Andrew B Leslie1, Jeremy Beaulieu2, Garth Holman3, Christopher S Campbell3, Wenbin Mei4, Linda R Raubeson5, Sarah Mathews6. 1. Department of Ecology and Evolutionary Biology, Brown University, Box G-W, 80 Waterman Street, Providence, Rhode Island, 02912, USA. 2. Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA. 3. School of Biology and Ecology, University of Maine, Orono, Maine, 04469, USA. 4. Department of Plant Sciences, University of California, Davis, 1 Shields Avenue, Davis, California, 95616, USA. 5. Department of Biological Sciences, Central Washington University, 400 E. University Way, Ellensburg, Washington, 98926, USA. 6. CSIRO National Research Collections Australia, Australian National Herbarium, Canberra, ACT, 2601, Australia.
Abstract
PREMISE OF THE STUDY: Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. METHODS: We surveyed the current state of knowledge in conifer phylogenetics to present a new time-calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species-rich and well known from fossils. KEY RESULTS: Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. CONCLUSIONS: Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.
PREMISE OF THE STUDY: Conifers are an important living seed plant lineage with an extensive fossil record spanning more than 300 million years. The group therefore provides an excellent opportunity to explore congruence and conflict between dated molecular phylogenies and the fossil record. METHODS: We surveyed the current state of knowledge in conifer phylogenetics to present a new time-calibrated molecular tree that samples ~90% of extant species diversity. We compared phylogenetic relationships and estimated divergence ages in this new phylogeny with the paleobotanical record, focusing on clades that are species-rich and well known from fossils. KEY RESULTS: Molecular topologies and estimated divergence ages largely agree with the fossil record in Cupressaceae, conflict with it in Araucariaceae, and are ambiguous in Pinaceae and Podocarpaceae. Molecular phylogenies provide insights into some fundamental questions in conifer evolution, such as the origin of their seed cones, but using them to reconstruct the evolutionary history of specific traits can be challenging. CONCLUSIONS: Molecular phylogenies are useful for answering deep questions in conifer evolution if they depend on understanding relationships among extant lineages. Because of extinction, however, molecular datasets poorly sample diversity from periods much earlier than the Late Cretaceous. This fundamentally limits their utility for understanding deep patterns of character evolution and resolving the overall pattern of conifer phylogeny.
Authors: Alexis R Sullivan; Yrin Eldfjell; Bastian Schiffthaler; Nicolas Delhomme; Torben Asp; Kim H Hebelstrup; Olivier Keech; Lisa Öberg; Ian Max Møller; Lars Arvestad; Nathaniel R Street; Xiao-Ru Wang Journal: Genome Biol Evol Date: 2020-01-01 Impact factor: 3.416
Authors: Fabien L Condamine; Daniele Silvestro; Eva B Koppelhus; Alexandre Antonelli Journal: Proc Natl Acad Sci U S A Date: 2020-11-02 Impact factor: 11.205
Authors: Alison D Scott; Aleksey V Zimin; Daniela Puiu; Rachael Workman; Monica Britton; Sumaira Zaman; Madison Caballero; Andrew C Read; Adam J Bogdanove; Emily Burns; Jill Wegrzyn; Winston Timp; Steven L Salzberg; David B Neale Journal: G3 (Bethesda) Date: 2020-11-05 Impact factor: 3.154
Authors: Fabiany Herrera; Gongle Shi; Chris Mays; Niiden Ichinnorov; Masamichi Takahashi; Joseph J Bevitt; Patrick S Herendeen; Peter R Crane Journal: PLoS One Date: 2020-01-15 Impact factor: 3.240