دورية أكاديمية
Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis).
| العنوان: | Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis). |
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| المؤلفون: | Chan KO; Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377 Singapore., Hutter CR; Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Dyche Hall, 1345 Jayhawk Blvd, Lawrence, Kansas 66045-7561, USA.; Museum of Natural Sciences and Department of Biological Sciences, 119, Foster Hall. Louisiana State University, Baton Rouge, LA 70803, USA., Wood PL; Department of Biological Sciences & Museum of Natural History, Auburn University, 101 Rouse Life Sciences Building, Auburn, Alabama 36849., Su YC; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd, Kaohsiung City, 80708, Taiwan., Brown RM; Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Dyche Hall, 1345 Jayhawk Blvd, Lawrence, Kansas 66045-7561, USA. |
| المصدر: | Systematic biology [Syst Biol] 2021 Dec 16; Vol. 71 (1), pp. 40-57. |
| نوع المنشور: | Journal Article; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 9302532 Publication Model: Print Cited Medium: Internet ISSN: 1076-836X (Electronic) Linking ISSN: 10635157 NLM ISO Abbreviation: Syst Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2009- : Oxford : Oxford University Press Original Publication: Washington, D.C., USA : Society of Systematic Biologists, [1992- |
| مواضيع طبية MeSH: | DNA, Mitochondrial*/genetics , Gene Flow*, Animals ; Anura/genetics ; Genetic Variation ; Philippines ; Phylogeny |
| مستخلص: | In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: 1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and 2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear $p$-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow. [Cryptic species; gene flow; introgression; isolation-by-distance; isolation-by-environment; phylogenetic network; species delimitation.]. (© The Author(s) 2021. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.) |
| سلسلة جزيئية: | Dryad 10.5061/dryad.34tmpg4j1 |
| المشرفين على المادة: | 0 (DNA, Mitochondrial) |
| تواريخ الأحداث: | Date Created: 20210508 Date Completed: 20220307 Latest Revision: 20220307 |
| رمز التحديث: | 20221213 |
| DOI: | 10.1093/sysbio/syab034 |
| PMID: | 33964168 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1076-836X |
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| DOI: | 10.1093/sysbio/syab034 |