Conservation Genetics最新文献

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Loss of genetic diversity and isolation by distance and by environment in populations of a keystone ungulate species 一种关键性蹄类动物种群遗传多样性的丧失以及因距离和环境造成的隔离
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-04-03 DOI: 10.1007/s10592-024-01614-w
Fernanda de Góes Maciel, Sean O’Rourke, Melissa Jones, William Hemstrom, Michael Ryan Miller, Gabriela Schmaedecke, Leandro Reverberi Tambosi, Mozart Sávio Pires Baptista, Alexine Keuroghlian, Alessandra Ferreira Dales Nava, Marcello Schiavo Nardi, Anah Tereza de Almeida Jácomo, Leandro Silveira, Mariana Malzoni Furtado, Natália Mundim Tôrres, Cibele Biondo
{"title":"Loss of genetic diversity and isolation by distance and by environment in populations of a keystone ungulate species","authors":"Fernanda de Góes Maciel, Sean O’Rourke, Melissa Jones, William Hemstrom, Michael Ryan Miller, Gabriela Schmaedecke, Leandro Reverberi Tambosi, Mozart Sávio Pires Baptista, Alexine Keuroghlian, Alessandra Ferreira Dales Nava, Marcello Schiavo Nardi, Anah Tereza de Almeida Jácomo, Leandro Silveira, Mariana Malzoni Furtado, Natália Mundim Tôrres, Cibele Biondo","doi":"10.1007/s10592-024-01614-w","DOIUrl":"https://doi.org/10.1007/s10592-024-01614-w","url":null,"abstract":"<p>Adaptive genetic and neutral variations are essential for maintaining population viability in changing environmental conditions. Habitat loss and fragmentation can be reflected in the patterns of genetic variation in the populations. White-lipped peccaries (WLPs, <i>Tayassu pecari</i>) are wide-ranging Neotropical ungulates with important ecological roles in the ecosystem suffering local extinctions worldwide. Here, we used a RAD-seq protocol to genotype 192 individuals. After filtering, we identified sets of SNP markers (ranging from 147 to 151,792 SNPs) to assess the genetic diversity and population structure of WLPs from Pantanal, Cerrado, and Atlantic Forest in Brazil. We found signals of loss (θw &lt; θπ) and lower genetic diversity (allelic richness, nucleotide diversity, and observed and expected heterozygosities) in the Central Cerrado and Atlantic Forest populations. Principal Component Analysis (PCA) and admixture analyses (NGSAdmix) using genome-wide and neutral SNP data sets showed three major genetic clusters according to the biomes. Multiple matrix regression with randomization (MMRR) analysis found an isolation-by-distance pattern explaining the neutral genetic differentiation. We used Latent Factor Mixed Models (LFMM) and Redundancy Analysis (RDA) to identify candidate SNPs involved in different biological processes, such as metabolism and immune and neuronal responses, mainly associated with temperature and precipitation variables. We found an adaptive population genetic structure, suggesting three adaptive units with significant patterns of isolation-by-distance and isolation-by-environment. Our results highlighted the importance of conservation strategies for maintaining the genetic diversity of WLP populations. Furthermore, conservation plans and translocation programs should preserve and consider the adaptive variation.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"213 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140595633","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}
引用次数: 0
Early detection of rare and elusive endangered species using environmental DNA: a case study for the Eurasian otter and the white-clawed crayfish in northwestern Italy 利用环境 DNA 早期检测稀有和难以捉摸的濒危物种:意大利西北部欧亚水獭和白爪螯虾案例研究
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-04-02 DOI: 10.1007/s10592-024-01619-5
Lorenzo Ballini, Dario Ottonello, Valentina Repetto, Chiara Natali, Giacomo Chini, Livia Tolve, Claudio Ciofi, Sara Fratini, Alessio Iannucci
