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Ali M, Dey R, Das M, Kumar V, Chandra K, Uniyal VP, Gupta SK. Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India. RESEARCH SQUARE 2024:rs.3.rs-4392854. [PMID: 38826425 PMCID: PMC11142357 DOI: 10.21203/rs.3.rs-4392854/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani . Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.
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2
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Klesser R, Blick T, Fritze MA, Marten A, Hemauer M, Kastner L, Höfer H, Jäger G, Husemann M. Ice cage: new records and cryptic, isolated lineages in wingless snow flies (Diptera, Limoniidae: Chionea spp.) in German lower mountain ranges. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:15. [PMID: 38478046 PMCID: PMC10937758 DOI: 10.1007/s00114-024-01900-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
In Earth's history warm and cold periods have alternated. Especially, during the Pleistocene, the alternation between these different climatic conditions has led to frequent range expansions and retractions of many species: while thermophilic species dispersed during warm periods, cold adapted species retracted to cold refugia and vice versa. After the last Pleistocene cycle many cold adapted taxa found refuges in relict habitats in mountain ranges. One example for such a cold adapted relict is the flightless snow fly Chionea araneoides (Dalman, 1816). It can be found in lower mountain ranges of Central Europe exclusively in stone runs and stony accumulations which provide cold microclimates. Imagines develop only in winter. They have strongly restricted ranges and hence experienced strong isolation predicting that local populations may show local adaptation and hence also genetic differentiation. We investigated this for several middle mountain ranges of Germany using the COI barcoding gene. Our analyses revealed two distinct lineages, one in the Bavarian Forest and a second one in all other more northern locations up to Scandinavia. These lineages likely go back to post-Pleistocene isolation and should be studied in more detail in the future, also to confirm the taxonomic status of both lineages. Further, we confirmed former records of the species for Germany and report new records for the federal states of Saxony, Lower Saxony, Saxony-Anhalt and Thuringia. Finally, we provide the first evidence of two types of males for the species, a small and a larger male type.
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Affiliation(s)
- Robert Klesser
- Leibniz Institut zur Analyse des Biodiversitätswandels, ztm, Zoologisches Museum Hamburg Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany.
- Naturkundemuseum Leipzig, Lortzingstraße 3, D-04105, Leipzig, Germany.
| | - Theo Blick
- Private researcher, Heidloh 8, D-95503, Hummeltal, Germany
| | - Michael-Andreas Fritze
- Arbeitsgruppe für Tierökologie und Planung GmbH, Johann-Strauß-Str. 22, 70794, Filderstadt, Germany
| | - Andreas Marten
- Harz National Park, Lindenallee 35, D-38855, Wernigerode, Germany
| | - Michael Hemauer
- Private researcher, Wallbergstraße 20, D-81539, Munich, Germany
| | - Laura Kastner
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| | - Hubert Höfer
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
| | - Gero Jäger
- Private researcher, Fuldatalstraße 55, D-34125, Kassel, Germany
| | - Martin Husemann
- Leibniz Institut zur Analyse des Biodiversitätswandels, ztm, Zoologisches Museum Hamburg Martin-Luther-King-Platz 3, D-20146, Hamburg, Germany
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133, Karlsruhe, Germany
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3
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Picq S, Wu Y, Martemyanov VV, Pouliot E, Pfister SE, Hamelin R, Cusson M. Range‐wide population genomics of the spongy moth,
Lymantria dispar
(Erebidae): Implications for biosurveillance, subspecies classification and phylogeography of a destructive moth. Evol Appl 2023; 16:638-656. [PMID: 36969137 PMCID: PMC10033852 DOI: 10.1111/eva.13522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/10/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
The spongy moth, Lymantria dispar, is an irruptive forest pest native to Eurasia where its range extends from coast to coast and overspills into northern Africa. Accidentally introduced from Europe in Massachusetts in 1868-1869, it is now established in North America where it is considered a highly destructive invasive pest. A fine-scale characterization of its population genetic structure would facilitate identification of source populations for specimens intercepted during ship inspections in North America and would enable mapping of introduction pathways to help prevent future incursions into novel environments. In addition, detailed knowledge of L. dispar's global population structure would provide new insight into the adequacy of its current subspecies classification system and its phylogeographic history. To address these issues, we generated >2000 genotyping-by-sequencing-derived SNPs from 1445 contemporary specimens sampled at 65 locations in 25 countries/3 continents. Using multiple analytical approaches, we identified eight subpopulations that could be further partitioned into 28 groups, achieving unprecedented resolution for this species' population structure. Although reconciliation between these groupings and the three currently recognized subspecies proved to be challenging, our genetic data confirmed circumscription of the japonica subspecies to Japan. However, the genetic cline observed across continental Eurasia, from L. dispar asiatica in East Asia to L. d. dispar in Western Europe, points to the absence of a sharp geographical boundary (e.g., the Ural Mountains) between these two subspecies, as suggested earlier. Importantly, moths from North America and the Caucasus/Middle East displayed high enough genetic distances from other populations to warrant their consideration as separate subspecies of L. dispar. Finally, in contrast with earlier mtDNA-based investigations that identified the Caucasus as L. dispar's place of origin, our analyses suggest continental East Asia as its evolutionary cradle, from where it spread to Central Asia and Europe, and to Japan through Korea.
