Ancient mitogenomes reveal the evolutionary history and biogeography of sloths

Supplementary Material for:

Delsuc F., Kuch M., Gibb G.C., Karpinski E., Hackenberger D., Szpak P., Martínez J.G., Mead J.I., McDonald H.G., MacPhee R.D.E., Billet G., Hautier L., and Poinar H.N. (2019). Ancient mitogenomes reveal the evolutionary history and biogeography of sloths. Current Biology. doi:10.1016/j.cub.2019.05.043.

Delsuc-CurrBiol-2019_capture_baits.fasta: Sequence baits designed from living xenarthran mitogenomes and reconstructed ancestral sequences used to capture ancient sloth mitogenomes.  

Delsuc-CurrBiol-2019_dataset.fasta: Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in fasta format.

Delsuc-CurrBiol-2019_dataset.phylip: Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in phylip format.

Delsuc-CurrBiol-2019_dataset_partitions.nex: Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in nexus format with partitions.

Delsuc-CurrBiol-2019_FigS2_RAxML_MLtree_100BP_nexus_for_FigTree.tree: Maximum likelihood mitogenomic tree inferred under the best-fitting partitioned model using RAxML. Related to Figure 1. Maximum-likelihood bootstrap percentages are indicating at nodes (100 replicates). Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree.

Delsuc-CurrBiol-2019_FigS3_IQ-TREE_MLtree_100BP_nexus_for_FigTree.tree: Maximum likelihood mitogenomic tree inferred under the best-fitting partitioned model using IQ-TREE. Related to Figure 1. Maximum-likelihood bootstrap percentages are indicating at nodes (100 replicates). Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree.

Delsuc-CurrBiol-2019_FigS4_MrBayes_consensus_nexus_for_FigTree.tree: Bayesian consensus mitogenomic tree inferred under the best-fitting partitioned model using MrBayes. Related to Figure 1. Clade posterior probabilities (PP) are indicated at nodes. Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree. 

Delsuc-CurrBiol-2019_FigS5_PhyloBayes_consensus_nexus_for_FigTree.tree: Bayesian consensus mitogenomic tree inferred under the CAT-GTR+G₄ mixture model using PhyloBayes. Related to Figure 1. Clade posterior probabilities (PP) are indicated at nodes. Tree is rooted on midpoint. Scale is in mean number of substitutions per site. Tree in nexus format viewable with FigTree.

Delsuc-CurrBiol-2019_FigS6_PhyloBayes_chronogram_nexus_for_FigTree.tree: Bayesian mitogenomic chronogram. Related to Figure 2. This chronogram was inferred under the CAT-GTR+G₄ mixture model and an autocorrelated lognormal model of clock relaxation using PhyloBayes. Tree in nexus format viewable with FigTree.

Delsuc-CurrBiol-2019_Megatherium_bone_extraction_protocol.pdf: Detailed protocol for Megatherium americanum MAPB4R 3965 bone sample preparation.

Delsuc-CurrBiol-2019_ML_ancestral_reconstruction_MOL_constraint.pdf: Maximum likelihood ancestral character state reconstruction. Related to Figure 3. Maximum likelihood estimation of ancestral states for six dental characters from Varela et al. (2019) under the Mk model on the maximum likelihood topology obtained using the molecular topology as a backbone constraint. 

Delsuc-CurrBiol-2019_ML_ancestral_reconstruction_MORPH_constraint.pdf: Maximum likelihood ancestral character state reconstruction. Related to Figure 3. Maximum likelihood estimation of ancestral states for six dental characters from Varela et al. (2019) under the Mk model on the maximum likelihood topology obtained using the same topological constraint that these authors used in their Bayesian phylogenetic reconstructions. 

Delsuc-CurrBiol-2019_MP_ancestral_reconstruction_MOL_constraint.pdf: Maximum parsimony ancestral character state reconstruction. Related to Figure 3. Maximum parsimony estimation of ancestral states for six dental characters from Varela et al. obtained using the molecular topology as a backbone constraint.

Delsuc-CurrBiol-2019_MP_ancestral_reconstruction_MORPHO_constraint.pdf: Maximum parsimony ancestral character state reconstruction. Related to Figure 3. Maximum parsimony estimation of ancestral states for six dental characters from Varela et al. (2019) on the maximum parsimony topology obtained using the same topological constraint that these authors used in their Bayesian phylogenetic reconstructions. 

Delsuc-CurrBiol-2019_TableS1_PartitionFinder_RAxML_best_partition_scheme.txt: Detailed results of the PartitionFinder analysis for RAxML.

Delsuc-CurrBiol-2019_TableS2_ModelFinder_IQ-TREE_best_partition_scheme.txt: Detailed results of the ModelFinder analysis for IQ-TREE.

Delsuc-CurrBiol-2019_TableS3_PartitionFinder_MrBayes_best_partition_scheme.txt: Detailed results of the PartitionFinder analysis for MrBayes.