Conservation Genetics最新文献

{"title":"Distinct spatial patterns of genetic structure and diversity in the butterfly Marbled White (Melanargia galathea) inhabiting fragmented grasslands","authors":"Evelyn Terzer, Max Schmid, Barbara Bauert, Daniela Weidmann-Csencsics, Stefan Birrer, Janine Bolliger, Sabine Brodbeck, Felix Gugerli","doi":"10.1007/s10592-023-01593-4","DOIUrl":"https://doi.org/10.1007/s10592-023-01593-4","url":null,"abstract":"<p>We adopted a landscape-scale approach to analyze the genetic patterns (diversity, structure, and differentiation) of the Marbled White (<i>Melanargia galathea</i>). This butterfly species is characteristic of semi-dry grasslands, which have substantially declined in Switzerland during past decades. We sampled individuals on a regular grid of the established Biodiversity Monitoring program of Switzerland over five consecutive years, obtaining 1639 genotyped individuals from 185 locations. Results showed that <i>M. galathea</i> populations cluster into five spatially aggregated clusters that largely coincide with the biogeographic regions of Switzerland. Genetic diversity (allelic richness) was higher in the South of the Alps, likely related to immigration dynamics that suggest recolonisation from the South after the last glaciation. Demographic history resulted in distinct isolation by distance (IBD) and by cumulative elevational difference (isolation by altitude, IBA) at large scale, while regional IBD and IBA were less pronounced. This pattern was likely induced by the barrier effect of the high mountains of the Alps impeding continuous northward migration after the last glacial maximum. A temporal analysis revealed that regional genetic diversity did not change strongly during the five sampling years. This result indicates that the genetic diversity pattern in <i>M. galathea</i> has not been noticeably affected by historical land-use change or that the sampling period of five years is too short to detect any changes. Our findings highlight the regionally, topography-induced distinct genetic clusters, relevant for consideration as conservation units and likely reflecting genetic structures similar to those found in other butterfly species of conservation concern.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"9 2","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138503977","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":"Phylogeographic analysis points toward invasion of the Timanfaya National Park (Lanzarote; Canary Islands) by a translocated native plant (Rumex lunaria)","authors":"Mario A. González Carracedo, Mariano Hernández Ferrer, Raimundo Cabrera, María Bernardos, José A. Pérez Pérez","doi":"10.1007/s10592-023-01592-5","DOIUrl":"https://doi.org/10.1007/s10592-023-01592-5","url":null,"abstract":"<p><i>Rumex lunaria</i> is an endemic shrub of the Canary Islands, which is colonizing the Timanfaya National Park (TNP) in Lanzarote. Whether the arrival of <i>R. lunaria</i> to Lanzarote has been natural or by human intervention is still a matter of debate. To address this question, 100 specimens of <i>R. lunaria</i> were collected from the seven main Canary Islands, and genetic analysis of four chloroplast DNA <i>loci</i> were performed, covering a total length of 4809 nucleotide positions. Multiple alignments revealed 49 nucleotide substitutions, which define 30 different haplotypes. Island-specific haplotypes were found in Tenerife, La Gomera, La Palma and Gran Canaria, with the greatest diversity found in the first island. Interestingly, the unique haplotype detected in El Hierro is shared with almost all plants from Lanzarote (95%), including all individuals sampled in the TNP. The most frequent haplotype present in Gran Canaria was detected in only one sample from Lanzarote (5%). These results were corroborated by a robust phylogenetic analysis, which supports the hypothesis of a common origin of <i>R. lunaria</i> populations from El Hierro and the vast majority of those from Lanzarote. In addition, this study rules out the genetic singularity of the <i>R. lunaria</i> specimens that are colonizing the TNP.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"9 3","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138503976","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":"What mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate","authors":"Anna Weber, Jackie Lighten, Cock van Oosterhout, Amour Guibinga Mickala, Stephan Ntie, Patrick Mickala, David Lehmann, Katharine Abernethy, Nicola Anthony","doi":"10.1007/s10592-023-01587-2","DOIUrl":"https://doi.org/10.1007/s10592-023-01587-2","url":null,"abstract":"<p>The major histocompatibility complex (MHC) can be useful in guiding conservation planning because of its influence on immunity, fitness, and reproductive ecology in vertebrates. The mandrill (<i>Mandrillus sphinx</i>) is a threatened primate endemic to central Africa. Considerable research in this species has shown that the MHC is important for disease resistance, mate choice, and reproductive success. However, all previous MHC research in mandrills