Conservation Genetics最新文献

Marine turtles undertake long migrations across different geographies and habitats, exposing them to a wide range of threats throughout their lifespan. Analysing population structure and connectivity is key to informing effective conservation management. We expand knowledge of Atlantic-wide connectivity of green turtles (Chelonia mydas) by characterising the genetic structure of the Ascension Island nesting population, one of the largest in the Atlantic Ocean, and carrying out Atlantic population structure and mixed stock analyses using high-resolution genetic markers. We amplified a ~ 738 bp fragment (extended D-loop) and a highly polymorphic mitochondrial short tandem repeat (mtSTR) fragment of the mitochondrial DNA control region, designating haplotypes based on (1) extended D-loop and (2) the extended D-loop and mtSTR combined. Overall, 11 extended D-loop and 33 combined haplotypes were found, the dominant haplotypes being CM-A8.1 and CM-A8.1/7-12-4-4. Population structure analysis found three main genetic groups: Northwest Atlantic, Northern South America, and South and East Atlantic. Mixed stock analyses indicate Ascension Island as a major source for juvenile foraging aggregations in the Southwest Atlantic (34-55%) and Central Africa (18-78%), with some contribution to West Africa (3-20%). Green turtles are vulnerable to fishery bycatch in the coastal waters of the South and East Atlantic. Our study underlines how improving sample sizes of Atlantic mtSTR haplotypes could further elucidate green turtle connectivity across threatened regions. We urge international collaboration to minimise mtSTR data gaps, in order to enhance connectivity assessments and improve conservation measures between countries that share populations.

Supplementary information: The online version contains supplementary material available at 10.1007/s10592-025-01720-3.

Assisted gene flow can restore genetic diversity when genetic drift has driven deleterious alleles to high frequencies in small, isolated populations. Previous crosses among 20 populations of Gymnadenia conopsea documented the strongest heterosis and the weakest inbreeding depression in sparse and small populations, consistent with fixation of mildly deleterious alleles by genetic drift. We genotyped the populations used for crosses, and used 1200–1728 SNPs to test the following predictions: (1) heterosis increases with genetic differentiation (F_ST) to donor populations and decreases with genetic diversity in the recipient population, (2) inbreeding depression increases with genetic diversity, and (3) genetic diversity increases, and mean F_ST to other populations decreases, with population size and density. Pairwise F_ST ranged from very low to moderate (0.005–0.20) and genetic diversity varied moderately among populations (proportion of polymorphic loci = 0.52–0.75). However, neither F_ST between populations, nor genetic diversity in the recipient population, were related to the strength of heterosis. There was also no association between genetic diversity and the strength of inbreeding depression. Genetic diversity increased and mean F_ST decreased with population size, consistent with reduced diversity and increased differentiation of small populations by genetic drift. The results indicate that the loci conferring heterosis are not mirrored by overall population differentiation, and limited additional information on potential source populations for genetic rescue is gained by the genetic data. Instead, the use of controlled crosses can directly reveal positive effects of introducing new genetic material, and is a simple method with high potential in conservation.

The North American freshwater genus Forbesichthys is composed of facultative cave-dwelling fishes restricted to springs and caves in southern Illinois, southeastern Missouri, southwestern Kentucky, and central Tennessee. These fishes were previously considered a single species, the Spring Cavefish (F. agassizii), but recent molecular evidence led to the recognition of the Shawnee Hills Cavefish (F. papilliferus). The Shawnee Hills Cavefish is hypothesized to be restricted to Illinois, Missouri, Kentucky and north-central Tennessee, whereas the Spring Cavefish is restricted to the Eastern Highland Rim of central Tennessee. However, the distributions of Forbesichthys are difficult to ascertain due to their intermittent appearance in surface springs, making sampling challenging. We assessed the species status, distribution, connectivity, and population sizes of the Forbesichthys spp. using Restriction-site Associated DNA sequencing (RADseq) and the mitochondrial NADH dehydrogenase 2 locus. Our results corroborate the recognition and hypothesized distributions of the Shawnee Hills Cavefish and Spring Cavefish. Furthermore, we suggest the recognition of three Evolutionary Significant Units (ESUs) and two Management Units (MUs) within the Shawnee Hills Cavefish. Although all populations analyzed appear to have reasonable genetic diversity and population stability over time, this regionalization has implications for both groundwater policy and management. Our study provides important information relevant to understanding potential population distributions and the identification of unique lineages that may deserve additional protection.

