DOI: 10.5061/dryad.r7sqv9sj3
title: Integrating genomics and biogeography to unravel the origin of a mountain biota: The case of a reptile endemicity hotspot in Arabia

description: Advances 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.
description: 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. 
description: # Title of Dataset: Integrating genomics and biogeography to unravel the
 origin of a mountain biota: The case of a reptile endemicity hotspot in
 Arabia --- *Brief summary of dataset contents.* Data archive for:\
 **Integrating genomics and biogeography to unravel the origin of a
 mountain biota: The case of a reptile endemicity hotspot in Arabia** by
 Bernat Burriel-Carranza, Hctor Tejero-Cicundez, Albert Carn, Gabriel Riao,
 Adrin Talavera, Saleh Al Saadi, Johannes Els, Ji md, Karin Tamar, Pedro
 Tarroso and Salvador Carranza 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. \################################################## ##
 Description of the Data and file structure ### Summary of data Data 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. ###
 Schema of data archive \|- Datasets/ \|- Asaccus/ \| |- 1.ADMIXTURE/ \| |
 |- Admixture_Asaccus_arnoldii.ped \| | |- Admixture_Asaccus_margaritae.ped
 \| | |- Admixture_Asaccus_caudivolvulus.ped \| | |-
 Admixture_Asaccus_montanus.ped \| | |- Admixture_Asaccus_gallagheri.ped \|
 | |- Admixture_Asaccus_playrhynchus.ped \| | |-
 Admixture_Asaccus_gardneri.ped \| |- 2.RAXML/ \| | |- ML_Asaccus.phy \| |-
 3.BEAST/ \| | |- BI_Asaccus.nex \| |- 4.BFD_SNAPP/ \| | |-
 BFD_Asaccus_arnoldi_Agallagheri_Aplatyrhynchus.nex \| | |-
 BFD_Asaccus_caudivolvulus_Agardneri_Amargaritae.nex \| | |-
 BFD_Asaccus_montanus.nex \| | |- SNAPP_Asaccus.vcf \| |- 5.feems/ \| | |-
 A.arnoA.gall/ \| | | |- A.arnoA.gall.bed \| | | |- A.arnoA.gall.coords \|
 | | |- A.arnoA.gall.bim \| | | |- A.arnoA.gall.fam \| | |- A.gard/ \| | |
 |- A.gard.bed \| | | |- A.gard.bim \| | | |- A.gard.coords \| | | |-
 A.gard.fam \| | |- A.marg/ \| | | |- A.marg.bed \| | | |- A.marg.bim \| |
 | |- A.marg.coords \| | | |- A.marg.fam \| | |- A.montanus/ \| | | |-
 A.montanus.bed \| | | |- A.montanus.bim \| | | |- A.montanus.coords \| | |
 |- A.montanus.fam \| | |- A.plat/ \| | | |- A.plat.bed \| | | |-
 A.plat.bim \| | | |- A.plat.coords \| | | |- A.plat.fam \|- Echis/ \| |-
 1.ADMIXTURE/ \| | |- Admixture_Echis_omanensis.ped \| |- 2.RAXML/ \| | |-
 ML_Echis_omanensis.phy \| |- 3.BEAST/ \| | |- BI_Echis.nex \| |-
 4.BFD_SNAPP/ \| | |- SNAPP_echis.nex \| | |- SNAPP_echis.vcf \| |-
 5.feems/ \| | |- Echis.bed \| | |- Echis.bim \| | |- Echis.coords \| | |-
 Echis.fam \|- Hemidactylus/ \| |- 1.ADMIXTURE/ \| | |-
 Admixture_Hemidactylus.ped \| |- 2.RAXML/ \| | |- ML_Hemidactylus.phy \|
