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de Miranda GS, Kulkarni SS, Tagliatela J, Baker CM, Giupponi APL, Labarque FM, Gavish-Regev E, Rix MG, Carvalho LS, Fusari LM, Harvey MS, Wood HM, Sharma PP. The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi). Syst Biol 2024:syae021. [PMID: 38733598 DOI: 10.1093/sysbio/syae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Indexed: 05/13/2024] Open
Abstract
Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils, which bears upon the ancestral range reconstruction for the group. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa", and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy.
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Affiliation(s)
- Gustavo S de Miranda
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC, 20560, USA
| | - Siddharth S Kulkarni
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jéssica Tagliatela
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, campus São Carlos, Rodovia Washington Luís, Km 235, 13565-905, São Paulo, Brazil
| | - Caitlin M Baker
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alessandro P L Giupponi
- Laboratório de Referência Nacional em Vetores das Riquetsioses, LIRN-FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Facundo M Labarque
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, campus São Carlos, Rodovia Washington Luís, Km 235, 13565-905, São Paulo, Brazil
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Michael G Rix
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD 4101, Australia
| | - Leonardo S Carvalho
- Campus Amílcar Ferreira Sobral, Universidade Federal do Piauí, 64808-605, Floriano, PI, Brazil
| | - Lívia Maria Fusari
- Departamento de Hidrobiologia, Universidade Federal de São Carlos, campus São Carlos, Rodovia Washington Luís, Km 235, 13565-905, São Paulo, Brazil
| | - Mark S Harvey
- Collections and Research Centre, Western Australian Museum, Welshpool, Western Australia 6106, Australia
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Hannah M Wood
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave. NW, Washington, DC, 20560, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Lizano AM, Smolina I, Choquet M, Kopp M, Hoarau G. Insights into the species evolution of Calanus copepods in the northern seas revealed by de novo transcriptome sequencing. Ecol Evol 2022; 12:e8606. [PMID: 35228861 PMCID: PMC8861592 DOI: 10.1002/ece3.8606] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 01/07/2023] Open
Abstract
Copepods of the zooplankton genus Calanus play a key role in marine ecosystems in the northern seas. Although being among the most studied organisms on Earth, due to their ecological importance, genomic resources for Calanus spp. remain scarce, mostly due to their large genome size (from 6 to 12 Gbps). As an alternative to whole-genome sequencing in Calanus spp., we sequenced and de novo assembled transcriptomes of five Calanus species: Calanus glacialis, C. hyperboreus, C. marshallae, C. pacificus, and C. helgolandicus. Functional assignment of protein families based on clusters of orthologous genes (COG) and gene ontology (GO) annotations showed analogous patterns of protein functions across species. Phylogenetic analyses using maximum likelihood (ML) of 191 protein-coding genes mined from RNA-seq data fully resolved evolutionary relationships among seven Calanus species investigated (five species sequenced for this study and two species with published datasets), with gene and site concordance factors showing that 109 out of 191 protein-coding genes support a separation between three groups: the C. finmarchicus group (including C. finmarchicus, C. glacialis, and C. marshallae), the C. helgolandicus group (including C. helgolandicus, C. sinicus, and C. pacificus) and the monophyletic C. hyperboreus group. The tree topology obtained in ML analyses was similar to a previously proposed phylogeny based on morphological criteria and cleared certain ambiguities from past studies on evolutionary relationships among Calanus species.
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Affiliation(s)
| | - Irina Smolina
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Marvin Choquet
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Martina Kopp
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Galice Hoarau
- Faculty of Biosciences and AquacultureNord UniversityBodøNorway
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Abstract
We implement two measures for quantifying genealogical concordance in phylogenomic data sets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org/doc/Concordance-Factor, last accessed May 13, 2020).
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Affiliation(s)
- Bui Quang Minh
- Research School of Computer Science, Australian National University, Canberra, ACT, Australia.,Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN.,Department of Computer Science, Indiana University, Bloomington, IN
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM. Target-capture phylogenomics provide insights on gene and species tree discordances in Old World treefrogs (Anura: Rhacophoridae). Proc Biol Sci 2020; 287:20202102. [PMID: 33290680 PMCID: PMC7739936 DOI: 10.1098/rspb.2020.2102] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/13/2020] [Indexed: 11/12/2022] Open
Abstract
Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as bootstrapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topology. Furthermore, relatively little attention has been given to assessing discordances between gene and species trees, and the underlying processes that produce phylogenetic conflict. We generated novel genomic datasets to characterize and determine the causes of discordance in Old World treefrogs (Family: Rhacophoridae)-a group that is fraught with conflicting and poorly supported topologies among major clades. Additionally, a suite of data filtering strategies and analytical methods were applied to assess their impact on phylogenetic inference. We showed that incomplete lineage sorting was detected at all nodes that exhibited high levels of discordance. Those nodes were also associated with extremely short internal branches. We also clearly demonstrate that bootstrap values do not reflect uncertainty or confidence for the correct topology and, hence, should not be used as a measure of branch support in phylogenomic datasets. Overall, we showed that phylogenetic discordances in Old World treefrogs resulted from incomplete lineage sorting and that species tree inference can be improved using a multi-faceted, total-evidence approach, which uses the most amount of data and considers results from different analytical methods and datasets.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, 2 Conservatory Drive, Singapore 117377, Republic of Singapore
| | - Carl R. Hutter
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L. Wood
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - L. Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA 92505, USA
| | - Rafe M. Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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