Genetic diversity is the foundation of biodiversity, and preserving it is therefore fundamental to conservation practice. However, global conservation efforts face significant challenges integrating genetic and genomic approaches into applied management and policy. As collaborative partnerships are increasingly recognized as key components of successful conservation efforts, we explore their role and relevance in the Australian context, by engaging with key entities from across the conservation sector, including academia, botanic gardens, herbaria, seed banks, governmental/non-governmental organisations, private industry, museums, Traditional Owners, Indigenous rangers, and zoos and aquaria. By combining perspectives from these entities with comprehensive literature review, we identified five guiding principles for conservation genetic and genomic research and explored the different elements of, and approaches to, collaboration. Our reflections suggest that there is a substantial overlap in research interests across the Australian conservation sector, and our findings show that collaboration is increasing. We discuss approaches to building collaborative partnerships, the reciprocal benefits of collaborating, and some remaining challenges associated with data generation, data collection, and cross-cultural considerations. We emphasise the need for long-term national resourcing for sample and data storage and consistency in collecting, generating and reporting genetic data. While informed by the Australian experience, our goal is to support researchers and practitioners to foster meaningful collaborations that achieve measurable management outcomes in conservation genetics and genomics, both in Australia and globally.

Understanding factors that influence the viability of populations is central to conservation biology. Small and isolated populations have elevated risk of extinction due to demographic and genetic stochasticity. The Apostle Islands National Lakeshore features a genetically unique and culturally important population of archipelagic black bears (Makwa; Ursus americanus). While dispersal is central to population viability, previous studies of this population did not sample the adjacent mainland black bear population on the Red Cliff Reservation (Gaa-miskwaabikaang). Therefore, we lack robust estimates of dispersal, gene flow and overall connectivity among the islands and with the mainland population. In partnership with Red Cliff Band of Lake Superior Chippewa and the National Park Service, we non-invasively collected black bear hair, and used 17 microsatellite markers to genotype 141 black bears. We then estimated genetic diversity, population structure, dispersal, and conducted a pedigree network analysis to identify areas of the archipelago important for connectivity and reproduction. We found evidence of a well-connected archipelagic bear population structured into five clusters and characterized by moderate dispersal between islands and mainland. We found that three of the islands are disproportionately important for genetically connecting the archipelago, but the islands were nevertheless reliant upon the mainland for gene flow and genetic diversity. The high connectivity between islands and the mainland demonstrates a potential metapopulation dynamic, where islands may serve as a reservoir of individuals for the mainland and the mainland supplying individuals likely important for maintaining genetic diversity of island populations. Given the importance of island–mainland connectivity, future tribal and federal collaboration will be important to maintain a genetically and demographically viable population of black bears.

Integrating molecular data is essential for clarifying the distributions and genetic structures of species that have histories of misidentification and misapplication of names. There has been confusion about the species limits of the Vulnerable Prostanthera cineolifera with respect to morphologically similar specimens in the Hunter Valley, New South Wales, Australia and morphologically dissimilar specimens in the Lower Hawkesbury Valley, New South Wales, and from north-eastern New South Wales. To test the species limits of P. cineolifera, and related taxa, specimens were collected from across the range and augmented with herbarium specimens. We used morphometric analysis of 18 morphological characters across 51 samples. Using the DArTseq reduced representation sequencing platform, 4010 single-nucleotide polymorphisms (SNPs) across 110 individuals were recovered for molecular analysis. Both morphological and molecular analyses produced three concordant clusters (A) P. cineolifera, (B) a group sharing similarities with P. sp. Hawkesbury (B.J.Conn 2591), and (C) a group allied with P. lanceolata and P. ovalifolia. These results indicate that the specimens form north-eastern New South Wales are more likely to be P. lanceolata, not P. cineolifera, and that specimens from the Lower Hawkesbury are of an undescribed species with the phrase name P. sp. Hawkesbury (B.J.Conn 2591). Within P. cineolifera there was pronounced genetic differentiation among populations. Little evidence of inbreeding was observed, but the newly recognised, more isolated populations had the lowest genetic diversity. This study provides new information about the range of the species and its genetic structure that informs the conservation priorities for this species.

