Development and validation of microsatellite markers for the tiny dragonfly, <Emphasis Type="Italic">Nannophya pygmaea</Emphasis> (Odonata: Libellulidae), which is endangered in South Korea

The tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae), is listed as a second-degree endangered wild animal in South Korea. The application of molecular markers to assess genetic diversity and population relationships can provide information necessary to establish an effective conservation strategy. In this study, we developed 12 microsatellite markers specific to N. pygmaea using the NextSeq 500 platform. Forty individuals of N. pygmaea collected from three currently known localities in South Korea were genotyped to validate these markers and to preliminarily assess population genetic characteristics. The observed number of alleles, observed heterozygosity, and expected heterozygosity at a locus ranged from 2 to 9, 0.421–1.0, and 0.508–0.766 in a population with the largest sample size (20 individuals), respectively, thereby validating the suitability of the markers for population analysis. Five of 12 loci showed significant deviation from the Hardy–Weinberg equilibrium in the population. Our preliminary data indicate an absence of inbreeding in all populations and an absence of obvious genetic difference. The microsatellite markers developed in this study will be useful for studying the population genetics of N. pygmaea collected from other regions worldwide, including additional sites in South Korea.     

Isolation and Characterization of Microsatellite Markers for <Emphasis Type="Italic">Viola websteri</Emphasis> (Violaceae) and Cross-Species Amplification within the Genus <Emphasis Type="Italic">Viola</Emphasis>

We isolated and characterized microsatellite loci in Viola websteri (Violaceae), an endangered species from Korea and endemic to Northeast Asia. A total of 27 microsatellite loci were developed and tested in Korean and Chinese populations. The number of alleles per locus varied from two to eight. The observed and expected heterozygosities within two populations were 0.000 to 1.000 and 0.080 to 0.816, respectively. Korean and Chinese populations were clearly distinguished by the private alleles from 16 loci. A total of 21 loci out of the 27 developed loci were successfully cross-amplified in 39 other Viola species. We believe that these microsatellite loci will be useful for future studies on genetic diversity and population structure of V. websteri, as well as other Viola species.     

Genetic diversity and genetic structure of the endangered Manchurian trout, <Emphasis Type="Italic">Brachymystax lenok tsinlingensis</Emphasis>, at its southern range margin: conservation implications for future restoration

The Manchurian trout, Brachymystax lenok tsinlingensis (family: Salmonidae), is a cold freshwater fish endemic to Northeast Asia. South Korean populations of this species, which comprise its southern range limit, have recently decreased markedly in size and are now becoming critically endangered. We assessed the current population status of this species in South Korea by estimating the levels of genetic diversity and genetic structure of five natural and four restored populations using mitochondrial DNA (mtDNA) control region sequences and eight nuclear microsatellite loci. Levels of within-population genetic diversity were low, suggesting that past effective population sizes (N _e) have been small. Each population had one or a maximum of two mtDNA haplotypes. Microsatellite allelic richness (AR) was significantly higher for natural populations (mean AR?=?3.51; 95% confidence interval, 3.00–4.03) than for restored populations (mean AR?=?2.61; 2.38–2.98). South Korean populations were significantly genetically isolated from one another, with private mtDNA haplotypes and microsatellite alleles, suggesting that limited gene flow has been occurring among populations. A mtDNA phylogeny revealed that South Korean lineages were more closely related to those of China than to those of North Korea and Russia. Overall, we suggest that future restoration efforts aimed at South Korean populations should consider the genetic characteristics reported here, which should help to fulfil effective conservation strategies for this highly cherished species. Our results will inform other conservation efforts, including assisted migration of freshwater fish populations at the equatorial end of the geographical range limit of the species.     

