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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>
The phylogeny of ceutorhynchine weevils (Ceutorhynchinae, Curculionidae): mitogenome data improve the resolution of tribal relationships.
Open the record for dataset details and reuse information.
Fig. 7 in Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation
Fig. 7 (opposite page). Kalloconus canariensis sp. nov. A–B. Holotype (dorsal and ventral views), 89.0 mm (MNCN 15.05/200091H). C. Paratype 1, 85.3 mm (MNCN 15.05/200091P). D. Paratype 5, 76.3 mm (MNCN 15.05/200092). E. Paratype 3, 92.1 mm (MNCN 15.05/200093). F. Paratype 2, 132.0 mm (MNCN 15.05/200094). G. Paratype 4, 93.9 mm (MNCN 15.05/200092). H. Paratype 6, 47.4 mm (MNCN 5.05.200091P). I. Paratype 7, 43.3 mm (MNCN 15.05/200095). J–K. Radular tooth. K. K. canariensis sp. nov., paratype 1. K. K. pulcher ([Lightfoot], 1786), Joal Fadiouth, Senegal (MJT), SL = 96.7 mm. Scale bars = 10 mm unless otherwise indicated
Fig. 8 in Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation
Fig. 8. Plot of maximum diameter (MD, mm) versus shell length (SL, mm) for K. canariensis sp. nov. (Ɨ) and K. pulcher ([Lightfoot], 1786) (-). The lectotype of K. siamensis (Hwass in Bruguiére, 1792) (A) is also shown.
Fig. 6 in Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation
Fig. 6 (opposite page). A. Conus navarroi navarroi Rolán, 1986, holotype, 16 mm (MNCN 15.05/1008). B. Africonus angeluquei Tenorio, Abalde & Zardoya, 2018 (= perrineae Cossignani & Fiadeiro, 2018), holotype, 30.0 mm (MNCN 15.05/78710). C. Conus raulsilvai Rolán, Monteiro & Fernandes, 1998, holotype, 19.7 mm (MNCN 15.05/27230). D. Conus regonae Rolán & Trovão, 1990, holotype, 32.7 mm (MNCN 15.05/1092). E. Conus roeckeli Rolán, 1980, holotype, 13.2 mm (MNCN 15.05/1049). F. Africonus salletae Cossignani, 2014, holotype, 15.5 mm (MMM). G. Africonus santaluziensis Cossignani & Fiadeiro, 2015, paratype, 28.1 mm (Paul Kersten coll.). H. Africonus santanaensis Afonso & Tenorio, 2014, holotype, 17.1 mm (MNCN 15.05/60118). I. Conus saragasae Rolán, 1986, holotype, 21.8 mm (MNCN 15.05/1009). J. Africonus verdensis (Trovão, 1979), 22.5 mm (MNCN 15.05/78864). K. Conus vulcanus Tenorio & Afonso, 2004, holotype, 25.2 mm (MNCN 15.05/46652). L. Chelyconus ermineus (Born, 1778), 54.3 mm (MNCN 15.05/80014). M. Genuanoconus genuanus (Linnaeus, 1758), 50.2 mm (MNCN 15.05/78547). N. Kalloconus ateralbus (Kiener, 1850), 40.1 mm (MNCN 15.05/79649). O. Kalloconus byssinus (Röding, 1798), 56.4 mm (MNCN 15.05/90429). Scale bars = 10 mm.
Fig. 2 in Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation
Fig. 2. Phylogenetic relationships of West African cones and species delimitation. A time tree (relaxed molecular clock) was reconstructed following methods and calibrations in Abalde et al. (2017a). Dates are in million years. Bold names indicate new mitogenomes. A red line indicates the threshold (uncorrected p distance of 0.2%, based on the divergences between Africonus verdensis (Trovão, 1979) and its sister group and Varioconus guanche (Lauer, 1993) and its sister group) for species delimitation.