has focused on an inbred semi-captive population, so their genetic diversity may have been underestimated. Here we expand our current knowledge of mandrill MHC variation by performing next-generation sequencing of non-invasively collected fecal samples from a large wild horde in central Gabon. We observe MHC lineages and alleles shared with other primates, and we uncover 45 putative new class II MHC DRB alleles, including representatives of the DRB9 pseudogene, which has not previously been identified in mandrills. We also document methodological challenges associated with fecal samples in NGS-based MHC research. Even with high read depth, the replicability of alleles from fecal samples was lower than that of tissue samples, and allele assignments are inconsistent between sample types. Further, the common assumption that variants with very high read depth should represent true alleles does not appear to be reliable for fecal samples. Nevertheless, the use of degraded DNA in the present study still enabled significant progress in quantifying immunogenetic diversity and its evolution in wild primates.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"9 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138503975","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":"Contemporary reproductive patterns of Snake River Oncorhynchus nerka in Pettit Lake","authors":"Kendra R. Eaton, Kurt A. Tardy, Rebecca M. Croy","doi":"10.1007/s10592-023-01585-4","DOIUrl":"https://doi.org/10.1007/s10592-023-01585-4","url":null,"abstract":"<p>Maintaining genetic biodiversity is a focal point for conservation of endangered species. As such, reproductive patterns and behaviors are key to understanding how to aid in species conservation. Snake River Sockeye Salmon (<i>Oncorhynchus nerka)</i> are an endangered species with reproductive complexity created by intermixing life history strategies including: anadromous Sockeye Salmon, residual Sockeye Salmon, kokanee, and introgressed populations. We explore the reproductive behaviors, intermixing life history groups, and resulting juvenile production of Pettit Lake <i>O. nerka</i> using genetic stock identification and parentage-based tagging of outmigrating juveniles and returning or released adults. We also compared how production varied between equal and female-biased sex ratio years of adult releases and used this data to explore a sex ratio that can be used to maximize production for management purposes. In this study, Pettit Lake was found to have consistent intermixing between every known life history group in the lake. We determined that a female-biased sex ratio led to larger females selecting for captive males, more production from residual males spawning with captive females, and increased production of age-1 outmigrants. At higher female-biased sex ratios, we found evidence of males spawning with multiple females and an increase in outmigrant production. Our data supports maximizing production by adopting a captive adult release sex ratio of two females per male in a system limited by available adults. These findings provide further understanding on the complexity of reproductive patterns and demonstrate the importance of monitoring and utilizing scientific findings to maximize conservation efforts and management decisions.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"9 5","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138503974","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":"Genome-wide analysis of the harbour porpoise (Phocoena phocoena) indicates isolation-by-distance across the North Atlantic and potential local adaptation in adjacent waters","authors":"Marijke Autenrieth, Katja Havenstein, Binia De Cahsan, Julia Canitz, Harald Benke, Anna Roos, Christophe Pampoulie, Guðjón Már Sigurðsson, Ursula Siebert, Morten Tange Olsen, Vincent Biard, Mads Peter Heide-Jørgensen, Ayaka Amaha Öztürk, Bayram Öztürk, John W. Lawson, Ralph Tiedemann","doi":"10.1007/s10592-023-01589-0","DOIUrl":"https://doi.org/10.1007/s10592-023-01589-0","url":null,"abstract":"<p>The harbour porpoise (<i>Phocoena phocoena</i>), a highly mobile cetacean species of the Northern Hemisphere, inhabits basins that vary broadly in salinity, temperature, and food availability; such variation can drive divergent adaptation among local populations. To shed light on range-wide population structure and local adaptation, we generated ddRAD sequencing data spanning the entire North Atlantic and the Baltic Sea, as well as the Black Sea as an outgroup, and mapped this data to the high-quality draft genome of the species. We identified 11,978 genome-wide SNPs from 150 individuals, which we used for population genetic inferences. Our results support genetic differentiation between North Atlantic and Baltic Sea populations, with Kattegat as a transition zone. Across the North Atlantic the population differentiation is subtle from west to east, congruent with an isolation-by-distance pattern, but indicates a separation of southern North Sea harbour porpoises. We identified genomic outlier regions, i.e., scaffold regions where SNPs with high <i>F</i>_ST across North Atlantic populations co-occur. Together with the draft genome annotation, these regions could point towards candidate genes for differential local adaptation processes among populations. Furthermore, they enable the development of a SNP panel for routine population assignment which will be useful in a conservation and management context. We identified six outlier loci putatively under positive selection, based on the population structure inferred from the complete SNP set. Our study highlights the value of genome resources in conservation and management and provides a crucial additional resource for the study of harbour porpoise evolution and phylogeny.