Genetic assessment of <Emphasis Type="Italic">Abies koreana</Emphasis> (Pinaceae), the endangered Korean fir,and conservation implications

To establish a management plan for endangered and rare species, genetic assessment must first be conducted. The genetic characteristics of plant species are affected by demographic history, reproductive strategy, and distributional range as well as anthropological effects. Abies koreana E. H. Wilson (Pinaceae), Korean fir, is endemic to Korea and found only in sub-alpine areas of the southern Korean Peninsula and Jejudo Island. This species has been designated as critically endangered by the International Union for Conservation of Nature due to a continuous decline in its range and population fragmentation. We genotyped 176 individuals from seven natural populations and two afforested populations on the Korean Peninsula using 19 microsatellite loci. STRUCTURE analysis revealed two genetic clusters in natural populations (F _st  = 0.040 and R _st  = 0.040) despite low differentiation. We did not detect a significant reduction in genetic diversity or the signature of a genetic bottleneck despite population fragmentation and small population size. We deduced that this species exhibits a metapopulation structure, with the population on Jirisan Mountain acting as a source of genetic diversity for other local small populations on the Korean Peninsula, through contemporary asymmetric gene flow. However, the majority of afforested individuals on the Korean Peninsula originated from a different gene cluster. Thus, we recommend a conservation strategy that maintains two genetically unique clusters.     

Genetic diversity and structure analyses on the natural populations of diploids and triploids of tiger lily, <Emphasis Type="Italic">Lilium lancifolium</Emphasis> Thunb., from Korea,China, and Japan

Tiger lily, Lilium lancifolium Thumb. is an endemic species in Korea. Genetic structure and diversity of diploid and triploid tiger lily accessions were analyzed using SSRP and IRAP molecular markers. All genetic indices analyzed showed that the diploids hold higher genetic variations compared to the triploids which were collected from Korea, China, and Japan. All variations found in triploids were also found in diploids to support the autotriploidy of L. lancifolium. It was also revealed that the triploid populations have experienced population regrowth from small population after population bottleneck. The population and phylogenetic analyses showed that analyzed tiger lilies were partitioned into three populations, Pop 1 from West Sea of Korean Peninsula, Pop 2 from South Sea of Korean Peninsula and Pop 3 of triploids in which many accessions of West Sea and South Sea were admixed in each partitioned group. Although the level of population differentiation is not extensive, F_ST analysis revealed some level of differentiation among the three populations. The analyses of genetic structure and phylogenetic dendrogram revealed admixture in some accessions among populations. All the results obtained in our analyses imply that autotriploid tiger lilies were originated from a small number of accessions of diploid L. lancifolium.     

Genetic variability comparison of cultured Israeli carp (<Emphasis Type="Italic">Cyprinus carpio</Emphasis>) from Korea using microsatellites

In aquaculture, cultured fish often undergo continuous cross-fertilization without any inflow of new broodstock. This lowers genetic diversity, leading to increased disease rates and decreased survival rates. To improve the mass production and easy culture of Israeli carp, it is essential to investigate the population structure and genetic diversity of these fish. However, such a survey has not yet been performed on Korean Israeli carp. In this study, we used seven microsatellite markers to analyze the genetic diversity and association of cultured Israeli carp from Korea and China. The average numbers of alleles per locus (N _A ) for two Korean (KorA and KorB) and two Chinese (ChA and ChB) populations were as follows: KorA (10.42), KorB (14.43), ChA (20.57) and ChB (20.71). The expected heterozygosity (H _e ) ranged from 0.672 to 0.897 and from 0.827 to 0.938 in the Korean sample and Chinese sample respectively. The genetic diversity of the Korean Israeli carp was about half that of the Chinese carp. The diversity of the Korean Israeli carp was very low, suggesting that the immunity of this population could be weak, and that diversity–recovery studies are urgently needed. Therefore, our results may therefore form the foundation for future research efforts towards genetic monitoring and selective breeding, continuous research needs to be conducted in order to recover the genetic diversity of the Korean Israeli carp.     

Genetic diversity and genetic structure of the Siberian roe deer (<Emphasis Type="Italic">Capreolus pygargus</Emphasis>) populations from Asia

Background

The roe deer, Capreolus sp., is one of the most widespread meso-mammals of Palearctic distribution, and includes two species, the European roe deer, C. capreolus inhabiting mainly Europe, and the Siberian roe deer, C. pygargus, distributed throughout continental Asia. Although there are a number of genetic studies concerning European roe deer, the Siberian roe deer has been studied less, and none of these studies use microsatellite markers. Natural processes have led to genetic structuring in wild populations. To understand how these factors have affected genetic structure and connectivity of Siberian roe deer, we investigated variability at 12 microsatellite loci for Siberian roe deer from ten localities in Asia.

