Molecular Ecology Resources最新文献

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Individual-based landscape genomics for conservation: An analysis pipeline. 基于个体的景观基因组学保护:分析管道。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-26 DOI: 10.1111/1755-0998.13884
E Anne Chambers, Anusha P Bishop, Ian J Wang
{"title":"Individual-based landscape genomics for conservation: An analysis pipeline.","authors":"E Anne Chambers,&nbsp;Anusha P Bishop,&nbsp;Ian J Wang","doi":"10.1111/1755-0998.13884","DOIUrl":"https://doi.org/10.1111/1755-0998.13884","url":null,"abstract":"<p><p>Landscape genomics can harness environmental and genetic data to inform conservation decisions by providing essential insights into how landscapes shape biodiversity. The massive increase in genetic data afforded by the genomic era provides exceptional resolution for answering critical conservation genetics questions. The accessibility of genomic data for non-model systems has also enabled a shift away from population-based sampling to individual-based sampling, which now provides accurate and robust estimates of genetic variation that can be used to examine the spatial structure of genomic diversity, population connectivity and the nature of environmental adaptation. Nevertheless, the adoption of individual-based sampling in conservation genetics has been slowed due, in large part, to concerns over how to apply methods developed for population-based sampling to individual-based sampling schemes. Here, we discuss the benefits of individual-based sampling for conservation and describe how landscape genomic methods, paired with individual-based sampling, can answer fundamental conservation questions. We have curated key landscape genomic methods into a user-friendly, open-source workflow, which we provide as a new R package, A Landscape Genomics Analysis Toolkit in R (algatr). The algatr package includes novel added functionality for all of the included methods and extensive vignettes designed with the primary goal of making landscape genomic approaches more accessible and explicitly applicable to conservation biology.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54227139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review 连锁不平衡方法在估计当代有效人口规模中的实际应用:综述。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-24 DOI: 10.1111/1755-0998.13879
Robin S. Waples
{"title":"Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review","authors":"Robin S. Waples","doi":"10.1111/1755-0998.13879","DOIUrl":"10.1111/1755-0998.13879","url":null,"abstract":"<p>The method to estimate contemporary effective population size (<i>N</i><sub>e</sub>) based on patterns of linkage disequilibrium (LD) at unlinked loci has been widely applied to natural and managed populations. The underlying model makes many simplifying assumptions, most of which have been evaluated in numerous studies published over the last two decades. Here, these performance evaluations are reviewed and summarized, with a focus on information that facilitates practical application to real populations in nature. Potential sources of bias that are discussed include calculation of <i>r</i><sup>2</sup> (a measure of LD), adjustments for sampling error, physical linkage, age structure, migration and spatial structure, mutation and selection, mating systems, changes in abundance, rare alleles, missing data, genotyping errors, data filtering choices and methods for combining multiple <i>N</i><sub>e</sub> estimates. Factors that affect precision are reviewed, including pseudoreplication that limits the information gained from large genomics datasets, constraints imposed by small samples of individuals, and the challenges in obtaining robust estimates for large populations. Topics that merit further research include the potential to weight <i>r</i><sup>2</sup> values by allele frequency, lump samples of individuals, use genotypic likelihoods rather than called genotypes, prune large LD values and apply the method to species practising partial monogamy.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49687386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Journeying towards best practice data management in biodiversity genomics. 生物多样性基因组学最佳实践数据管理之旅。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-24 DOI: 10.1111/1755-0998.13880
Natalie J Forsdick, Jana Wold, Anton Angelo, François Bissey, Jamie Hart, Mitchell Head, Libby Liggins, Dinindu Senanayake, Tammy E Steeves
