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Foley NM, Mason VC, Harris AJ, Bredemeyer KR, Damas J, Lewin HA, Eizirik E, Gatesy J, Karlsson EK, Lindblad-Toh K, Springer MS, Murphy WJ, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. A genomic timescale for placental mammal evolution. Science 2023; 380:eabl8189. [PMID: 37104581 DOI: 10.1126/science.abl8189] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Victor C Mason
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Joana Damas
- The Genome Center, University of California, Davis, CA, USA
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elinor K Karlsson
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, University of Massachussetts Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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Gheerbrant E, Schmitt A, Billet G. Petrosal and bony labyrinth morphology of the stem paenungulate mammal (Paenungulatomorpha) Ocepeia daouiensis from the Paleocene of Morocco. J Anat 2022; 240:595-611. [PMID: 32735727 PMCID: PMC8930808 DOI: 10.1111/joa.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 11/29/2022] Open
Abstract
Based on high-resolution computed tomography, we describe in detail the petrosal and inner ear anatomy of one of the few known African stem paenungulates (Paenungulatomorpha), Ocepeia daouiensis from the Selandian of the Ouled Abdoun phosphate basin (Morocco). The petrosal of Ocepeia displays some remarkable, probably derived features (among eutherians) such as relatively small pars cochlearis, pars canalicularis labyrinth (including small semicircular canals), a large wing-like pars mastoidea, a large and inflated tegmen tympani, and the dorsoventral orientation of the large canal for the ramus superior. The presence of small semicircular canals in Ocepeia is an interesting shared trait with tenrecoidean afrotherians. Otherwise, and consistent with a general primitive skull morphology, the middle ear and labyrinth of Ocepeia daouiensis is characterised by many plesiomorphic traits close to the eutherian generalised plan. This adds to the rather generalised morphology of the earliest crown paenungulates such as Eritherium, Phosphatherium and Seggeurius to support an ancestral paenungulatomorph morphotype poorly derived from the eutherian pattern. As a result, Ocepeia provides key morphological and fossil data to test phylogenetic relationships of the Afrotheria (including Paenungulatomorpha) at the placental root mostly inferred from molecular studies.
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Affiliation(s)
- Emmanuel Gheerbrant
- CR2PCentre de Recherche en Paléontologie ParisUMR 7207 (CNRS, MNHN, UPMC, Sorbonne Universités)ParisFrance
| | - Arnaud Schmitt
- CR2PCentre de Recherche en Paléontologie ParisUMR 7207 (CNRS, MNHN, UPMC, Sorbonne Universités)ParisFrance
| | - Guillaume Billet
- CR2PCentre de Recherche en Paléontologie ParisUMR 7207 (CNRS, MNHN, UPMC, Sorbonne Universités)ParisFrance
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Springer MS. Afrotheria. Curr Biol 2022; 32:R205-R210. [DOI: 10.1016/j.cub.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wagner F, Ruf I, Lehmann T, Hofmann R, Ortmann S, Schiffmann C, Hiller M, Stefen C, Stuckas H. Reconstruction of evolutionary changes in fat and toxin consumption reveals associations with gene losses in mammals: a case study for the lipase inhibitor PNLIPRP1 and the xenobiotic receptor NR1I3. J Evol Biol 2021; 35:225-239. [PMID: 34882899 DOI: 10.1111/jeb.13970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/28/2022]
Abstract
The inactivation of ancestral protein-coding genes (gene loss) can be associated with phenotypic modifications. Within placental mammals, repeated losses of PNLIPRP1 (gene inhibiting fat digestion) occurred preferentially in strictly herbivorous species, while repeated NR1I3 losses (gene involved in detoxification) occurred preferentially in strictly carnivorous species. It was hypothesized that lower fat contents of herbivorous diets and lower toxin contents of carnivorous diets cause relaxed selection pressure on these genes resulting in the accumulation of mutations and ultimately to convergent gene losses. However, since herbivorous and carnivorous diets differ vastly in their composition, a fine-grained analysis is required for hypothesis testing. We generated a trait matrix recording diet and semi-quantitative estimates of fat and toxin consumption for 52 placental species. By including data from 31 fossil taxa, we reconstructed the ancestral diets in major lineages (grundplan reconstruction). We found support that PNLIPRP1 loss is primarily associated with low levels of fat intake and not simply with herbivory/carnivory. In particular, PNLIPRP1 loss also occurred in carnivorous lineages feeding on a fat-poor diet, suggesting that the loss of this gene may be beneficial for occupying ecological niches characterized by fat-poor food resources. Similarly, we demonstrated that carnivorous species are indeed less exposed to diet-related toxins suggesting that the loss of NR1I3 and related genes (NR1I2, UGT1A6) resulted from relaxed selection pressure. This study illustrates the need of detailed phenotype studies to obtain a deeper understanding of factors underlying gene losses and to progress in understanding genomic causes of phenotypic variation in mammals.