Results

Moderate levels of genetic diversity (H _E = 0.522 to 0.628) were found in all populations except in Jeju Island, South Korea, where the diversity was lowest?(H _E?= 0.386). Western populations showed relatively low genetic diversity and higher degrees of genetic differentiation compared with eastern populations (mean Ar = 3.54 (east), 2.81 (west), mean F _ST = 0.122). Bayesian-based clustering analysis revealed the existence of three genetically distinct groups (clusters) for Siberian roe deer, which comprise of the Southeastern group (Mainland Korea, Russian Far East, Trans-Baikal region and Northern part of Mongolia), Northwestern group (Western Siberia and Ural in Russia) and Jeju Island population. Genetic analyses including AMOVA (F _RT = 0.200), Barrier and PCA also supported genetic differentiation among regions separated primarily by major mountain ridges, suggesting that mountains played a role in the genetic differentiation of Siberian roe deer. On the other hand, genetic evidence also suggests an ongoing migration that may facilitate genetic admixture at the border areas between two groups.

Conclusions

Our results reveal an apparent pattern of genetic differentiation among populations inhabiting Asia, showing moderate levels of genetic diversity with an east-west gradient. The results suggest at least three distinct management units of roe deer in continental Asia, although genetic admixture is evident in some border areas. The insights obtained from this study shed light on management of Siberian roe deer in Asia and may be applied in conservation of local populations of Siberian roe deer.

     

Genetic structure and diversity in relation to the recently reduced population size of the rare conifer, <Emphasis Type="Italic">Pseudotsuga japonica</Emphasis>, endemic to Japan

Rare species consisting of small populations are subject to random genetic drift, which reduces genetic diversity. Thus, determining the relationship between population size and genetic diversity would provide key information for planning a conservation strategy for rare species. We used six microsatellite markers to investigate seven extant populations of the rare conifer Pseudotsuga japonica, which is endemic to the Kii Peninsula and Shikoku Island regions that are geographically separated by the Kii Channel in southwest Japan. The population differentiation of P. japonica was relatively high (F_ST = 0.101) for a coniferous species, suggesting limited gene flow among populations. As expected, significant regional differentiation (AMOVA; p?<?0.05) indicated genetic divergence across the Kii Channel. A strong positive correlation between census population size and the number of rare alleles (r?=?0.862, p?<?0.05) was found, but correlations with major indices of genetic diversity were not significant (allelic richness: r?=?0.649, p?=?0.104, expected heterozygosity: r?=?0.361, p?=?0.426). The observed order of magnitude of correlation with three genetic diversity indices corresponded with the theoretically expected order of each index’ sensitivity (i.e., the rate of decline per generation) to the bottleneck event. Thus, features that exhibit a faster response, i.e., the number of rare alleles, would have been subject to deleterious effects of the recent decline in population size, which is presumably caused by the development of extensive artificial plantations of other tree species over the last several decades. Finally, we propose a conservation plan for P. japonica based on our findings.     

Genetic diversity and population structure of <Emphasis Type="Italic">Melia azedarach</Emphasis> in North-Western Plains of India

Key message

Genetic structure among M. azedarach populations was detected and two subpopulations were present among them. A significant ‘isolation by distance’ was found in M. azedarach population in North-Western Plains of India.

Abstract

Melia azedarach is an important forest tree with pharmaceutical, insecticidal, pesticidal, and commercial significance. It is a good reforestation tree because of its fast growth and drought hardy nature. Genetic variation in a species allows itself to adapt, evolve and respond to environmental stress. It provides the basis for survival of a species and critically influences its evolutionary potential. Assessment of genetic diversity is necessary for improvement and conservation of a species. For this, microsatellite markers are of particular interest given the attributes like co-dominance, reproducibility, hyper variability and abundance throughout the genome. In the present study, we analyzed the genetic diversity and population structure of M. azedarach, an ecologically imperative species growing in the North-Western Plains of India. We developed 43 microsatellite markers, of which 20 were subsequently employed for analysis of diversity and population structure among 33 populations encompassing 318 genotypes representing North-Western Plains of India. A moderate level of diversity (Na = 5.1, Ho = 0.506, He = 0.712, I = 1.386) was assessed. The highest value of ΔK estimated using STRUCTURE indicated 2 subpopulations (K = 2). AMOVA exhibited 73 % variation within populations and 12 % variation was found among regions. Significant positive correlation between geographical and genetic distance was found (Rxy = 0.365, P = 0.010). The present study lays a foundation on a better understanding of genetic dynamics of the species and reveals its diversity and population structure in North-Western Plains of India.