{"title":"Early detection of rare and elusive endangered species using environmental DNA: a case study for the Eurasian otter and the white-clawed crayfish in northwestern Italy","authors":"Lorenzo Ballini, Dario Ottonello, Valentina Repetto, Chiara Natali, Giacomo Chini, Livia Tolve, Claudio Ciofi, Sara Fratini, Alessio Iannucci","doi":"10.1007/s10592-024-01619-5","DOIUrl":"https://doi.org/10.1007/s10592-024-01619-5","url":null,"abstract":"<p> Monitoring, management and conservation of rare and elusive species often requires early detection of individuals, especially for re-introduced and endangered taxa. Environmental DNA (eDNA) approaches can enhance the detection power of traditional biomonitoring methods for low-density, newly-established populations. In this study, we used species-specific Real Time PCR TaqMan assays to assess the presence of two endangered freshwater species, the white-clawed crayfish <i>Austropotamobius pallipes</i> and the Eurasian otter <i>Lutra lutra</i> at eight sites in four river catchments in Liguria (northwestern Italy). The Eurasian otter was considered extinct in the study area since the 1980s. However, recent, although scattered sightings indicated a recolonisation by a few individuals. The white-clawed crayfish populations declined drastically and became increasingly dispersed in the western part of Liguria. Our eDNA analysis confirmed the presence of both species in some of the selected rivers and detected Eurasian otter DNA where the species was not recorded through traditional monitoring methods. This study confirms eDNA-based monitoring approaches as valuable tools to assess the presence of rare and elusive species and help implement protection plans at a local scale.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"41 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140595650","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}
引用次数: 0
eDNA metabarcoding reveals a rich but threatened and declining elasmobranch community in West Africa’s largest marine protected area, the Banc d’Arguin eDNA 代谢标定揭示了西非最大的海洋保护区--阿尔金湾丰富但濒临灭绝的箭亚纲动物群落
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-02-22 DOI: 10.1007/s10592-024-01604-y
Carolina de la Hoz Schilling, Rima W. Jabado, Ana Veríssimo, Luca Caminiti, Ebaye Sidina, Cheikhna Yero Gandega, Ester A. Serrão
{"title":"eDNA metabarcoding reveals a rich but threatened and declining elasmobranch community in West Africa’s largest marine protected area, the Banc d’Arguin","authors":"Carolina de la Hoz Schilling, Rima W. Jabado, Ana Veríssimo, Luca Caminiti, Ebaye Sidina, Cheikhna Yero Gandega, Ester A. Serrão","doi":"10.1007/s10592-024-01604-y","DOIUrl":"https://doi.org/10.1007/s10592-024-01604-y","url":null,"abstract":"<p>Elasmobranchs (sharks and rays) are the most threatened marine vertebrates, particularly in tropical and subtropical areas. Their population status is often poorly understood due to insufficient information. Despite reportedly harbouring critical elasmobranch habitats, the Banc d’Arguin National Park (PNBA) in Mauritania lacks comprehensive and updated information on the diversity of elasmobranch species in the area. We developed a baseline inventory based on morphological and molecular identification and metabarcoding. DNA barcoding of tissue samples from elasmobranch processing sites and freshly sampled specimens was used to build a genetic reference database of local elasmobranch species. The richness and diversity of species in the PNBA were described via metabarcoding of seawater eDNA samples using an elasmobranch-specific assay and our reference database. We detected 27 species, including 12 new species records for the PNBA. We further uncover potentially undescribed species of <i>Gymnura</i> and <i>Torpedo</i>, while taxonomic corrections are noted for previously reported species. In particular, the reportedly abundant <i>Mustelus mustelus</i> was absent from tissue and eDNA samples, while <i>M. punctulatus</i> was detected instead. Taxa that have anecdotally become regionally extinct or rare (e.g., sawfishes, wedgefishes, lemon sharks) were not detected, highlighting local species diversity shifts within the last few decades. Results show that 67.9% of elasmobranch species in the PNBA are threatened with extinction according to the IUCN Red List of Threatened Species. This study emphasises the importance of taxonomic identification in support of species management and provides a baseline to inform future studies and conservation measures to avoid further species losses.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"7 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139956471","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}
