Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia

[Methods] Raw ddRADseq demultiplexed reads are available and can be processed with ipyrad (https://ipyrad.readthedocs.io/). Supplementary figures, supplementary tables datasets and tree files are uploaded as separate files.

Detalles Bibliográficos
Autores: Burriel-Carranza, Bernat, Tejero-Cicuéndez, Héctor, Carné, Albert, Mochales-Riaño, Gabriel, Talavera, Adrián, Al Saadi, Saleh, Els, Johannes, Šmíd, Jiří, Tamar, Karin, Tarroso, Pedro, Carranza, Salvador
Tipo de recurso: conjunto de datos
Fecha de publicación:2024
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/394203
Acceso en línea:http://hdl.handle.net/10261/394203
Access Level:acceso abierto
Palabra clave:Biogeography
Desertification
Genomics
Reptiles
Natural sciences
Arabia
Arid environments
ddRADseq
Hajar Mountains
Mountain building
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dc.title.none.fl_str_mv Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
title Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
spellingShingle Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
Burriel-Carranza, Bernat
Biogeography
Desertification
Genomics
Reptiles
Natural sciences
Arabia
Arid environments
ddRADseq
Hajar Mountains
Mountain building
title_short Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
title_full Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
title_fullStr Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
title_full_unstemmed Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
title_sort Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia
dc.creator.none.fl_str_mv Burriel-Carranza, Bernat
Tejero-Cicuéndez, Héctor
Carné, Albert
Mochales-Riaño, Gabriel
Talavera, Adrián
Al Saadi, Saleh
Els, Johannes
Šmíd, Jiří
Tamar, Karin
Tarroso, Pedro
Carranza, Salvador
author Burriel-Carranza, Bernat
author_facet Burriel-Carranza, Bernat
Tejero-Cicuéndez, Héctor
Carné, Albert
Mochales-Riaño, Gabriel
Talavera, Adrián
Al Saadi, Saleh
Els, Johannes
Šmíd, Jiří
Tamar, Karin
Tarroso, Pedro
Carranza, Salvador
author_role author
author2 Tejero-Cicuéndez, Héctor
Carné, Albert
Mochales-Riaño, Gabriel
Talavera, Adrián
Al Saadi, Saleh
Els, Johannes
Šmíd, Jiří
Tamar, Karin
Tarroso, Pedro
Carranza, Salvador
author2_role author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
Agencia Estatal de Investigación (España)
European Commission
La Caixa
Fundação para a Ciência e a Tecnologia (Portugal)
Czech Science Foundation
Charles University (Czech Republic)
Burriel-Carranza, Bernat [0000-0001-9832-1782]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Biogeography
Desertification
Genomics
Reptiles
Natural sciences
Arabia
Arid environments
ddRADseq
Hajar Mountains
Mountain building
topic Biogeography
Desertification
Genomics
Reptiles
Natural sciences
Arabia
Arid environments
ddRADseq
Hajar Mountains
Mountain building
description [Methods] Raw ddRADseq demultiplexed reads are available and can be processed with ipyrad (https://ipyrad.readthedocs.io/). Supplementary figures, supplementary tables datasets and tree files are uploaded as separate files.