     

Mesoscale investigations based on microsatellite analysis of the freshwater sponge <Emphasis Type="Italic">Ephydatia fluviatilis</Emphasis> in the River-Sieg system (Germany) reveal a genetic divergence

Freshwater sponges play a major role in freshwater ecological system as important filter-feeding organisms and bioindicators. There are only few data about their ecological diversity and population genetic structure available, though a deeper knowledge is needed to propose proper conservation and effective management. The aim of this study was to assess data on distribution patterns of freshwater sponges to study the connectivity of genotypes of Ephydatia fluviatilis in a river system. We sampled specimens from River-Sieg system (River Agger and River Sieg, Germany). We hypothesized that strong anthropogenic influence would cause a uniform distribution of population structures. The genetic structure of E. fluviatilis populations was analysed with a set of eleven microsatellite loci from seven locations in River-Sieg system. Besides of E. fluviatilis, three other species co-occurred (Ephydatia mülleri, Spongilla lacustris, Eunapius fragilis). In contrast to our hypothesis, we observed an overall correlation between genetic and geographic distances among populations of this sessile species, which follows a clear isolation-by-distance pattern. A significant microsatellite polymorphism and high levels of genetic divergence between populations (F_ST) in upstream reaches were present. These results will provide important information for conservation management of populations with limited dispersal ability in connected river systems.     

Development and characterization of twelve microsatellite markers for <Emphasis Type="Italic">Porphyra linearis</Emphasis> Greville

The genus Porphyra (and its sister genus Pyropia) contains important red algal species that are cultivated and/or harvested for human consumption, sustaining a billion-dollar aquaculture industry. A vast amount of research has been focused on species of this genus, including studies on genetics and genomics among other areas. Twelve novel microsatellite markers were developed here for Porphyra linearis. Markers were characterized using 32 individuals collected from four natural populations of P. linearis with total heterozygosity varying from 0.098 to 0.916. The number of alleles per locus ranged from 2 to 18. All markers showed cross amplification with Porphyra umbilicalis and/or Porphyra dioica. These polymorphic microsatellite markers are useful for investigating population genetic diversity and differentiation in P. linearis and may become useful for other genetic research on the reproductive biology of this important species.     

Development and characterization of 24 chloroplast microsatellite markers for two species of <Emphasis Type="Italic">Eranthis</Emphasis> (Ranunculaceae)

Chloroplast microsatellites for two Korean endemic species, Eranthis byunsanensis and E. pungdoensis (Ranunculaceae), were isolated to address the questions of their distributional patterns and evolutionary relationships, using next-generation sequencing. Twenty-four polymorphic chloroplast microsatellite markers for these two species were developed, and then characterized in 65 individuals (55 individuals of E. byunsanensis and 10 individuals of E. pungdoensis). The number of alleles per locus ranged from 2 to 9; the average number of alleles across all the loci scored 4.792. The unbiased diversity per locus ranged from 0.089 to 0.880; the unbiased diversity averaged over all the loci was 0.646. The developed markers were successfully amplified for three congeneric species, E. stellata, E. pinnatifida, and E. longistipitata. The markers developed in this study can provide a valuable and important tool for understanding genetic variations, population structures, evolutionary histories and phylogeography of E. byunsanensis, E. pungdoensis, and related species.     

