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Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
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Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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Bell CJ, Cadena C, Meza A, Rudie L, Lewis PJ. Cranial anatomy of the "round-headed" Amphisbaenian Zygaspis quadrifrons (Squamata, Amphisbaenia) based on high-resolution x-ray computed tomography. Anat Rec (Hoboken) 2024; 307:495-532. [PMID: 37849246 DOI: 10.1002/ar.25304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 10/19/2023]
Abstract
Amphisbaenians are a poorly understood clade of fossorial lizards. Because of their derived anatomy and relative scarcity, the systematics of the clade and its placement within squamates has long been controversial. Traditional approaches grouped species into four assemblages according to burrowing behavior and cranial morphology, resulting in the recognition of "shovel-headed," "round-headed," "keel-headed," and "spade-headed" morphotypes. Recent phylogenetic analyses do not support the monophyly of the taxa that share those morphotypes. Detailed analyses of cranial osteology were previously accomplished using high-resolution x-ray computed tomography (HRXCT) for the "shovel-headed" Rhineura hatcherii (Rhineruidae) and the "spade-headed" Diplometopon zarudnyi (Trogonophidae). A detailed description of the "round-headed" Amphisbaena alba was previously completed based upon traditional "dry" skeletal specimens. Seven species of the "round-headed" Blanus (Blanidae) were also analyzed using HRXCT. The goal of that project was a comparative analysis of all extant species of Blanus rather than a detailed, bone-by-bone description of one species, but certainly is useful for comparison with another "round-headed" taxon. The "round-headed" morphotype is by far the most common among amphisbaenians and is much in need of further documentation. We use HRXCT imagery to provide additional data about the disparity in cranial morphology among amphisbaenians. Those data allow us to provide another detailed description of a "round-headed" amphisbaenian, the poorly known southern African species Zygaspis quadrifrons. HRXCT is ideal for this relatively rare and diminutive species. We are able to visualize and describe a detailed reconstruction of the entire skull as well as individual cranial elements. Comparisons with other species that were described in similar detail-D. zarudnyi, Spathorhynchus fossorium, R. hatcherii, and A. alba-and to a lesser degree with Blanus, reveal a complex mosaic of morphological features of the skull in Zygaspis. Preliminary data suggest that intraspecific variation is present within Z. quadrifrons, and interspecific variation among other species of Zygaspis may be sufficient for species-level recognition based on cranial osteology. Our description is, therefore, also intended to serve as a baseline for comparative analysis of other specimens of Z. quadrifrons and of other species within the genus.
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Affiliation(s)
- Christopher J Bell
- Department of Earth and Planetary Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Cristhian Cadena
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Antonio Meza
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Lauren Rudie
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Patrick J Lewis
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
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Brownstein CD, Meyer DL, Fabbri M, Bhullar BAS, Gauthier JA. Evolutionary origins of the prolonged extant squamate radiation. Nat Commun 2022; 13:7087. [PMID: 36446761 PMCID: PMC9708687 DOI: 10.1038/s41467-022-34217-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/18/2022] [Indexed: 11/30/2022] Open
Abstract
Squamata is the most diverse clade of terrestrial vertebrates. Although the origin of pan-squamates lies in the Triassic, the oldest undisputed members of extant clades known from nearly complete, uncrushed material come from the Cretaceous. Here, we describe three-dimensionally preserved partial skulls of two new crown lizards from the Late Jurassic of North America. Both species are placed at the base of the skink, girdled, and night lizard clade Pan-Scincoidea, which consistently occupies a position deep inside the squamate crown in both morphological and molecular phylogenies. The new lizards show that several features uniting pan-scincoids with another major lizard clade, the pan-lacertoids, in trees using morphology were convergently acquired as predicted by molecular analyses. Further, the palate of one new lizard bears a handful of ancestral saurian characteristics lost in nearly all extant squamates, revealing an underappreciated degree of complex morphological evolution in the early squamate crown. We find strong evidence for close relationships between the two new species and Cretaceous taxa from Eurasia. Together, these results suggest that early crown squamates had a wide geographic distribution and experienced complicated morphological evolution even while the Rhynchocephalia, now solely represented by the tuatara, was the dominant clade of lepidosaurs.