{"title":"Journeying towards best practice data management in biodiversity genomics.","authors":"Natalie J Forsdick,&nbsp;Jana Wold,&nbsp;Anton Angelo,&nbsp;François Bissey,&nbsp;Jamie Hart,&nbsp;Mitchell Head,&nbsp;Libby Liggins,&nbsp;Dinindu Senanayake,&nbsp;Tammy E Steeves","doi":"10.1111/1755-0998.13880","DOIUrl":"https://doi.org/10.1111/1755-0998.13880","url":null,"abstract":"<p><p>Advances in sequencing technologies and declining costs are increasing the accessibility of large-scale biodiversity genomic datasets. To maximize the impact of these data, a careful, considered approach to data management is essential. However, challenges associated with the management of such datasets remain, exacerbated by uncertainty among the research community as to what constitutes best practices. As an interdisciplinary team with diverse data management experience, we recognize the growing need for guidance on comprehensive data management practices that minimize the risks of data loss, maximize efficiency for stand-alone projects, enhance opportunities for data reuse, facilitate Indigenous data sovereignty and uphold the FAIR and CARE Guiding Principles. Here, we describe four fictional personas reflecting differing user experiences with data management to identify data management challenges across the biodiversity genomics research ecosystem. We then use these personas to demonstrate realistic considerations, compromises and actions for biodiversity genomic data management. We also launch the Biodiversity Genomics Data Management Hub (https://genomicsaotearoa.github.io/data-management-resources/), containing tips, tricks and resources to support biodiversity genomics researchers, especially those new to data management, in their journey towards best practice. The Hub also provides an opportunity for those biodiversity researchers whose expertise lies beyond genomics and are keen to advance their data management journey. We aim to support the biodiversity genomics community in embedding data management throughout the research lifecycle to maximize research impact and outcomes.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49687385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database 用于地下进化比较研究的合作骨干资源:世界昆虫科数据库。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-21 DOI: 10.1111/1755-0998.13882
Nathanaelle Saclier, Louis Duchemin, Lara Konecny-Dupré, Philippe Grison, David Eme, Chloé Martin, Cécile Callou, Tristan Lefébure, Clémentine François, Colin Issartel, Julian J. Lewis, Fabio Stoch, Boris Sket, Sanja Gottstein, Teo Delić, Maja Zagmajster, Michal Grabowski, Dieter Weber, Ana Sofia P. S. Reboleira, Dmitry Palatov, Kaloust Paragamian, Lee R. F. D. Knight, Georges Michel, Francois Lefebvre, Mohammad-Javad Malek Hosseini, Ana I. Camacho, Begoña Gartzia De Bikuña, Amina Taleb, Nouria Belaidi, Raoul P. Tuekam Kayo, Diana Maria Paola Galassi, Oana Teodora Moldovan, Christophe J. Douady, Florian Malard
{"title":"A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database","authors":"Nathanaelle Saclier,&nbsp;Louis Duchemin,&nbsp;Lara Konecny-Dupré,&nbsp;Philippe Grison,&nbsp;David Eme,&nbsp;Chloé Martin,&nbsp;Cécile Callou,&nbsp;Tristan Lefébure,&nbsp;Clémentine François,&nbsp;Colin Issartel,&nbsp;Julian J. Lewis,&nbsp;Fabio Stoch,&nbsp;Boris Sket,&nbsp;Sanja Gottstein,&nbsp;Teo Delić,&nbsp;Maja Zagmajster,&nbsp;Michal Grabowski,&nbsp;Dieter Weber,&nbsp;Ana Sofia P. S. Reboleira,&nbsp;Dmitry Palatov,&nbsp;Kaloust Paragamian,&nbsp;Lee R. F. D. Knight,&nbsp;Georges Michel,&nbsp;Francois Lefebvre,&nbsp;Mohammad-Javad Malek Hosseini,&nbsp;Ana I. Camacho,&nbsp;Begoña Gartzia De Bikuña,&nbsp;Amina Taleb,&nbsp;Nouria Belaidi,&nbsp;Raoul P. Tuekam Kayo,&nbsp;Diana Maria Paola Galassi,&nbsp;Oana Teodora Moldovan,&nbsp;Christophe J. Douady,&nbsp;Florian Malard","doi":"10.1111/1755-0998.13882","DOIUrl":"10.1111/1755-0998.13882","url":null,"abstract":"<p>Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species-rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large-scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade-offs during groundwater colonization.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Conservation in a litre of air 保存在一升空气中。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-21 DOI: 10.1111/1755-0998.13883
David M. Lodge