Phylogeography of the Asian lesser white-toothed shrew, <Emphasis Type="Italic">Crocidura shantungensis</Emphasis>, in East Asia: role of the Korean Peninsula as refugium for small mammals

Many peninsulas in the temperate zone played an important role as refugia of various flora and fauna, and the southern Korean Peninsula also served as a refugium for many small mammals in East Asia during the Pleistocene. The Asian lesser white-toothed shrew, Crocidura shantungensis, is a widely distributed species in East Asia, and is an appropriate model organism for exploring the role of the Korean Peninsula as a refugium of small mammals. Here, we investigated phylogenetic relationships and genetic diversity based on the entire sequence of the mitochondrial cytochrome b gene (1140 bp). A Bayesian tree for 98 haplotypes detected in 228 C. shantungensis specimens from East Asia revealed the presence of three major groups with at least 5 subgroups. Most haplotypes were distributed according to their geographic proximity. Pairwise F_ST’s and analysis of molecular variance (AMOVA) revealed a high degree of genetic differentiation and variance among regions as well as among populations within region, implying little gene flow among local populations. Genetic evidence from South Korean islands, Jeju-do Island of South Korea, and Taiwan leads us to reject the hypothesis of recent population expansion. We observed unique island-type genetic characteristics consistent with geographic isolation and resultant genetic drift. Phylogeographic inference, together with estimates of genetic differentiation and diversity, suggest that the southern most part the Korean Peninsula, including offshore islands, played an important role as a refugium for C. shantungensis during the Pleistocene. However, the presence of several refugia on the mainland of northeast Asia is also proposed.     

Isolation and characterization of species-specific microsatellite markers for blue and black wildebeest (<Emphasis Type="BoldItalic">Connochaetes taurinus</Emphasis> and <Emphasis Type="BoldItalic">C. gnou</Emphasis>)

The blue wildebeest (Connochaetes taurinus) is distributed throughout southern and east Africa while the black wildebeest (Connochaetes gnou) is endemic to South Africa and was driven to near extinction in the early 1900s due to hunting pressure and disease outbreaks. Extensive translocation of both species throughout South Africa is threatening the genetic integrity of blue and black wildebeest. To effectively manage these species, genetic tools that can be used to detect hybrid individuals, identify genetically unique subpopulations and determine the levels of genetic diversity are required. In this study, 11 microsatellite markers were developed for wildebeest through next-generation sequencing. The microsatellite loci displayed 2.00–4.14 alleles, unbiased heterozygosity values ranged from 0.32 to 0.60 and observed heterozygosity values ranged from 0.26 to 0.52. The comparatively high level of polymorphism observed in the microsatellite markers indicates that these markers can contribute significantly to our knowledge of population genetic structure, relatedness, genetic diversity and hybridization in these species.     

Development of microsatellite markers for <Emphasis Type="Italic">Manilkara maxima</Emphasis> T.D. Penn. (Sapotaceae) and their use in conservation genetics

Manilkara maxima is an endemic tree species of the Atlantic Forest in southern Bahia, Brazil. It is considered important for forest conservation due to its mutualistic interactions with endemic and endangered animals. Our aim was to develop microsatellite markers to estimate genetic diversity in order to provide information for effectiveness of future conservation programs. We used next generation sequencing technology to develop the first specific microsatellite markers for M. maxima. Seventeen new microsatellite loci were applied in 72 individuals sampled in three natural populations. On average, the number of alleles per loci was 8.8. The expected heterozygosity varied between 0.72 and 0.77, indicating that the developed set of molecular markers is useful for genetic diversity studies. Additionally, the estimated value for the combined probability of exclusion (Q) was greater than 0.999, which indicates the powerful of these molecular tools for paternity and kinship analysis. Our results demonstrate that the set of microsatellites developed in this work is a powerful tool for population genetics, molecular ecology and conservation biology purposes.     

Genetic diversity and population structure of the northern snakehead (<Emphasis Type="Italic">Channa argus</Emphasis> Channidae: Teleostei) in central China: implications for conservation and management

Major threats to freshwater fish diversity now include loss of native genetic diversity as a consequence of translocations of fishes between sites and from hatcheries to sites, and small effective population sizes resulting from overfishing and/or habitat loss. Ten polymorphic microsatellite markers were employed to evaluate genetic diversity, population genetic structure and gene flow amongst nine populations of the ecologically and economically important fish, the northern snakehead (Channa argus), in three river systems in central China. Multiple analyses revealed evidence of high genetic diversity and pronounced subdivision based on both regional separation and on river systems. A lack of evidence of genetic bottleneck over recent generations was consistent with the long-term stability of population size and contemporary distribution. The effective population sizes for most C. argus populations were small, suggesting the need for future conservation efforts focusing on these populations. Different lines of evidence point to the local enhancement of stocks by both aquaculture-reared fish and the transfer of wild fish. This study illustrates how human activities may affect genetic diversity and population genetic structure of C. argus populations, and highlights the need for new management regimes to protect native freshwater fish genetic diversity.     