 |- 3.BEAST/ \| | |- BI_Hemidactylus.nex \| |- 4.BFD_SNAPP/ \| | |-
 SNAPP_hemidactylus.vcf \| | |- SNAPP_hemidactylus.xml \| |- 5.feems/ \| |
 |- H.haj/ \| | | |- H.haj.bed \| | | |- H.haj.bim \| | | |- H.haj.coords
 \| | | |- H.haj.fam \| | |- H.luq/ \| | | |- H.luq.bed \| | | |- H.luq.bim
 \| | | |- H.luq.coords \| | | |- H.luq.fam \|- Omanosaura/ \| |-
 1.ADMIXTURE/ \| | |- Admixture_Omanosaura.ped \| |- 2.RAXML/ \| | |-
 ML_Omanosaura.phy \| |- 3.BEAST/ \| | |- BI_Omanosaura.nex \| |-
 4.BFD_SNAPP/ \| | |- SNAPP_Omanosaura.vcf \| | |- SNAPP_Omanosaura.xml \|
 |- 5.feems/ \| | |- O.cyan \| | | |- O.cyan.bed \| | | |- O.cyan.bim \| |
 | |- O.cyan.coords \| | | |- O.cyan.fam \| | |- O.jaya \| | | |-
 O.jaya.bed \| | | |- O.jaya.bim \| | | |- O.jaya.coords \| | | |-
 O.jaya.fam \|- Pristurus celerrimus/ \| |- 1.ADMIXTURE/ \| | |-
 Admixture_Pristurus_celerrimus.ped \| |- 2.RAXML/ \| | |-
 ML_Pcelerrimus.phy \| |- 3.BEAST/ \| | |- BI_Pristurus_celerrimus.nex \|
 |- 4.BFD_SNAPP/ \| | |- SNAPP_Pristurus_celerrimus.vcf \| | |-
 SNAPP_Pristurus_celerrimus.xml \| |- 5.feems/ \| | |- P.cele.bed \| | |-
 P.cele.bim \| | |- P.cele.coords \| | |- P.cele.fam \|- Pristurus
 gallagheri/ \| |- 1.ADMIXTURE/ \| | |- Admixture_Pristurus_gallagheri.ped
 \| |- 2.RAXML/ \| | |- ML_Pgall.phy \| |- 3.BEAST/ \| | |-
 BI_Pristurus_gallagheri.nex \| |- 4.BFD_SNAPP/ \| | |- RunA.xml \| | |-
 SNAPP_Pristurus_gallagheri.vcf \| |- 5.feems/ \| | |- P.gall.bed \| | |-
 P.gall.bim \| | |- P.gall.coord \| | |- P.gall.fam \|- Pristurus
 rupestris/ \| |- 1.ADMIXTURE/ \| | |-
 Admixture_Pristurus_rupestris_BFD1-3_6-12.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD1-3_7-12.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD1-3_12.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD1-3.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD1-12.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD4_5.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD6.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD7-11.vcf \| | |-
 Admixture_Pristurus_rupestris_BFD8-9.vcf \| |- 2.RAXML/ \| | |-
 ML_Pristurus_rupestris.phy \| |- 3.BEAST/ \| | |-
 BI_Pristurus_rupestris.nexus \| |- 4.BFD_SNAPP/ \| | |-
 SNAPP_Pristurus_rupestris.vcf \| |- 5.feems/ \| | |- P.rupestris_BFD1-3 \|
 | | |- P.rupestris_BFD1-3.bed \| | | |- P.rupestris_BFD1-3.bim \| | | |-
 P.rupestris_BFD1-3.coords \| | | |- P.rupestris_BFD1-3.fam \| | |-
 P.rupestris_BFD4-5 \| | | |- P.rupestris_BFD4-5.bed \| | | |-
 P.rupestris_BFD4-5.bim \| | | |- P.rupestris_BFD4-5.coords \| | | |-
 P.rupestris_BFD4-5.fam \| | |- P.rupestris_BFD7-11 \| | | |-
 P.rupestris_BFD7-11.bed \| | | |- P.rupestris_BFD7-11.bim \| | | |-