Fig. 10 in Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation
Fig. 10 (opposite page). A. Conus ambiguus Reeve, 1844, neotype, 39.3 mm (NBC). B. Conus bellocqae van Rossum, 1996, paratype, 60 mm (F. Gubbioli coll., Marbella, Spain). C. Monteiroconus tabidus (Reeve, 1844), 33.6 mm (MNCN 15.05/78864). D. Conus belairensis Pin & Leung Tack in Pin, 1989, holotype, 36.7 mm (MNHN IM-2000-32668). E. Varioconus bruguieresi (Kiener, 1846) comb. nov., 32.1 mm (MNCN 15.05/78497). F. Varioconus cloveri (Walls, 1978) comb. nov., 23.2 mm (MNCN 15.05/78457). G. Varioconus echinophilus (Petuch, 1975b) comb. nov., 22.0. mm (MNCN 15.05/90430). H. Conus franciscanus Hwass in Bruguière, 1792, lectotype, 56.6 mm (MHNG-MOLL-52625). I. Varioconus franciscanus (Hwass in Bruguière, 1792) comb. nov., 53.6 mm (MNCN 15.05/78491). J. Varioconus franciscanus f. hybridus (Kiener, 1847), 40.0 mm (MNCN 15.05/78427). K. Conus guanche Lauer, 1993, holotype, 34.0 mm (MNHN IM-2000-2553). L. Conus guinaicus Hwass in Bruguière, 1792, lectotype, 43.0 mm (MHNG-MOLL-52638). M. Varioconus guinaicus (Hwass in Bruguière, 1792) comb. nov., 50.2 mm (MNCN 15.05/78443). N. Lautoconus wolof Petuch & Berschauer, 2018, holotype, 21.1 mm (MNHN IM-2000-34015). O. Conus pineaui Pin & Leung Tack in Pin, 1989, holotype, 28.7 mm (MNHN IM-2000-2528). P. Conus dorotheae Monnier & Limpalaër, 2010, holotype, 26.8 mm (MNHN IM-2009-8702). Scale bars = 10 mm.
Fig. 4 in Taxonomic revision of West African cone snails (Gastropoda: Conidae) based upon mitogenomic studies: implications for conservation
Fig. 4 (opposite page). A. Conus felitae Rolán, 1990, holotype, 12.7 mm (MNCN 15.05/1099). B. Africonus fernandesi (Tenorio, Afonso & Rolán, 2008), 14.5 mm (MNCN 15.05/78598). C. Africonus freitasi Tenorio, Afonso, Rolán, Pires, Vasconcelos, Abalde & Zardoya, 2018, holotype, 13.7 mm (MNCN 15.05/200008) D. Conus verdensis furnae Rolán, 1990, holotype, 21.1 mm (MNCN 15.05/1097). E. Africonus fuscoflavus (Röckel, Rolán & Monteiro, 1980), 22.3 mm (MNCN 15.05/80407). F. Conus damottai galeao Rolán, 1990, holotype, 21.3 mm (MNCN 15.05/1093). G. Africonus gonsaloi Afonso & Tenorio, 2014, holotype, 19.3 mm (MNCN 15.05/60119). H. Africonus grahami (Röckel, Cosel & Burnay, 1980), 24.0 mm (MNCN 15.05/78549). I. Conus infinitus Rolán, 1990, holotype, 20.8 mm (MNCN, 15.05/1095). J. Conus isabelarum Tenorio & Afonso, 2004, holotype, 22.8 mm (MNCN 15.05/46654). K. Conus josephinae Rolán, 1980, holotype, 25.8 mm (MNCN 15.05/1050). L. Africonus kersteni (Tenorio, Afonso & Rolán, 2008), holotype, 20.8 mm (MNCN 15.05/47051). M. Africonus longilineus (Röckel, Rolán & Monteiro, 1980), 21.7 mm (MNCN 15.05/79738). N. Africonus lugubris (Reeve, 1849), 14.5 mm (MNCN 15.05/90431). O. Africonus maioensis (Trovão, Rolán & Félix-Alves, 1990), 29.5 mm (MNCN 15.05/78689). P. Africonus miruchae (Röckel, Rolán & Monteiro, 1980), 12.9 mm (MNCN 15.05/79789). Scale bars = 10 mm.
Evolutionary history of the Galápagos Rail revealed by ancient mitogenomes and modern samples
<p>Beast v. 2.6.3 input (<em>.xml</em>) files and output (<em>.log</em> and <em>.trees</em>) files for phylogenetic analyses of rails, used to determined the evolutionary history of the Galápagos Rail <em>Laterallus spilonota</em>. There are two main datasets: coding sequences of the mitochondrial genome ('mtCDS'), partitioned per codon position, and a two mitochondrial/one nuclear marker dataset ('2mt1nc'). For each of the datasets, separate runs have been made in which the fossil calibration of Rallidae is applied to the stem of the present-day family ('calRallidaeStem') or the crown node ('calRallidaeCrown), and finally all runs have been replicated with three different starting seeds ('seed_NNNNNNNNN', with the different seeds 123456789, 456789123, and 789123456).</p> <p>We provide raw output (<em>.log</em> and <em>.raw.trees</em>) as well as maximum clade credibility ('mcc') trees (<em>.mcc.trees</em>), calculated after discarding 10% of the trees as burn-in, using median ('heights_median') or mean ('heights_mean') node heights as estimated node age.</p> <p>The runs used for Table 1 (and Figure 2) in the accompanying paper are:</p> <ul> <li>Dataset mtCDS, Rallidae calibration of stem: seed 123456789</li> <li>Dataset mtCDS, Rallidae calibration of crown: seed 456789123 </li> <li>Dataset 2mt1nc, Rallidae calibration of stem: seed 789123456</li> <li>Dataset 2mt1nc, Rallidae calibration of crown: seed 123456789</li> </ul> <p>This version of the data includes <em>Pellornis mikkelseni</em> among the fossils making up the calibration distribution for crown Gruiformes. In a previous version of this data deposit, that data point was represented by <em>Messelornis cristata </em>(see accompanying paper).</p>
Supplementary Figure S7 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S7 Infant Trachypithecus popa sp. nov. with creamy white fur coloration at Popa Mountain Park, Myanmar (Photo: Thaung Win).
