Conservation Genetics最新文献

{"title":"Genetic structure of Atlantic Puffins (Fratercula arctica) breeding in Atlantic Canada","authors":"Quinn B. Carvey, Scott A. Pavey, Antony W. Diamond, Gail K. Davoren, Raphael A. Lavoie, Nathalie M. LeBlanc, Matthew J. Legard, Gregory J. Robertson, Emily S. Runnells, Christina Petalas, Heather L. Major","doi":"10.1007/s10592-024-01629-3","DOIUrl":"https://doi.org/10.1007/s10592-024-01629-3","url":null,"abstract":"<p>The Atlantic Puffin (<i>Fratercula arctica</i>; hereafter ‘puffin’) breeds at the southern limit of its range in the Gulf of Maine, where waters are warming faster than most of the world’s oceans. Puffin productivity and survival have decreased in the Gulf of Maine with warming, but population-level declines have not been detected. Understanding the connectivity between Gulf of Maine breeding colonies and colonies to the north has become a priority to determine the demographic importance of immigration, but mark-recapture and tracking studies have yet to resolve this question. In this study, we used double digest restriction-site associated DNA sequencing (ddRADseq) to quantify neutral genetic differentiation among five breeding colonies in Atlantic Canada, identify outlier single nucleotide polymorphisms (SNPs), and determine if puffins can be reliably assigned to their breeding colony. We identified a new genetic cluster of puffins, represented by Machias Seal Island, and recommend that this colony be considered separately from Newfoundland and Québec for management. We found three outlier SNPs, with the rare alleles predominantly present in Machias Seal Island puffins, and recommend further research to determine the extent that selection may be contributing to the differentiation of Machias Seal Island. Puffins could be reliably assigned to the Machias Seal Island or the northern-colony genetic cluster, including with a subset of the 200 highest-<span>(F_{ST})</span> SNPs. Finally, we did not identify evidence of inbreeding at any colony, suggesting that effective population sizes are large enough to buffer against these negative effects.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"22 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Urbanisation has impacted the population genetic structure of the Eurasian red squirrel in Japan within a short period of 30 years","authors":"Yu Takahata, Kenta Uchida, Nobuyuki Kutsukake, Tatsuki Shimamoto, Yushin Asari, Yohey Terai","doi":"10.1007/s10592-024-01631-9","DOIUrl":"https://doi.org/10.1007/s10592-024-01631-9","url":null,"abstract":"<p>Human activities often induce maladaptive effects in urban wildlife, such as increased inbreeding and decreased gene flow, consequently leading to a loss of biodiversity. Although maladaptive effects are commonly reported in urban wildlife, some wildlife species are not affected. Understanding the conditions and factors that affect the genetic structure of wildlife is crucial for its conservation in urban environments. Eurasian red squirrels <i>Sciurus vulgaris</i> in Obihiro City, Hokkaido, Japan, have settled in large residential lots with a high risk of vehicle collisions for approximately 30 years, raising the possibility that the urban population would be genetically isolated from nearby rural populations and may experience a rapid decrease in genetic diversity. In this study, we analysed the population structure, genetic distance, and nucleotide diversity of squirrels in the Obihiro area using genome-wide single nucleotide polymorphisms (SNPs). Principal component analysis and ADMIXTURE showed that urban and rural squirrel populations formed distinct clusters with intermediate urban and rural boundary populations. Genetic distances between the urban populations were greater than that of other pairs. Nucleotide diversities were lower in urban populations than in other populations, suggesting limited gene flow between urban and other populations, possibly due to urbanisation. The change in the genetic characteristics of urban squirrel populations during this short period demonstrates the strong impact of urbanisation. Our findings suggest that a genome-wide approach to the genetic structure of wildlife contributes to its conservation in urban environments.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"8 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142208231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning approaches to assess microendemicity and conservation risk in cave-dwelling arachnofauna","authors":"Hugh G. Steiner, Shlomi Aharon, Jesús Ballesteros, Guilherme Gainett, Efrat Gavish-Regev, Prashant P. Sharma","doi":"10.1007/s10592-024-01627-5","DOIUrl":"https://doi.org/10.1007/s10592-024-01627-5","url":null,"abstract":"<p>The biota of cave habitats faces heightened conservation risks, due to geographic isolation and high levels of endemism. Molecular datasets, in tandem with ecological surveys, have the potential to precisely delimit the nature of cave endemism and identify conservation priorities for microendemic species. Here, we sequenced ultraconserved elements of <i>Tegenaria</i> within, and at the entrances of, 25 cave sites to test phylogenetic relationships, combined with an unsupervised machine learning approach for detecting species. Our analyses identified clear and well-supported genetic breaks in the dataset that accorded closely with morphologically diagnosable units. Through these analyses, we also detected some previously unidentified, potential cryptic morphospecies. We then performed conservation assessments for seven troglobitic Israeli species of this genus and determined five of these to be critically endangered.