引用次数: 0
Genomic data identify genetic structure in Enoploctenus cyclothorax (Araneae: Ctenidae), revealing two distinct taxonomic units in the southern region of the Brazilian Atlantic Forest 基因组数据确定了 Enoploctenus cyclothorax(鹤形目:栉水母科)的遗传结构,揭示了巴西大西洋森林南部地区两个不同的分类单元
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-02-17 DOI: 10.1007/s10592-024-01609-7
Mariana Costa Terra, Antonio Domingos Brescovit, Rogério Fernandes de Souza, Ana Lúcia Dias, Matheus Pires Rincão, Renata da Rosa
{"title":"Genomic data identify genetic structure in Enoploctenus cyclothorax (Araneae: Ctenidae), revealing two distinct taxonomic units in the southern region of the Brazilian Atlantic Forest","authors":"Mariana Costa Terra, Antonio Domingos Brescovit, Rogério Fernandes de Souza, Ana Lúcia Dias, Matheus Pires Rincão, Renata da Rosa","doi":"10.1007/s10592-024-01609-7","DOIUrl":"https://doi.org/10.1007/s10592-024-01609-7","url":null,"abstract":"<p>Habitat fragmentation is among the greatest threats to arachnids present in the forests, especially to <i>Enoploctenus cyclothorax</i> (Ctenidae), which is widely distributed in the Atlantic Forest of southern and southeastern Brazil. Fragmented populations, whether due to anthropic or stochastic factors, tend to be more susceptible to extinction, since genetic diversity is reduced in small and isolated populations. Considering this, the current work aimed to understand how the genetic variability is distributed in six populations of <i>E. cyclothorax</i> (120 individuals sampled), sampled in fragments of the Atlantic Forest in Paraná (Brazil), based on Single Nucleotide Polymorphism (SNP) genotyping. The results obtained support the separation of <i>E. cyclothorax</i> into two distinct genetic groups in the state, based mainly on analyses of genetic structure and connectivity. A strong and significant genetic structure was observed in the species, supported by the k = 3 estimated using Bayesian analysis, by the high values of <i>F</i><sub><i>ST</i></sub> genetic differentiation, and by the low gene flow identified between the genetic groups. Corroborating these results, isolation by distance and the presence of a genetic barrier in the evaluated populations were evidenced. Population genomic analysis also revealed non-homogeneous genetic diversity in <i>E. cyclothorax</i> (<i>H</i><sub><i>E</i></sub> = 0.14 to 0.31). The hypothesis that population fragmentation could possibly impact the genetic variability of <i>E. cyclothorax</i> throughout the state was confirmed by the inferred data, which point to phytophysiognomy, geographical distance, and forest fragmentation as factors that shaped the current genetic structure identified in the evaluated populations.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"186 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139902379","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}
引用次数: 0
The importance of understanding clonal structure for species listing and recovery: case studies from the rare oconee bells (shortia brevistyla and shortia galacifolia; Diapensiaceae) and the federally endangered bunched arrowhead (sagittaria fasciculata; Alismataceae) 了解克隆结构对物种列名和恢复的重要性:对珍稀物种奥科尼钟(shortia brevistyla 和 shortia galacifolia;Diapensiaceae)和联邦濒危物种束箭草(sagittaria fasciculata;Alismataceae)的案例研究
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-02-14 DOI: 10.1007/s10592-024-01608-8
Skyler Fox, Lauren Eberth, J. Banks Floyd, Calla Pederson, Lily Stafford, Nora Tillmanns, Lo Vodo, Ashley B. Morris
{"title":"The importance of understanding clonal structure for species listing and recovery: case studies from the rare oconee bells (shortia brevistyla and shortia galacifolia; Diapensiaceae) and the federally endangered bunched arrowhead (sagittaria fasciculata; Alismataceae)","authors":"Skyler Fox, Lauren Eberth, J. Banks Floyd, Calla Pederson, Lily Stafford, Nora Tillmanns, Lo Vodo, Ashley B. Morris","doi":"10.1007/s10592-024-01608-8","DOIUrl":"https://doi.org/10.1007/s10592-024-01608-8","url":null,"abstract":"<p>Understanding genetic structure in rare plant populations is essential to making informed decisions for recovery actions, particularly in species