{"title":"Conservation in a litre of air","authors":"David M. Lodge","doi":"10.1111/1755-0998.13883","DOIUrl":"10.1111/1755-0998.13883","url":null,"abstract":"<p>Since Ficetola et al. (2008) alerted ecologists and conservation biologists to the existence of environmental DNA (eDNA), the number of studies using eDNA has exploded, with a rapidly increasing diversity of research, monitoring, and management objectives. Initial applications focused on amphibians and fishes while today's taxonomic targets span the phylogenetic tree. The environmental media that are sampled have expanded from freshwater to saltwater to soils, and, most recently, to air. In this issue of Molecular Ecology Resources, Lynggaard et al. (Molecular Ecology Resources, 2023) use eDNA captured on air filters to census vertebrate biodiversity in a forest. With a three day, six sample period, 143 sample effort in a nature park in a rural area of Zealand, Denmark, their wild species detections comprised about 25% of the terrestrial vertebrates that are known to occur in the area, including about 33% of the mammal, 17% of the bird, and 60% of the amphibian species. This study demonstrates that air sampling for eDNA has the potential to become a powerful standard method for terrestrial biodiversity assessment that is complementary to traditional methods (e.g., trapping, visual and acoustic observation, collection of scat and hair).</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13883","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49672120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa. 条形码和传统健康从业者的观点有助于监测和保护南非城市中以传统药物交易的青蛙和爬行动物。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-16 DOI: 10.1111/1755-0998.13873
Fortunate M Phaka, Edward C Netherlands, Maarten Van Steenberge, Erik Verheyen, Gontran Sonet, Jean Hugé, Louis H du Preez, Maarten P M Vanhove
{"title":"Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa.","authors":"Fortunate M Phaka,&nbsp;Edward C Netherlands,&nbsp;Maarten Van Steenberge,&nbsp;Erik Verheyen,&nbsp;Gontran Sonet,&nbsp;Jean Hugé,&nbsp;Louis H du Preez,&nbsp;Maarten P M Vanhove","doi":"10.1111/1755-0998.13873","DOIUrl":"https://doi.org/10.1111/1755-0998.13873","url":null,"abstract":"<p><p>Previous literature suggests that Indigenous cultural practices, specifically traditional medicine, are commonplace among urban communities contrary to the general conception that such practices are restricted to rural societies. We reviewed previous literature for records of herptiles (frog and reptile species) sold by traditional health practitioners in urban South Africa, then used visual confirmation surveys, DNA barcoding and folk taxonomy to identify the herptile species that were on sale. Additionally, we interviewed 11 IsiZulu and SePedi speaking traditional health practitioners to document details of the collection and pricing of herptile specimens along with the practitioners' views of current conservation measures for traditional medicine markets. The 34 herptile species recorded in previous literature on traditional medicine markets included endangered and non-native species. Spectrophotometry measurements of the DNA we extracted from the tissue of herptiles used in traditional medicine were an unreliable predictor of whether those extractions would be suitable for further experimental work. From our initial set of 111 tissue samples, 81 sequencing reactions were successful and 55 of those sequences had species-level matches to COI reference sequences on the NCBI GenBank and/or BOLD databases. Molecular identification revealed that traditional health practitioners correctly labelled 77% of the samples that we successfully identified with DNA barcoding in this study. Our mixed methodology approach is useful for conservation planning as it updates knowledge of animal use in Indigenous remedies and can accurately identify species of high conservation priority. Furthermore, this study highlights the possibility of collaborative conservation planning with traditional health practitioners.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41230987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites 使用纳米孔长读测序进行代谢编码,以无偏地表征顶端复合体类血寄生虫。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-14 DOI: 10.1111/1755-0998.13878
Lucas G. Huggins, Vito Colella, Neil D. Young, Rebecca J. Traub
