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140 results for “Mammal Evolution”
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
<p>Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all ~6000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our 'backbone-and-patch' approach to tree-building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (i) backbone relationships and ages among major lineages, using fossil node- or tip-dating; and (ii) species-level 'patch' phylogenies with non-overlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ('DNA-only' trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ('completed' trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (i) node ages are broadly concordant among studies, and (ii) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous 'supertree' approaches where unresolved nodes led to branch length artifacts. Credible sets of mammalian phylogenetic history are now available for download at <a href="http://vertlife.org/phylosubsets">http://vertlife.org/phylosubsets</a>, enabling investigations of long-standing questions in comparative biology.</p>
Diversity and evolution of cerebellar folding in mammals
<p>Coronal cerebellar mid-sections for 56 mammalian species, at the same scale.</p> <p> </p> <p>This figure is from our open access paper:</p> <p>Heuer, K., Traut, N., de Sousa, A. A., Valk, S., & Toro, R. (2022). Diversity and evolution of cerebellar folding in mammals. bioRxiv. <a href="https://doi.org/10.1101/2022.12.30.522292">https://doi.org/10.1101/2022.12.30.522292</a></p> <p> </p> <p>Abstract</p> <p>The process of brain folding is thought to play an important role in the development and organisation of the cerebrum and the cerebellum. The study of cerebellar folding is challenging due to the small size and abundance of its folia. In consequence, little is known about its anatomical diversity and evolution. We constituted an open collection of histological data from 56 mammalian species and manually segmented the cerebrum and the cerebellum. We developed methods to measure the geometry of cerebellar folia and to estimate the thickness of the molecular layer. We used phylogenetic comparative methods to study the diversity and evolution of cerebellar folding and its relationship with the anatomy of the cerebrum. Our results show that the evolution of cerebellar and cerebral anatomy follows a stabilising selection process. We observed 2 groups of phenotypes changing concertedly through evolution: a group of “diverse” phenotypes – varying over several orders of magnitude together with body size, and a group of “stable” phenotypes varying over less than 1 order of magnitude across species. Our analyses confirmed the strong correlation between cerebral and cerebellar volumes across species, and showed in addition that large cerebella are disproportionately more folded than smaller ones. Compared with the extreme variations in cerebellar surface area, folial anatomy and molecular layer thickness varied only slightly, showing a much smaller increase in the larger cerebella. We discuss how these findings could provide new insights into the diversity and evolution of cerebellar folding, the mechanisms of cerebellar and cerebral folding, and their potential influence on the organisation of the brain across species.</p>
Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation
Open the record for dataset details and reuse information.
Fig. 4 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig. 4. Upper molars of the trechnotherian mammal Lactodens sheni Han and Meng, 2016, from Aptian, Lower Cretaceous Jiufotang Formation, Caoyang City, Liaoning Province, China. A. Holotype (HG-M016) from Shangheshou area; right ultimate premolar and M1–M6 in buccal (A1) and occlusal (A2) views, showing the corresponding cusps on different teeth. B. ZGY0053 from Dapingfang; left upper molars (M1–M6) in occlusal (B1), buccal (B2), and lingual (B3) views. Image in B3 is horizontally flipped for convenience of comparison.
Fig. 5 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig. 5. Lower teeth of the trechnotherian mammal Lactodens sheni Han and Meng, 2016 (ZGY0053) from Aptian, Lower Cretaceous Jiufotang Formation of Dapingfang, Caoyang City, Liaoning Province, China), right c–m6 in lingual (A1) and occlusal (A2) views (with the dentary bone segmented away) and in posterobuccal view (A5), left p5–m6 in buccal (A3) and occlusal (A4) views. See also Figs. 3 and 7.
Fig. 3 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig. 3. CT-rendered lower jaws and dentitions of the trechnotherian mammal Lactodens sheni Han and Meng, 2016 (ZGY0053), from Aptian, Lower Cretaceous Jiufotang Formation of Dapingfang, Caoyang City, Liaoning Province, China. A1–A3, left upper and lower dentition and dentary in medial (only teeth), lateral, and occlusal views, respectively. A4–A6, right upper and lower dentition and dentary in lateral, medial, and occlusal views, respectively. Note: angular end is not the mandibular condyle (see Fig. 6); coronoid tubercle, mis-labelled as "cp" in Han and Meng (2016: fig. 10). Upper and lower teeth in A1, A2, A4, A5 are in the original position that were preserved. Arrows in A2, A4 point to mental foramina (note the difference between the two mandibles). Question mark in A5 points to a faint groove that is not the Meckelian groove (compared to that of Origolestes lii in Fig. 6B).
Fig. 1 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig. 1. New specimen of Lactodens sheni Han and Meng, 2016 (ZGY0053) from Aptian, Lower Cretaceous Jiufotang Formation of Dapingfang, Caoyang City, Liaoning Province, China. A. Partial skeleton in dorsal view that is preserved in the main slab. B. CT rendered partial skull; mostly ventral portion with teeth in dorsal (B1) and ventral (B2) views and mainly the skull roof in dorsal (B3) and ventral (B4) views.
