Evolutionary Applications最新文献

{"title":"Genomic Data Support the Revision of Provenance Regions Delimitation for Scots Pine","authors":"Martyna Lasek,&nbsp;Julia Zaborowska,&nbsp;Bartosz Łabiszak,&nbsp;Daniel J. Chmura,&nbsp;Witold Wachowiak","doi":"10.1111/eva.70038","DOIUrl":"10.1111/eva.70038","url":null,"abstract":"<p>Scots pine is a crucial component of ecosystems in Europe and Asia and a major utility species that comprises more than 60% of total forest production in Poland. Despite its importance, the genetic relationships between key conservation and the commercial value of Scots pine ecotypes in Poland remain unclear. To address this problem, we analyzed 27 populations (841 trees) of the most valuable Polish Scots pine ecotypes, including the oldest natural stands in all 24 regions of provenance established for the species in the country. By examining maternally inherited mitochondrial markers, nuclear microsatellite loci, and thousands of SNP markers from a genotyping array, we evaluated the genetic structure between and within them. These multilevel genomic data revealed high genetic similarity and a homogeneous structure in most populations, suggesting a common historical origin and admixture of populations after the postglacial recolonization of Central Europe. This research presents novel data on existing genomic resources among local ecotypes defined within strictly managed Polish regions of provenance, challenging their validity. Formal tests of the progeny of seed stands are needed to check whether the diversity in adaptation and quantitative traits still supports the delineation of provenance regions. In parallel, the health status of selected populations and the viability of seeds from these regions should be monitored to detect early-stage symptoms of their environmental stress. It seems reasonable that periodic shortages of forest reproductive material (FRM) in a given region of provenance could be supplemented with the one from other regions that match their climatic envelope. Together, our results have important implications for the management of native Scots pine stands, particularly elite breeding populations, as they contribute to the discussion of the boundaries of provenance regions and the transfers of FRM that face increasing climate change.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 11","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11568063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142646285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex Pheromone Mediates Resource Partitioning Between Drosophila melanogaster and D. suzukii","authors":"Charles A. Kwadha,&nbsp;Guillermo Rehermann,&nbsp;Deni Tasso,&nbsp;Simon Fellous,&nbsp;Marie Bengtsson,&nbsp;Erika A. Wallin,&nbsp;Adam Flöhr,&nbsp;Peter Witzgall,&nbsp;Paul G. Becher","doi":"10.1111/eva.70042","DOIUrl":"10.1111/eva.70042","url":null,"abstract":"<p>The spotted-wing drosophila, <i>Drosophila suzukii</i> and the cosmopolitan vinegar fly <i>D. melanogaster</i> feed on soft fruit and berries and widely overlap in geographic range. The presence of <i>D. melanogaster</i> reduces egg-laying in <i>D. suzukii</i>, possibly because <i>D. melanogaster</i> outcompetes <i>D. suzukii</i> larvae feeding in the same fruit substrate. Flies use pheromones to communicate for mating, but pheromones also serve a role in reproductive isolation between related species. We asked whether a <i>D. melanogaster</i> pheromone also modulates oviposition behaviour in <i>D. suzukii</i>. A dual-choice oviposition assay confirms that <i>D. suzukii</i> lays fewer eggs on blueberries exposed to <i>D. melanogaster</i> flies and further shows that female flies have a stronger effect than male flies. This was corroborated by treating berries with synthetic pheromones. Avoidance of <i>D. suzukii</i> oviposition is mediated by the female <i>D. melanogaster</i> pheromone (<i>Z</i>)-4-undecenal (Z4-11Al). Significantly fewer eggs were laid on berries treated with synthetic Z4-11Al. In comparison, the male pheromone (<i>Z</i>)-11-octadecenyl acetate (cVA) had no effect on <i>D. suzukii</i> oviposition. Z4-11Al is a highly volatile compound that is perceived via olfaction and it is accordingly behaviourally active at a distance from the source. <i>D. suzukii</i> is known to engage in mutual niche construction with the yeast <i>Hanseniaspora uvarum</i>, which strongly attracts flies. Adding Z4-11Al to fermenting <i>H. uvarum</i> significantly decreased <i>D. suzukii</i> flight attraction in a laboratory wind tunnel and a field trapping assay. That a <i>D. melanogaster</i> pheromone regulates oviposition in <i>D. suzukii</i> demonstrates that heterospecific pheromone communication contributes to reproductive isolation and resource partitioning in cognate species. Stimulo-deterrent diversion or push-pull methods, building on combined use of attractant and deterrent compounds, have shown promise for control of <i>D. suzukii</i>. A pheromone that specifically reduces <i>D. suzukii</i> attraction and oviposition adds to the toolbox for <i>D. suzukii</i> integrated management.