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Affiliation(s)
- Chase D. Brownstein
- grid.47100.320000000419368710Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT USA ,Stamford Museum and Nature Center, Stamford, CT USA
| | - Dalton L. Meyer
- grid.47100.320000000419368710Department of Earth and Planetary Sciences, Yale University, New Haven, CT USA
| | - Matteo Fabbri
- grid.47100.320000000419368710Department of Earth and Planetary Sciences, Yale University, New Haven, CT USA ,grid.299784.90000 0001 0476 8496Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL USA
| | - Bhart-Anjan S. Bhullar
- grid.47100.320000000419368710Department of Earth and Planetary Sciences, Yale University, New Haven, CT USA ,grid.47100.320000000419368710Yale Peabody Museum, Yale University, New Haven, CT USA
| | - Jacques A. Gauthier
- grid.47100.320000000419368710Department of Earth and Planetary Sciences, Yale University, New Haven, CT USA ,grid.47100.320000000419368710Yale Peabody Museum, Yale University, New Haven, CT USA
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5
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Hawkins RK, Bell CJ, Olori JC, Stocker MR. Intraspecific variation in the cranial osteology of Diplometopon zarudnyi (Squamata: Amphisbaenia: Trogonophidae). J Morphol 2022; 283:1359-1375. [PMID: 35998301 PMCID: PMC9826134 DOI: 10.1002/jmor.21508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/06/2022] [Accepted: 08/17/2022] [Indexed: 01/11/2023]
Abstract
A snake-like body plan and burrowing lifestyle characterize numerous vertebrate groups as a result of convergent evolution. One such group is the amphisbaenians, a clade of limbless, fossorial lizards that exhibit head-first burrowing behavior. Correlated with this behavior, amphisbaenian skulls are more rigid and coossified than those of nonburrowing lizards. However, due to their lifestyle, there are many gaps in our understanding of amphisbaenian anatomy, including how their cranial osteology varies among individuals of the same species and what that reveals about constraints on the skull morphology of head-first burrowing taxa. We investigated intraspecific variation in the cranial osteology of amphisbaenians using seven individuals of the trogonophid Diplometopon zarudnyi. Variation in both skull and individual skull element morphology was examined qualitatively and quantitatively through three-dimensional (3D) models created from microcomputed tomography data. Qualitative examination revealed differences in the number and position of foramina, the interdigitation between the frontals and parietal, and the extent of coossification among the occipital complex, fused basioccipital and parabasisphenoid ("parabasisphenoid-basioccipital complex"), and elements X. We performed 3D landmark-based geometric morphometrics for the quantitative assessment, revealing shape differences in the skull, premaxilla, maxilla, frontal, and parietal. The observed intraspecific variation may be the result of different stages of ontogenetic development or biomechanical optimization for head-first burrowing. For example, variation in the coossification of the occipital region suggests a potential ontogenetic coossification sequence. Examination of these areas of variation across other head-first burrowing taxa will help determine if the variation is clade-specific or part of a broader macroevolutionary pattern of head-first burrowing.
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Affiliation(s)
- Rebecca K. Hawkins
- Department of Fish and Wildlife ConservationVirginia TechBlacksburgVirginiaUSA,Present address:
Museum Studies Program, Lippincott Hall Room 61410 Jayhawk BlvdLawrenceKansasUSA
| | - Christopher J. Bell
- Department of Geological SciencesThe University of Texas at AustinAustinTexasUSA
| | - Jennifer C. Olori
- Biological Sciences DepartmentState University of New York at OswegoOswegoNew YorkUSA
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Bolet A, Stubbs TL, Herrera-Flores JA, Benton MJ. The Jurassic rise of squamates as supported by lepidosaur disparity and evolutionary rates. eLife 2022; 11:e66511. [PMID: 35502582 PMCID: PMC9064307 DOI: 10.7554/elife.66511] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
The squamates (lizards, snakes, and relatives) today comprise more than 10,000 species, and yet their sister group, the Rhynchocephalia, is represented by a single species today, the tuatara. The explosion in squamate diversity has been tracked back to the Cretaceous Terrestrial Revolution, 100 million years ago (Ma), the time when flowering plants began their takeover of terrestrial ecosystems, associated with diversification of coevolving insects and insect-eating predators such as lizards, birds, and mammals. Squamates arose much earlier, but their long pre-Cretaceous history of some 150 million years (Myr) is documented by sparse fossils. Here, we provide evidence for an initial radiation of squamate morphology in the Middle and Late Jurassic (174-145 Ma), and show that they established their key ecological roles much earlier than had been assumed, and they have not changed them much since.
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Affiliation(s)
- Arnau Bolet
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de BarcelonaCerdanyola del VallèsSpain
- School of Earth Sciences, University of BristolBristolUnited Kingdom
| | - Thomas L Stubbs
- School of Earth Sciences, University of BristolBristolUnited Kingdom
| | | | - Michael J Benton
- School of Earth Sciences, University of BristolBristolUnited Kingdom
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Georgalis GL, Szyndlar Z. First occurrence of Psammophis (Serpentes) from Europe witnesses another Messinian herpetofaunal dispersal from Africa - biogeographic implications and a discussion of the vertebral morphology of psammophiid snakes. Anat Rec (Hoboken) 2022; 305:3263-3282. [PMID: 35139258 DOI: 10.1002/ar.24892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 11/08/2022]
Abstract
We here describe abundant new snake material from the late Miocene (MN 13) of Salobreña, Spain. Vertebral morphology suggests a referral of the specimens to the extant psammophiid Psammophis, documenting the first occurrence of this genus in Europe. The diversity and disparity across the vertebral morphology of different psammophiid genera is discussed. We identify vertebral features that could diagnose Psammophis and therefore enable the recognition of the genus in the fossil record. A comparison of the new Spanish form with other taxa is conducted. We provide a detailed review of the psammophiid fossil record. Material previously described from the middle Miocene of Beni Mellal, Morocco is here tentatively referred to as? Psammophis sp., an action that renders that occurrence as the oldest (probable) record of the genus and Psammophiidae as a whole, providing thus a potential calibration point. On the other hand, Eastern European Pliocene material that had been previously supposedly referred to Psammophis is here discarded as being rather fragmentary, not affording any more precise determination. The two psammophiid genera Psammophis and Malpolon appear almost simultaneously in the European fossil record (MN 13), with the former achieving only a short-lived and apparently geographically limited distribution in the continent, while the latter still exists in its modern herpetofauna. We assess biogeographic implications of the new find, suggesting a direct dispersal event from northwestern Africa to the Iberian Peninsula during the late Miocene, facilitated by the Messinian Salinity Crisis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Georgios L Georgalis
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Zbigniew Szyndlar
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
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8
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Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction. Nat Commun 2021; 12:5335. [PMID: 34521829 PMCID: PMC8440539 DOI: 10.1038/s41467-021-25136-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 07/22/2021] [Indexed: 02/08/2023] Open
Abstract
Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes-a major clade of predators comprising over 3,700 living species-remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth's extant vertebrate faunas.