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"59 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141937850","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic support for discrete conservation units of the fossorial rodent Geomys pinetis","authors":"Sarah I. Duncan, Robert A. McCleery, Celine M. Carneiro, J. T. Pynne, Elizabeth I. Parsons, L. Mike Conner, Steven B. Castleberry, Robert A. Gitzen, James D. Austin","doi":"10.1007/s10592-024-01626-6","DOIUrl":"https://doi.org/10.1007/s10592-024-01626-6","url":null,"abstract":"<p>Knowledge of the population genetic structure and diversity of at-risk species is essential to accurately evaluate population viability and define units for conservation and management. The southeastern pocket gopher (<i>Geomys pinetis)</i> is a fossorial rodent native to the imperiled longleaf pine savannas of the southeastern United States. Its recent decline has made it a species of ‘high conservation concern’ by state agencies. Previous phylogenetic analyses suggested two distinct lineages within the species occurring east (<i>G. p. pinetis</i>) and west (<i>G. p. mobilensis</i>) of the Apalachicola-Chattahoochee-Flint River (ACF) Basin, a phylogeographic break for many species. However, little is known about the genetic substructure within each region. We examined neutral and putatively adaptive variation in 9373 single nucleotide polymorphisms (SNPs) to assess the extent of genetic structure across the species' geographic range. We confirmed significant genetic divergence of populations east–west of the ACF Basin, predating the Last Glacial Maximum, supporting the presence of two evolutionary independent lineages. Our results indicate additional strong genetic substructuring within each lineage and possible non-neutral variation across latitudes. Given the high degree of genetic differentiation and lack of evidence for secondary contact among populations within the ACF Basin, we recommend that <i>G. pinetis</i> be managed as two conservation units corresponding to distinct lineages representing <i>G. pinetis</i> and <i>G. mobiliensis</i>.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"68 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population genetic structure of the European pond turtle (Emys orbicularis) at the northern edge of the Pannonian Basin","authors":"Peter Mikulíček, Petr Papežík, Stanislav Danko, Róbert Dankovics, Daniel Gruľa, Bálint Halpern, Peter Havaš, Botond Heltai, Enikő Horváth, Tomáš Kušík, Peter Puchala, Maria Schindler, Viliam Vongrej, Marcel Uhrin","doi":"10.1007/s10592-024-01624-8","DOIUrl":"https://doi.org/10.1007/s10592-024-01624-8","url":null,"abstract":"<p>Populations of plants and animals at the edge of a species’ range may exhibit lower genetic diversity due to a combination of historical (e.g., postglacial dispersal) and contemporary (e.g., low effective population size, strong genetic drift or bottlenecks) processes. In this study, we analysed the genetic structure of populations of the European pond turtle (<i>Emys orbicularis</i>) in the northern part of the Pannonian Basin (Slovakia, Hungary, Austria), which represents the edge of the species’ range. Using mitochondrial DNA (mtDNA) and microsatellite markers, we aimed to assign individuals and populations into phylogeographic lineages and to determine genetic variation and population structure. Our study revealed that most individuals from natural populations belong to mtDNA lineage II (widely distributed haplotype IIa, and likely endemic haplotypes IIl and IIo), which is typical for the whole Pannonian region. However, non-native haplotypes were detected in one Slovak population (haplotype Ib) and in the Austrian Donau Auen National Park (haplotype IVa). Microsatellite markers revealed high variability comparable to that in other parts of the range, suggesting that marginal populations may not necessarily have reduced genetic diversity. A genetically mixed population was found in the Donau Auen National Park, consisting of turtles belonging to mtDNA lineage II (taxonomically assessed as subspecies <i>E. orbicularis orbicularis</i>) and lineage IV (taxonomically assessed as <i>E. orbicularis hellenica</i>), which is native to the circum-Adriatic region. The admixture suggests intense hybridization and introgression between the two lineages (subspecies).