Supplementary Figure S5 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S5 Dorsal (A), lateral (B), and ventral (C) view of skull and mandible of holotype (NHMUK ZD.1914.7.19.3) of Trachypithecus popa sp. nov. (Photo: Courtesy of the Trustees of the Natural History Museum, London).
Supplementary Figure S6 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S6 Ventral view of skull without mandible (A), and dorsal (B), lateral (C), and ventral (D) views of mandible of holotype (NHMUK ZD.1914.7.19.3) of Trachypithecus popa sp. nov. (Photo: Courtesy of the Trustees of the Natural History Museum, London).
Figure 6 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Figure 6 Photos of Trachypithecus phayrei (A, B), Trachypithecus popa sp. nov. (C, D) and Trachypithecus melamera (formerly T. p. shanicus) (E, F) A: Adult female T. phayrei at Yangon Zoo, Myanmar (photo by Tilo Nadler); B: Adult male T. phayrei from Lawachara National Park, Bangladesh (photo by Tanvir Ahmed); C, D: Subadult male T. popa from Mount Popa, Myanmar (photo by Lay Win); E: Adult female T. melamera at Mandalay Zoo, Myanmar (photo by Tilo Nadler), F: Adult female T. melamera with offspring from Gaoligong Mountains National Park, China (photo by Chi Ma).
Supplementary Figure S1 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S1 Ultrametric tree showing phylogenetic relationships and divergence times among all investigated taxa inferred from BEAST analysis (node bars indicate 95% HPDs and node supports of <100% ML BS and <1.0 BI PP are given at respective nodes).
Figure 5 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Figure 5 Geographical distribution of mitochondrial clades found in Trachypithecus phayrei Sample locations are numbered as in Figures 1, 2 (see also Supplementary Table S1) and colored according to their mitochondrial clade assignment. Limits of the Central clade to the northeast and East clade to the southwest, depicted in light green, are not yet firmly resolved. Samples from locations 6–9 form Central clade A, while those from locations 10–12 cluster in Central clade B. Note, at location 10, haplotypes of the Central and East clades were found. Museum specimen from location 13 cluster unexpectedly with Central clade A (see Results).
Supplementary Figure S3 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S3 Morphometric comparisons (PCA performed on 12 molar measurements (A-B, same analysis as in Figure 4), 24 molar and cranial measurements (C-D), and 12 cranial measurements (E-F)) among Trachypithecus phayrei individuals representing West (red), Central (blue), and East (yellow) clades. Shown is projection of specimen scores on first and second principal components extracted with percentage of variance explained by each component (Tables S7-8). Specimens are clustered by species and represented by maturity (right panels) and sex (left panels) to show the influence of age and sex on comparisons.
Supplementary Figure S4 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S4 Dorsal (A), lateral (B), and ventral (C) view of stuffed holotype (NHMUK ZD.1914.7.19.3) of Trachypithecus popa sp. nov. (Photo: Courtesy of the Trustees of the Natural History Museum, London).
Figure 3 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Figure 3 Head-body length (A), tail length (B), and tail/head-body length ratio (C) of adult male and female Trachypithecus phayrei representing West, Central, and East clades (median, quartiles, min-max) Numbers in brackets: sample sizes; post-hoc pair-wise population comparisons of traits; Mann-Whitney U-test, with Bonferroni correction for multiple testing: *: P<0.025, (*): P<0.05; see Supplementary Table S6.
Supplementary Figure S2 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Supplementary Figure S2 Morphometric comparisons (PCA performed on 12 molar measurements) among Trachypithecus phayrei individuals representing West (red), Central (blue), and East (yellow) clades. Shown is projection of specimen scores on first and second versus third (A and B, respectively) principal components extracted (Supplementary Table S7).
Figure 4 in Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species
Figure 4 Morphometric comparisons (principal component analysis performed on 12 molar measurements) among Trachypithecus phayrei individuals representing West (red), Central (blue), and East (yellow) clades Shown is projection of specimen scores of first and second principal components, with variance explained by each component (graphical depictions of third principal component appear in Supplementary Figure S2 and underlying statistics are provided in Supplementary Table S7.)
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