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Affiliation(s)
- Sandrine Picq
- Laurentian Forestry Centre Natural Resources Canada Quebec Quebec City Canada
| | - Yunke Wu
- United States Department of Agriculture, APHIS, PPQ, Science and Technology Forest Pest Methods Laboratory Massachusetts Buzzards Bay USA
- Department of Ecology and Evolutionary Biology Cornell University New York Ithaca USA
| | - Vyacheslav V. Martemyanov
- Institute of Systematics and Ecology of Animals SB RAS Novosibirsk Russia
- Biological Institute National Research Tomsk State University Tomsk Russia
| | - Esther Pouliot
- Laurentian Forestry Centre Natural Resources Canada Quebec Quebec City Canada
| | - Scott E. Pfister
- United States Department of Agriculture, APHIS, PPQ, Science and Technology Forest Pest Methods Laboratory Massachusetts Buzzards Bay USA
| | - Richard Hamelin
- Department of Forest and Conservation Sciences The University of British Columbia British Columbia Vancouver Canada
| | - Michel Cusson
- Laurentian Forestry Centre Natural Resources Canada Quebec Quebec City Canada
- Département de biochimie, de microbiologie et de bio‐informatique Université Laval Quebec Quebec City Canada
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4
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Polic D, Yıldırım Y, Lee KM, Franzén M, Mutanen M, Vila R, Forsman A. Linking large-scale genetic structure of three Argynnini butterfly species to geography and environment. Mol Ecol 2022; 31:4381-4401. [PMID: 35841126 PMCID: PMC9544544 DOI: 10.1111/mec.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022]
Abstract
Understanding which factors and processes are associated with genetic differentiation within and among species remains a major goal in evolutionary biology. To explore differences and similarities in genetic structure and its association with geographical and climatic factors in sympatric sister species, we conducted a large‐scale (>32° latitude and >36° longitude) comparative phylogeographical study on three Argynnini butterfly species (Speyeria aglaja, Fabriciana adippe and F. niobe) that have similar life histories, but differ in ecological generalism and dispersal abilities. Analyses of nuclear (ddRAD‐sequencing derived SNP markers) and mitochondrial (COI sequences) data revealed differences between species in genetic structure and how genetic differentiation was associated with climatic factors (temperature, solar radiation, precipitation, wind speed). Geographical proximity accounted for much of the variation in nuclear and mitochondrial structure and evolutionary relationships in F. adippe and F. niobe, but only explained the pattern observed in the nuclear data in S. aglaja, for which mitonuclear discordance was documented. In all species, Iberian and Balkan individuals formed genetic clusters, suggesting isolation in glacial refugia and limited postglacial expansion. Solar radiation and precipitation were associated with the genetic structure on a regional scale in all species, but the specific combinations of environmental and geographical factors linked to variation within species were unique, pointing to species‐specific responses to common environments. Our findings show that the species share similar colonization histories, and that the same ecological factors, such as niche breadth and dispersal capacity, covary with genetic differentiation within these species to some extent, thereby highlighting the importance of comparative phylogeographical studies in sympatric sister species.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Markus Franzén
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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5
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Lohse K, Setter D. The genome sequence of the small pearl-bordered fritillary butterfly, Boloria selene (Schiffermüller, 1775). Wellcome Open Res 2022; 7:76. [PMID: 36507315 PMCID: PMC9713055 DOI: 10.12688/wellcomeopenres.17734.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/15/2022] Open
Abstract
We present a genome assembly from an individual female Boloria selene (the small pearl-bordered fritillary, also known as the silver meadow fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400 megabases in span. The complete assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.
