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Revely L, Eggleton P, Clement R, Zhou C, Bishop TR. The diversity of social complexity in termites. Proc Biol Sci 2024; 291:20232791. [PMID: 38835273 DOI: 10.1098/rspb.2023.2791] [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: 12/11/2023] [Accepted: 05/03/2024] [Indexed: 06/06/2024] Open
Abstract
Sociality underpins major evolutionary transitions and significantly influences the structure and function of complex ecosystems. Social insects, seen as the pinnacle of sociality, have traits like obligate sterility that are considered 'master traits', used as single phenotypic measures of this complexity. However, evidence is mounting that completely aligning both phenotypic and evolutionary social complexity, and having obligate sterility central to both, is erroneous. We hypothesize that obligate and functional sterility are insufficient in explaining the diversity of phenotypic social complexity in social insects. To test this, we explore the relative importance of these sterility traits in an understudied but diverse taxon: the termites. We compile the largest termite social complexity dataset to date, using specimen and literature data. We find that although functional and obligate sterility explain a significant proportion of variance, neither trait is an adequate singular proxy for the phenotypic social complexity of termites. Further, we show both traits have only a weak association with the other social complexity traits within termites. These findings have ramifications for our general comprehension of the frameworks of phenotypic and evolutionary social complexity, and their relationship with sterility.
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Affiliation(s)
- Lewis Revely
- Soil Biodiversity Group, Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Paul Eggleton
- Soil Biodiversity Group, Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Rebecca Clement
- Computational Biology Institute, George Washington University, Washington, DC 20052, USA
| | - Chuanyu Zhou
- Soil Biodiversity Group, Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Tom R Bishop
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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2
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Staggemeier VG, Amorim B, Bünger M, Costa IR, de Faria JEQ, Flickinger J, Giaretta A, Kubo MT, Lima DF, Dos Santos LL, Lourenço AR, Lucas E, Mazine FF, Murillo-A J, de Oliveira MIU, Parra-O C, Proença CEB, Reginato M, Rosa PO, Santos MF, Stadnik A, Tuler AC, Valdemarin KS, Vasconcelos T. Towards a species-level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies. AMERICAN JOURNAL OF BOTANY 2024; 111:e16330. [PMID: 38725388 DOI: 10.1002/ajb2.16330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
PREMISE Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification. METHODS Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling. RESULTS The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented. CONCLUSIONS We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported.
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Affiliation(s)
- Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, 59092-970, RN, Brazil
| | - Bruno Amorim
- Programa de Pós-Graduação em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | - Mariana Bünger
- Programa de Pós-Graduação em Sistemática, Uso e Conservação da Biodiversidade, Department de Biologia, Universidade Federal do Ceará, Fortaleza, 60355-636, CE, Brazil
| | - Itayguara R Costa
- Programa de Pós-Graduação em Sistemática, Uso e Conservação da Biodiversidade, Department de Biologia, Universidade Federal do Ceará, Fortaleza, 60355-636, CE, Brazil
| | - Jair Eustáquio Quintino de Faria
- Instituto Interamericano de Cooperação para a Agricultura - IICA - SHIS QI 5, Chácara 16, Lago Sul, Brasília, 71600-530, DF, Brazil
| | - Jonathan Flickinger
- Lady Bird Johnson Wildflower Center, The University of Texas at Austin, 4801 La Crosse Ave., Austin, 78739, TX, USA
| | - Augusto Giaretta
- Universidade Federal da Grande Dourados, Faculdade de Ciências Biológicas e Ambientais, Unidade II, Dourados, 79804-970, MS, Brazil
| | - Marcelo T Kubo
- Departamento de Botânica, Laboratório de Sistemática Vegetal, Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-900, São Paulo, Brazil
| | - Duane Fernandes Lima
- Programa de Pós-Graduação em Biologia de Fungos, Algas e Plantas, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | | | | | - Eve Lucas
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Fiorella Fernanda Mazine
- Universidade Federal de São Carlos, Campus Sorocaba, Rodovia João Leme dos Santos (SP-264), km 110, Sorocaba, 18052-780, SP, Brazil
| | - José Murillo-A
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Marla Ibrahim Uehbe de Oliveira
- Departamento de Biologia, Universidade Federal de Sergipe, Av. Marcelo Déda Chagas, s/n, Bairro Jardim Rosa Elze, São Cristóvão, 49107-230, SE, Brazil
| | - Carlos Parra-O
- Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Bogotá, Colombia
| | - Carolyn E B Proença
- Departamento de Botânica, Universidade de Brasília, Brasília, 70910-900, DF, Brazil
| | - Marcelo Reginato
- Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90650-001, RS, Brazil
| | - Priscila Oliveira Rosa
- Jardim Botânico de Brasília, Diretoria de Vegetação e Flora, Área Especial SMDB Estação Ecológica Jardim Botânico de Brasília, Brasília, 71.680-001, DF, Brazil
| | - Matheus Fortes Santos
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Alameda da Universidade s/n, Anchieta, São Bernardo do Campo, 09606-045, SP, Brazil