publishDate 2024
dc.date.none.fl_str_mv 2024
2025
2025
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url http://hdl.handle.net/10261/394203
dc.language.none.fl_str_mv Inglés
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info:eu-repo/grantAgreement/AEI//PRE2019-088729
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-098290-B-I00
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-128901NB-I00
info:eu-repo/grantAgreement/AEI//FPU18
info:eu-repo/grantAgreement/AEI//FJC2021-046832-I
Burriel-Carranza, Bernat; Tejero-Cicuéndez, Héctor; Carné, Albert; Mochales-Riaño, Gabriel; Talavera, Adrián; Al Saadi, Saleh; Els, Johannes; Šmíd, Jiří; Tamar, Karin; Tarroso, Pedro; Carranza, Salvador. Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia. https://doi.org/10.1093/sysbio/syae032 . http://hdl.handle.net/10261/392336
Burriel-Carranza, Bernat; Tejero-Cicuéndez, Héctor; Carné, Albert; Mochales-Riaño, Gabriel; Talavera, Adrián; Al Saadi, Saleh; Els, Johannes; Šmíd, Jiří; Tamar, Karin; Tarroso, Pedro; Carranza, Salvador; 2023; The origin of a mountain biota: hyper-aridity shaped reptile diversity in an Arabian biodiversity hotspot [Preprint]; https://doi.org/10.1101/2023.04.07.536010
Burriel-Carranza, Bernat; Tejero-Cicuéndez, Héctor; Carné, Albert; Mochales-Riaño, Gabriel; Talavera, Adrián; Al Saadi, Saleh; Els, Johannes; Šmíd, Jiří; Tamar, Karin; Tarroso, Pedro; Carranza, Salvador; 2024; Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia [Software]; Zenodo; Version 1; https://doi.org/10.5281/zenodo.10534366
https://doi.org/10.5061/dryad.r7sqv9sj3
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dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Dryad
publisher.none.fl_str_mv Dryad
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
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spelling Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in ArabiaBurriel-Carranza, BernatTejero-Cicuéndez, HéctorCarné, AlbertMochales-Riaño, GabrielTalavera, AdriánAl Saadi, SalehEls, JohannesŠmíd, JiříTamar, KarinTarroso, PedroCarranza, SalvadorBiogeographyDesertificationGenomicsReptilesNatural sciencesArabiaArid environmentsddRADseqHajar MountainsMountain building[Methods] Raw ddRADseq demultiplexed reads are available and can be processed with ipyrad (https://ipyrad.readthedocs.io/). Supplementary figures, supplementary tables datasets and tree files are uploaded as separate files.This dataset contains ddRADseq raw reads, data files that should allow replication of the workflow, and the resulting phylogenomic and pylogenetic trees produced in this work. Also, this dataset contains supplementary material (Figures and Tables), and the extended methods related to this publication. In the present work, we assembled a large genomic database (n = 661) for all endemic reptiles of the Hajar Mountains. We investigated the diversity, population structure and the biogeography of all the endemic reptile fauna of this mountain range providing, for the first time, an holistic understanding of how a montane reptile community has originated, diversified, and dispersed in a mountain system.Published May 12, 2023; Updated Jun 27, 2024 on DryadAdvances in genomics have greatly enhanced our understanding of mountain biodiversity, providing new insights into the complex and dynamic mechanisms that drive the formation of mountain biotas. These span from broad biogeographic patterns to population dynamics and adaptations to these environments. However, significant challenges remain in integrating large-scale and fine-scale findings to develop a comprehensive understanding of mountain biodiversity. One significant challenge is the lack of genomic data, particularly in historically understudied arid regions where reptiles are a particularly diverse vertebrate group. In the present study, we assembled a de novo genome-wide SNP dataset for the complete endemic reptile fauna of a mountain range (19 described species with more than 600 specimens sequenced), and integrated state-of-the-art biogeographic analyses at the population, species and community level. Thus, we provide for the first time a holistic integration of how a whole endemic reptile community has originated, diversified and dispersed through a mountain system. Our results show that reptiles independently colonized the Hajar Mountains of southeastern Arabia 11 times. After colonization, species delimitation methods suggest high levels of within-mountain diversification, supporting up to 49 putative species. This diversity is strongly structured following local topography, with the highest peaks acting as a broad