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Affiliation(s)
- Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Derek Setter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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6
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Trense D, Hoffmann AA, Fischer K. Large- and small-scale geographic structures affecting genetic patterns across populations of an Alpine butterfly. Ecol Evol 2021; 11:14697-14714. [PMID: 34765135 PMCID: PMC8571576 DOI: 10.1002/ece3.8157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.
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Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| | - Ary A. Hoffmann
- Pest & Environmental Adaptation Research GroupSchool of BiosciencesBio21 InstituteParkvilleVic.Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
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7
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McGreevy TJ, Michaelides S, Djan M, Sullivan M, Beltrán DM, Buffum B, Husband T. Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails. Front Genet 2021; 12:708871. [PMID: 34659333 PMCID: PMC8511500 DOI: 10.3389/fgene.2021.708871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
The environment plays an important role in the movement of individuals and their associated genes among populations, which facilitates gene flow. Gene flow can help maintain the genetic diversity both within and between populations and counter the negative impact of genetic drift, which can decrease the fitness of individuals. Sympatric species can have different habitat preferences, and thus can exhibit different patterns of genetic variability and population structure. The specialist-generalist variation hypothesis (SGVH) predicts that specialists will have lower genetic diversity, lower effective population sizes (Ne), and less gene flow among populations. In this study, we used spatially explicit, individual-based comparative approaches to test SGVH predictions in two sympatric cottontail species and identify environmental variables that influence their gene flow. New England cottontail (Sylvilagus transitionalis) is the only native cottontail in the Northeast US, an early successional habitat specialist, and a species of conservation concern. Eastern cottontail (S. floridanus) is an invasive species in the Northeast US and a habitat generalist. We characterized each species' genomic variation by developing double-digest Restriction-site Associated DNA sequence single nucleotide polymorphism markers, quantified their habitat with Geographic Information System environmental variables, and conducted our analyses at multiple scales. Surprisingly, both species had similar levels of genetic diversity and eastern cottontail's Ne was only higher than New England cottontail in one of three subregions. At a regional level, the population clusters of New England cottontail were more distinct than eastern cottontail, but the subregional levels showed more geographic areas of restricted gene flow for eastern cottontail than New England cottontail. In general, the environmental variables had the predicted effect on each species' gene flow. However, the most important environmental variable varied by subregion and species, which shows that location and species matter. Our results provide partial support for the SGVH and the identification of environmental variables that facilitate or impede gene flow can be used to help inform management decisions to conserve New England cottontail.
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Affiliation(s)
- Thomas J McGreevy
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI, United States
| | | | - Mihajla Djan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Mary Sullivan
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, Kingston, RI, United States
| | - Diana M Beltrán
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI, United States
| | - Bill Buffum
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI, United States
| | - Thomas Husband
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI, United States
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8
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Kohli M, Djernæs M, Sanchez Herrera M, Sahlen G, Pilgrim E, Simonsen TJ, Olsen K, Ware J. Comparative phylogeography uncovers evolutionary past of Holarctic dragonflies. PeerJ 2021; 9:e11338. [PMID: 34221703 PMCID: PMC8236228 DOI: 10.7717/peerj.11338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/02/2021] [Indexed: 12/05/2022] Open
Abstract
Here, we investigate the evolutionary history of five northern dragonfly species to evaluate what role the last glaciation period may have played in their current distributions. We look at the population structure and estimate divergence times for populations of the following species: Aeshna juncea (Linnaeus), Aeshna subarctica Walker, Sympetrum danae (Sulzer), Libellula quadrimaculata Linnaeus and Somatochlora sahlbergi Trybom across their Holarctic range. Our results suggest a common phylogeographic pattern across all species except for S. sahlbergi. First, we find that North American and European populations are genetically distinct and have perhaps been separated for more than 400,000 years. Second, our data suggests that, based on genetics, populations from the Greater Beringian region (Beringia, Japan and China) have haplotypes that cluster with North America or Europe depending on the species rather than having a shared geographic affinity. This is perhaps a result of fluctuating sea levels and ice sheet coverage during the Quaternary period that influenced dispersal routes and refugia. Indeed, glacial Beringia may have been as much a transit zone as a refugia for dragonflies. Somatochlora sahlbergi shows no genetic variation across its range and therefore does not share the geographic patterns found in the other circumboreal dragonflies studied here. Lastly, we discuss the taxonomic status of Sympetrum danae, which our results indicate is a species complex comprising two species, one found in Eurasia through Beringia, and the other in North America east and south of Beringia. Through this study we present a shared history among different species from different families of dragonflies, which are influenced by the climatic fluctuations of the past.