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Recoder R, Prates I, Marques-Souza S, Camacho A, Nunes PMS, Dal Vechio F, Ghellere JM, McDiarmid RW, Rodrigues MT. Lizards from the Lost World: two new species and evolutionary relationships of the Pantepui highland Riolama (Gymnophthalmidae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlz168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Pantepui region of northern South America harbours an endemic fauna that differs dramatically from those of the surrounding lowland rainforests and savannas. A component of this unique fauna is Riolama, a poorly known genus of microteiid lizards with four described and two undescribed species restricted to tepui mountains. We here implement an integrative approach to formally describe the two unnamed species and investigate the phylogenetic relationships and timing of diversification in Riolama using a fossil-calibrated molecular approach. Our results suggest that diversification initiated in Riolama during the Oligocene (c. 28 Mya), thereby characterizing the genus as an ancient lineage. This supports the Plateau biogeographic hypothesis to explain the diversification of the Pantepui fauna. Our divergence time estimation analysis also provides an updated temporal framework for the diversification of the highly diverse Gymnophthalmidae clade.
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Affiliation(s)
- Renato Recoder
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Sergio Marques-Souza
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Agustín Camacho
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Pedro M Sales Nunes
- Departamento de Zoologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Francisco Dal Vechio
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - José Mario Ghellere
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Roy W McDiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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10
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Scarpetta SG. Unusual lizard fossil from the Miocene of Nebraska and a minimum age for cnemidophorine teiids. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200317. [PMID: 32968509 PMCID: PMC7481707 DOI: 10.1098/rsos.200317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Teiid lizards are well represented in the fossil record and are common components of modern ecosystems in North and South America. Many fossils were referred to the cnemidophorine teiid group (whiptails, racerunners and relatives), particularly from North America. However, systematic interpretations of morphological features in cnemidophorines were hampered by the historically problematic taxonomy of the clade, and the biogeography and chronology of cnemidophorine evolution in North America is poorly understood from the fossil record. Few fossil cnemidophorines were identified with an apomorphy-based diagnosis, and there are almost no fossil cnemidophorines that could be used to anchor node calibrations. Here, I describe a cnemidophorine from the Miocene Ogallala Group of Nebraska and diagnose the fossil using apomorphies. In that process, I clarify the systematic utility of several morphological features of cnemidophorine lizards. I refer the fossil to the least inclusive clade containing Aspidoscelis, Holcosus and Pholidoscelis. The most conservative minimum age of the locality of the fossil is a fission-track date of 6.3 Ma, but mammal biochronology provides a more refined age of 9.4 Ma, which can be used as a minimum age for the crown cnemidophorine clade in divergence time analyses. The fossil indicates that a cnemidophorine lineage that does not live in Nebraska today inhabited the area during the Miocene. I refrain from naming a new taxon pending discovery of additional fossil material of the lineage to which the fossil belonged.
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Affiliation(s)
- Simon G. Scarpetta
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA
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11
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Jenkins KM, Shaw JO. Bite force data suggests relationship between acrodont tooth implantation and strong bite force. PeerJ 2020; 8:e9468. [PMID: 32656000 PMCID: PMC7333653 DOI: 10.7717/peerj.9468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/11/2020] [Indexed: 12/22/2022] Open
Abstract
Extant and extinct reptiles exhibit numerous combinations of tooth implantation and attachment. Tooth implantation ranges from those possessing roots and lying within a socket (thecodonty), to teeth lying against the lingual wall of the jawbone (pleurodonty), to teeth without roots or sockets that are attached to the apex of the marginal jawbones (acrodonty). Attachment may be ligamentous (gomphosis) or via fusion (ankylosis). Generally speaking, adaptative reasonings are proposed as an underlying driver for evolutionary changes in some forms of tooth implantation and attachment. However, a substantiated adaptive hypothesis is lacking for the state of acrodont ankylosis that is seen in several lineages of Lepidosauria, a clade that is plesiomorphically pleurodont. The convergent evolution of acrodont ankylosis in several clades of lepidosaurs suggests a selective pressure shaped the evolution of the trait. We hypothesize that acrodont ankylosis as seen in Acrodonta and Sphenodon punctatus, is an adaptation either resulting from or allowing for a stronger bite force. We analyzed bite force data gathered from the literature to show that those taxa possessing acrodont dentition possess a stronger bite force on average than those taxa with pleurodont dentition. Dietary specialists with pleurodont dentition may also possess relatively high bite forces, though body size may also play a role in their ability to bite hard. Furthermore, our results have implications for the evolution of acrodont ankylosis and potential behaviors related to strong bite force that influenced the evolution of acrodonty within Acrodonta and Rhynchocephalia.
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Affiliation(s)
- Kelsey M Jenkins
- Department of Earth and Planetary Sciences, Yale University, New Haven, United States of America
| | - Jack O Shaw
- Department of Earth and Planetary Sciences, Yale University, New Haven, United States of America
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12
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Abstract
We present a quantitative test of end-Cretaceous extinction scenarios and how these would have affected dinosaur habitats. Combining climate and ecological modeling tools, we demonstrate a substantial detrimental effect on dinosaur habitats caused by an impact winter scenario triggered by the Chicxulub asteroid. We were not able to obtain such an extinction state with several modeling scenarios of Deccan volcanism. We further show that the concomitant prolonged eruption of the Deccan traps might have acted as an ameliorating agent, buffering the negative effects on climate and global ecosystems that the asteroid impact produced at the Cretaceous–Paleogene boundary. The Cretaceous/Paleogene mass extinction, 66 Ma, included the demise of non-avian dinosaurs. Intense debate has focused on the relative roles of Deccan volcanism and the Chicxulub asteroid impact as kill mechanisms for this event. Here, we combine fossil-occurrence data with paleoclimate and habitat suitability models to evaluate dinosaur habitability in the wake of various asteroid impact and Deccan volcanism scenarios. Asteroid impact models generate a prolonged cold winter that suppresses potential global dinosaur habitats. Conversely, long-term forcing from Deccan volcanism (carbon dioxide [CO2]-induced warming) leads to increased habitat suitability. Short-term (aerosol cooling) volcanism still allows equatorial habitability. These results support the asteroid impact as the main driver of the non-avian dinosaur extinction. By contrast, induced warming from volcanism mitigated the most extreme effects of asteroid impact, potentially reducing the extinction severity.