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"9 6","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138503973","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":"Evolutionary history of the salt marsh harvest mouse mitogenome is concordant with ancient patterns of sea level rise","authors":"Cody M. Aylward, Laureen Barthman-Thompson, Douglas A. Kelt, Benjamin N. Sacks, Mark J. Statham","doi":"10.1007/s10592-023-01588-1","DOIUrl":"https://doi.org/10.1007/s10592-023-01588-1","url":null,"abstract":"Abstract Coastal wetland ecosystems support unique biodiversity and are imminently threatened by climate change-driven sea level rise. However, the impact of climate change on their demographic and evolutionary histories is poorly understood. To improve our understanding, we examined how past climatic events have shaped the evolutionary history of the salt marsh harvest mouse ( Reithrodontomys raviventris ), an endangered species and a salt marsh habitat specialist, completely restricted to coastal wetlands in the San Francisco Estuary (SFE). We used whole mitochondrial genome sequences of 102 salt marsh harvest mice to characterize phylogeography and demographic history. Then, we predicted the ancient distribution of salt marsh habitat and examined correspondence between divergence, demographic history, and changes in ancient marsh habitat caused by sea level rise. A Bayesian Skyline Plot revealed demographic expansions during periods of sea level rise, particularly during the formation of the modern SFE (~ 10 kya), and rapid decline consistent with recent anthropogenic landscape change. Bayesian estimates of divergence time were consistent with subspecies divergence ~ 10 kya, and subpopulation divergence ~ 5 kya, consistent with multiple episodes of vicariance caused by Holocene sea level rise. Spatial Analysis of Molecular Variance and Φ ST revealed a mismatch between the morphological and molecular subspecies assignment of two populations. Our study implicates sea level rise as a force of demographic change and evolutionary divergence in coastal marsh ecosystems. Our study also aids conservation of an endangered species by clarifying genetic subspecies boundaries and highlighting the unique nature of isolated populations that are increasingly threatened by modern sea level rise.","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"48 16","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135042967","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":"Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking","authors":"Oksana Burimski, Anti Vasemägi, Riho Gross","doi":"10.1007/s10592-023-01582-7","DOIUrl":"https://doi.org/10.1007/s10592-023-01582-7","url":null,"abstract":"Abstract Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders ( N b ) over the study period. Furthermore, we found that immigration rates ( m ) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation.","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"8 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135774354","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":"Michael (Mike) William Bruford (6th June 1963–13th April 2023)","authors":"Benoit Goossens, Pablo Orozco-terWengel","doi":"10.1007/s10592-023-01583-6","DOIUrl":"https://doi.org/10.1007/s10592-023-01583-6","url":null,"abstract":"","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"105 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135934979","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":"A comprehensive strategy for the conservation of forest tree genetic diversity: an example with the protected Pinus nigra subsp. salzmannii (Dunal) Franco in France","authors":"C. Scotti-Saintagne, A. de Sousa Rodrigues, A. Roig, B. Fady","doi":"10.1007/s10592-023-01581-8","DOIUrl":"https://doi.org/10.1007/s10592-023-01581-8","url":null,"abstract":"","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"2 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135221164","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":"Correction: Beyond Bonferroni: less conservative analyses for conservation genetics","authors":"Shawn R. Narum","doi":"10.1007/s10592-023-01576-5","DOIUrl":"https://doi.org/10.1007/s10592-023-01576-5","url":null,"abstract":"","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135512028","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}