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Costa GJ, Nunes VL, Marabuto E, Mendes R, Silva DN, Pons P, Bas JM, Hertach T, Paulo OS, Simões PC. The effect of the Messinian salinity crisis on the early diversification of the
Tettigettalna
cicadas. ZOOL SCR 2022. [DOI: 10.1111/zsc.12571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gonçalo J. Costa
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Vera L. Nunes
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Raquel Mendes
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Diogo N. Silva
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Pere Pons
- Departament de Ciències Ambientals Universitat de Girona Girona Catalonia Spain
| | - Josep M. Bas
- Departament de Ciències Ambientals Universitat de Girona Girona Catalonia Spain
| | - Thomas Hertach
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Natural History Museum of Bern Bern Switzerland
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Paula C. Simões
- Centre for Ecology, Evolution and Environmental Changes & CHANGE ‐ Global Change and Sustainability Institute, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
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Mongiardino Koch N, Thompson JR, Hiley AS, McCowin MF, Armstrong AF, Coppard SE, Aguilera F, Bronstein O, Kroh A, Mooi R, Rouse GW. Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record. eLife 2022; 11:72460. [PMID: 35315317 PMCID: PMC8940180 DOI: 10.7554/elife.72460] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Earth & Planetary Sciences, Yale University, New Haven, United States.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Jeffrey R Thompson
- Department of Earth Sciences, Natural History Museum, London, United Kingdom.,University College London Center for Life's Origins and Evolution, London, United Kingdom
| | - Avery S Hiley
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - Marina F McCowin
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
| | - A Frances Armstrong
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Simon E Coppard
- Bader International Study Centre, Queen's University, Herstmonceux Castle, East Sussex, United Kingdom
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Omri Bronstein
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,Steinhardt Museum of Natural History, Tel-Aviv, Israel
| | - Andreas Kroh
- Department of Geology and Palaeontology, Natural History Museum Vienna, Vienna, Austria
| | - Rich Mooi
- Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, United States
| | - Greg W Rouse
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, United States
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3
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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4
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Carruthers T, Scotland RW. exTREEmaTIME: a method for incorporating uncertainty into divergence time estimates. Biol Open 2022; 11:274355. [PMID: 35147180 PMCID: PMC8845097 DOI: 10.1242/bio.059181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022] Open
Abstract
We present a method of divergence time estimation (exTREEmaTIME) that aims to effectively account for uncertainty in divergence time estimates. The method requires a minimal set of assumptions, and, based on these assumptions, estimates the oldest possible divergence times and youngest possible divergence times that are consistent with the assumptions. We use a series of simulations and empirical analyses to illustrate that exTREEmaTIME is effective at representing uncertainty. We then describe how exTREEmaTIME can act as a basis to determine the implications of the more stringent assumptions that are incorporated into other methods of divergence time estimation that produce more precise estimates. This is critically important given that many of the assumptions that are incorporated into these methods are highly complex, difficult to justify biologically, and as such can lead to estimates that are highly inaccurate. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Tom Carruthers
- The Jodrell Building, Royal Botanic Gardens Kew, Richmond, London TW9 3AE, UK
| | - Robert W Scotland
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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