capable of clonal reproduction. Here, we present three case studies using microsatellites to assess clonal structure in rare plants: Northern Oconee bells (<i>S. brevistyla</i> (P.A. Davies) Gaddy) and Southern Oconee bells (<i>Shortia galacifolia</i> Torr &amp; Gray) (Diapensiaceae); and bunched arrowhead (<i>Sagittaria fasciculata</i> E.O. Beal (Alismataceae)). We used six loci to genotype <i>Shortia brevistyla</i> (<i>n</i> = 62 ramets; three sites) and <i>S. galacifolia</i> (<i>n</i> = 111 ramets; seven sites) and five loci in <i>Sagittaria fasciculata</i> (<i>n</i> = 162 ramets; eight sites). Ramets were systematically mapped and sampled to allow for clonal assignment in a spatial context. All ramets for <i>S. brevistyla</i> were genetically identical across all loci, while <i>S. galacifolia</i> exhibited variation consistent with a mixed reproductive strategy. <i>Sagittaria fasciculata</i> also exhibited a mixed reproductive strategy with emphasis on clonality. Our data indicate that stem counts are not effective measures for recovery assessment in these species, and a more complex demographic monitoring protocol should be developed. Additional implications for conservation of these species are discussed, including a consideration for federal listing for <i>Shortia brevistyla</i>.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"27 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767221","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}
引用次数: 0
Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape 在高度破碎化的地貌中,残存的肯古尔(Phascogale calura)保留了遗传连接性和遗传多样性
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-02-13 DOI: 10.1007/s10592-024-01603-z
{"title":"Remnant kenngoor (Phascogale calura) retain genetic connectivity and genetic diversity in a highly fragmented landscape","authors":"","doi":"10.1007/s10592-024-01603-z","DOIUrl":"https://doi.org/10.1007/s10592-024-01603-z","url":null,"abstract":"<h3>Abstract</h3> <p>Kenngoor (<em>Phascogale calura</em>) persist in &lt; 1% of their original distribution, occupying highly fragmented remnant habitat in south-west Western Australia, with very little known of the genetic diversity of the remaining wild populations. Recently, the species has been translocated to managed reserves to improve its conservation. Understanding genetic structure and patterns of genetic diversity is crucial to inform conservation translocations for species recovery. This study aims to (1) assess genetic structure and genetic diversity across remaining wild locations, (2) assess long-term genetic outcomes of a mixed-source wild-to-wild translocation, and (3) estimate global effective population size. We genotyped 209 samples from 13 locations of fragmented remnant habitat using reduced representation sequencing. An isolation by distance model best explained genetic structure across the survey areas, with evidence of fine scale divergence of two northern locations. Allelic richness and autosomal heterozygosity measures indicated that diversity is spread uniformly across locations, and no locations showed signs of inbreeding or strong genetic drift. The mixed-source translocation has retained the diversity of the wider species ten years post-translocation. Overall, our results suggest that connectivity between survey areas has largely been maintained and that no location has substantially lower genetic diversity, despite the highly fragmented nature of remnant kenngoor habitat. Future translocations should aim to represent a mixture of genetically divergent locations to maintain the diversity present at the species level. Ongoing conservation management will be required to ensure the long-term viability of the species in this fragmented landscape.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"308 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767153","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}
引用次数: 0
Effective population size of adult and offspring cohorts as a genetic monitoring tool in two stand-forming and wind-pollinated tree species: Fagus sylvatica L. and Picea abies (L.) Karst. 将成株和后代群体的有效种群数量作为两种林木和风媒花树种的遗传监测工具:Fagus sylvatica L. 和 Picea abies (L. Karst):Fagus sylvatica L. 和 Picea abies (L.) Karst.