barrier to gene flow among the entire community. Surprisingly, orogenic events do not seem key drivers of the biogeographic history of reptiles in this system. Instead, past climatic events seem to have had a major role in this community assemblage. We observe an increase of vicariant events from Late Pliocene onwards, coinciding with an unstable climatic period of rapid shifts between hyper-arid and semiarid conditions that led to the ongoing desertification of Arabia. We conclude that paleoclimate, and particularly extreme aridification, acted as a main driver of diversification in arid mountain systems which is tangled with the generation of highly adapted endemicity. Overall, our study does not only provide a valuable contribution to understanding the evolution of mountain biodiversity, but also offers a flexible and scalable approach that can be reproduced into any taxonomic group and at any discrete environment.MCIN/AEI/10.13039/501100011033 : PGC2018-098290-B-I00 (MCIU/AEI/FEDER, UE) European Regional Development Fund : PID2021-128901NB-I00 Ministerio de Ciencia e Innovación : FPU18/04742 CaixaBank : LCF/BQ/DR20/11790007, Doctoral fellowship programme MCIN/AEI/10.13039/501100011033 : FJC2021-046832-I, European Union NextGenerationEU/PRTR Fundação para a Ciência e Tecnologia : DL57/2016/CP1440/CT0008 Czech Science Foundation : 22-12757S Charles University : 204069, Research Centre Ministerio de Ciencia e Innovación : PRE2019-088729Data in this repository is structured into different subfolders. ** Demultiplexed reads: This zipped folder contains all demultiplexed reads obtained through ddRAD sequencing in the present study. There are 606 fastq.gz files and each file is identified by the specimen code given to each individual in Table S4 (see Sup_tables folder). The remaining 55 samples used in this work were extracted from a previous study and correspond to all Trachydactylus samples (Burriel-Carranza, Bernat; Estarellas, Maria; Riao, Gabriel; Talavera, Adrin; Tejero-Cicundez, Hctor; Els, Johannes; Carranza, Salvador (2023), Data from: Species boundaries to the limit: validating species delimitation methods is critical to avoid taxonomic inflation in the genomic era, Mendeley Data, V2, doi: 10.17632/dnsrsmkzkg.2) ** Datasets: This folder contains all datasets needed to reproduce the study. This folder is structured into 10 subfolders representing each of the different colonization groups in the Hajar Mountain range. Within each subfolder there are 5 analysis folders\ ** Scripts: Folder containing all scripts used in this publication.Peer reviewedDryadMinisterio de Ciencia e Innovación (España)Agencia Estatal de Investigación (España)European CommissionLa CaixaFundação para a Ciência e a Tecnologia (Portugal)Czech Science FoundationCharles University (Czech Republic)Burriel-Carranza, Bernat [0000-0001-9832-1782]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202520252024info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1http://hdl.handle.net/10261/394203reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI//PRE2019-088729info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PGC2018-098290-B-I00info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023/PID2021-128901NB-I00info:eu-repo/grantAgreement/AEI//FPU18info:eu-repo/grantAgreement/AEI//FJC2021-046832-IBurriel-Carranza, Bernat; Tejero-Cicuéndez, Héctor; Carné, Albert; Mochales-Riaño, Gabriel; Talavera, Adrián; Al Saadi, Saleh; Els, Johannes; Šmíd, Jiří; Tamar, Karin; Tarroso, Pedro; Carranza, Salvador. Integrating Genomics and Biogeography to Unravel the Origin of a Mountain Biota: The Case of a Reptile Endemicity Hotspot in Arabia. https://doi.org/10.1093/sysbio/syae032 . http://hdl.handle.net/10261/392336Burriel-Carranza, Bernat; Tejero-Cicuéndez, Héctor; Carné, Albert; Mochales-Riaño, Gabriel; Talavera, Adrián; Al Saadi, Saleh; Els, Johannes; Šmíd, Jiří; Tamar, Karin; Tarroso, Pedro; Carranza, Salvador; 2023; The origin of a mountain biota: hyper-aridity shaped reptile diversity in an Arabian biodiversity hotspot [Preprint]; https://doi.org/10.1101/2023.04.07.536010Burriel-Carranza, Bernat; Tejero-Cicuéndez, Héctor; Carné, Albert; Mochales-Riaño, Gabriel; Talavera, Adrián; Al Saadi, Saleh; Els, Johannes; Šmíd, Jiří; Tamar, Karin; Tarroso, Pedro; Carranza, Salvador; 2024; Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia [Software]; Zenodo; Version 1; https://doi.org/10.5281/zenodo.10534366https://doi.org/10.5061/dryad.r7sqv9sj3Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3942032026-05-22T06:33:51Z
score 15,811543

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