 P.rupestris_BFD7-11.coords \| | | |- P.rupestris_BFD7-11.fam \|-
 Pseudotrapelus/ \| |- 1.ADMIXTURE/ \| | |- Admixture_Pseudotrapelus.ped \|
 |- 2.RAXML/ \| | |- ML_Pseudotrapelus.phy \| |- 3.BEAST/ \| | |-
 BI_Pseudotrapelus.nex \| |- 4.BFD_SNAPP/ \| | |- SNAPP_Pseudotrapelus.vcf
 \| |- 5.feems/ \| | |- P.jens.bed \| | |- P.jens.bim \| | |- P.jens.coords
 \| | |- P.jens.fam \|- Ptyodactylus/ \| |- 1.ADMIXTURE/ \| | |-
 Admixture_Ptyodactylus.ped \| |- 2.RAXML/ \| | |- ML_Ptyodactylus.phy \|
 |- 3.BEAST/ \| | |- BI_Ptyodactylus.nex \| |- 4.BFD_SNAPP/ \| | |-
 SNAPP_Ptyodactylus.vcf \| | |- snapp.xml \| |- 5.feems/ \| | |- Ptyo.bed
 \| | |- Ptyo.bim \| | |- Ptyo.coords \| | |- Ptyo.fam \|- Trachydactylus/
 \| |- 1.ADMIXTURE/ \| | |- Admixture_Trachydactylus.ped \| |- 2.RAXML/ \|
 | |- ML_Trachydactylus.phy \| |- 3.BEAST/ \| | |-
 Trach_all_loci_5219_gen.nex \| |- 4.BFD_SNAPP/ \| | |-
 SNAPP_Trachydactylus.vcf \| | |- Trach_5spp.xml \| |- 5.feems/ \| | |-
 Trach.bed \| | |- Trach.bim \| | |- Trach.fam \| | |- Trach06.coords \|-
 Demultiplexed Reads: Raw Demultiplexed reads for all the specimens
 produced de novo in the present study. Each file starts by the specimen
 code assigned to the individual. To determine and extract specific
 indivuals refer to TableS4_ddrad_individuals. \|- Trees/: All phylogenomic
 trees produced in the present study. They are separated by colonization
 group and by analysis (Maximum Likelihood, Bayesian Inference and Species
 trees). We also provide a time calibrated phylogenetic reconstruction of
 all Squamates. \|- Calibrated_BI_Gene_trees \| |- 01Asaccus_all.tree \| |-
 02Echis.tree \| |- 03Hemidactylus.tree \| |- 04Omanosaura.tree \| |-
 05Pcele.tree \| |- 06Pgall.tree \| |- 07Prup.tree \| |-
 08Pseudotrapelus.tree \| |- 09Ptyodactylus.tree \| |-
 10Trachidactylus.tree \|- ML_Gene_trees \| |-
 01.Asaccus.phy.raxml.support.tree \| |-
 02.Echis_omanensis.phy.raxml.support.tree \| |-
 03.Hemidactylus.phy.raxml.support.tree \| |-
 04.Omanosaura.phy.raxml.support.support.tree \| |-
 05.Pristurus_celerrimus.phy.raxml.support.tree \| |-
 06.Pgall.phy.raxml.support.tree \| |-
 07.Prupestris.phy.raxml.rba.raxml.support.tree \| |-
 08.Pseudotrapelus.phy.raxml.support.tree \| |-
 09.Ptyodactylus.phy.raxml.support.tree \| |- 10.Trachydactylus.tree \|-
 Species_Trees \| |- 01Asaccus.tree \| |- 02Echis.tree \| |-
 03Hemidactylus.tree \| |- 04Omanosaura.tree \| |- 05Pcele.tree \| |-
 07Prup.tree \| |- 09Ptyodactylus.tree \| |- 10Trachydactylus.tree \|-
 Squamate_tree \| |- SQUAMATA_ALL_PF.tree\ \| |-
 Squamata_StarBEAST_1billionGen.tree \|- Supplementary Figures: PDF file
 with all supplementary figures of the study \|- Sup_tables/ \| |-
 TableS1_squamata_phylogeny.xlsx \| |- TableS2_Calibration_nodes.xlsx \| |-