</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"41 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141740784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity in the traditional cultivars and wild ancestor of near-threatened Japanese iris (Iris ensata Thunb.)","authors":"Makiko Mimura, Marina Takeuchi, Takayuki Kobayashi, Shun K. Hirota, Yoshihisa Suyama, Hirofumi Yamaguchi, Toshihito Tabuchi","doi":"10.1007/s10592-024-01625-7","DOIUrl":"https://doi.org/10.1007/s10592-024-01625-7","url":null,"abstract":"<p>Wild relatives of cultivars are crucial sources of genetic variation for further enhancement, yet they face potential threats due to contemporary environmental changes. <i>Iris ensata</i> var. <i>spontanea</i>, a wild progenitor of the Japanese iris cultivars (<i>I. ensata</i> var. <i>ensata</i>), is extensively cultivated in Japanese gardens, is distributed across mesic meadows and wetlands in Japan and East Asia. This species is currently threatened owing to habitat loss linked to land use alterations. We assessed genetic diversity and phylogenetic relationships in 32 wild accessions and the 14 principal Edo Group of Japanese iris cultivars, originally bred during the Edo period (1600–1868). In the phylogenetic tree, the cultivars formed a cluster with low inbreeding coefficients, suggesting a singular origin and interbreeding between the genetically distinct accessions. Conversely, wild accessions exhibited greater overall genetic diversity and higher inbreeding coefficients than cultivars, indicating frequent inbreeding within divergent natural populations. Our findings highlight the distinct genetic reservoirs of both wild accessions and Edo cultivars, although the former may face inbreeding challenges. Urgent conservation action is needed to ensure the genetic diversity of wild populations as natural resources.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"23 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141745942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep genetic divergence underlies within-island eco-morphological variation in the endangered day gecko Phelsuma borbonica: implications for conservation","authors":"Josselin Cornuault, Mickaël Sanchez, Thomas Duval, Antoine Fouquet, Christophe Thébaud","doi":"10.1007/s10592-024-01622-w","DOIUrl":"https://doi.org/10.1007/s10592-024-01622-w","url":null,"abstract":"<p>The day gecko <i>Phelsuma borbonica</i> displays marked differences in coloration and occupies a variety of habitats across its very small range on the volcanic oceanic island of Reunion in the southwestern Indian Ocean. Such differences might reflect geographic and ecological divergence and thus be associated with an underlying genetic differentiation. We examined the partitioning of genetic diversity in <i>Phelsuma borbonica</i> across Reunion at a very small spatial scale (&lt; 10 km) using mtDNA and nuDNA sequences, along with microsatellite genotype data. This study provides an account of the evolutionary history of <i>Phelsuma borbonica</i>, along with a quantification of effective population sizes, which constitute important information for the conservation of this endangered species, which may represent a previously unrecognized case of incipient speciation. We found that populations of <i>Phelsuma borbonica</i> are genetically strongly differentiated, highlighting historically low levels of gene flow. Phylogenetic analyses suggest that <i>Phelsuma borbonica</i> reached its present range through two parallel southward expansions from an ancestral population located in the northern part of the island.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"1 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141506003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Population genetics of caribou in the Alaska-Yukon border region: implications for designation of conservation units and small herd persistence","authors":"Karen H. Mager, Michael J. Suitor, Thanh Khoa Nguyen, My Hanh Hoang, Jim D. Herriges, Jeffrey B. Stetz, Kelsey L. Russell","doi":"10.1007/s10592-024-01612-y","DOIUrl":"https://doi.org/10.1007/s10592-024-01612-y","url":null,"abstract":"<p>Better knowledge of genetic relationships between the Fortymile caribou herd and its neighbors is needed for conservation decision-making in Canada. Here, we contribute the first fine-scale analysis of genetic population structure in nine contiguous caribou herds at the geographic boundaries between Barren-ground and Northern Mountain caribou, and at the Alaska-Yukon border. Using pairwise differentiation metrics, STRUCTURE, and discriminant analysis of principal components (DAPC) to analyze 15 microsatellite loci in 379 caribou, we found complex patterns of genetic differentiation. The Fortymile was the only herd assigned to more than one genetic cluster, indicative of its history as a larger herd whose range expansions and gene flow to other herds were likely important to maintaining diversity across a functioning genetic metapopulation. Some small herds (Chisana, Klaza, and White Mountains) were genetically distinct, while others (Hart River, Clear Creek, Mentasta) exhibited little differentiation from herds they occasionally overlap, including herds assigned to different conservation units (DUs). This genetic connectivity does not result from demographic connectivity, as episodic contact during rut, rather than herd switching, is the likely mechanism. Unusually, one small herd (White Mountains) maintained genetic differentiation despite rut overlap with Fortymile. Our data reveal that some herds with different ecological and behavioral attributes are demographically independent but nonetheless genetically connected. Thus, we suggest that managing caribou for an appropriate level of genetic connectivity, while also supporting herd persistence, will be essential to conserve caribou genetic diversity in the region.