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Affiliation(s)
- F Wagner
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - I Ruf
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Goethe-University, Department of Geosciences, Altenöferallee 1, 60438, Frankfurt am Main, Germany
| | - T Lehmann
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - R Hofmann
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Goethe-University, Department of Geosciences, Altenöferallee 1, 60438, Frankfurt am Main, Germany
| | - S Ortmann
- Leibniz Institut für Zoo- und Wildtierforschung, Abteilung für Evolutionäre Ökologie, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - C Schiffmann
- Leibniz Institut für Zoo- und Wildtierforschung, Abteilung für Evolutionäre Ökologie, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - M Hiller
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Goethe University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - C Stefen
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany
| | - H Stuckas
- Senckenberg, Leibniz Institution for Biodiversity and Earth System Research, Senckenberg Natural History Collections Dresden, Königsbrücker Landstraße 159, 01109, Dresden, Germany
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Avilla LS, Mothé D. Out of Africa: A New Afrotheria Lineage Rises From Extinct South American Mammals. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.654302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The South American native ungulates (SANUs) are usually overlooked in Eutherian phylogenetic studies. In the rare studies where they were included, the diversity of SANUs was underrated, keeping their evolutionary history poorly known. Some authors recognized the SANUs as a monophyletic lineage and formally named it Meridiungulata. Here, we recognized and defined a new supraordinal lineage of Eutheria, the Sudamericungulata, after performing morphological phylogenetic analyses including all lineages of SANUs and Eutheria. The SANUs resulted as non-monophyletic; thus, Meridiungulata is not a natural group; Litopterna and “Didolodontidae” are Panameriungulata and closer to Laurasiatheria than to other “Meridiungulata” (Astrapotheria, Notoungulata, Pyrotheria, and Xenungulata). The other “Meridiungulata” is grouped in the Sudamericungulata, as a new monophyletic lineage of Afrotheria Paenungulata, and shared a common ancestor with Hyracoidea. The divergence between the African and South American lineages is estimated to Early Paleocene, and their interrelationships support the Atlantogea biogeographic model. Shortly afterward, the Sudamericungulata explosively diversified in its four lineages. Confronting the Sudamericungulata evolutionary patterns and the Cenozoic natural events (such as tectonics and climatic and environmental changes, among others) helps to unveil a new chapter in the evolution of Gondwanan Eutheria, as well as the natural history of South America during the Cenozoic.
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Endocranial Morphology of a Middle Miocene South American Dugongid and the Neurosensorial Evolution of Sirenians. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09555-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
Giant land vertebrates have evolved more than 30 times, notably in dinosaurs and mammals. The evolutionary and biomechanical perspectives considered here unify data from extant and extinct species, assessing current theory regarding how the locomotor biomechanics of giants has evolved. In terrestrial tetrapods, isometric and allometric scaling patterns of bones are evident throughout evolutionary history, reflecting general trends and lineage-specific divergences as animals evolve giant size. Added to data on the scaling of other supportive tissues and neuromuscular control, these patterns illuminate how lineages of giant tetrapods each evolved into robust forms adapted to the constraints of gigantism, but with some morphological variation. Insights from scaling of the leverage of limbs and trends in maximal speed reinforce the idea that, beyond 100-300 kg of body mass, tetrapods reduce their locomotor abilities, and eventually may lose entire behaviours such as galloping or even running. Compared with prehistory, extant megafaunas are depauperate in diversity and morphological disparity; therefore, turning to the fossil record can tell us more about the evolutionary biomechanics of giant tetrapods. Interspecific variation and uncertainty about unknown aspects of form and function in living and extinct taxa still render it impossible to use first principles of theoretical biomechanics to tightly bound the limits of gigantism. Yet sauropod dinosaurs demonstrate that >50 tonne masses repeatedly evolved, with body plans quite different from those of mammalian giants. Considering the largest bipedal dinosaurs, and the disparity in locomotor function of modern megafauna, this shows that even in terrestrial giants there is flexibility allowing divergent locomotor specialisations.
