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Pérez-Escobar OA, Bogarín D, Przelomska NAS, Ackerman JD, Balbuena JA, Bellot S, Bühlmann RP, Cabrera B, Cano JA, Charitonidou M, Chomicki G, Clements MA, Cribb P, Fernández M, Flanagan NS, Gravendeel B, Hágsater E, Halley JM, Hu AQ, Jaramillo C, Mauad AV, Maurin O, Müntz R, Leitch IJ, Li L, Negrão R, Oses L, Phillips C, Rincon M, Salazar GA, Simpson L, Smidt E, Solano-Gomez R, Parra-Sánchez E, Tremblay RL, van den Berg C, Tamayo BSV, Zuluaga A, Zuntini AR, Chase MW, Fay MF, Condamine FL, Forest F, Nargar K, Renner SS, Baker WJ, Antonelli A. The origin and speciation of orchids. THE NEW PHYTOLOGIST 2024; 242:700-716. [PMID: 38382573 DOI: 10.1111/nph.19580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024]
Abstract
Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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Affiliation(s)
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
- Naturalis Biodiversity Centre, Leiden, CR 2333, the Netherlands
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - James D Ackerman
- University of Puerto Rico - Rio Piedras, San Juan, PR, 00925-2537, USA
| | | | | | | | - Betsaida Cabrera
- Jardín Botánico Rafael Maria Moscoso, Santo Domingo, 21-9, Dominican Republic
| | | | | | | | - Mark A Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Melania Fernández
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Nicola S Flanagan
- Universidad Pontificia Javeriana, Seccional Cali, Cali, 760031, Colombia
| | | | | | | | - Ai-Qun Hu
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 257494, Singapore
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Apartado, Panama City, 0843-03092, Panama
| | | | | | - Robert Müntz
- Reserva Biológica Guaitil, Eisenstadt, 7000, Austria
| | | | - Lan Li
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Lizbeth Oses
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Charlotte Phillips
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Milton Rincon
- Jardín Botánico Jose Celestino Mutis, Bogota, 111071, Colombia
| | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
| | - Eric Smidt
- Universidade Federal do Paraná, Curitiba, 19031, Brazil
| | | | | | | | - Cassio van den Berg
- Universidade Estadual de Feira de Santana, Feira de Santana, 44036-900, Brazil
| | | | | | | | - Mark W Chase
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia
| | | | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugène Bataillon, Montpellier, 34000, France
| | | | - Katharina Nargar
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
- Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Gothenburg, 417 56, Sweden
- University of Gothenburg, Gothenburg, 417 56, Sweden
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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Title PO, Singhal S, Grundler MC, Costa GC, Pyron RA, Colston TJ, Grundler MR, Prates I, Stepanova N, Jones MEH, Cavalcanti LBQ, Colli GR, Di-Poï N, Donnellan SC, Moritz C, Mesquita DO, Pianka ER, Smith SA, Vitt LJ, Rabosky DL. The macroevolutionary singularity of snakes. Science 2024; 383:918-923. [PMID: 38386744 DOI: 10.1126/science.adh2449] [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: 02/22/2023] [Accepted: 01/02/2024] [Indexed: 02/24/2024]
Abstract
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity.
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Environmental Resilience Institute, Indiana University, Bloomington, IN 47408, USA
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747, USA
| | - Michael C Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel C Costa
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
| | - Timothy J Colston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00680, Puerto Rico
| | - Maggie R Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ivan Prates
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Natasha Stepanova
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc E H Jones
- Science Group: Fossil Reptiles, Amphibians and Birds Section, Natural History Museum, London SW7 5BD, UK
- Research Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
- Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Lucas B Q Cavalcanti
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | | | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Daniel O Mesquita
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba 58051-900, Brazil
| | - Eric R Pianka
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie J Vitt
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Romeiro-Brito M, Taylor NP, Zappi DC, Telhe MC, Franco FF, Moraes EM. Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing. ANNALS OF BOTANY 2023; 132:989-1006. [PMID: 37815357 PMCID: PMC10808018 DOI: 10.1093/aob/mcad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND AND AIMS Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe. METHODS We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches. KEY RESULTS Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae. CONCLUSIONS We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, Gibraltar
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas Universidade de Brasília (UNB), Brasília, Distrito Federal, Brazil
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
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Portik DM, Streicher JW, Wiens JJ. Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species. Mol Phylogenet Evol 2023; 188:107907. [PMID: 37633542 DOI: 10.1016/j.ympev.2023.107907] [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: 01/15/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the higher-level relationships estimated are discordant with recent phylogenomic estimates based on much larger numbers of loci. Here, we attempted to rectify this problem by generating an expanded supermatrix and combining this with data from phylogenomic studies. To assist in aligning ribosomal sequences for this supermatrix, we developed a new program (TaxonomyAlign) to help perform taxonomy-guided alignments. The new combined matrix contained 5,242 anuran species with data from 307 markers, but with 95% missing data overall. This dataset represented a 71% increase in species sampled relative to the previous largest supermatrix analysis of anurans (adding 2,175 species). Maximum-likelihood analyses generated a tree in which higher-level relationships (and estimated clade ages) were generally concordant with those from phylogenomic analyses but were more discordant with the previous largest supermatrix analysis. We found few obvious problems arising from the extensive missing data in most species. We also generated a set of 100 time-calibrated trees for use in comparative analyses. Overall, we provide an improved estimate of anuran phylogeny based on the largest number of combined taxa and markers to date. More broadly, we demonstrate the potential to combine phylogenomic and supermatrix analyses in other groups of organisms.
