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Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex

In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator...

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Autores principales: Çiftçi, Ozan, Alverson, Andrew J., van Bodegom, Peter, Roberts, Wade R., Mertens, Adrienne, Van de Vijver, Bart, Trobajo, Rosa, Mann, David G., Pirovano, Walter, van Eijk, Iris, Gravendeel, Barbara
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9804273/
https://www.ncbi.nlm.nih.gov/pubmed/35861132
http://dx.doi.org/10.1111/jpy.13281
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author Çiftçi, Ozan
Alverson, Andrew J.
van Bodegom, Peter
Roberts, Wade R.
Mertens, Adrienne
Van de Vijver, Bart
Trobajo, Rosa
Mann, David G.
Pirovano, Walter
van Eijk, Iris
Gravendeel, Barbara
author_facet Çiftçi, Ozan
Alverson, Andrew J.
van Bodegom, Peter
Roberts, Wade R.
Mertens, Adrienne
Van de Vijver, Bart
Trobajo, Rosa
Mann, David G.
Pirovano, Walter
van Eijk, Iris
Gravendeel, Barbara
author_sort Çiftçi, Ozan
collection PubMed
description In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear‐lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene‐tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes.
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spelling pubmed-98042732023-01-03 Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex Çiftçi, Ozan Alverson, Andrew J. van Bodegom, Peter Roberts, Wade R. Mertens, Adrienne Van de Vijver, Bart Trobajo, Rosa Mann, David G. Pirovano, Walter van Eijk, Iris Gravendeel, Barbara J Phycol Research Articles In contrast to surveys based on a few genes that often provide limited taxonomic resolution, transcriptomes provide a wealth of genomic loci that can resolve relationships among taxonomically challenging lineages. Diatoms are a diverse group of aquatic microalgae that includes important bioindicator species and many such lineages. One example is Nitzschia palea, a widespread species complex with several morphologically defined taxonomic varieties, some of which are critical pollution indicators. Morphological differences among the varieties are subtle and phylogenetic studies based on a few genes fail to resolve their evolutionary relationships. We conducted morphometric and transcriptome analyses of 10 Nitzschia palea strains to resolve the relationships among strains and taxonomic varieties. Nitzschia palea was resolved into three clades, one of which corresponds to a group of strains with narrow linear‐lanceolate valves. The other morphological group recovered in the shape outline analysis was not monophyletic and consisted of two clades. Gene‐tree concordance analyses and phylogenetic network estimations revealed patterns of incomplete lineage sorting and gene flow between intraspecific lineages. We detected reticulated evolutionary patterns among lineages with different morphologies, resulting in a putative recent hybrid. Our study shows that phylogenomic analyses of unlinked nuclear loci, complemented with morphometrics, can resolve complex evolutionary histories of recently diverged species complexes. John Wiley and Sons Inc. 2022-08-08 2022-10 /pmc/articles/PMC9804273/ /pubmed/35861132 http://dx.doi.org/10.1111/jpy.13281 Text en © 2022 The Authors. Journal of Phycology published by Wiley Periodicals LLC on behalf of Phycological Society of America. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Çiftçi, Ozan
Alverson, Andrew J.
van Bodegom, Peter
Roberts, Wade R.
Mertens, Adrienne
Van de Vijver, Bart
Trobajo, Rosa
Mann, David G.
Pirovano, Walter
van Eijk, Iris
Gravendeel, Barbara
Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
title Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
title_full Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
title_fullStr Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
title_full_unstemmed Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
title_short Phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
title_sort phylotranscriptomics reveals the reticulate evolutionary history of a widespread diatom species complex
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9804273/
https://www.ncbi.nlm.nih.gov/pubmed/35861132
http://dx.doi.org/10.1111/jpy.13281
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