An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods

Abstract Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site...

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Autores principales:	Juan Moles, Shahan Derkarabetian, Stefano Schiaparelli, Michael Schrödl, Jesús S. Troncoso, Nerida G. Wilson, Gonzalo Giribet
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c14996ce4b6f43f1864862064fbfcf48
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spelling	oai:doaj.org-article:c14996ce4b6f43f1864862064fbfcf482021-12-02T18:27:48ZAn approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods10.1038/s41598-021-87244-52045-2322https://doaj.org/article/c14996ce4b6f43f1864862064fbfcf482021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-87244-5https://doaj.org/toc/2045-2322Abstract Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.Juan MolesShahan DerkarabetianStefano SchiaparelliMichael SchrödlJesús S. TroncosoNerida G. WilsonGonzalo GiribetNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Juan Moles Shahan Derkarabetian Stefano Schiaparelli Michael Schrödl Jesús S. Troncoso Nerida G. Wilson Gonzalo Giribet An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
description	Abstract Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.
format	article
author	Juan Moles Shahan Derkarabetian Stefano Schiaparelli Michael Schrödl Jesús S. Troncoso Nerida G. Wilson Gonzalo Giribet
author_facet	Juan Moles Shahan Derkarabetian Stefano Schiaparelli Michael Schrödl Jesús S. Troncoso Nerida G. Wilson Gonzalo Giribet
author_sort	Juan Moles
title	An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
title_short	An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
title_full	An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
title_fullStr	An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
title_full_unstemmed	An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
title_sort	approach using ddradseq and machine learning for understanding speciation in antarctic antarctophilinidae gastropods
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/c14996ce4b6f43f1864862064fbfcf48
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An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods

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