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Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA; California Academy of Sciences, San Francisco, CA 94118, USA
| | | | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721 USA.
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5
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Wogan GOU, Yuan ML, Mahler DL, Wang IJ. Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards. Syst Biol 2023; 72:874-884. [PMID: 37186031 PMCID: PMC10687355 DOI: 10.1093/sysbio/syad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 04/01/2023] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought to reduce or constrain divergence between 2 species, hybridization can, paradoxically, promote divergence by increasing genetic variation or providing novel combinations of alleles that selection can act upon to move lineages toward new adaptive peaks. Hybridization may, then, play a key role in adaptive radiation by allowing lineages to diversify into new ecological space. Here, we test for signatures of historical hybridization in the Anolis lizards of Puerto Rico and evaluate 2 hypotheses for the role of hybridization in facilitating adaptive radiation-the hybrid swarm origins hypothesis and the syngameon hypothesis. Using whole genome sequences from all 10 species of Puerto Rican anoles, we calculated D and f-statistics (from ABBA-BABA tests) to test for introgression across the radiation and employed multispecies network coalescent methods to reconstruct phylogenetic networks that allow for hybridization. We then analyzed morphological data for these species to test for patterns consistent with transgressive evolution, a phenomenon in which the trait of a hybrid lineage is found outside of the range of its 2 parents. Our analyses uncovered strong evidence for introgression at multiple stages of the radiation, including support for an ancient hybrid origin of a clade comprising half of the extant Puerto Rican anole species. Moreover, we detected significant signals of transgressive evolution for 2 ecologically important traits, head length and toepad width, the latter of which has been described as a key innovation in Anolis. [Adaptive radiation; introgression; multispecies network coalescent; phenotypic evolution; phylogenetic network; reticulation; syngameon; transgressive segregation.].
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Affiliation(s)
- Guinevere O U Wogan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael L Yuan
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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6
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Seo CW, Kim SH, Lim YW, Park MS. Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine. MYCOBIOLOGY 2022; 50:231-237. [PMID: 36158042 PMCID: PMC9467555 DOI: 10.1080/12298093.2022.2116816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Penicillium species have been actively studied in various fields, and many new and unrecorded species continue to be reported in Korea. Moreover, unidentified and misidentified Korean Penicillium species still exist in GenBank. Therefore, it is necessary to revise the Korean Penicillium inventory based on accurate identification. We collected Korean Penicillium nucleotide sequence records from GenBank using the newly developed software, GenMine, and re-identified Korean Penicillium based on the maximum likelihood trees. A total of 1681 Korean Penicillium GenBank nucleotide sequence records were collected from GenBank. In these records, 1208 strains with four major genes (Internal Transcribed Spacer rDNA region, β-tubulin, Calmodulin and RNA polymerase II) were selected for Penicillium re-identification. Among 1208 strains, 927 were identified, 82 were identified as other genera, the rest remained undetermined due to low phylogenetic resolution. Identified strains consisted of 206 Penicillium species, including 156 recorded species and 50 new species candidates. However, 37 species recorded in the national list of species in Korea were not found in GenBank. Further studies on the presence or absence of these species are required through literature investigation, additional sampling, and sequencing. Our study can be the basis for updating the Korean Penicillium inventory.
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Affiliation(s)
- Chang Wan Seo
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Sung Hyun Kim
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Young Woon Lim
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Myung Soo Park
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju, South Korea
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Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life. FRONTIERS IN PLANT SCIENCE 2022; 13:909768. [PMID: 36092417 PMCID: PMC9449725 DOI: 10.3389/fpls.2022.909768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/12/2022] [Indexed: 05/31/2023]
Abstract
Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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Gould AL, Fritts-Penniman A, Gaisiner A. Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish. Front Ecol Evol 2021; 9:630207. [PMID: 34485316 PMCID: PMC8412414 DOI: 10.3389/fevo.2021.630207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how stable they are over host generations. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio family. Primarily using museum specimens, we investigated the codivergence of host and symbiont and test for patterns of divergence that correlate with both biogeography and time. Contrary to expectations, we determined that the light organ symbionts of all 14 Siphamia species examined belong to one genetic clade of Photobacterium mandapamensis (Clade II), indicating that the association is highly specific and conserved throughout the host genus. Thus, we did not find evidence of codivergence among hosts and symbionts. We did observe that symbionts hosted by individuals sampled from colder water regions were more divergent, containing more than three times as many single nucleotide polymorphisms than the rest of the symbionts examined. Overall, our findings indicate that the symbiosis between Siphamia fishes and P. mandapamensis Clade II has been highly conserved across host taxa and over a broad geographic range despite the facultative nature of the bacterial symbiont. We also present a new approach to simultaneously recover genetic information from a bacterial symbiont and its vertebrate host from formalin-fixed specimens, enhancing the utility of museum collections.
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Affiliation(s)
- Alison L. Gould
- California Academy of Sciences, San Francisco, CA, United States
| | | | - Ana Gaisiner
- California Academy of Sciences, San Francisco, CA, United States
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9
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Portik DM, Wiens JJ. Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? Syst Biol 2020; 70:440-462. [PMID: 32797207 DOI: 10.1093/sysbio/syaa064] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/14/2022] Open
Abstract
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming].
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Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.,California Academy of Sciences, San Francisco, CA 94118, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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