 TableS3_information_of_285_spp_Phylogenies.xlsx \| |-
 TableS4_ddrad_individuals.xlsx \| |- TableS5_Datasets_summary.xlsx \| |-
 TableS6_Marginal_likelihoods_species.xlsx \| |-
 TableS7_bayesian_specifications_and dataset_calibrations.xlsx \| |-
 TableS8_Biogeography_best_fitted_models.xlsx \|- Extended methods:
 Microsoft Office Word document with the extended version of the methods
 used in the present study \|- SCRIPTS\ \| |- Biogeography\ \| | |-
 Biogeobears: Folder containing all necessary scripts and data to reproduce
 biogeobears analyses generated in this study\ \| | | |- biogeo_tmp: Folder
 to store temporary files produced over the analyses\ \| | | |-
 name_correspondance\ \| | | | |- 01Asaccus.txt\ \| | | | |- 02Echis.txt\
 \| | | | |- 03Hemidactylus.txt\ \| | | | |- 04Omanosaura.txt\ \| | | | |-
 05Pcele.txt\ \| | | | |- 07Prup.txt\ \| | | | |- 09Ptyodactylus.txt\ \| |
 | | |- 10Trachydactylus.txt \| | | |- tree_files\ \| | | | |-
 01Asaccus.tree\ \| | | | |- 02Echis.tree\ \| | | | |- 03Hemidactylus.tree\
 \| | | | |- 04Omanosaura.tree\ \| | | | |- 05Pcele.tree\ \| | | | |-
 07Prup.tree\ \| | | | |- 09Ptyodactylus.tree\ \| | | | |-
 10Trachydactylus.tree\ \| | | |- functions\ \| | | | |-
 bears_optim_run_nexus.R\ \| | | | |-
 BioGeoBEARS_calc_transition_matrices_v1.R\ \| | | | |-
 BioGeoBEARS_DNA_cladogenesis_sim_v1.R\ \| | | | |-
 BioGeoBEARS_extract_Qmat_COOmat_v1.R\ \| | | | |-
 BioGeoBEARS_simulate_v1.R\ \| | | | |- BioGeoBEARS_SSEsim_v1.R\ \| | | |
 |- check_BioGeoBEARS_run_nexus.R\ \| | | | |- check_trfn_nexus.R\ \| | | |
 |- get_Qmat_COOmat_from_BioGeoBEARS_run_object_nexus.R\ \| | | | |-
 get_Qmat_COOmat_from_res_nexus.R\ \| | | | |- modsel.R\ \| | | | |-
 readfiles_BioGeoBEARS_run_nexus.R\ \| | | |- objects: Folder to store
 objects generated over the analyses\ \| | | |- location\ \| | | | |-
 08Pseudotrapelus.txt\ \| | | | |- locations corrected\ \| | | | | |-
 01Asaccus.txt\ \| | | | | |- 02Echis.txt\ \| | | | | |-
 03Hemidactylus.txt\ \| | | | | |- 04Omanosaura.txt\ \| | | | | |-
 05Pcele.txt\ \| | | | | |- 07Prup.txt\ \| | | | | |- 09Ptyodactylus.txt\
 \| | | | | |- 10Trachydactylus.txt\ \| | | |- scripts\ \| | | | |-
 biogeobears_Masterfile_edited_all.R\ \| | | | |-
 cumulative+transition_nodes.R\ \| | | | |- plot_biogeobears.R\ \| | | | |-
 plot_cumulative_plots_1.R\ \| | | | |-
 plot_cumulative_plots_2_simulations.R\ \| | | | |-
 plot_events_ggplot_edited.R \| | |- Mountain Simmap: Folder containing all
 necessary scripts to reproduce simmap analyses generated in this study\ \|
 | | |- GENUS\ \| | | | |- Asaccus.txt\ \| | | | |- Echis.txt\ \| | | | |-
 Hemidactylus.txt\ \| | | | |- Omanosaura.txt\ \| | | | |- Pristurus.txt\