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 11","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11555161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimating Demographic Parameters for Bearded Seals, Erignathus barbatus, in Alaska Using Close-Kin Mark-Recapture Methods","authors":"Brian D. Taras,&nbsp;Paul B. Conn,&nbsp;Mark V. Bravington,&nbsp;Andrzej Kilian,&nbsp;Aimée R. Lang,&nbsp;Anna Bryan,&nbsp;Raphaela Stimmelmayr,&nbsp;Lori Quakenbush","doi":"10.1111/eva.70035","DOIUrl":"10.1111/eva.70035","url":null,"abstract":"<p>Reliable estimates of population abundance and demographics are essential for managing harvested species. Ice-associated phocids, “ice seals,” are a vital resource for subsistence-dependent coastal Native communities in western and northern Alaska, USA. In 2012, the Beringia distinct population segment of the bearded seal, <i>Erignathus barbatus nauticus</i>, was listed as “threatened” under the US Endangered Species Act requiring greater scrutiny for management assessments. We sought to estimate requisite population parameters from harvested seals by using close-kin mark-recapture (CKMR) methods, the first such application for marine mammals. Samples from 1758 bearded seals harvested by Bering, Chukchi, and Beaufort Sea communities during 1998–2020 were genotyped, genetically sexed, and aged by tooth annuli. After rigorous quality control, kin relationships were established for 1484 seals including two parent–offspring pairs (POPs) and 25 potential second-order kin pairs. Most of the second-order kin were half-sibling pairs (HSPs), but four were potential grandparent-grandchild pairs (GGPs). There were no full sibling pairs, suggesting a lack of mate fidelity. Mitochondrial DNA analysis identified 17 potential HSPs as paternally related, providing substantial evidence of persistent heterogeneity in reproductive success among adult males. The statistical CKMR model incorporates probabilities associated with POPs, HSPs, and GGPs and assumes known ages and a stable population. Our top model accommodates heterogeneity in adult male breeding success and yields an abundance estimate of ~409,000 with a coefficient of variation (CV) = 0.35, which is substantially greater than the “non-heterogeneity” model estimate of ~232,000 (CV = 0.21), an important difference for managing a harvested species. Using CKMR methods with harvested species provides estimates of abundance with the added opportunity to acquire information about adult survival, fecundity, and breeding success that could be applied to other species of concern, marine and terrestrial.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 11","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and Habitat Rescue Improve Population Viability in Self-Incompatible Plants","authors":"Francisco Encinas-Viso,&nbsp;Peter H. Thrall,&nbsp;Andrew G. Young","doi":"10.1111/eva.70037","DOIUrl":"10.1111/eva.70037","url":null,"abstract":"<p>Habitat fragmentation and the acceleration of environmental change threaten the survival of many plant species. The problem is especially pronounced for plant species with self-incompatibility mating systems, which are obligate outcrossers, thus requiring high mate availability to persist. In such situations, plant populations suffering decreased fitness could be rescued by: (a) improving local habitat conditions (habitat rescue), (b) increasing the number of individuals (demographic rescue), or (c) introducing new genetic variation (genetic rescue). In this study, we used a spatially and genetically explicit individual-based model to approximate the demography of a small (<i>N</i> = 250) isolated self-incompatible population using a timescale of 500 years. Using this model, we quantified the effectiveness of the different types of rescues described above, singly and in combination. Our results show that individual genetic rescue is the most effective type of rescue with respect to improving fitness and population viability. However, we found that introducing a high number of individuals (<i>N</i> &gt; 30) to a small population (<i>N</i> = 50) at the brink of extinction through demographic rescue can also have a positive effect on viability, improving average fitness by 55% compared to introducing a low number of individuals (<i>N</i> = 10) over a long timescale (&gt; 500 years). By itself, habitat rescue showed the lowest effects on viability. However, combining genetic and habitat rescue provided the best results overall, increasing both persistence (&gt; 30%) and mate availability (&gt; 50%). Interestingly, we found that the addition of even a small number of new S alleles (20%) can be highly beneficial to increase mate availability and persistence. We conclude that genetic rescue through the introduction of new S alleles and an increase in habitat suitability is the best management strategy to improve mate availability and population viability of small isolated SI plant populations to overcome the effects of demographic stochasticity and positive density dependence.