Fig. 7 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig. 7. Comparison of molars between of Origolestes and Lactodens. A. Origolestes lii Mao, Hu, Li, Wang, Chase, Smith, and Meng, 2020 (IVPP V13604) from Lower Cretaceous Lujiatun beds of the Yixian Formation of the Lujiatun locality, Beipiao County, Liaoning Province, China; upper molars (M1–M2) in buccal (A1) and occlusal (A2) views; lower molars (m1–m3) in occlusal (A3) and lingual (A4) views (modified from Mao et al. 2020). B. Lactodens sheni Han and Meng, 2016 (ZGY0053) from Aptian, Lower Cretaceous Jiufotang Formation of Dapingfang, Caoyang City, Liaoning Province, China; upper molars (M1–M4) in buccal (B1) and occlusal (B2) views; lower molars (m1–m4) in occlusal (B3) and lingual (B4) views. Image in B1 has been vertically reversed for convenience of comparison. The lower teeth (m1–m4) in B3 and B4 were composite from better preserved left m2–m3 (reversed) and right dentitions (m1, m4). The angular lines indicate the symmetrical (O. lii) and asymmetrical (L. sheni) crown outline and the embrasure.
Fig 6 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig 6. Comparison of the mandibular morphologies of Origolestes and Lactodens. A. Lactodens sheni Han and Meng, 2016 (holotype, HG-M016) from Aptian, Lower Cretaceous Jiufotang Formation of Shangheshou area, Caoyang City, Liaoning Province, China; posterior portion of the right mandible in buccal (A1) and lingual (A2) views. B. Origolestes lii Mao, Hu, Li, Wang, Chase, Smith, and Meng, 2020 (IVPP V13604) from Lower Cretaceous Lujiatun beds of the Yixian Formation of the Lujiatun locality, Beipiao County, Liaoning Province, China; right mandible in buccal (B1) and lingual (B2) views. The mandible in B was slightly displaced at the crack (marked with the arrow) and has been digitally restored (see Mao et al. 2020).
Fig. 2 in New material of the trechnotherian mammal Lactodens from the Early Cretaceous Jehol Biota: Comparison with Origolestes and implications for mammal evolution
Fig. 2. CT-images of the trechnotherian mammal Lactodens sheni Han and Meng, 2016, from Aprian, Lower Cretaceous Jiufotang Formation, Caoyang City, Liaoning Province, China. A. Holotype (HG-M016) from Shangheshou area; A1, virtual skull remains with the lingual side of the right mandible exposed (see Han and Meng 2016: fig. 1); A2, virtual skull remains with the lateral side of the right mandible exposed (this side of the skull is embeded in the matrix and not visible except for the part of cheek teeth that were needle-prepared from the back side of the slab (Han and Meng 2016: figs. 1, 5); A3, a CT-slice showing the contrast of bone and matrix and revealing the roots of some teeth. B. ZGY0053 from Dapingfang, a CT-section through the skull (showing the root conditions). Note there is no tooth germ under any cheek teeth in both specimens in A3 and B.
FIGURE 18 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 18. Ancestral state reconstruction of prey capture strategies and prey type preference in stem and crown Mysticeti. Topology follows Gatesy et al. (2013) and Fordyce and Marx (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
FIGURE 3 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 3. Anatomical features associated with suction feeding in walrus (Odobenus rosmarus skull, from Jefferson et al., 2015) and North Sea beaked whale (Mesoplodon bidens skull, authors' work).
FIGURE 11 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 11. Sirenia stem and familial level diversity through time. "Protosirenidae / Prorastomidae" includes all taxa that are not included in the two extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 7 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 7. Pinnipedimorpha stem taxa and familial level diversity through time. "Stem-Pinnipedimorpha" includes all stem taxa that are not included in Desmatophocidae and the three extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 5 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 5. Anatomical features associated with grazing in African manatee (Trichechus senegalensis skull, from Werth, 2000), Desmostylia (Paleoparadoxia skull, public domain), and aquatic sloth (Thalassocnus sp. skull, modified from de Muizon et al., 2004).
FIGURE 8 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 8. Cetacean stem and Neoceti taxa diversity through time. "Archaeoceti" includes all stem taxa that are not included in the two extant groups. Dashed vertical lines: black, epoch boundaries; gray, age boundaries.
FIGURE 16 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 16. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in Odobenidae. Topology follows Berta et al. (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information uploaded to Dryad repository (https:// doi.org/10.6086/d14671).
FIGURE 17 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 17. Ancestral state reconstruction of prey type preference in stem and crown Pinnipedimorpha. Topology follows Rybczynski et al. (2009), Dewaele et al. (2017), and Berta et al. (2018). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch can be found in the Supplementary Information (https:// doi.org/10.6086/d14671).
FIGURE 19 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 19. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in stem Odontoceti. Topology follows Gatesy et al. (2013) and Boessenecker et al. (2017). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
FIGURE 20 in Feeding in marine mammals: An integration of evolution and ecology through time
FIGURE 20. Ancestral state reconstruction of prey capture strategies and tooth pattern and cusp shape in crown Odontoceti. Topology follows McGowen et al. (2009) and Gatesy et al. (2013). Details on the tree can be found in Appendix 1. All data matrices and complete trees with branch lengths can be found in the Supplementary Information (https://doi.org/10.6086/d14671).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.