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13
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Junior MT, Vechio FD, Recoder R, Cassimiro J, De Sena MA, Rodrigues MT. Two New Highland Species of Amphisbaena Linnaeus, 1758 (Amphisbaenia, Amphisbaenidae) from Bahia State, Brazil. SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2019. [DOI: 10.2994/sajh-d-17-00097.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Mauro Teixeira Junior
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090, São Paulo, SP, Brazil
| | - Francisco Dal Vechio
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090, São Paulo, SP, Brazil
| | - Renato Recoder
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090, São Paulo, SP, Brazil
| | - José Cassimiro
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090, São Paulo, SP, Brazil
| | - Marco Aurélio De Sena
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090, São Paulo, SP, Brazil
| | - Miguel Trefaut Rodrigues
- Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, CEP 05508-090, São Paulo, SP, Brazil
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14
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Perez R, Borges-Martins M. Integrative taxonomy of small worm lizards from Southern South America, with description of three new species (Amphisbaenia: Amphisbaenidae). ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Abstract
Abstract
The Afrotropics house a diverse freshwater ichthyofauna with > 3000 species, almost all of which are endemic. Recent progress in dated phylogenetics and palaeontology of several groups of Afrotropical freshwater fishes (AFFs) has allowed the testing of palaeoecology- and palaeogeography-based hypotheses explaining their early presence in Africa. Seven hypotheses were tested for 37 most-inclusive monophyletic groups of AFFs. Results indicated that ten lineages originated from direct, but asynchronous, marine-to-freshwater shifts. These lineages contribute < 2% to the current AFF species richness. Eleven lineages colonized the Afrotropics from the Orient after the Afro-Arabian plate collided with Eurasia in the early Oligocene. These lineages contribute ~20% to the total diversity. There are seven sister relationships between Afrotropical and Neotropical taxa. For only three of them (4% of the species diversity), the continental drift vicariance hypothesis was not rejected. Distributions of the other four younger trans-Atlantic lineages are better explained by post-drifting long-distance dispersal. In those cases, I discuss the possibility of dispersal through the Northern Hemisphere as an alternative to direct trans-Atlantic dispersal. The origins of ten AFF lineages, including the most species-rich Pseudocrenilabrinae (> 1100 species), are not yet established with confidence.
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Affiliation(s)
- Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
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16
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Čerňanský A, Stanley EL. The atlas-axis complex in Dibamidae (Reptilia: Squamata) and their potential relatives: The effect of a fossorial lifestyle on the morphology of this skeletal bridge. J Morphol 2019; 280:1777-1797. [PMID: 31566797 DOI: 10.1002/jmor.21064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 11/10/2022]
Abstract
We report on the first detailed study of the atlas-axis complex in the lizard clade Dibamidae, a family of poorly known fossorial squamates distributed in tropical or subtropical climates. This skeletal bridge is characterized by several features, such as the complete absence of the first intercentrum or the appearance of the first free cervical rib on the axis (usually less developed in Dibamus relative to that in Anelytropsis). Our study shows morphological differences of the atlas-axis complex in the Mexican blind lizard Anelytropsis relative to those of Asian Dibamus, the only two known extant genera of this clade. With regard to taxonomy and phylogenetic topology of the Dibamidae within Squamata, a huge conflict exists between morphology versus molecules. The morphology of the atlas-axis complex is therefore compared with several potential sister clades + Sphenodon. Dibamids share several features with limbless Gekkota, Scincoidea, and Amphisbaenia. The complete absence of the first intercentrum is observed in Rhineura floridana and in Ateuchosaurus chinensis as well, and the free rib associated with the synapophyses of the axis is also present in Acontias meleagris. However, some of these features may result from a limbless, burrowing ecology and thus could represent homoplastic characters. In any case, the morphology of the atlas-axis shows that dibamids share most character states with skinks. Although the atlas-axis complex forms only an additional source of information, this conclusion is consistent with most morphological rather than molecular tree topologies.
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Affiliation(s)
- Andrej Čerňanský
- Department of Ecology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Edward L Stanley
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
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17
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Čerňanský A. The first potential fossil record of a dibamid reptile (Squamata: Dibamidae): a new taxon from the early Oligocene of Central Mongolia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Dibamid reptiles have a known current distribution on two continents (Asia and North America). Although this clade represents an early-diverging group in the Squamata and thus should have a long evolutionary history, no fossil record of these peculiar burrowing squamate reptiles has been documented so far. The fossil material described here comes from the early Oligocene of the Valley of Lakes in Central Mongolia. This material consists of jaws and is placed in the clade Dibamidae on the basis of its morphology, which is further confirmed by phylogenetic analyses. In spite of the fragmentary nature of this material, it thus forms the first, but putative, fossil evidence of this clade. If correctly interpreted, this material demonstrates the occurrence of Dibamidae in East Asia in the Palaeogene, indicating its distribution in higher latitudes than today. The preserved elements possess a unique combination of character states, and a new taxon name is therefore erected: Hoeckosaurus mongoliensis sp. nov. The dentary of Hoeckosaurus exhibits some characters of the two extant dibamid taxa. However, the open Meckel’s groove, together with other characters, show that this group was morphologically much more diverse in the past.
