hector’s dolphin populations using mitochondrial (mt) DNA and microsatellite genotypes from 438 samples. Results confirmed earlier reports of a single unique mtDNA control region haplotype fixed in the Maui’s dolphin, and provided new evidence of reproductive isolation from Hector’s dolphins (9-locus microsatellite F _ST?=?0.167, P?<?0.001). Independent evolutionary trajectories were also supported for Hector’s dolphin populations of the East Coast, West Coast, Te Waewae Bay and Toetoe Bay. Low asymmetrical migration rates were found among several Hector’s dolphin populations and assignment tests identified five Hector’s dolphins likely to have a migrant father from another regional population. There appears to be sufficient step-wise gene flow to maintain genetic diversity within the East and West Coasts; however, the two local South Coast populations exhibited a high degree of differentiation given their close proximity (~100?km). To maintain the evolutionary potential and long-term survival of both subspecies, genetic monitoring and conservation management must focus on maintaining corridors to preserve gene flow and prevent further population fragmentation and loss of genetic diversity, in addition to maintaining local population abundances.