Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river

Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutio...

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Autores: Alda, Fernando, Alter, S. Elizabeth, Kurata, Naoko P., Chakrabarty, Prosanta
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/413207
Acceso en línea:http://hdl.handle.net/10261/413207
Access Level:acceso abierto
Palabra clave:African cichlids
Ultraconserved elements
Congo River
UCEs
Diversification
Phylogenomics
Hybridization
Lamprologini
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spelling Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo riverAlda, FernandoAlter, S. ElizabethKurata, Naoko P.Chakrabarty, ProsantaAfrican cichlidsUltraconserved elementsCongo RiverUCEsDiversificationPhylogenomicsHybridizationLamprologiniUnderstanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutionary history has been difficult to untangle with previous data sets, particularly with regard to river-dwelling lineages in the genus Lamprologus. This clade notably includes the only known blind and depigmented cichlid, Lamprologus lethops. Here, we reconstructed the evolutionary, population, and biogeographic history of a Lamprologus clade from the Congo River by leveraging genomic data and sampling over 50 lamprologine species from the entire Lake Tanganyika radiation. This study provides the most comprehensive species-level coverage to date of the riverine taxa within this lacustrine-origin clade. We found that in the mid-late Pliocene, two lineages of Lake Tanganyika lamprologines independently colonized the Congo River, where they subsequently hybridized and diversified, forming the current monophyletic group of riverine Lamprologus. Our estimates for divergence time and introgression align with the region’s geological history and suggest rapid speciation in Lamprologus species from the Congo River marked by rapids-driven vicariance and water level fluctuations, and repeated episodes of secondary contact and reticulation. As a result of our analyses, we propose the taxonomic restriction of the genus Lamprologus to Congo River taxa only. The complex evolutionary history of this group—characterized by introgressive hybridization followed by a rapid series of isolation and reconnection—illustrates the multifaceted dynamics of speciation that have shaped the rich biodiversity of this region.This work was supported by the National Science Foundation [DEB 1655227 to M.L.J.S., 1655694 to S.E.A.].Peer reviewedOxford University PressNational Science Foundation (US)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202620262025info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionapplication/pdfhttp://hdl.handle.net/10261/413207reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésAlda, Fernando; Alter, S. Elizabeth; Kurata, Naoko P.; Chakrabarty, Prosanta; Stiassny, Melanie L. J.; 2025; Data for: Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo River [Dataset]; Dryad; https://doi.org/10.5061/dryad.8931zcs13https://doi.org/10.1093/sysbio/syaf032Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/4132072026-05-22T06:33:51Z
dc.title.none.fl_str_mv Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
title Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
spellingShingle Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
Alda, Fernando
African cichlids
Ultraconserved elements
Congo River
UCEs
Diversification
Phylogenomics
Hybridization
Lamprologini
title_short Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
title_full Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
title_fullStr Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
title_full_unstemmed Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
title_sort Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo river
dc.creator.none.fl_str_mv Alda, Fernando
Alter, S. Elizabeth
Kurata, Naoko P.
Chakrabarty, Prosanta
author Alda, Fernando
author_facet Alda, Fernando
Alter, S. Elizabeth
Kurata, Naoko P.
Chakrabarty, Prosanta
author_role author
author2 Alter, S. Elizabeth
Kurata, Naoko P.
Chakrabarty, Prosanta
author2_role author
author
author
dc.contributor.none.fl_str_mv National Science Foundation (US)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv African cichlids
Ultraconserved elements
Congo River
UCEs
Diversification
Phylogenomics
Hybridization
Lamprologini
topic African cichlids
Ultraconserved elements
Congo River
UCEs
Diversification
Phylogenomics
Hybridization
Lamprologini
description Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutionary history has been difficult to untangle with previous data sets, particularly with regard to river-dwelling lineages in the genus Lamprologus. This clade notably includes the only known blind and depigmented cichlid, Lamprologus lethops. Here, we reconstructed the evolutionary, population, and biogeographic history of a Lamprologus clade from the Congo River by leveraging genomic data and sampling over 50 lamprologine species from the entire Lake Tanganyika radiation. This study provides the most comprehensive species-level coverage to date of the riverine taxa within this lacustrine-origin clade. We found that in the mid-late Pliocene, two lineages of Lake Tanganyika lamprologines independently colonized the Congo River, where they subsequently hybridized and diversified, forming the current monophyletic group of riverine Lamprologus. Our estimates for divergence time and introgression align with the region’s geological history and suggest rapid speciation in Lamprologus species from the Congo River marked by rapids-driven vicariance and water level fluctuations, and repeated episodes of secondary contact and reticulation. As a result of our analyses, we propose the taxonomic restriction of the genus Lamprologus to Congo River taxa only. The complex evolutionary history of this group—characterized by introgressive hybridization followed by a rapid series of isolation and reconnection—illustrates the multifaceted dynamics of speciation that have shaped the rich biodiversity of this region.
publishDate 2025
dc.date.none.fl_str_mv 2025
2026
2026
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/413207
url http://hdl.handle.net/10261/413207
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Alda, Fernando; Alter, S. Elizabeth; Kurata, Naoko P.; Chakrabarty, Prosanta; Stiassny, Melanie L. J.; 2025; Data for: Phylogenomic and population genomic analyses of ultraconserved elements reveal deep coalescence and introgression shaped diversification patterns in Lamprologine cichlids of the Congo River [Dataset]; Dryad; https://doi.org/10.5061/dryad.8931zcs13
https://doi.org/10.1093/sysbio/syaf032
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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