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-02-11 DOI: 10.1007/s10592-024-01600-2
Heike Liesebach, Pascal Eusemann, Aki M. Höltken, Ute Tröber, Oleksandra Kuchma, Manuel Karopka, Frank Becker, Ralf Kätzel, Barbara Fussi
{"title":"Effective population size of adult and offspring cohorts as a genetic monitoring tool in two stand-forming and wind-pollinated tree species: Fagus sylvatica L. and Picea abies (L.) Karst.","authors":"Heike Liesebach, Pascal Eusemann, Aki M. Höltken, Ute Tröber, Oleksandra Kuchma, Manuel Karopka, Frank Becker, Ralf Kätzel, Barbara Fussi","doi":"10.1007/s10592-024-01600-2","DOIUrl":"https://doi.org/10.1007/s10592-024-01600-2","url":null,"abstract":"<p>Genetic diversity is considered to be a prerequisite for adaptation and adaptability as it is a key element of biological diversity. However, the monitoring of genetic diversity has tended to be ignored in biodiversity monitoring. We report a comprehensive genetic monitoring effort in two dominant forest tree species, which was started with a baseline survey in 12 European beech populations and 10 Norway spruce populations in Germany. The standardized experimental design is based on collecting samples of at least 250 adult trees, and 400 natural regeneration and 400 seed samples and their genotyping with 15–16 high-resolution SSR markers. In addition to commonly used mean values across the markers to quantify genetic diversity, we placed special emphasis on various marker-based, pedigree-based and demographic models for estimating the contemporary effective population size N<sub>e</sub> of the different generations. In both beech and spruce, no variation in genetic diversity with mean values across markers was detectable between the studied stands and between age cohorts. We detected that stable allelic diversity in progeny generations is ensured by sufficient gene flow from surrounding forests. However, estimates of effective population size show marked differentiation among populations and among age cohorts. Natural regeneration samples appear to converge on the parent generation, while seed samples show a clear bottleneck effect. The N<sub>e</sub> parameter can be used to derive conclusions for sustainable natural regeneration management in forest stands and for seed stand approvals including adequate seed collections for appropriate artificial regenerations.The sibship frequency-based method for N<sub>e</sub> estimates is presented as much more robust than the widely used LD estimates, which often fail for samples with too weak relatedness. Despite the distinct kinship structure in our monitoring plots, the contemporary effective population size proves to be an essential parameter for assessing the integrity of the reproductive system.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"1 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767220","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}
引用次数: 0
Towards a genomic resolution of the Phengaris alcon species complex 实现 Phengaris alcon 物种复合体的基因组解析
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-01-28 DOI: 10.1007/s10592-024-01605-x
Kay Lucek, Lucas Blattner, Camille Cornet, Yannick Chittaro, Andreas Erhardt, Andreas Jaun, Bernhard Jost, Nathalie Winiger, Hans-Peter Wymann, Goran Dušej
{"title":"Towards a genomic resolution of the Phengaris alcon species complex","authors":"Kay Lucek, Lucas Blattner, Camille Cornet, Yannick Chittaro, Andreas Erhardt, Andreas Jaun, Bernhard Jost, Nathalie Winiger, Hans-Peter Wymann, Goran Dušej","doi":"10.1007/s10592-024-01605-x","DOIUrl":"https://doi.org/10.1007/s10592-024-01605-x","url":null,"abstract":"<p>Taxonomic entities below the species level often pose difficulties for conservation practice, especially when they are ecologically distinct from the nominal species. Genomic tools provide the opportunity to study and potentially resolve such cryptic diversity. The Alcon blue butterfly <i>Phengaris alcon</i> species complex is such a cryptic example, comprising different ecotypes or even subspecies, one of them is the high elevation taxon <i>P. rebeli</i> from the European Alps. We sequenced a first reference genome for <i>Phengaris alcon</i>. Furthermore, we generated whole genome resequence data for individuals of three Swiss ecotypes, i.e., the low elevation <i>P. alcon</i>, the mid elevation and high elevation alpine <i>P. rebeli</i> and integrated genomic data from across Europe to study the relationship among these ecotypes. At a European scale, our results suggest that for the <i>P. alcon</i> complex, biogeography and the evolutionary context of diversification is more multifaceted than previously suggested, falling in the range of more recent ecological speciation. In Switzerland, the three ecotypes were genetically isolated with only limited current gene flow between them. Past gene flow, however, could have given rise to the mid elevation ecotype. Our findings emphasise that high elevation <i>P. rebeli</i> in the Alps should be treated as a distinct species. Our study highlights how the availability of reference genome assemblies allows to address so far open taxonomic questions in conservation research and that broadscale studies are needed to understand the biogeographic history of apparent diversification.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"39 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139588188","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}
引用次数: 0