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Affiliation(s)
- Manpreet Kohli
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, United States
| | | | | | - Göran Sahlen
- The Rydberg Laboratory for Applied Sciences, Halmstad University, Halmstad, Sweden
| | - Erik Pilgrim
- Department of Biology, Utah State University, Logan, Utah, United States
| | - Thomas J Simonsen
- Natural History Museum Aarhus, Aarhus, Denmark
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Kent Olsen
- Natural History Museum Aarhus, Aarhus, Denmark
| | - Jessica Ware
- Department of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States
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9
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Sedano-Cruz RE, Calero-Mejía H. CARACTERIZACIÓN GENÉTICA DE LA POBLACIÓN DE Heliconius sara (Nymphalidae) EN LA ISLA GORGONA, COLOMBIA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.86205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
La estructura genética de poblaciones de mariposas con distribución en islas y sus pares continentales ha sido poco documentada para el neotrópico. Este estudio presenta la caracterización de una población de Heliconius sara con distribución en la Isla Gorgona, ubicada en la región del Pacífico Oriental Colombiano. Para esto se examinaron secuencias parciales de un marcador mitocondrial incluyendo información obtenida del GenBank. Se comparó la diversidad y estructura genética con sus conespecíficos continentales y también con congéneres, con los que comparte un ancestro común cercano en el clado Sapho-Sara. Para el análisis de diversidad y estructura genética se realizó un análisis molecular de varianza. Este análisis muestra que la distancia entre la población de la isla y sus pares en el continente es consistente con la variación intraespecífica observada en otras especies del género Heliconius. Para la reconstrucción de la genealogía y datación reciente en el Pleistoceno superior del grupo monofilético de secuencias de H. sara, se realizó un análisis de inferencia bayesiana, así como una de máxima verosimilitud. Del análisis demográfico se seleccionó un modelo histórico de flujo asimétrico desde la isla hacia el continente que sugiere baja resistencia de la discontinuidad geográfica a la dispersión de esta mariposa diurna desde la isla. Este es el primer estudio en examinar un posible evento de aislamiento de una población insular de mariposas en Colombia.
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10
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Faltýnek Fric Z, Rindoš M, Konvička M. Radical pruning of distribution data may result in loss of knowledge (Response to Larsen & Shirey). Ecol Lett 2021; 24:1290-1292. [PMID: 33756000 DOI: 10.1111/ele.13739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/15/2020] [Accepted: 03/03/2021] [Indexed: 11/26/2022]
Abstract
Larsen & Shirey (2020) criticised our analysis of latitudinal changes in butterfly phenology on the grounds of improper data management. We admit some imprecisions, but show that stringent reanalyses did not change the overall results. We also show that unreasonable treatment of data may result in critical information loss.
