DOI: 10.5281/zenodo.15747478
title: A comprehensive phylogenomic view of the living xenarthran radiation

description: A comprehensive phylogenomic view of the living xenarthran radiation

Mathilde Barthe*, Rémi Allio, Nadia Moraes-Barros, Christopher A. Emerling, Marie-Ka Tilak, Amandine Magdeleine, Fabienne Justy, Melanie Kuch, Roberto Portela Miguez, Benoit de Thoisy, Lionel Hautier, Hendrik N. Poinar, Benoit Nabholz and Frédéric Delsuc*

*Corresponding authors: mathilde.barthe.pro@gmail.com; frederic.delsuc@umontpellier.fr 

 

01_Figures_of_the_main_text.zip 





Figure 1: Mitochondrial phylogenetic relationships reconstructed by maximum likelihood, species delimitation methods, and maps representing the distribution of individuals according to their lineage.




Figure 2: Principal Component Analysis of genetic variance (PCA) conducted on the most complete Bradypus spp., Cyclopes spp. and Dasypus spp. individuals. 




Figure 3: Pairwise genetic differentiation between xenarthran species estimated with the Genetic Differentiation Index (GDI).




Figure 4: Phylogenetic relationships of 40 xenarthran species or subspecies reconstructed by maximum likelihood based on 1,908 BUSCO genes. 




Figure 5: Divergence time tree of 40 xenarthran species or subspecies based on 100 most clock-like and less discordant BUSCO genes reconstructed using MCMCTree. 




Figure 6: Genomic diversity (He) and inbreeding (RoHs) indicators in the genomes of xenarthran species. 




Figure 7: Demographic histories of xenarthran species or lineages estimated by pairwise sequential Markovian coalescent (PSMC).



 

02_Supplementary_tables_&_figures.zip 





Table S1: List of samples and mitochondrial sequences used.




Table S2: Completeness of BUSCO genes for all 94 xenarthran individuals. 




Table S3: Quality of the 40 best xenarthran representative genomes based on 2,006 BUSCO genes.




Table S4: Mean posterior divergence times estimated in Myr for 36 clades, and comparison with previous molecular dating studies (Gibb et al. 2016; Delsuc et al. 2004, 2012).




Table S5: IUCN Red List categories of xenarthran species.




Table S6: List of whole genome sequences used.




Table S7: List and details of the reference genome used to map resequenced individuals.




Table S8: Quality of the 2,006 BUSCO genes sequenced in at least 37 individuals.




Table S9: Generation times of xenarthran species used in PSMC demographic analyses.




Figure S1: Phylogenetic relationships reconstructed by maximum likelihood based on 15 partitioned mitochondrial genes for 261 xenarthran individuals (including 7 extinct species).




Figure S2: Mitochondrial phylogenetic relationships reconstructed by maximum likelihood, with diagrams representing partitions supporting species delimitation methods.




Figure S3: Distribution of 48 Bradypus spp. evaluated in this study. 




Figure S4: Distribution of 23 pygmy anteaters (Cyclopes spp.) evaluated in this study plus 33 individuals from Coimbra et al (2017). 




Figure S5: Species delimitation based on 222 mitogenomes estimated using bPTP-h.




Figure S6: Species delimitation based on 222 mitogenomes estimated using GMYC.




Figure S7: Principal Component Analysis of genetic variance (PCA) conducted on the 5 most complete Cyclopes spp. individuals.




Figure S8: Pairwise genetic divergence comparisons (Dxy) between pairs of xenarthran individuals.




Figure S9:  Net divergence (Da) comparisons between pairs of xenarthran individuals. 




Figure S10: Summary of pairwise genetic differentiation (GDI) and divergence (Da and Dxy) between xenarthran species. 




Figure S11: Phylogenetic relationships of the 40 best representative xenarthran genomes plus 3 outgroups (Dugong dugon, Orycteropus afer, Loxodonta africana) obtained using Astral on the 1908 ML BUSCO gene trees.