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Affiliation(s)
- Andrej Čerňanský
- Department of Ecology, Laboratory of Evolutionary Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova, Bratislava, Slovakia
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18
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Blom MPK, Matzke NJ, Bragg JG, Arida E, Austin CC, Backlin AR, Carretero MA, Fisher RN, Glaw F, Hathaway SA, Iskandar DT, McGuire JA, Karin BR, Reilly SB, Rittmeyer EN, Rocha S, Sanchez M, Stubbs AL, Vences M, Moritz C. Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate. Proc Biol Sci 2019; 286:20182575. [PMID: 31161911 DOI: 10.1098/rspb.2018.2575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal. Cryptoblepharus species that occur in coastal habitats have on average dispersed 13 to 14 times more frequently than non-coastal species and coastal specialization has, therefore, led to an extraordinarily widespread distribution that includes multiple continents and distant island archipelagoes. Furthermore, their presence across the Pacific substantially predates the age of human colonization and we can explicitly reject the possibility that these patterns are solely shaped by human-mediated dispersal. Overall, by combining new analytical methods with a comprehensive phylogenomic dataset, we use a quantitative framework to show how coastal specialization can influence dispersal capacity and eventually shape geographical distributions at a macroevolutionary scale.
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Affiliation(s)
- Mozes P K Blom
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,2 Museum für Naturkunde, Leibniz Institut für Evolutions- und Biodiversitätsforschung , Berlin , Germany
| | - Nicholas J Matzke
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,3 School of Biological Sciences, University of Auckland , Auckland , New Zealand
| | - Jason G Bragg
- 1 Research School of Biology, The Australian National University , Canberra , Australia
| | - Evy Arida
- 4 Research Center for Biology, The Indonesian Institute of Sciences , Cibinong , Indonesia
| | | | - Adam R Backlin
- 6 U.S. Geological Survey, Western Ecological Research Center , Santa Ana, CA , USA
| | | | - Robert N Fisher
- 8 U.S. Geological Survey, Western Ecological Research Center , San Diego, CA , USA
| | - Frank Glaw
- 9 Department of Herpetology, Zoologische Staatssamlung Münich , Munich , Germany
| | - Stacie A Hathaway
- 8 U.S. Geological Survey, Western Ecological Research Center , San Diego, CA , USA
| | - Djoko T Iskandar
- 10 School of Life Sciences and Technology, Institut Teknologi , Bandung , Indonesia
| | - Jimmy A McGuire
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Benjamin R Karin
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Sean B Reilly
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Eric N Rittmeyer
- 1 Research School of Biology, The Australian National University , Canberra , Australia.,5 Museum of Natural Science, Louisiana State University , Baton Rouge, LA , USA
| | - Sara Rocha
- 12 Department of Biochemistry, Genetics and Immunology & Biomedical Research Center (CINBIO), University of Vigo , Vigo , Spain
| | | | - Alexander L Stubbs
- 11 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley , Berkeley, CA , USA
| | - Miguel Vences
- 14 Zoological Institute, Technische Universität Braunschweig , Braunschweig , Germany
| | - Craig Moritz
- 1 Research School of Biology, The Australian National University , Canberra , Australia
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19
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Westphal N, Mahlow K, Head JJ, Müller J. Pectoral myology of limb-reduced worm lizards (Squamata, Amphisbaenia) suggests decoupling of the musculoskeletal system during the evolution of body elongation. BMC Evol Biol 2019; 19:16. [PMID: 30630409 PMCID: PMC6329177 DOI: 10.1186/s12862-018-1303-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 11/20/2018] [Indexed: 01/10/2023] Open
Abstract
Background The evolution of elongated body forms in tetrapods has a strong influence on the musculoskeletal system, including the reduction of pelvic and pectoral girdles, as well as the limbs. However, despite extensive research in this area it still remains unknown how muscles within and around bony girdles are affected by these reductions. Here we investigate this issue using fossorial amphisbaenian reptiles, or worm lizards, as a model system, which show substantial variation in the degree of reductions of girdles and limbs. Using iodine-based contrast-enhanced computed tomography (diceCT), we analyze the composition of the shoulder muscles of the main clades of Amphisbaenia and their outgroups relative to the pectoral skeleton. Results All investigated amphisbaenian taxa retain the full set of 17 shoulder muscles, independent of the degree of limb and girdle reductions, whereas in some cases muscles are fused to complexes or changed in morphology relative to the ancestral condition. Bipes is the only taxon that retains forelimbs and an almost complete pectoral girdle. All other amphisbaenian families show more variation concerning the completeness of the pectoral girdle having reduced or absent girdle elements. Rhineura, which undergoes the most severe bone reductions, differs from all other taxa in possessing elongated muscle strands instead of discrete shoulder muscles. In all investigated amphisbaenians, the shoulder muscle agglomerate is shortened and shifted anteriorly relative to the ancestral position as seen in the outgroups. Conclusions Our results show that pectoral muscle anatomy does not necessarily correspond to the loss or reduction of bones, indicating a decoupling of the musculoskeletal system. Muscle attachment sites change from bones to non-skeletal areas, such as surrounding muscles, skin or connective tissue, whereas muscle origins themselves remain in the same region where the pectoral bones were ancestrally located. Our findings indicate a high degree of developmental autonomy within the musculoskeletal system, we predict that the observed evolutionary rearrangements of amphisbaenian shoulder muscles were driven by functional demands rather than by developmental constraints. Nevertheless, worm lizards display a spatial offset of both pectoral bones and muscles relative to the ancestral position, indicating severe developmental modifications of the amphisbaenian body axis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1303-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natascha Westphal
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany.