 \| | | | |- Pseudotrapelus.txt\ \| | | | |- Ptyodactylus.txt\ \| | | | |-
 Trachydactylus.txt\ \| | | |- Geologic_regions\ \| | | | |-
 lowland_midland_highland\ \| | | | | |- continuous_trait\ \| | | | | | |-
 Simmaps_mountain_colonization.r\ \| | | | | |- data\ \| | | | | | |-
 elevation\ \| | | | | | | |- Asaccus_elevation.txt\ \| | | | | | | |-
 Echis_elevation.txt\ \| | | | | | | |- Hemidactylus_elevation.txt\ \| | |
 | | | | |- Omanosaura_elevation.txt\ \| | | | | | | |-
 Pcele_elevation.txt\ \| | | | | | | |- Pgall_elevation.txt\ \| | | | | | |
 |- Prup_elevation.txt\ \| | | | | | | |- Pseudotrapelus_elevation.txt\ \|
 | | | | | | |- Ptyodactylus_elevation.txt\ \| | | | | | | |-
 Trachydactylus_elevation.txt\ \| | | | | | |- names\ \| | | | | | | |-
 01Asaccus.txt\ \| | | | | | | |- 02Echis.txt\ \| | | | | | | |-
 03Hemidactylus.txt\ \| | | | | | | |- 04Omanosaura.txt\ \| | | | | | | |-
 05Pcele.txt\ \| | | | | | | |- 06Pgall.txt\ \| | | | | | | |- 07Prup.txt\
 \| | | | | | | |- 08Pseudotrapelus.txt\ \| | | | | | | |-
 09Ptyodactylus.txt\ \| | | | | | | |- 10Trachydactylus.txt\ \| | | | | |
 |- species\ \| | | | | | | |- 01Asaccus.txt\ \| | | | | | | |-
 02Echis.txt\ \| | | | | | | |- 03Hemidactylus.txt\ \| | | | | | | |-
 04Omanosaura.txt\ \| | | | | | | |- 05Pcele.txt\ \| | | | | | | |-
 06Pgall.txt\ \| | | | | | | |- 07Prup.txt\ \| | | | | | | |-
 08Pseudotrapelus.txt\ \| | | | | | | |- 09Ptyodactylus.txt\ \| | | | | | |
 |- 10Trachydactylus.txt\ \| | | | | |- elevation_events\ \| | | | | | |-
 elevation_events.csv\ \| | | | | |- objects: Folder to store produced
 objects during analyses\ \| | | | | |- plots: Folder to store produced
 plots during analyses\ \| | | | | |- scripts\ \| | | | | | |-
 names_and_elevation.R\ \| | | | | | |-
 script_plotting_merged_upslope_migration.R\ \| | | | | | |-
 Simmaps_mountain_colonization.r\ \| | | | | |- trees\ \| | | | | |
 |-01Asaccus_all.tree\ \| | | | | | |-02Echis.tree\ \| | | | | |
 |-03Hemidactylus.tree\ \| | | | | | |-04Omanosaura.tree\ \| | | | | |
 |-05Pcele.tree\ \| | | | | | |-06Pgall.tree\ \| | | | | | |-07Prup.tree\
 \| | | | | | |-08Pseudotrapelus.tree\ \| | | | | | |-09Ptyodactylus.tree\
 \| | | | | | |-10Trachidactylus.tree\ \| | | | |- mountain_blocks\ \| | |
 | | |- data\ \| | | | | | |- names\ \| | | | | | | |- 01Asaccus_all.txt\
 \| | | | | | | |- 02Echis.txt\ \| | | | | | | |- 03Hemidactylus.txt\ \| |
 | | | | | |- 04Omanosaura.txt\ \| | | | | | | |- 05Pcele.txt\ \| | | | | |
 | |- 06Pgall.txt\ \| | | | | | | |- 07Prup.txt\ \| | | | | | | |-
 08Pseudotrapelus.txt\ \| | | | | | | |- 09Ptyodactylus.txt\ \| | | | | | |
 |- 10Trachydactylus.txt\ \| | | | | | |- species\ \| | | | | | | |-