| | - Aline Stadnik
- Instituto Interamericano de Cooperação para a Agricultura - IICA - SHIS QI 5, Chácara 16, Lago Sul, Brasília, 71600-530, DF, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s/n, Feira de Santana, 44036-900, BA, Brazil
| | - Amélia Carlos Tuler
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Campus Paricarana, Av. Cap. Ene Garcez, 2413, Boa Vista, 69304-000, RR, Brazil
| | - Karinne Sampaio Valdemarin
- Departamento de Ciências Biológicas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, 13418-260, SP, Brazil
| | - Thais Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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Stieb SM, Cortesi F, Mitchell L, Jardim de Queiroz L, Marshall NJ, Seehausen O. Short-wavelength-sensitive 1 ( SWS1) opsin gene duplications and parallel visual pigment tuning support ultraviolet communication in damselfishes (Pomacentridae). Ecol Evol 2024; 14:e11186. [PMID: 38628922 PMCID: PMC11019301 DOI: 10.1002/ece3.11186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
Damselfishes (Pomacentridae) are one of the most behaviourally diverse, colourful and species-rich reef fish families. One remarkable characteristic of damselfishes is their communication in ultraviolet (UV) light. Not only are they sensitive to UV, they are also prone to have UV-reflective colours and patterns enabling social signalling. Using more than 50 species, we aimed to uncover the evolutionary history of UV colour and UV vision in damselfishes. All damselfishes had UV-transmitting lenses, expressed the UV-sensitive SWS1 opsin gene, and most displayed UV-reflective patterns and colours. We find evidence for several tuning events across the radiation, and while SWS1 gene duplications are generally very rare among teleosts, our phylogenetic reconstructions uncovered two independent duplication events: one close to the base of the most species-rich clade in the subfamily Pomacentrinae, and one in a single Chromis species. Using amino acid comparisons, we found that known spectral tuning sites were altered several times in parallel across the damselfish radiation (through sequence change and duplication followed by sequence change), causing repeated shifts in peak spectral absorbance of around 10 nm. Pomacentrinae damselfishes expressed either one or both copies of SWS1, likely to further finetune UV-signal detection and differentiation. This highly advanced and modified UV vision among damselfishes, in particular the duplication of SWS1 among Pomacentrinae, might be seen as a key evolutionary innovation that facilitated the evolution of the exuberant variety of UV-reflectance traits and the diversification of this coral reef fish lineage.
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Affiliation(s)
- Sara M. Stieb
- Center for Ecology, Evolution and BiogeochemistryEAWAG Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Institute for Ecology and EvolutionUniversity of BernBernSwitzerland
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Fabio Cortesi
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
- School of the EnvironmentThe University of QueenslandBrisbaneAustralia
| | - Laurie Mitchell
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
- Marine Eco‐Evo‐Devo UnitOkinawa Institute of Science and TechnologyOnna sonOkinawaJapan
| | - Luiz Jardim de Queiroz
- Center for Ecology, Evolution and BiogeochemistryEAWAG Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Institute for Ecology and EvolutionUniversity of BernBernSwitzerland
| | - N. Justin Marshall
- Queensland Brain InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Ole Seehausen
- Center for Ecology, Evolution and BiogeochemistryEAWAG Federal Institute of Aquatic Science and TechnologyKastanienbaumSwitzerland
- Institute for Ecology and EvolutionUniversity of BernBernSwitzerland
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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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Ramírez-Barahona S, González-Serrano FM, Martínez-Ugalde E, Soto-Pozos A, Parra-Olea G, Rebollar EA. Host phylogeny and environment shape the diversity of salamander skin bacterial communities. Anim Microbiome 2023; 5:52. [PMID: 37828573 PMCID: PMC10571319 DOI: 10.1186/s42523-023-00271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
The composition and diversity of animal-associated microbial communities are shaped by multiple ecological and evolutionary processes acting at different spatial and temporal scales. Skin microbiomes are thought to be strongly influenced by the environment due to the direct interaction of the host's skin with the external media. As expected, the diversity of amphibian skin microbiomes is shaped by climate and host sampling habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on salamander skin microbiomes remains poorly understood. Here, we analysed sequence data from 1164 adult salamanders of 44 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host sampling habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that bacterial alpha diversity was mainly associated with host sampling habitat and climate, but that bacterial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogenetic effect predominantly occurred at intermediate levels of host divergence (0-50 Mya). Our results support the importance of environmental factors shaping the diversity of salamander skin microbiota, but also support host phylogenetic history as a major factor shaping these bacterial communities.
