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Brennan IG, Lemmon AR, Moriarty Lemmon E, Hoskin CJ, Donnellan SC, Keogh JS. Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification. Syst Biol 2024; 73:1-11. [PMID: 37527840 DOI: 10.1093/sysbio/syad048] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/21/2023] [Accepted: 08/01/2023] [Indexed: 08/03/2023] Open
Abstract
The Australian continent's size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia's plants and animals are unique and endemic, including the continent's frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups that vary from Gondwanan relics to recent immigrants from Asia and include arguably the continent's oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continent's most visible faunas. [Anuran; adaptive radiation; Gondwana; phylogenetics].
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Affiliation(s)
- Ian G Brennan
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32316, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Stephen C Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J Scott Keogh
- Division of Ecology & Evolution, The Australian National University, Canberra, ACT 2601, Australia
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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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Gonzlez CR, Saldarriaga-Cordoba M, Aguilera O, Miranda-Esquivel DR. Coenura Bigot as a valid genus: A molecular and morphological phylogenetic analysis of Pelecorhynchus Macquart sensu lato (Diptera: Pelecorhynchidae). Zootaxa 2023; 5383:297-324. [PMID: 38221247 DOI: 10.11646/zootaxa.5383.3.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Indexed: 01/16/2024]
Abstract
The phylogeny of the genus Pelecorhynchus Macquart (Diptera: Pelecorhynchidae) was analyzed using three genes, cytochrome oxidase I, 28S ribosomal DNA, and CAD5, with 112 morphological characteristics. A total of 59 specimens (13 outgroups and 46 ingroups) were included in the analysis. The monophyly of Pelecorhynchidae was recovered under all analyses, with Glutops Burgess as the sister group of Pelecorhynchus s.l., while Pseudoerinna jonesi (Cresson) was the sister group. Within Pelecorhynchus there are three main clades with unresolved affinities. Clade I was formed by P. personatus (Walker), P. vulpes (Macquart), P. penai Pechuman and P. kroeberi (Lindner), a well-supported clade. Clade II corresponds to the set of species of Chilean Pelecorhynchus, conformed to P. biguttatus (Philippi), P. toltensis Llanos & Gonzlez, P. elegans (Philippi), P. xanthopleura (Philippi), P. hualqui Llanos & Gonzlez, and P. longicauda (Bigot), a well-supported clade. Clade III is represented exclusively by P. fulvus Ricardo, which has an exclusively Australian distribution. The monophyly of P. fulvus and its nomenclature remain an open question, as only a single species of this taxon was included. Our study demonstrated that the concept of Pelecorhynchus should be revisited. Therefore, we restore Coenura Bigot, 1857 to generic status for part of the southern South American species of Pelecorhynchus conformed by the species C. biguttata, C. elegans, C. hualqui, C. longicauda, C. toltensis, and C. xanthopleura which are monophyletic, supported by molecular and morphological data, and consistent with a Chilean distribution.
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Affiliation(s)
- Christian R Gonzlez
- Instituto de Entomologa; Facultad de Ciencias Bsicas; Universidad Metropolitana de Ciencias de la Educacin; Santiago; Chile.
| | - Mnica Saldarriaga-Cordoba
- Centro de Investigacin en Recursos Naturales y Sustentabilidad; Universidad Bernardo OHiggins; Santiago; Chile.
| | - Omayra Aguilera
- Centro de Investigacin en Recursos Naturales y Sustentabilidad; Universidad Bernardo OHiggins; Santiago; Chile.
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Farman RM, Archer M, Hand SJ. A geometric morphometric analysis of variation in Australian frog ilia and taxonomic interpretations. J Morphol 2023; 284:e21642. [PMID: 37708503 DOI: 10.1002/jmor.21642] [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: 02/28/2023] [Revised: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
Anurans including frogs and toads exhibit an ilium that is often regarded as taxonomically diagnostic. The ilium, one of the three paired bones that make up the pelvic girdle, has been important in the fossil record for identifying anuran morphotypes. Osteological collections for Australian frogs are rare in herpetological museums, and skeletonizing whole-bodied specimens requires destroying soft tissue morphology which is valuable to anuran specialists working on living species. Computed tomography scans provide the opportunity to study anuran osteology without the loss of soft tissues. Our study, based on microcomputed tomography scans of extant Australian frogs from the public repository Morphosource and from museum collections focuses on the morphological differences between Australian frogs at the familial and generic levels using geometric morphometrics to compare the diagnostic shape of the ilium. Principal component analysis (PCA) and canonical variate analysis (CVA) were conducted to assess differences in the ilium between supraspecific groups of Australian frogs. The canonical variates analysis accurately predicted group membership (i.e., the correct family) with up to 76.2% success for cross-validated predictions and 100% of original group predictions. While the sample was limited to familial and generic level analyses, our research shows that ilial morphology in Australian frogs is taxonomically informative. This research provides a guide for identifying Australian anurans, including fossils, as well as new information relevant to considerations about their phylogenetic relationships, and the potential use of the fossil record to enhance efforts to conserve threatened living frog species.