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"17 11","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11549066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada","authors":"Sarah J. Lehnert,&nbsp;Ian R. Bradbury,&nbsp;Brendan F. Wringe,&nbsp;Mallory Van?Wyngaarden,&nbsp;Paul Bentzen","doi":"10.1111/eva.13587","DOIUrl":"https://doi.org/10.1111/eva.13587","url":null,"abstract":"<p>Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed “designatable units”; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to “big data” is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non-model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (<i>Salmo salar</i>, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in-depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"16 9","pages":"1568-1585"},"PeriodicalIF":4.1,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13587","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41081535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Domestication in dry-cured meat Penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision","authors":"Ying-Chu Lo,&nbsp;Jade Bruxaux,&nbsp;Ricardo C. Rodríguez?de?la?Vega,&nbsp;Samuel O'Donnell,&nbsp;Alodie Snirc,&nbsp;Monika Coton,&nbsp;Mélanie Le?Piver,&nbsp;Stéphanie Le?Prieur,&nbsp;Daniel Roueyre,&nbsp;Jo?lle Dupont,&nbsp;Jos Houbraken,&nbsp;Robert Debuchy,&nbsp;Jeanne Ropars,&nbsp;Tatiana Giraud,&nbsp;Antoine Branca","doi":"10.1111/eva.13591","DOIUrl":"https://doi.org/10.1111/eva.13591","url":null,"abstract":"<p>Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates is of fundamental and applied importance for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly related <i>Penicillium</i> species used for dry-cured meat production, <i>P. nalgiovense</i>, the most common species in the dry-cured meat food industry, and <i>P. salamii</i>, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those of <i>P. nalgiovense</i> were whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of available <i>Penicillium</i> genomes from various environments revealed HGTs, particularly between <i>P. nalgiovense</i> and <i>P. salamii</i> (representing almost 1.5 Mb of cumulative length). HGTs additionally involved <i>P. biforme</i>, also found in dry-cured meat products. We further detected positive selection based on amino acid changes. Our findings suggest that selection by humans has shaped the <i>P. salamii</i> and <i>P. nalgiovense</i> populations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar in <i>P. salamii</i>, <i>P. nalgiovense</i> and <i>P. biforme</i>, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"16 9","pages":"1637-1660"},"PeriodicalIF":4.1,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13591","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41081767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fine-scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic","authors":"Barbara L. Langille,&nbsp;Tony Kess,&nbsp;Matthew Brachmann,&nbsp;Cameron M. Nugent,&nbsp;Amber Messmer,&nbsp;Steven J. Duffy,&nbsp;Melissa K. Holborn,&nbsp;Mallory Van?Wyngaarden,&nbsp;Tim Martin Knutsen,&nbsp;Matthew Kent,&nbsp;Danny Boyce,&nbsp;Robert S. Gregory,&nbsp;Johanne Gauthier,&nbsp;Elizabeth A. Fairchild,&nbsp;Michael Pietrak,&nbsp;Stephen Eddy,&nbsp;Carlos Garcia de Leaniz,&nbsp;Sofia Consuegra,&nbsp;Ben Whittaker,&nbsp;Paul Bentzen,&nbsp;Ian R. Bradbury","doi":"10.1111/eva.13590","DOIUrl":"https://doi.org/10.1111/eva.13590","url":null,"abstract":"<p>Lumpfish, <i>Cyclopterus lumpus</i>, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at-risk wild populations. Here, we characterize the spatial population structure and genomic-environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole-genome re-sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome-wide variation in <i>F</i>_ST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at-risk species throughout Atlantic Canada.