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Ancient mitogenomes reveal the evolutionary history and biogeography of sloths
<p><strong>Supplementary Material for:</strong></p> <p>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.</p> <p> </p> <p><strong>Delsuc-CurrBiol-2019_capture_baits.fasta: </strong>Sequence baits designed from living xenarthran mitogenomes and reconstructed ancestral sequences used to capture ancient sloth mitogenomes. </p> <p><strong>Delsuc-CurrBiol-2019_dataset.fasta:</strong> Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in fasta format.</p> <p><strong>Delsuc-CurrBiol-2019_dataset.phylip:</strong> Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in phylip format.</p> <p><strong>Delsuc-CurrBiol-2019_dataset_partitions.nex:</strong> Mitogenomic dataset used for phylogenetic reconstruction and molecular dating in nexus format with partitions.</p> <p><strong>Delsuc-CurrBiol-2019_FigS2_RAxML_MLtree_100BP_nexus_for_FigTree.tree: </strong>Maximum likelihood mitogenomic tree inferred under the best-fitting partitioned model using RAxML. Related to Figure 1.<strong> </strong>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.</p> <p><strong>Delsuc-CurrBiol-2019_FigS3_IQ-TREE_MLtree_100BP_nexus_for_FigTree.tree</strong><strong>:</strong> 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.</p> <p><strong>Delsuc-CurrBiol-2019_FigS4_MrBayes_consensus_nexus_for_FigTree.tree: </strong>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. </p> <p><strong>Delsuc-CurrBiol-2019_FigS5_PhyloBayes_consensus_nexus_for_FigTree.tree: </strong>Bayesian consensus mitogenomic tree inferred under the CAT-GTR+G<sub>4</sub> 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.</p> <p><strong>Delsuc-CurrBiol-2019_FigS6_PhyloBayes_chronogram_nexus_for_FigTree.tree</strong><strong>: </strong>Bayesian mitogenomic chronogram. Related to Figure 2. This chronogram was inferred under the CAT-GTR+G<sub>4</sub> mixture model and an autocorrelated lognormal model of clock relaxation using PhyloBayes. Tree in nexus format viewable with FigTree.</p> <p><strong>Delsuc-CurrBiol-2019_Megatherium_bone_extraction_protocol.pdf: </strong>Detailed protocol for <em>Megatherium americanum</em> MAPB4R 3965 bone sample preparation.</p> <p><strong>Delsuc-CurrBiol-2019_ML_ancestral_reconstruction_MOL_constraint.pdf: </strong>Maximum likelihood ancestral character state reconstruction.<strong> </strong>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. </p> <p><strong>Delsuc-CurrBiol-2019_ML_ancestral_reconstruction_MORPH_constraint.pdf: </strong>Maximum likelihood ancestral character state reconstruction.<strong> </strong>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. </p> <p><strong>Delsuc-CurrBiol-2019_MP_ancestral_reconstruction_MOL_constraint.pdf: </strong>Maximum parsimony ancestral character state reconstruction.<strong> </strong>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.</p> <p><strong>Delsuc-CurrBiol-2019_MP_ancestral_reconstruction_MORPHO_constraint.pdf: </strong>Maximum parsimony ancestral character state reconstruction.<strong> </strong>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. </p> <p><strong>Delsuc-CurrBiol-2019_TableS1_PartitionFinder_RAxML_best_partition_scheme.txt: </strong>Detailed results of the PartitionFinder analysis for RAxML.</p> <p><strong>Delsuc-CurrBiol-2019_TableS2_ModelFinder_IQ-TREE_best_partition_scheme.txt: </strong>Detailed results of the ModelFinder analysis for IQ-TREE.</p> <p><strong>Delsuc-CurrBiol-2019_TableS3_PartitionFinder_MrBayes_best_partition_scheme.txt: </strong>Detailed results of the PartitionFinder analysis for MrBayes.</p> <p> </p>
Triangular Mesh of the Brain of a Sloth Bear (Melursus ursinus)
<p>Triangular Mesh of the Brain of a Sloth Bear (<i>Melursus ursinus</i>) from http://braincatalogue.org/Sloth_bear</p>
FIGURE 4 in A new Megatheriinae skull (Xenarthra, Tardigrada) from the Pliocene of Northern Venezuela - implications for a giant sloth dispersal to Central and North America
FIGURE 4. Skulls of Bradypus marmoratus (sic) of the PIMUZ comparative collection in dorsal view; females on the left and males on the right, in three different sutural ages: 1 and 4, young adults (with most of the posterior sutures opened); 2 and 5, adults (with most of the posterior sutures closed but visible); and, 3 and 6, old adults (with most of the posterior sutures closed and not visible). In all the skulls the right temporal line was marked with a black line showing a great variation among sexes and ages.