The Peninsular Indian population of the endangered Asian elephant occurs in the Western and Eastern Ghats, and further north-east in the Eastern Central Indian (ECI) range. Using DNA obtained from fresh elephant dung, this study assessed the genetic variation, population structure, and gene flow in the two southern populations, SI1 and SI2, separated by the Palghat Gap in the Western Ghats, and the third population in the ECI range. As these populations have been shown to be genetically associated in previous studies, the hypotheses that their combined genetic diversity would be high and gene flow via migration would be evident, were tested. A total of 379 elephants were genotyped at 10 microsatellite markers, and a 630 bp mitochondrial DNA (mtDNA) fragment from the D-loop region was sequenced from 33 individuals. Four previously documented mtDNA haplotypes were identified: SI1 and ECI each had a single haplotype (BN and BL, respectively), while SI2 had two haplotypes (BA and BF). The mtDNA markers indicated substantial genetic differentiation among the populations, while differentiation using microsatellite data was moderate. The populations were assigned to three genetic groups: SI1, SI2, and the ECI. However, 39% of these individuals showed mixed ancestry, indicating ongoing gene flow despite natural and human-made barriers. Several first-generation male migrants were identified providing further evidence of contemporary gene flow. The sex ratio was female-biased, which is consistent with the existing census data. These three populations should be managed as a single conservation unit to ensure their long term viability.

In this era of global warming, southwestern Shikoku is a strong candidate as a refugium for tropical reef corals in the Pacific. In this study, we documented patterns of species composition among pocilloporid recruits, the dominant coral family being recruited to southern Shikoku, and we evaluated genetic population relationships between recruits and adults at four sites, using seven nuclear microsatellite markers. Pocilloporid recruits in the area comprised two genera and three species, including the most heavily recruited species, Pocillopora damicornis, and the minor P. acuta. This is the first observation of the latter species in this area. In P. damicornis, clonality differed among the four sites and clonal recruits were observed at two sites. However, proportions of clones were relatively low. Strong genetic differentiation among the four sites was observed in populations of P. damicornis, although three genetic clusters were shared among these sites. In addition, compositions of these three clusters were similar between recruits and adults at each site. This indicates that populations of P. damicornis in southwestern Shikoku are maintained primarily by sexual reproduction and that larvae derived from sexual reproduction are supplied mainly from their natal habitats at all sites. As local population persistence and self-recruitment are important to maintain populations of this species in southwestern Shikoku, conservation efforts should be directed at protecting extant local populations.

Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic studies, when available, provide detailed information that is important for management, such as estimates of gene flow, inbreeding, genetic erosion and adaptation. In this article, we argue that the development and advancement of genetic diversity indicators is a complementary approach to genetic studies in conservation biology, but not a substitute. Genetic diversity indicators and empirical genetic data can provide different information for conserving genetic diversity. Genetic diversity indicators enable affordable tracking, reporting, prioritization and communication, although, being proxies, do not provide comprehensive evaluation of the genetic status of a species. Conversely, genetic methods offer detailed analysis of the genetic status of a given species or population, although they remain challenging to implement for most species globally, given current capacity and resourcing. We conclude that indicators and genetic studies are both important for genetic conservation actions and recommend they be used in combination for conserving and monitoring genetic diversity.