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"16 9","pages":"1619-1636"},"PeriodicalIF":4.1,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13590","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41081932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatial and temporal patterns in the population genomics of the European cockchafer Melolontha melolontha in the Alpine region","authors":"Chiara Pedrazzini,&nbsp;Hermann Strasser,&nbsp;Niklaus Zemp,&nbsp;Rolf Holderegger,&nbsp;Franco Widmer,&nbsp;Jürg Enkerli","doi":"10.1111/eva.13588","DOIUrl":"https://doi.org/10.1111/eva.13588","url":null,"abstract":"<p>The European cockchafer <i>Melolontha melolontha</i> is an agricultural pest in many European countries. Populations have a synchronized 3 or 4 years life cycle, leading to temporally isolated populations. Despite the economic importance and availability of comprehensive historical as well as current records on cockchafer occurrence, population genomic analyses of <i>M. melolontha</i> are missing. For example, the effects of geographic separation caused by the mountainous terrain of the Alps and of temporal isolation on the genomic structure of <i>M. melolontha</i> still remain unknown. To address this gap, we genotyped 475 <i>M. melolontha</i> adults collected during 3 years from 35 sites in a central Alpine region. Subsequent population structure analyses discriminated two main genetic clusters, i.e., the South Tyrol cluster including collections located southeast of the Alpine mountain range, and a northwestern alpine cluster with all the other collections, reflecting distinct evolutionary history and geographic barriers. The “passo di Resia” linking South and North Tyrol represented a regional contact zone of the two genetic clusters, highlighting genomic differentiation between the collections from the northern and southern regions. Although the collections from northwestern Italy were assigned to the northwestern alpine genetic cluster, they displayed evidence of admixture with the South Tyrolean genetic cluster, suggesting shared ancestry. A linear mixed model confirmed that both geographic distance and, to a lower extent, also temporal isolation had a significant effect on the genetic distance among <i>M. melolontha</i> populations. These effects may be attributed to limited dispersal capacity and reproductive isolation resulting from synchronized and non-synchronized swarming flights, respectively. This study contributes to the understanding of the phylogeography of an organism that is recognized as an agricultural problem and provides significant information on the population genomics of insect species with prolonged temporally shifted and locally synchronized life cycles.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"16 9","pages":"1586-1597"},"PeriodicalIF":4.1,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13588","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41081486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex","authors":"Carlos Congrains,&nbsp;Julian R. Dupuis,&nbsp;Erick J. Rodriguez,&nbsp;Allen L. Norrbom,&nbsp;Gary Steck,&nbsp;Bruce Sutton,&nbsp;Norma Nolazco,&nbsp;Reinaldo A. de Brito,&nbsp;Scott M. Geib","doi":"10.1111/eva.13589","DOIUrl":"https://doi.org/10.1111/eva.13589","url":null,"abstract":"<p>Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus <i>Anastrepha</i> Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the <i>Anastrepha fraterculus</i> (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the <i>fraterculus</i> species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the <i>A. fraterculus</i> complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole-genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the <i>A. fraterculus</i> complex. Furthermore, network analysis indicated introgression across lineages in the <i>fraterculus</i> group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the <i>A. fraterculus</i> complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome-scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"16 9","pages":"1598-1618"},"PeriodicalIF":4.1,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13589","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41081742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer","authors":"Hamish A. Burnett,&nbsp;Vanessa C. Bieker,&nbsp;Mathilde Le?Moullec,&nbsp;Bart Peeters,&nbsp;J?rgen Rosvold,&nbsp;?shild ?nvik Pedersen,&nbsp;Love Dalén,&nbsp;Leif Egil Loe,&nbsp;Henrik Jensen,&nbsp;Brage B. Hansen,&nbsp;Michael D. Martin","doi":"10.1111/eva.13585","DOIUrl":"https://doi.org/10.1111/eva.13585","url":null,"abstract":"<p>Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (<i>Rangifer tarandus platyrhynchus</i>) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"16 9","pages":"1531-1548"},"PeriodicalIF":4.1,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13585","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41081552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}