| | - Kristin Mahlow
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany
| | - Jason James Head
- Department of Zoology and University Museum of Zoology, University of Cambridge, Downing St, Cambridge, CB2 3EJ, UK
| | - Johannes Müller
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Invalidenstr. 43, 10115, Berlin, Germany
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20
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Vullo R, Rage JC. The first Gondwanan borioteiioid lizard and the mid-Cretaceous dispersal event between North America and Africa. Naturwissenschaften 2018; 105:61. [PMID: 30291449 DOI: 10.1007/s00114-018-1588-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 10/28/2022]
Abstract
Borioteiioidea are an enigmatic group of Cretaceous lizards widely distributed in northern continents (Laurasia). Here, we describe the first borioteiioid lizard from Gondwana, represented by a new species of the polyglyphanodontine genus Bicuspidon, B. hogreli sp. nov., from the Cenomanian Kem Kem beds of Morocco. The discovery of Bicuspidon hogreli sp. nov., which is one of the oldest known member of Polyglyphanodontini, challenges previous assumptions on the center of origin and dispersal of the group. In addition, the known distribution of Bicuspidon (Cenomanian of Utah and Morocco, and Santonian-Maastrichtian of eastern Europe) suggests a complex palaeobiogeographical history for the genus. The existence of a terrestrial dispersal route persisting during the whole Early Cretaceous between North America and Africa is hypothesized to explain some similarities observed between the Cenomanian squamate assemblages of these two continents. Alternatively, dispersal between the two landmasses may have occurred by transatlantic rafting. During the Cenomanian-Santonian interval, Bicuspidon colonized the European archipelago probably from North Africa, like many "Eurogondwanan" taxa.
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Affiliation(s)
- Romain Vullo
- Univ Rennes, CNRS, Géosciences Rennes, UMR 6118, F-35000, Rennes, France.
| | - Jean-Claude Rage
- Sorbonne Universités, CR2P, UMR 7207, CNRS-Muséum national d'Histoire naturelle-Université Paris 6, F-75005, Paris, France
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21
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Mongiardino Koch N, Gauthier JA. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 2018; 13:e0202729. [PMID: 30133514 PMCID: PMC6105018 DOI: 10.1371/journal.pone.0202729] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
- Yale Peabody Museum of Natural History, New Haven, Connecticut, United States of America
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22
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Kazi S, Hipsley CA. Conserved evolution of skull shape in Caribbean head-first burrowing worm lizards (Squamata: Amphisbaenia). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Sakib Kazi
- University of Melbourne, School of BioSciences, Parkville, VIC, Australia
- Museums Victoria, Melbourne, VIC, Australia
| | - Christy A Hipsley
- University of Melbourne, School of BioSciences, Parkville, VIC, Australia
- Museums Victoria, Melbourne, VIC, Australia
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23
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McIntyre SRN, Lineweaver CH, Groves CP, Chopra A. Global biogeography since Pangaea. Proc Biol Sci 2018; 284:rspb.2017.0716. [PMID: 28592675 DOI: 10.1098/rspb.2017.0716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/09/2017] [Indexed: 11/12/2022] Open
Abstract
The break-up of the supercontinent Pangaea around 180 Ma has left its imprint on the global distribution of species and resulted in vicariance-driven speciation. Here, we test the idea that the molecular clock dates, for the divergences of species whose geographical ranges were divided, should agree with the palaeomagnetic dates for the continental separations. Our analysis of recently available phylogenetic divergence dates of 42 pairs of vertebrate taxa, selected for their reduced ability to disperse, demonstrates that the divergence dates in phylogenetic trees of continent-bound terrestrial and freshwater vertebrates are consistent with the palaeomagnetic dates of continental separation.
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Affiliation(s)
- Sarah R N McIntyre
- Research School of Astronomy and Astrophysics, Australian National University, Canberra, Australia
| | - Charles H Lineweaver
- Research School of Astronomy and Astrophysics, Australian National University, Canberra, Australia.,Research School of Earth Sciences, Australian National University, Canberra, Australia
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, Australia
| | - Aditya Chopra
- Research School of Earth Sciences, Australian National University, Canberra, Australia
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24
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Anderson FE, Williams BW, Horn KM, Erséus C, Halanych KM, Santos SR, James SW. Phylogenomic analyses of Crassiclitellata support major Northern and Southern Hemisphere clades and a Pangaean origin for earthworms. BMC Evol Biol 2017; 17:123. [PMID: 28558722 PMCID: PMC5450073 DOI: 10.1186/s12862-017-0973-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 05/18/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Earthworms (Crassiclitellata) are a diverse group of annelids of substantial ecological and economic importance. Earthworms are primarily terrestrial infaunal animals, and as such are probably rather poor natural dispersers. Therefore, the near global distribution of earthworms reflects an old and likely complex evolutionary history. Despite a long-standing interest in Crassiclitellata, relationships among and within major clades remain unresolved. METHODS In this study, we evaluate crassiclitellate phylogenetic relationships using 38 new transcriptomes in combination with publicly available transcriptome data. Our data include representatives of nearly all extant earthworm families and a representative of Moniligastridae, another terrestrial annelid group thought to be closely related to Crassiclitellata. We use a series of differentially filtered data matrices and analyses to examine the effects of data partitioning, missing data, compositional and branch-length heterogeneity, and outgroup inclusion. RESULTS AND DISCUSSION We recover a consistent, strongly supported ingroup topology irrespective of differences in methodology. The topology supports two major earthworm clades, each of which consists of a Northern Hemisphere subclade and a Southern Hemisphere subclade. Divergence time analysis results are concordant with the hypothesis that these north-south splits are the result of the breakup of the supercontinent Pangaea. CONCLUSIONS These results support several recently proposed revisions to the classical understanding of earthworm phylogeny, reveal two major clades that seem to reflect Pangaean distributions, and raise new questions about earthworm evolutionary relationships.