Sampling through space and time: multi-year analysis reveals dynamic population genetic patterns for an amphibian metapopulation 时空取样:多年分析揭示两栖动物元种群的动态种群遗传模式
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-01-28 DOI: 10.1007/s10592-024-01602-0
Chloe E. Moore, Meryl C. Mims
{"title":"Sampling through space and time: multi-year analysis reveals dynamic population genetic patterns for an amphibian metapopulation","authors":"Chloe E. Moore, Meryl C. Mims","doi":"10.1007/s10592-024-01602-0","DOIUrl":"https://doi.org/10.1007/s10592-024-01602-0","url":null,"abstract":"<p>Metapopulations are dynamic, and population genetics can reveal both spatial and temporal metapopulation variation. Yet, population genetic studies often focus on samples collected within a single time period or combine samples taken across time periods due to limited resources and the assumption that these approaches capture patterns and processes occurring over decadal and longer temporal scales. However, this may leave important fine-scale temporal variation in genetic composition undetected, particularly for metapopulations in which dynamic populations are expected. We investigated temporal patterns of population genetic diversity, effective population size, and differentiation across three sample periods for a dryland amphibian metapopulation. We sampled nine distinct Arizona treefrog (<i>Hyla (Dryophytes) wrightorum</i>) breeding ponds in 2014, 2018/2019, and 2021 and genotyped 17 microsatellite loci to quantify spatial and temporal population genetic dynamics. Genetic diversity within and between populations varied significantly among years. Most notably, we identified a concerning decline in allelic richness across populations, with an average − 26.11% difference between a population’s first and last sample period. Effective population sizes were generally small (N<sub>e</sub> &lt; 100) and variable within and among populations over time, with many populations falling below common conservation thresholds by the final sample period. Trends in global genetic diversity, as measured by heterozygosity, and population differentiation were relatively consistent across all sampling periods. Overall, we found that “snapshot” or single-time sampling approaches may miss temporal variability in genetic composition that has important conservation implications, including early warning signs of decline in genetic diversity.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"5 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139588303","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}
引用次数: 0
Genetic diversity and inbreeding in an endangered island-dwelling parrot population following repeated population bottlenecks 濒危岛栖鹦鹉种群在反复出现种群瓶颈后的遗传多样性和近亲繁殖问题
IF 2.2 3区 环境科学与生态学
Conservation Genetics Pub Date : 2024-01-23 DOI: 10.1007/s10592-023-01599-y
Daniel Gautschi, Robert Heinsohn, Luis Ortiz-Catedral, Dejan Stojanovic, Melinda Wilson, Ross Crates, Nicholas A. Macgregor, Penny Olsen, Linda Neaves
{"title":"Genetic diversity and inbreeding in an endangered island-dwelling parrot population following repeated population bottlenecks","authors":"Daniel Gautschi, Robert Heinsohn, Luis Ortiz-Catedral, Dejan Stojanovic, Melinda Wilson, Ross Crates, Nicholas A. Macgregor, Penny Olsen, Linda Neaves","doi":"10.1007/s10592-023-01599-y","DOIUrl":"https://doi.org/10.1007/s10592-023-01599-y","url":null,"abstract":"<p>Genetic diversity and population structure can have important implications for the management of threatened species. This is particularly true for small, isolated populations that have experienced significant declines or population bottlenecks. The Norfolk Island green parrot <i>Cyanoramphus cookii</i> is an endangered species at risk of inbreeding and loss of genetic diversity due to its restricted range and the population bottlenecks experienced in recent decades. To assess the severity of inbreeding and loss of genetic diversity in the population we analyzed single nucleotide polymorphisms (SNPs) for 157 unique genetic samples collected from nestlings and randomly captured adult birds between 2015 and 2022. We also assessed the population for genetic structure, calculated sex ratios, and looked for evidence of past population bottlenecks. Our analysis revealed that 17.83% of individuals sampled were highly inbred (<i>F</i> &gt; 0.125), although expected heterozygosity (<i>H</i><sub>E</sub>) did not significantly differ from observed heterozygosity (<i>H</i><sub>O</sub>) and the average inbreeding coefficient was low. The estimated effective population size (<i>N</i><sub>e</sub>) was 43.8 and we found no evidence of genetic structure. Demographic simulations provided support for scenarios including multiple population bottlenecks, when compared to those with a single population bottleneck or no past bottlenecks. We discuss the implications of our findings for the future management of the species including any potential attempt to establish an insurance population via translocation. Our study highlights the importance of considering population genetics when determining appropriate management actions for threatened species and the need to assess non-model species on an individual basis.</p>","PeriodicalId":55212,"journal":{"name":"Conservation Genetics","volume":"10 1","pages":""},"PeriodicalIF":2.2,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139555776","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}
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