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Affiliation(s)
- John R. Hutchinson
- Structure & Motion Lab, Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hawkshead Lane, North Mymms, Hertfordshire AL9 7TA,UK
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Abstract
Although viruses have threatened our ancestors for millions of years, prehistoric epidemics of viruses are largely unknown. Endogenous bornavirus-like elements (EBLs) are ancient bornavirus sequences derived from the viral messenger RNAs that were reverse transcribed and inserted into animal genomes, most likely by retrotransposons. These elements can be used as molecular fossil records to trace past bornaviral infections. In this study, we systematically identified EBLs in vertebrate genomes and revealed the history of bornavirus infections over nearly 100 My. We confirmed that ancient bornaviral infections have occurred in diverse vertebrate lineages, especially in primate ancestors. Phylogenetic analyses indicated that primate ancestors were infected with various bornaviral lineages during evolution. EBLs in primate genomes formed clades according to their integration ages, suggesting that bornavirus lineages infected with primate ancestors had changed chronologically. However, some bornaviral lineages may have coexisted with primate ancestors and underwent repeated endogenizations for tens of millions of years. Moreover, a bornaviral lineage that coexisted with primate ancestors also endogenized in the genomes of some ancestral bats. The habitats of these bat ancestors have been reported to overlap with the migration route of primate ancestors. These results suggest that long-term virus-host coexistence expanded the geographic distributions of the bornaviral lineage along with primate migration and may have spread their infections to these bat ancestors. Our findings provide insight into the history of bornavirus infections over geological timescales that cannot be deduced from research using extant viruses alone, thus broadening our perspective on virus-host coevolution.
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Gheerbrant E, Khaldoune F, Schmitt A, Tabuce R. Earliest Embrithopod Mammals (Afrotheria, Tethytheria) from the Early Eocene of Morocco: Anatomy, Systematics and Phylogenetic Significance. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09509-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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Eocene metatherians from Anatolia illuminate the assembly of an island fauna during Deep Time. PLoS One 2018; 13:e0206181. [PMID: 30427946 PMCID: PMC6235269 DOI: 10.1371/journal.pone.0206181] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
Island biotas have disproportionately influenced the history and development of evolutionary biology, but understanding their genesis and evolution across geological timescales has been hindered by a poor fossil record. Here we augment the insular Eocene (~43 Ma) mammalian fauna known from the Pontide terrane of central Anatolia by describing two new metatherian taxa (stem marsupials) from the Lülük Member of the Uzunçarşıdere Formation in the Orhaniye Basin. Geological and paleontological data indicate that the Pontide terrane was an island on the northern margin of Neotethys during the middle Eocene. Reflecting its geodynamic context in a region of active tectonic convergence, the Eocene Pontide terrane hosted a unique combination of Laurasian and Gondwanan mammals, including an anachronistic radiation of pleuraspidotheriids (archaic ungulates) that went extinct on the European mainland ~13 Ma earlier. Most of the mammalian clades occupying the Pontide terrane colonized it by dispersal across marine barriers rather than being stranded there through vicariance. Endemic radiations of pleuraspidotheriid ungulates and polydolopimorphian metatherians on the Pontide terrane reveal that in situ diversification was an important factor contributing to faunal assembly and evolution. The insular fauna that arose on the Pontide terrane is highly analogous to that of modern Sulawesi, which evolved under strikingly similar geological conditions. Illustrating the ephemeral nature of insular biotas across macroevolutionary timescales, the demise of the Pontide fauna coincided with paleogeographic changes enabling more cosmopolitan taxa to reach it for the first time. The high level of endemism shown by the mammalian fauna of the Uzunçarşıdere Formation eliminates the Pontide terrane as a potential early Eocene dispersal corridor between western Europe and India.
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