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Affiliation(s)
- Zdeněk Faltýnek Fric
- The Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic
| | - Michal Rindoš
- The Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, 1760, CZ-37005, Czech Republic
| | - Martin Konvička
- The Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31, České Budějovice, CZ-37005, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, 1760, CZ-37005, Czech Republic
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11
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Congruent Genetic and Demographic Dispersal Rates in a Natural Metapopulation at Equilibrium. Genes (Basel) 2021; 12:genes12030362. [PMID: 33802587 PMCID: PMC7999359 DOI: 10.3390/genes12030362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/01/2023] Open
Abstract
Understanding the functioning of natural metapopulations at relevant spatial and temporal scales is necessary to accurately feed both theoretical eco-evolutionary models and conservation plans. One key metric to describe the dynamics of metapopulations is dispersal rate. It can be estimated with either direct field estimates of individual movements or with indirect molecular methods, but the two approaches do not necessarily match. We present a field study in a large natural metapopulation of the butterfly Boloria eunomia in Belgium surveyed over three generations using synchronized demographic and genetic datasets with the aim to characterize its genetic structure, its dispersal dynamics, and its demographic stability. By comparing the census and effective population sizes, and the estimates of dispersal rates, we found evidence of stability at several levels: constant inter-generational ranking of population sizes without drastic historical changes, stable genetic structure and geographically-influenced dispersal movements. Interestingly, contemporary dispersal estimates matched between direct field and indirect genetic assessments. We discuss the eco-evolutionary mechanisms that could explain the described stability of the metapopulation, and suggest that destabilizing agents like inter-generational fluctuations in population sizes could be controlled by a long adaptive history of the species to its dynamic local environment. We finally propose methodological avenues to further improve the match between demographic and genetic estimates of dispersal.
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12
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Czajkowska M, Dawidowicz Ł, Borkowska A, Dziekańska I, Sielezniew M. Population Genetic Structure and Demography of the Critically Endangered Chequered Blue Butterfly ( Scolitantides orion) in a Highly Isolated Part of Its Distribution Range. INSECTS 2020; 11:insects11090608. [PMID: 32911638 PMCID: PMC7564389 DOI: 10.3390/insects11090608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
Scolitantides orion is a butterfly species threatened in many European countries. In Poland, it survived in a single highly isolated area (Vistula River valley), which is an example of the dramatic decline in the population number. We studied the two largest remaining populations inhabiting opposite banks of the river. Mark-release-recapture studies showed that both populations were small, and they fluctuated in numbers, but adult individuals were twice as numerous on the western site. Genetic analyses were carried out using a mitochondrial (COI, ND5) and nuclear markers (Wgl, EF-1α, and microsatellite loci). We found out that genetic variation was low at both sites but higher in the smaller eastern population. This pattern is likely to be better explained by past distribution, when the butterfly, as a continental species used to be much more widespread in the east. However, the genetic differentiation between populations was low. This could suggest that the existing gene flow is facilitated by dominant regional wind direction, which may also contribute to a better genetic condition of the western population. Finally, a comparison of the obtained COI sequences with others available enabled us to reveal the phylogeographic pattern of the S. orion from different localities within its range.
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Affiliation(s)
- Magdalena Czajkowska
- Department of Zoology and Genetics, Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245 Białystok, Poland; (A.B.); (I.D.); (M.S.)
| | - Łukasz Dawidowicz
- Department of Zoology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland;
| | - Anetta Borkowska
- Department of Zoology and Genetics, Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245 Białystok, Poland; (A.B.); (I.D.); (M.S.)
| | - Izabela Dziekańska
- Department of Zoology and Genetics, Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245 Białystok, Poland; (A.B.); (I.D.); (M.S.)
| | - Marcin Sielezniew
- Department of Zoology and Genetics, Faculty of Biology, University of Bialystok, Ciołkowskiego 1J, 15-245 Białystok, Poland; (A.B.); (I.D.); (M.S.)
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Yen EC, McCarthy SA, Galarza JA, Generalovic TN, Pelan S, Nguyen P, Meier JI, Warren IA, Mappes J, Durbin R, Jiggins CD. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience 2020; 9:giaa088. [PMID: 32808665 PMCID: PMC7433188 DOI: 10.1093/gigascience/giaa088] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/03/2020] [Accepted: 07/27/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. FINDINGS We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. CONCLUSIONS We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
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Affiliation(s)
- Eugenie C Yen
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Shane A McCarthy
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Juan A Galarza
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Tomas N Generalovic
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of
Entomology, Branišovská 1160/31, 370 05 České Budějovice, Czech
Republic
- University of South Bohemia, Faculty of Science, Branišovská
1645/31A, 370 05 České Budějovice, Czech Republic
| | - Joana I Meier
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
| | - Johanna Mappes
- Department of Biological and Environmental Science, University of
Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing
Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus,
Hinxton, Saffron Walden CB10 1SA, UK
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing
Street, Cambridge CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street,
Cambridge CB2 1TP, UK
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