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.     

Genetic diversity of endangered orchid <Emphasis Type="Italic">Phaius australis</Emphasis> across a fragmented Australian landscape

Historical events such as colonisation, spatial distribution across different habitats, and contemporary processes, such as human-mediated habitat fragmentation can leave lasting imprints on the population genetics of a species. Orchids currently comprise 17% of threatened flora species in Australia (Environment Protection and Biodiversity Conservation Act 1999) due to the combination of fragmentation and illegal harvesting (Benwell in Recovery plan, swamp orchids Phaius australis, Phaius tancarvilliae, NSW National Parks and Wildlife Service, Sydney, 1994; Jones in A complete guide to native orchids of Australia including the island territories, 2nd edn, Reed Natural History, Sydney, 2006; DE in Phaius australis in species profile and threats database, Department of the Environment. http://www.environment.gov.au/sprat, 2015). The federally endangered Swamp Orchid Phaius australis has a disjunct distribution across an almost 2000 km latitudinal range along Australia’s east coast but it was estimated that 95% of the populations have been lost since European settlement (Benwell 1994). Phaius australis is endangered due to illegal collection and habitat loss that has resulted in limited connectivity between populations, in ecosystems that are vulnerable to climate change. Thus the genetic impacts of its history combined with more recent fragmentation may have impacts on its future viability especially in light of changing environmental conditions. Thirty-four populations were sampled from tropical north Queensland to the southern edge of the subtropics in New South Wales. Population genetics analysis was conducted using 13 polymorphic microsatellite markers developed for the species using NextGen sequencing. Spatial genetic patterns indicate post-colonisation divergence from the tropics southwards to its current climate niche limits. Genetic diversity is low across all populations (A?=?1.5, H _e  = 0.171), and there is little evidence of genetic differentiation between regions. Consistent with population genetic theory, the historic loss of populations has resulted in significantly lower genetic diversity in small populations compared to large (P, A, He; p?<?0.05). The viability and persistence of P. australis populations now and in a changing climate are discussed in the context of conservation priorities.     

The contrasting genetic patterns of two sympatric flying fox species from the Comoros and the implications for conservation

Pteropus livingstonii and Pteropus seychellensis comorensis are endemic fruit bat species that are among the most threatened animals in the Comoros archipelago. Both species are pollinators and seed dispersers of native and cultivated plants and are thus of crucial importance for the regeneration of natural forests as well as for cultivated plantations. However, these species are subject to strong anthropogenic pressures and face one of the highest rates of natural habitat loss reported worldwide. Yet little is known about the population genetic structure of these two species, making it difficult to define relevant conservation strategies. In this study, we investigated for the two flying fox species (1) the level of genetic diversity within islands, as well as across the archipelago and (2) the genetic structure between the two islands (Anjouan and Mohéli) for P. livingstonii and between the four islands of the archipelago (Anjouan, Mohéli, Grande Comore and Mayotte) for P. s. comorensis using mitochondrial and microsatellite markers. The results revealed contrasting patterns of genetic structure, with P. s. comorensis showing low genetic structure between islands, whereas P. livingstonii exhibited high levels of inter-island genetic differentiation. Overall, the genetic analyses showed low genetic diversity for both species. These contrasting genetic patterns may be the result of different dispersal patterns and the populations’ evolutionary histories. Our findings lead us to suggest that in terms of conservation strategy, the two populations of P. livingstonii (on Anjouan and Mohéli islands) should be considered as two separate management units. We recommend focusing conservation efforts on the Anjouan population, which is the largest, exhibits the highest genetic diversity, and suffers the greatest anthropogenic pressure. As for P. s. comorensis, its four populations could be considered as a single unit for conservation management purposes. For this species, we recommend protecting roosting trees to reduce population disturbance.