Figure S12: Genome-wide heterozygosity (He) estimated for 274 mammalian species.




Figure S13: Genome-wide depth of coverage estimated from the Random_dataset for the 94 individuals used in this study. 




Figure S14: Completeness of orthologous genes of the Mammalia OrthoDB10 BUSCO gene set extracted for 14 reference genome assemblies. 





03_Mitogenomes.zip





Reference_Mitogenome: Mitogenome references of Cyclopes ida, C. dorsalis and C. thomasi generated using MitoFinder v1.4 and used to map reads and extract mitochondrial DNA of resequenced individuals. The location of 15 mitochondrial genes (13 protein-coding + 2 rRNAs) is indicated in the partition file. 




Concatenated_mitochondrial_genes_262_sequences.fasta: Concatenated nucleotide sequences of 15 mitochondrial genes (13 protein-coding + 2 rRNAs) for 262 xenarthrans including extinct species and unverified mitogenomes. 




Concatenated_mitochondrial_genes_222_sequences.fasta: Concatenated nucleotide sequences of 15 mitochondrial genes (13 protein-coding + 2 rRNAs) for 222 xenarthrans. 




Concatenated_mitochondrial_genes_partition.txt: Partition file of concatenated sequences of the 15 mitochondrial genes (13 protein-coding + 2 rRNAs). 




261_xenarthran_concatenated_mitochondrial_genes_TESTNEW.treefile: Maximum likelihood phylogenetic tree inferred from the concatenated sequences of the 15 mitochondrial genes for 261 xenarthrans using IQ-TREE under a partitioned model applying ModelFinder on each partition.




222_xenarthran_concatenated_mitochondrial_genes_TESTNEW.treefile: Maximum likelihood phylogenetic tree inferred from the concatenated sequences of the 15 mitochondrial genes for 222 xenarthrans using IQ-TREE under a partitioned model applying ModelFinder on each partition.




Depth_coverage_201_mitogenomes.csv: Table of mean depth of coverage and proportion of missing data (Ns) of the reconstructed mitochondrial genomes sequenced for this study. 



 

04_Species_delimitation.zip





bPTP 






bPTP_Support_Partition.txt: Details of the most supported species partition. 




bPTP_tree_partition.svg: Tree illustrating the most supported species partition. 





GMYC 






Script_GMYC.R: R script used to run the GMYC delimitation method on the ultrametric tree (11_Phylogenetic_inference/Ultrametric_Tree/Ultrametric_tree_concatenated_nuclear_loci.treefile).




Figure_GMYC.png: Figure illustrating the results of the GMYC species delimitation analysis.




222_xenarthran_concatenated_mitochondrial_genes_TESTNEW.timetree.nwk: Ultrametric reconstruction of the concatenated 15 mitochondrial genes for 222 individuals using IQ-TREE. 




 

05_WGS_dataset.zip

 





Table_reference_genomes.csv: List and details of the reference genomes used to map resequenced individuals. 



 

Random dataset (used for population genetics analyses)





Table_depth_of_coverage_random_regions.txt: Genome-wide depth of coverage estimated from the Random_dataset for the 94 individuals




Script_depth_of_coverage.R: R script used to plot depth of coverage estimated from the Random_dataset for the 94 individuals




Random_dataset: Diploid sequences of 10 regions of 100kb randomly sampled in the nuclear loci for the 94 individuals in PopPhyl format (Locus|lineage|individual|Allele).




Blobtools: folder with files resulting from Blobtools analysis for the 8 reference genomes used in this study (Bradypus tridactylus, Cyclopes didactylus, Myrmecophaga tridactyla, Tamandua tetradactyla, Euphractus sexcinctus, Chlamyphorus truncatus, Priodontes maximus, Cabassous unicinctus)




LastZ/*: List of scaffolds of reference genome aligning more than 50 % with Choloepus didactylus sexual chromosomes (NC_051334.1, NC_051335.1) using Lastz v1.04.22. 