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"4 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140926637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, small population size, and management influence inbreeding and reduced genetic variation in K’gari dingoes","authors":"Susan M. Miller, Linda Behrendorff, Benjamin L. Allen, Rose L. Andrew, Guy Ballard, J. William O. Ballard, Kylie M. Cairns, Gabriel C. Conroy, Peter J. S. Fleming, Catherine E. Grueber, Jane Oakey, Deane A. Smith, Danielle Stephens, Claire Wade, Jacqueline M. Bishop","doi":"10.1007/s10592-024-01616-8","DOIUrl":"https://doi.org/10.1007/s10592-024-01616-8","url":null,"abstract":"<p>Small island populations are vulnerable to genetic decline via demographic and environmental stochasticity. In the absence of immigration, founder effects, inbreeding and genetic drift are likely to contribute to local extinction risk. Management actions may also have a greater impact on small, closed populations. The demographic and social characteristics of a species can, however, delay the impact of threats. K’gari, a ~ 1 660 km² island off the Australian east coast and UNESCO World Heritage Site (Fraser Island 1842–2023), supports an isolated population of approximately 70–200 dingoes that represent an ideal opportunity to explore the small island paradigm. To examine temporal and spatial patterns of genetic diversity in this population we analysed single nucleotide polymorphism (SNP) genotype data (72 454 SNPS) for 112 K’gari dingoes collected over a 25-year period (1996 to 2020). Genetic diversity was lower in K’gari dingoes than mainland dingoes at the earliest time point in our study and declined significantly following a management cull in 2001. We did not find any spatial genetic patterns on the island, suggesting high levels of genetic connectivity between socially discrete packs. This connectivity, combined with the social structure and behaviour of dingoes, may act in concert to buffer the population from the impacts of genetic drift in the short term. Nevertheless, a general decline in genetic variation via inbreeding and drift has occurred over the past 20 years which we suggest should be considered in any future management planning for the population. Monitoring patterns of genetic variation, together with a clearer understanding of the social ecology of K’gari dingoes, will aid in the development of measurable genetic targets set over ecologically meaningful timelines, and help ensure continued survival of this culturally important population.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"20 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic patterns of native palms from the Leeward Antilles confirm single-island endemism and guide conservation priorities","authors":"James A. R. Clugston, Quirijn Coolen, Erik Houtepen, André S. J. van Proosdij, Ayress D. Grinage, M. Patrick Griffith","doi":"10.1007/s10592-024-01618-6","DOIUrl":"https://doi.org/10.1007/s10592-024-01618-6","url":null,"abstract":"<p>Systematic study of the palm (Arecaceae) flora from the Leeward Antilles marked both <i>Sabal antillensis</i> and <i>Sabal lougheediana</i> as endemic to Curaçao and Bonaire respectively. Although both species are emergent, obvious and charismatic elements of the Antillean flora, they were only described within the last decade. <i>Sabal lougheediana</i> is in demographic crisis as a result of constant ungulate pressure prohibiting seedling establishment, while <i>S. antillensis</i> is thriving as a result of careful management. Given the surprisingly recent discovery of these two species, and the severity of the conservation concern, genomic data can help inform whether these taxa are in fact well-circumscribed species, and help to guide further conservation actions. To investigate genomic diversity, we employed RADSeq data from samples throughout the range of both species. Results show significant genetic distance and fixation between the two taxa as currently circumscribed, as well as reduced genetic diversity and increased inbreeding in both species. Multivariate analysis of genetic distance and Bayesian clustering analysis both show clear and significant separation of the two taxa. Parallel assay of ex situ collections informs how future development of germplasm reserves can help support conservation of both species. We provide recommendations to help conserve these two unique and distinct species.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"68 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}