FIGURE 3 in A new Megatheriinae skull (Xenarthra, Tardigrada) from the Pliocene of Northern Venezuela - implications for a giant sloth dispersal to Central and North America
FIGURE 3. Skulls of 1: Eremotherium laurillardi, 2: Eremotherium eomigrans, 3: AMU-CURS 184, cf. Proeremotherium sp., and 4: Proeremotherium eljebe (AMU-CURS 126, type), compared in (from top to bottom) dorsal, lateral and palatal views. In light grey are the upper dental series alveoli contours of each skull; black arrows shows the outline and extension of the posterior palatal notch, and up to where it reaches in relation to the dental series (in 1 the dotted line is used because that part of the palatal notch was mechanically broken).
FIGURE 2 in A new Megatheriinae skull (Xenarthra, Tardigrada) from the Pliocene of Northern Venezuela - implications for a giant sloth dispersal to Central and North America
FIGURE 2. Skulls of AMU-CURS 184 and AMU-CURS 126 (Proeremotherium eljebe type specimen). AMU-CURS 184 in 1, dorsal; 3, lateral, and 5, palatal views. Proeremotherium eljebe in 2, dorsal; 4, lateral, and 6, palatal views.
FIGURE 1. Location map showing the locality where the AMU-CURS 184 in A new Megatheriinae skull (Xenarthra, Tardigrada) from the Pliocene of Northern Venezuela - implications for a giant sloth dispersal to Central and North America
FIGURE 1. Location map showing the locality where the AMU-CURS 184 specimen was recovered from San Gregorio Fm. outcrops.
Fig. 4 in Mass estimation of Santacrucian sloths from the Early Miocene Santa Cruz Formation of Patagonia, Argentina
Fig. 4. Phylogenetic tree following Asher and Helgen (2010), as used in the variance decomposition test. The nodes are arbitrarily labeled with numbers.
Fig. 3 in Mass estimation of Santacrucian sloths from the Early Miocene Santa Cruz Formation of Patagonia, Argentina
Fig. 3. Measurements used in this work, as illustrated using the left hind limb of Hapalops. A. Tibia in proximal view (A 1), anterior aspect down; anterior view (A 2), proximal end up; distal view (A 3), anterior aspect up. B. Fibula in anterior view, distal end down. C. Femur in anterior view (C 1), distal end down; distal view (C 2), anterior aspect up. D. Calcaneum in dorsal view, anterior aspect down. E. Astragalus in dorsal view, anterior aspect down. F. Pelvis in left lateral view.
Fig. 2 in Mass estimation of Santacrucian sloths from the Early Miocene Santa Cruz Formation of Patagonia, Argentina
Fig. 2. Measurements used in this work, as illustrated using the left forelimb of Hapalops. A. Scapula in lateral view, anteroventral aspect to the left. B. Humerus in proximal view (B 1), anterior aspect down; distal view (B 2), anterior aspect up; anterior view (B 3), proximal end up. C. Radius in anterior view, proximal end up. D. Ulna in medial view (D 1), anterior aspect right; anterior view (D 2).
Fig. 1 in Mass estimation of Santacrucian sloths from the Early Miocene Santa Cruz Formation of Patagonia, Argentina
Fig. 1. Cladogram showing the phylogenetic relationships among the xenarthrans included in this study. Modified from Gaudin (2004).
Fig. 2. A, B in Hypsodonty in Pleistocene ground sloths
Fig. 2. A, B. Paramylodon harlani (Owen, 1840), early Pleistocene, Hillsborough, Florida, USA. A. Left upper caniniform, UF 87042. B. Left M2, UF 87068. C, D. Glossotherium robustum (Owen, 1842), Pleistocene, General Belgrano, Buenos Aires province, Argentina. C. Left upper caniniform, MHM no catalogue number. D. Left M3, MHM no catalogue number.
