Ancient mitogenomes reveal the evolutionary history and biogeography of sloths
Notice bibliographique
Résumé
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.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».