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Affiliation(s)
- Frank E Anderson
- Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Bronwyn W Williams
- Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA
- North Carolina Museum of Natural Sciences, Research Laboratory, Raleigh, North Carolina, 27699, USA
| | - Kevin M Horn
- Department of Zoology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Christer Erséus
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30, Göteborg, SE, Sweden
| | - Kenneth M Halanych
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Scott R Santos
- Molette Biology Laboratory for Environmental and Climate Change Studies, Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Samuel W James
- Department of Biology, University of Iowa, Iowa City, Iowa, 52242, USA
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25
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Tennant JP, Mannion PD, Upchurch P, Sutton MD, Price GD. Biotic and environmental dynamics through the Late Jurassic-Early Cretaceous transition: evidence for protracted faunal and ecological turnover. Biol Rev Camb Philos Soc 2017; 92:776-814. [PMID: 26888552 PMCID: PMC6849608 DOI: 10.1111/brv.12255] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
Abstract
The Late Jurassic to Early Cretaceous interval represents a time of environmental upheaval and cataclysmic events, combined with disruptions to terrestrial and marine ecosystems. Historically, the Jurassic/Cretaceous (J/K) boundary was classified as one of eight mass extinctions. However, more recent research has largely overturned this view, revealing a much more complex pattern of biotic and abiotic dynamics than has previously been appreciated. Here, we present a synthesis of our current knowledge of Late Jurassic-Early Cretaceous events, focusing particularly on events closest to the J/K boundary. We find evidence for a combination of short-term catastrophic events, large-scale tectonic processes and environmental perturbations, and major clade interactions that led to a seemingly dramatic faunal and ecological turnover in both the marine and terrestrial realms. This is coupled with a great reduction in global biodiversity which might in part be explained by poor sampling. Very few groups appear to have been entirely resilient to this J/K boundary 'event', which hints at a 'cascade model' of ecosystem changes driving faunal dynamics. Within terrestrial ecosystems, larger, more-specialised organisms, such as saurischian dinosaurs, appear to have suffered the most. Medium-sized tetanuran theropods declined, and were replaced by larger-bodied groups, and basal eusauropods were replaced by neosauropod faunas. The ascent of paravian theropods is emphasised by escalated competition with contemporary pterosaur groups, culminating in the explosive radiation of birds, although the timing of this is obfuscated by biases in sampling. Smaller, more ecologically diverse terrestrial non-archosaurs, such as lissamphibians and mammaliaforms, were comparatively resilient to extinctions, instead documenting the origination of many extant groups around the J/K boundary. In the marine realm, extinctions were focused on low-latitude, shallow marine shelf-dwelling faunas, corresponding to a significant eustatic sea-level fall in the latest Jurassic. More mobile and ecologically plastic marine groups, such as ichthyosaurs, survived the boundary relatively unscathed. High rates of extinction and turnover in other macropredaceous marine groups, including plesiosaurs, are accompanied by the origin of most major lineages of extant sharks. Groups which occupied both marine and terrestrial ecosystems, including crocodylomorphs, document a selective extinction in shallow marine forms, whereas turtles appear to have diversified. These patterns suggest that different extinction selectivity and ecological processes were operating between marine and terrestrial ecosystems, which were ultimately important in determining the fates of many key groups, as well as the origins of many major extant lineages. We identify a series of potential abiotic candidates for driving these patterns, including multiple bolide impacts, several episodes of flood basalt eruptions, dramatic climate change, and major disruptions to oceanic systems. The J/K transition therefore, although not a mass extinction, represents an important transitional period in the co-evolutionary history of life on Earth.
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Affiliation(s)
- Jonathan P. Tennant
- Department of Earth Science and EngineeringImperial College LondonSouth KensingtonLondonSW7 2AZU.K.
| | - Philip D. Mannion
- Department of Earth Science and EngineeringImperial College LondonSouth KensingtonLondonSW7 2AZU.K.
| | - Paul Upchurch
- Department of Earth SciencesUniversity College LondonLondonWC1E 6BTU.K.
| | - Mark D. Sutton
- Department of Earth Science and EngineeringImperial College LondonSouth KensingtonLondonSW7 2AZU.K.
| | - Gregory D. Price
- School of Geography, Earth and Environmental SciencesPlymouth UniversityPlymouthPL4 8AAU.K.