 01Asaccus_all.txt\ \| | | | | | | |- 02Echis.txt\ \| | | | | | | |-
 03Hemidactylus.txt\ \| | | | | | | |- 04Omanosaura.txt\ \| | | | | | | |-
 05Pcele.txt\ \| | | | | | | |- 06Pgall.txt\ \| | | | | | | |- 07Prup.txt\
 \| | | | | | | |- 08Pseudotrapelus.txt\ \| | | | | | | |-
 09Ptyodactylus.txt\ \| | | | | | | |- 10Trachydactylus.txt\ \| | | | |
 |-objects: Folder to store all produced objects during the analyses\ \| |
 | | | |-plots: Folder to store produced plots during analyses\ \| | | | |
 |-scripts\ \| | | | | | |- Simmaps_mountain_colonization_blocks.r\ \| | |
 | | |-trees\ \| | | | | | |- 01Asaccus_all.tree\ \| | | | | | |-
 02Echis.tree\ \| | | | | | |- 03Hemidactylus.tree\ \| | | | | | |-
 04Omanosaura.tree\ \| | | | | | |- 05Pcele.tree\ \| | | | | | |-
 06Pgall.tree\ \| | | | | | |- 07Prup.tree\ \| | | | | | |-
 08Pseudotrapelus.tree\ \| | | | | | |- 09Ptyodactylus.tree\ \| | | | | |
 |- 10Trachidactylus.tree\ \| | | | | |-best_models.txt\ \| | | | |-
 plot_blocks_andelev.R\ \| | | |- scripts\ \| | | | |-
 Lineage_accumulation_first_col_plot.R\ \| | | | |-
 Simmaps_mountain_colonization.r\ \| | | |- simmaps_all_tree\ \| | | | |-
 data\ \| | | | | |- species_tree.csv\ \| | | | | |- tiplabels_to_plot.csv\
 \| | | | | |- calibration_nodes.txt\ \| | | | | |- species_tree.txt\ \| |
 | | |- objects: : Folder to store all produced objects during the
 analyses\ \| | | | |- plots: Folder to store produced plots during
 analyses\ \| | | |- TREES\ \| | | | |- SQUAMATA_ALL_PF.tree \| |-
 Population_structure\ \| | |- Admixture\ \| | | |-
 Admixture_qfiles_slection.R: Script to plot on a map admixture results \|
 | |- feems\ \| | | |- feems_with_export.py: Python scrupt to run feems
 analyses and export it in shapefile format for further processing. \ \| |
 | |- DGG_GRID_CONSTRUCT.R: R script to construct a geodesic grid for the
 entire area of study\ \| | | |- Merge_feems_results.R: R script to merge
 feems results and provide integrated metrics for different feems analyses\
 \| | | |- README.txt \| |- ddRAD_data_manipulation: Scripts used to
 process ddRADseq data\ \| | |- calculate_dataset_missingness.R\ \| | |-
 Post_processing_filtering.R \| |- Paleoclimate: Folder containing scripts
 to analyze paleoclimate data\ \| | |- script_paleoclimate.R\ \| | |-
 Teporal_autocorrelation.r\ \| |- README.md ## Sharing/access Information
 Links to other publicly accessible locations of the data: * The ddRAD
 sequencing data for all Trachydactylus specimens can be found in
 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 * Scripts
 necessary to reproduce or run the above datasets and results can be found
 at:
 [https://github.com/BernatBurriel/Hajar-Mountains](https://github.com/BernatBurriel/Hajar-Mountains)