Fig. 1. A. MLP 2−3 in Hypsodonty in Pleistocene ground sloths
Fig. 1. A. MLP 2−3, molariform of Megatherium americanum Cuvier, 1796, Pleistocene, Buenos Aires province, Argentina. B. UF 162356, molariform of Eremotherium eomigrans De Iuliis and Cartelle, 1999, Pleistocene, Alachua, Florida, USA. Because of the homodonty of the upper and lower megatheriine molariforms, determining the position of the isolated teeth is not reliable (except for M1, M5, and m5, but these do not have the ridges and grooves so prominent as in the illustrated material); thus, we have not attempted to identify the exact position of these teeth, but only figure them to show their occlusal features and the development of the tooth crown height.
FIGURE 6 in Description of the stylohyal bone of a giant sloth (Lestodon armatus)
FIGURE 6. Left femur of juvenile Lestodon (CAV 935) in posterior view showing the proximal (top) and distal (bottom) irregular surfaces of the diaphysis. Scale bar equals 100 mm.
FIGURE 5 in Description of the stylohyal bone of a giant sloth (Lestodon armatus)
FIGURE 5. Stylohyals of 1, juvenile ground sloth (CAV 476); 2, adult Glossotherium (MNHN 914); 3, adult Scelidotherium.(MLP 3-671); 4, Adult Megatherium (MNHN PAM 297). Scale bar equals 50 mm.
FIGURE 3 in Description of the stylohyal bone of a giant sloth (Lestodon armatus)
FIGURE 3. Three-dimensional reconstruction of the juvenile ground sloth stylohyal (CAV 476). Medial view (3D object see online Appendix 2 for animated PDF. palaeo-electronica.org/content/2015/1119-stylohyal-of-agiant-sloth).
FIGURE 2 in Description of the stylohyal bone of a giant sloth (Lestodon armatus)
FIGURE 2. Juvenile stylohyal (CAV 476) in 1, medial view; 2, lateral view. The glittering of the cylindrical part is due to its having been bathed in gold for SEM observations; 3, close up of the cut mark analyzed by Fariña et al (2014); 4, close up of the marks in the midshaft. White arrows indicate probable trampling marks; black arrows indicate probable cut marks. Scale bar equals 50 mm.
FIGURE 1 in Description of the stylohyal bone of a giant sloth (Lestodon armatus)
FIGURE 1. Left hyoid apparatus of the ground sloth Paramylodon harlani (modified from Stock, 1925). Shaded in grey is the fossil specimen analyzed in this work.
Text-fig. 6. Boxplots showing the proportion of mf2 in relation to the sum of the occlusal area in the five families of extinct sloths. in Unexpected Inhibitory Cascade In The Molariforms Of Sloths (Folivora, Xenarthra): A Case Study In Xenarthrans Honouring Gerhard Storch'S Open-Mindedness
Text-fig. 6. Boxplots showing the proportion of mf2 in relation to the sum of the occlusal area in the five families of extinct sloths.
Text-fig. 7. PGLS regressions for Mylodontidae, "Orophodontidae", and the rest of the sloths considered separately, Mylodontidae: dash double-dot line (-..-), "Orophodontidae": dash-dot line (-.-), rest of sloths: dash line (--). in Unexpected Inhibitory Cascade In The Molariforms Of Sloths (Folivora, Xenarthra): A Case Study In Xenarthrans Honouring Gerhard Storch'S Open-Mindedness
Text-fig. 7. PGLS regressions for Mylodontidae, "Orophodontidae", and the rest of the sloths considered separately, Mylodontidae: dash double-dot line (-..-), "Orophodontidae": dash-dot line (-.-), rest of sloths: dash line (--).
Text-fig. 5. Macroevolutionary trends related to the IC model in the first three teeth of the six families of extinct sloths, as well as specimens of the "basal Megatherioidea", Pseudoglyptodon, and Bradypus. Dashed line (- -) shows the regression including all data; solid line shows the regression after the exclusion of Octodontotherium (shown in the plot as a filled triangle). in Unexpected Inhibitory Cascade In The Molariforms Of Sloths (Folivora, Xenarthra): A Case Study In Xenarthrans Honouring Gerhard Storch'S Open-Mindedness
Text-fig. 5. Macroevolutionary trends related to the IC model in the first three teeth of the six families of extinct sloths, as well as specimens of the "basal Megatherioidea", Pseudoglyptodon, and Bradypus. Dashed line (- -) shows the regression including all data; solid line shows the regression after the exclusion of Octodontotherium (shown in the plot as a filled triangle).
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