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Affiliation(s)
- Roy M Farman
- School of Biological, Earth and Environmental Sciences, Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Archer
- School of Biological, Earth and Environmental Sciences, Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Suzanne J Hand
- School of Biological, Earth and Environmental Sciences, Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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Buček A, Wang M, Šobotník J, Hellemans S, Sillam-Dussès D, Mizumoto N, Stiblík P, Clitheroe C, Lu T, González Plaza JJ, Mohagan A, Rafanomezantsoa JJ, Fisher B, Engel MS, Roisin Y, Evans TA, Scheffrahn R, Bourguignon T. Molecular phylogeny reveals the past transoceanic voyages of drywood termites (Isoptera, Kalotermitidae). Mol Biol Evol 2022; 39:6577226. [PMID: 35511685 PMCID: PMC9113494 DOI: 10.1093/molbev/msac093] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ∼120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Ma (75–93 Ma 95% highest posterior density), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ∼40 disjunctions among biogeographic realms were dated at <50 Ma, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.
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Affiliation(s)
- A Buček
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - M Wang
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - J Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - S Hellemans
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - D Sillam-Dussès
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.,Laboratory of Experimental and Comparative Ethology, UR 4443, University Sorbonne Paris Nord, Villetaneuse, France
| | - N Mizumoto
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - P Stiblík
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - C Clitheroe
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - T Lu
- Tomer Lu, Total Hadbara Israel
| | - J J González Plaza
- International Research Centre in Critical Raw Materials-ICCRAM, University of Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - A Mohagan
- Center for Biodiversity Research and Extension in Mindanao, Central Mindanao University, Musuan, Maramag, Bukidnon 8710, Philippines.,Department of Biology, College of Arts and Sciences, Central Mindanao University, Musuan, Maramag, Bukidnon 8710, Philippines
| | - J J Rafanomezantsoa
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | - B Fisher
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar.,California Academy of the Sciences, San Francisco, California, USA
| | - M S Engel
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA.,Division of Entomology, Natural History Museum, University of Kansas, Lawrence, Kansas, USA
| | - Y Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Belgium
| | - T A Evans
- School of Animal Biology, University of Western Australia, Perth WA 6009, Australia
| | - R Scheffrahn
- Fort Lauderdale Research and Education Center, Institute for Food and Agricultural Sciences, 3205 College Avenue, Davie, Florida 33314, USA
| | - T Bourguignon
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.,Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
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Antarctica as an evolutionary arena during the Cenozoic global cooling. Proc Natl Acad Sci U S A 2021; 118:2108886118. [PMID: 34183404 DOI: 10.1073/pnas.2108886118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Kim SL, Zeichner SS, Colman AS, Scher HD, Kriwet J, Mörs T, Huber M. Probing the Ecology and Climate of the Eocene Southern Ocean With Sand Tiger Sharks Striatolamia macrota. PALEOCEANOGRAPHY AND PALEOCLIMATOLOGY 2020; 35:e2020PA003997. [PMID: 34222817 PMCID: PMC8246854 DOI: 10.1029/2020pa003997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 06/13/2023]
Abstract
Many explanations for Eocene climate change focus on the Southern Ocean-where tectonics influenced oceanic gateways, ocean circulation reduced heat transport, and greenhouse gas declines prompted glaciation. To date, few studies focus on marine vertebrates at high latitudes to discern paleoecological and paleoenvironmental impacts of this climate transition. The Tertiary Eocene La Meseta (TELM) Formation has a rich fossil assemblage to characterize these impacts; Striatolamia macrota, an extinct (†) sand tiger shark, is abundant throughout the La Meseta Formation. Body size is often tracked to characterize and integrate across multiple ecological dimensions. †S. macrota body size distributions indicate limited changes during TELMs 2-5 based on anterior tooth crown height (n = 450, mean = 19.6 ± 6.4 mm). Similarly, environmental conditions remained stable through this period based on δ18OPO4 values from tooth enameloid (n = 42; 21.5 ± 1.6‰), which corresponds to a mean temperature of 22.0 ± 4.0°C. Our preliminary ε Nd (n = 4) results indicate an early Drake Passage opening with Pacific inputs during TELM 2-3 (45-43 Ma) based on single unit variation with an overall radiogenic trend. Two possible hypotheses to explain these observations are (1) †S. macrota modified its migration behavior to ameliorate environmental changes related to the Drake Passage opening, or (2) the local climate change was small and gateway opening had little impact. While we cannot rule out an ecological explanation, a comparison with climate model results suggests that increased CO2 produces warm conditions that also parsimoniously explain the observations.
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Affiliation(s)
- Sora L. Kim
- Department of Geophysical SciencesUniversity of ChicagoChicagoILUSA
- Department of Life and Environmental SciencesUniversity of CaliforniaMercedCAUSA
| | - Sarah S. Zeichner
- Department of Geophysical SciencesUniversity of ChicagoChicagoILUSA
- Division of Geological and Planetary SciencesCalifornia Institute of TechnologyPasadenaCAUSA
| | - Albert S. Colman
- Department of Geophysical SciencesUniversity of ChicagoChicagoILUSA
- Department of Earth, Environment, and Planetary SciencesRice UniversityHoustonTXUSA
| | - Howie D. Scher
- Department of Earth, Ocean, and EnvironmentUniversity of South CarolinaColumbiaSCUSA
| | - Jürgen Kriwet
- Department of PalaeontologyUniversity of ViennaViennaAustria
| | - Thomas Mörs
- Department of PalaeobiologySwedish Museum of Natural HistoryStockholmSweden
- Bolin Centre for Climate ResearchStockholm UniversityStockholmSweden
| | - Matthew Huber
- Department of Earth, Atmosphere, and Planetary SciencesPurdue UniversityWest LafayetteINUSA
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