{"title":"Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites","authors":"Lucas G. Huggins,&nbsp;Vito Colella,&nbsp;Neil D. Young,&nbsp;Rebecca J. Traub","doi":"10.1111/1755-0998.13878","DOIUrl":"10.1111/1755-0998.13878","url":null,"abstract":"<p>Apicomplexan haemoparasites generate significant morbidity and mortality in humans and other animals, particularly in many low-to-middle income countries. Malaria caused by <i>Plasmodium</i> remains responsible for some of the highest numbers of annual deaths of any human pathogen, whilst piroplasmids, such as <i>Babesia</i> and <i>Theileria</i> can have immense negative economic effects through livestock loss. Diagnosing haemoparasites via traditional methods like microscopy is challenging due to low-level and transient parasitaemia. PCR-based diagnostics overcome these limitations by being both highly sensitive and specific, but they may be unable to accurately detect coinfections or identify novel species. In contrast, next-generation sequencing (NGS)-based methods can characterize all pathogens from a group of interest concurrently, although, the short-read platforms previously used have been limited in the taxonomic resolution achievable. Here, we used Oxford Nanopore Technologies' (ONT) long-read MinION™ sequencer to conduct apicomplexan haemoparasite metabarcoding via sequencing the near full-length 18S ribosomal RNA gene, demonstrating its ability to detect <i>Babesia</i>, <i>Hepatozoon</i>, <i>Neospora</i>, <i>Plasmodium</i>, <i>Theileria</i> and <i>Toxoplasma</i> species. This method was tested on blood-extracted DNA from 100 dogs and the results benchmarked against qPCR and Illumina-based metabarcoding. For two common haemoparasites, nanopore sequencing performed as well as qPCR (kappa agreement statistics &gt; 0.98), whilst also detecting one pathogen, <i>Hepatozoon felis</i>, missed by the other techniques. The long-reads obtained by nanopore sequencing provide an improved species-level taxonomic resolution whilst the method's broad applicability mean it can be used to explore apicomplexan communities from diverse mammalian hosts, on a portable sequencer that easily permits adaptation to field use.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 2","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13878","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41186638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons 通过两个夏季的定量环境DNA代谢编码调查监测多种鱼类。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-13 DOI: 10.1111/1755-0998.13875
Luhan Wu, Tomonori Osugi, Takashi Inagawa, Jiro Okitsu, Shogo Sakamoto, Toshifumi Minamoto
{"title":"Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons","authors":"Luhan Wu,&nbsp;Tomonori Osugi,&nbsp;Takashi Inagawa,&nbsp;Jiro Okitsu,&nbsp;Shogo Sakamoto,&nbsp;Toshifumi Minamoto","doi":"10.1111/1755-0998.13875","DOIUrl":"10.1111/1755-0998.13875","url":null,"abstract":"<p>Periodic monitoring can provide important information for the protection of endangered fish, sustainable use of fishery resources and management of alien species. Previous studies have attempted to monitor fish using non-invasive environmental DNA (eDNA) technology, generally employing quantitative PCR to quantify the eDNA concentration. However, the throughput was limited. High-throughput metabarcoding technology can detect the DNA of multiple species simultaneously in a single experiment but does not provide sufficient quantification. In this study, we applied a quantitative metabarcoding approach to simultaneously quantify the eDNA concentration of an entire fish assemblage in a small reservoir over two summer seasons. Traditional surveys were also conducted to investigate the individuals of fish. The eDNA concentrations were quantified using quantitative metabarcoding, and the fish species detected using this approach were highly consistent with the results of traditional fish monitoring. A significant positive relationship was observed between the eDNA concentration and fish species abundance. Seasonal changes in fish community structure were estimated using eDNA concentrations, which may reveal the activity seasons of different fish. The eDNA concentrations of different fish species peaked at different water temperatures, reflecting the differential responses of fish species to this environmental factor. Finally, by detecting outlier eDNA concentrations, the spawning activities of 13 fish species were estimated, 12 of which were roughly consistent with the current knowledge of fish spawning periods. These results indicate that quantitative eDNA metabarcoding with dozens of sampling times is useful for the simultaneous ecological monitoring of multiple fish species.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41186639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Demogenomic inference from spatially and temporally heterogeneous samples 来自空间和时间异质样本的人口基因组推断。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-11 DOI: 10.1111/1755-0998.13877
Nina Marchi, Adamandia Kapopoulou, Laurent Excoffier