BUSCO dataset (used for phylogenetic reconstructions)





Concatenated_1908_BUSCO_genes.fasta: Fasta sequences of the 1,908 BUSCO genes for the 40 best representative individuals.




Partition_1908_BUSCO_genes.txt: Partition of the 1,908 BUSCO genes concatenation



 

06_Phylogenetic_reconstructions.zip





Phylogram_Tree 






Species_tree_concatenated_1908_gene_TESTNEW_gCF_sCF.nex: Maximum likelihood phylogenetic tree inferred from the 1908 BUSCO genes concatenation using IQ-TREE under a partitioned model applying ModelFinder on each partition. Bootstrap support, and gene- and site-concordance factors (gCF/sCF) have also been estimated through IQ-TREE. 










Gene_Tree 






Concatenate_1908_gene_trees.treefile: File containing all gene trees reconstructed using IQ-TREE applying ModelFinder to each gene.




Astral_consensus_gene_tree.txt: Summary species tree reconstructed with Astral using Concatenate_gene_tree_TESTNEW.treefile








Time tree






Concat_100sequences_codon_partition.phy: 100 most clock-like BUSCO genes




Calibrated_tree.tre: Xenarthran topology including the calibration constraints used.




Convergence.csv: Posterior mean times of the different runs of approximation analyses.




mcmcR*.txt: Posterior age estimates for the different runs of approximation analyses.




MCMC_tree.tree: Divergence time tree of 40 xenarthran species or subspecies based on 100 most clock-like BUSCO genes and reconstructed using MCMCTree with relaxed clock with autocorrelated-rate and the HKY + Γ substitution model of sequence evolution.




07_Population_genetic_analyses.zip





PCA






./*/table_coord_PCA.txt: Output of the PopPhyl2PCA analysis.




./*/table_eigen_PCA.txt: Output of the PopPhyl2PCAanalysis.




Script_to_plot_PCA.R: R script used to plot PCA.




 





Stats_Da_Dxy_GDI






Pairwise_genetic_statistics.csv: Summary statistics computed using ABCstat_global.txt from the DILSmcsnp program for all pairwise combinations of individuals from the different lineages. 




Pairwise_GDI.csv: Genetic Differentiation Index estimates for all pairwise combinations of individuals from the different lineages. 




Plot_genetic_statistics.R: R script used to plot mean genetic statistics between lineages.





He_ROHs






IUCN_xenarthran.txt: IUCN status of the xenarthran species




Cumulative_ROH.txt: Cumulative size of run of homozygosity (ROH) categorized by homozygous fragment sizes: between 1 and 5 Mb, between 5 and 10 Mb, and more than 10 Mb.




 Heterozygocity.csv: Individual’s genome-wide heterozygosity (He) estimated from 1000 random regions of 100kb from the Random_dataset




Plot_He_ROH.R: R script used to plot genomic diversity and inbreeding 




 





PSMC: 






generation_time.csv: Generation time of xenarthran species used in PSMC analysis 




replacement_lineage: file used in Plot_PSMC.R script to assign the final name of individuals.




PSMC/*: PSMC output for different models: model 1 ‘4+10*3+4’ ; model 2 ‘4+30*2+4+6+10’; model 3 ‘4+25*2+4+6’ ; model ‘4+20*2+4+6+10’. 




Maps: Distribution maps of xenarthran species 




Plot_PSMC.R: R script used to plot PSMC and distribution maps of xenarthran species 




 

08_Distribution.zip 





Coordinates_Bradypus.csv: Table of GPS coordinates of Bradypus individuals according to their mitochondrial lineages.




Coordinates_Cyclopes.csv: Table of GPS coordinates of Bradypus individuals according to their mitochondrial lineages.




Plot_distribution.R: R script used to plot individuals on the Neotropical map according to the species partition supported by the bPTP species delimitation.