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26
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Cardoso D, Harris DJ, Wieringa JJ, São-Mateus WMB, Batalha-Filho H, Torke BM, Prenner G, Queiroz LPD. A molecular-dated phylogeny and biogeography of the monotypic legume genus Haplormosia, a missing African branch of the otherwise American-Australian Brongniartieae clade. Mol Phylogenet Evol 2016; 107:431-442. [PMID: 27965083 DOI: 10.1016/j.ympev.2016.12.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/02/2016] [Accepted: 12/09/2016] [Indexed: 11/17/2022]
Abstract
A comprehensively sampled reassessment of the molecular phylogeny of the genistoid legumes questions the traditional placement of Haplormosia, an African monotypic genus traditionally classified within tribe Sophoreae close to the Asian-American geographically disjunct genus Ormosia. Plastid matK sequences placed Haplormosia as sister to the American-Australian tribe Brongniartieae. Despite a superficial resemblance between Haplormosia and Ormosia, a re-examination of the morphology of Haplormosia corroborates the new phylogenetic result. The reciprocally monophyletic deep divergence of the Haplormosia stem lineage from the remaining Brongniartieae is dated to ca. 52Mya, thus supporting a signature of an old single long-distance dispersal during the early Eocene. Conversely, we estimated a relatively recent long-distance dispersal rooted in the Early Miocene for the Australian Brongniartieae clade emerging from within a grade of American Brongniartieae. The Bayesian ancestral area reconstruction revealed the coming and going of neotropical ancestors during the diversification history of the Brongniartieae legumes in Africa and all over the Americas and Australia.
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Affiliation(s)
- Domingos Cardoso
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil; Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil.
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Wallace M B São-Mateus
- Programa de Pós-Graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s.n., Ondina, 40170-115 Salvador, Bahia, Brazil
| | - Benjamin M Torke
- Institute of Systematic Botany, The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458-5126, USA
| | - Gerhard Prenner
- Royal Botanic Gardens, Kew, Jodrell Laboratory, Richmond, Surrey TW9 3DS, UK
| | - Luciano Paganucci de Queiroz
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
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27
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Abstract
The present-day distribution of velvet worms corresponds neatly to the ancient supercontinent Gondwana - except for a puzzling outpost in southeast Asia. Jaw-dropping new fossil material now establishes when and how peripatid onychophorans reached this isolated spot.
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28
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Müller J, Hipsley CA, Maisano JA. Skull osteology of the Eocene amphisbaenian Spathorhynchus fossorium (Reptilia, Squamata) suggests convergent evolution and reversals of fossorial adaptations in worm lizards. J Anat 2016; 229:615-630. [PMID: 27329946 DOI: 10.1111/joa.12513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2016] [Indexed: 11/29/2022] Open
Abstract
The fossorial amphisbaenians, or worm lizards, are characterized by a suite of specialized characters in the skull and postcranium, however fossil evidence suggests that at least some of these shared derived traits evolved convergently. Unfortunately the lack of detailed knowledge of many fossil taxa has rendered a more precise interpretation difficult. Here we describe the cranial anatomy of the oldest-known well-preserved amphisbaenian, Spathorhynchus fossorium, from the Eocene Green River Formation, Wyoming, USA, using high-resolution X-ray computed tomography (HRXCT). This taxon possesses one of the most strongly reinforced crania known among amphisbaenians, with many dermal bones overlapping each other internally. In contrast to modern taxa, S. fossorium has a paired orbitosphenoid, lacks a true compound bone in the mandible, and possesses a fully enclosed orbital rim. The last feature represents a highly derived structure in that the jugal establishes contact with the frontal internally, reinforcing the posterior orbital margin. S. fossorium also possesses a strongly modified Vidian canal with a previously unknown connection to the ventral surface of the parabasisphenoid. Comparison with the closely related fossil taxon Dyticonastis rensbergeri reveals that these derived traits are also shared by the latter species and potentially represent synapopmorphies of an extinct Paleogene clade of amphisbaenians. The presence of a reinforced orbital rim suggests selection against the loss of a functional eye and indicates an ecology potentially different from modern taxa. Given the currently accepted phylogenetic position of Spathorhynchus and Dyticonastis, we predict that supposedly 'unique' cranial traits traditionally linked to fossoriality such as a fused orbitosphenoid and the reduction of the eye show a more complex character history than previously assumed, including both parallel evolution and reversals to superficially primitive conditions.
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Affiliation(s)
- Johannes Müller
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany.
| | - Christy A Hipsley
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany.,Museum Victoria, Melbourne, VIC, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Jessica A Maisano
- Department of Geological Sciences, Jackson School of Geosciences, The University of Texas at Austin, Austin, TX, USA
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29
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Lavoué S. Was Gondwanan breakup the cause of the intercontinental distribution of Osteoglossiformes? A time-calibrated phylogenetic test combining molecular, morphological, and paleontological evidence. Mol Phylogenet Evol 2016; 99:34-43. [DOI: 10.1016/j.ympev.2016.03.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 11/16/2022]
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30
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Hipsley CA, Rentinck MN, Rödel MO, Müller J. Ontogenetic allometry constrains cranial shape of the head-first burrowing worm lizardCynisca leucura(Squamata: Amphisbaenidae). J Morphol 2016; 277:1159-67. [DOI: 10.1002/jmor.20564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/24/2016] [Accepted: 05/03/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Christy A. Hipsley
- School of BioSciences, University of Melbourne; Parkville Victoria Australia
- Museum Victoria; Melbourne Victoria Australia
- Museum Für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; Berlin Germany
| | - Marc-Nicolas Rentinck
- Museum Für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; Berlin Germany
| | - Mark-Oliver Rödel
- Museum Für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; Berlin Germany
| | - Johannes Müller
- Museum Für Naturkunde; Leibniz Institute for Evolution and Biodiversity Science; Berlin Germany
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31
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Affiliation(s)
- Mateusz Tałanda
- Department of Paleobiology and Evolution; Faculty of Biology, Biological and Chemical Research Centre; University of Warsaw; Żwirki i Wigury 101 Warszawa 02-089 Poland
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