{"title":"Demogenomic inference from spatially and temporally heterogeneous samples","authors":"Nina Marchi,&nbsp;Adamandia Kapopoulou,&nbsp;Laurent Excoffier","doi":"10.1111/1755-0998.13877","DOIUrl":"10.1111/1755-0998.13877","url":null,"abstract":"<p>Modern and ancient genomes are not necessarily drawn from homogeneous populations, as they may have been collected from different places and at different times. This heterogeneous sampling can be an issue for demographic inferences and results in biased demographic parameters and incorrect model choice if not properly considered. When explicitly accounted for, it can result in very complex models and high data dimensionality that are difficult to analyse. In this paper, we formally study the impact of such spatial and temporal sampling heterogeneity on demographic inference, and we introduce a way to circumvent this problem. To deal with structured samples without increasing the dimensionality of the site frequency spectrum (SFS), we introduce a new structured approach to the existing program <i>fastsimcoal2</i>. We assess the efficiency and relevance of this methodological update with simulated and modern human genomic data. We particularly focus on spatial and temporal heterogeneities to evidence the interest of this new SFS-based approach, which can be especially useful when handling scattered and ancient DNA samples, as in conservation genetics or archaeogenetics.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13877","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41186637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
One metric or many? Refining the analytical framework of landscape resistance estimation in individual-based landscape genetic analyses 一个度量还是多个度量?完善了基于个体的景观遗传分析中景观抗性估计的分析框架。
IF 7.7 1区 生物学
Molecular Ecology Resources Pub Date : 2023-10-11 DOI: 10.1111/1755-0998.13876
William E. Peterman
{"title":"One metric or many? Refining the analytical framework of landscape resistance estimation in individual-based landscape genetic analyses","authors":"William E. Peterman","doi":"10.1111/1755-0998.13876","DOIUrl":"10.1111/1755-0998.13876","url":null,"abstract":"<p>One of the allures of landscape genetics is the ability to leverage pairwise genetic distance metrics to infer how landscape features promote or constrain gene flow (i.e. landscape resistance surfaces). Critically, properly parameterized landscape resistance surfaces are foundational to applied conservation and management decisions. As such, there has been considerable effort expended assessing methods and metrics to estimate landscape resistance from genetic data (Balkenhol <i>et al</i>., <i>Ecography</i>, <i>32</i>, 2009, 818; Peterman <i>et al.</i>, <i>Landsc. Ecol.</i>, <i>34</i>, 2019, 2197; Shirk et al., <i>Mol. Ecol. Resour.</i>, <i>17</i>, 2017, 1308; Shirk et al., <i>Mol. Ecol. Resour.</i>, <i>18</i>, 2018, 55). Nonetheless, a primary challenge to assessing the effects of landscapes on gene flow is in the estimation of landscape resistance values, and this problem becomes increasingly challenging as more landscape features or land cover classes are considered. It quickly becomes infeasible to adequately assess the potential parameter space through manual or systematic assignment of resistance values. The development of ResistanceGA (Peterman, <i>Methods Ecol. Evol.</i>, <i>9</i>, 2018, 1638) provided a framework for using genetic algorithms to optimize landscape resistance values and identify the best statistical relationship between pairwise effective distances and genetic distances. ResistanceGA has seen extensive use in both population- and individual-based landscape genetic analyses. However, there has been relatively limited assessment of ResistanceGA's ability to identify the landscape features affecting gene flow (but see Peterman <i>et al.</i>, <i>Landsc. Ecol.</i>, <i>34</i>, 2019, 2197; Winiarski <i>et al.</i>, <i>Mol. Ecol. Resour</i>., <i>20</i>, 2020, 1583) or the sensitivity of ResistanceGA results to the choice of genetic distance metric used. In the current issue of <i>Molecular Ecology Resources</i>, Beninde <i>et al</i>. (2023) aim to address these knowledge gaps by examining the impact of individual-based genetic distance measures on landscape genetic inference.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"24 1","pages":""},"PeriodicalIF":7.7,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.13876","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41186640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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