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Affiliation(s)
- S Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - F M González-Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - E Martínez-Ugalde
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - A Soto-Pozos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - G Parra-Olea
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - E A Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
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Deanna R, Martínez C, Manchester S, Wilf P, Campos A, Knapp S, Chiarini FE, Barboza GE, Bernardello G, Sauquet H, Dean E, Orejuela A, Smith SD. Fossil berries reveal global radiation of the nightshade family by the early Cenozoic. THE NEW PHYTOLOGIST 2023; 238:2685-2697. [PMID: 36960534 DOI: 10.1111/nph.18904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023]
Abstract
Fossil discoveries can transform our understanding of plant diversification over time and space. Recently described fossils in many plant families have pushed their known records farther back in time, pointing to alternative scenarios for their origin and spread. Here, we describe two new Eocene fossil berries of the nightshade family (Solanaceae) from the Esmeraldas Formation in Colombia and the Green River Formation in Colorado (USA). The placement of the fossils was assessed using clustering and parsimony analyses based on 10 discrete and five continuous characters, which were also scored in 291 extant taxa. The Colombian fossil grouped with members of the tomatillo subtribe, and the Coloradan fossil aligned with the chili pepper tribe. Along with two previously reported early Eocene fossils from the tomatillo genus, these findings indicate that Solanaceae were distributed at least from southern South America to northwestern North America by the early Eocene. Together with two other recently discovered Eocene berries, these fossils demonstrate that the diverse berry clade and, in turn, the entire nightshade family, is much older and was much more widespread in the past than previously thought.
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Affiliation(s)
- Rocío Deanna
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, CO, 80309-0334, USA
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
- Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Medina Allende y Haya de la Torre, Córdoba, 5000, Argentina
| | - Camila Martínez
- Biological Science Department, Universidad EAFIT, Carrera 49, Cl. 7 Sur #50, Medellín, 050022, Antioquia, Colombia
- Center for Tropical Paleoecology and Archaeology, Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper Balboa Ancon, Panama City, 0843-03092, Panama
| | - Steven Manchester
- Florida Museum of Natural History, University of Florida, 3215 Hull Rd, Gainesville, FL, 32611, USA
| | - Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, State College, 201 Old Main, University Park, PA, 16802, USA
| | - Abel Campos
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, CO, 80309-0334, USA
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Franco E Chiarini
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Gabriel Bernardello
- Instituto Multidisciplinario de Biología Vegetal, IMBIV (CONICET-UNC), Vélez Sarsfield 299, Córdoba, 5000, Argentina
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW, 2000, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, High St Kensington, Sydney, NSW, 2052, Australia
| | - Ellen Dean
- Center for Plant Diversity, Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Andrés Orejuela
- Grupo de Investigación en Recursos Naturales Amazónicos - GRAM, Facultad de Ingenierías y Ciencias Básicas, Instituto Tecnológico del Putumayo - ITP, Calle 17, Carrera 17, Mocoa, Putumayo, Colombia
- Subdirección científica, Jardín Botánico de Bogotá José Celestino Mutis, Calle 63 #68-95, Bogotá, DC, Colombia
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1800 Colorado Avenue, Boulder, CO, 80309-0334, USA
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Zaharias P, Warnow T. Recent progress on methods for estimating and updating large phylogenies. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210244. [PMID: 35989607 PMCID: PMC9393559 DOI: 10.1098/rstb.2021.0244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022] Open
Abstract
With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the past few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g. incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements. This article is part of a discussion meeting issue 'Genomic population structures of microbial pathogens'.
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Affiliation(s)
- Paul Zaharias
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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8
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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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9
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Mctavish EJ, Sánchez-Reyes LL, Holder MT. OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life. Syst Biol 2021; 70:1295-1301. [PMID: 33970279 PMCID: PMC8513759 DOI: 10.1093/sysbio/syab033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 11/14/2022] Open
Abstract
The Open Tree of Life project constructs a comprehensive, dynamic, and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.[Evolution; open science; phylogenetics; Python; taxonomy.].
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Affiliation(s)
- Emily Jane Mctavish
- Department of Life and Environmental Sciences, University of California, Merced, CA 95343, USA
| | | | - Mark T Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
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10
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Combining molecular and geographical data to infer the phylogeny of Lamiales and its dispersal patterns in and out of the tropics. Mol Phylogenet Evol 2021; 164:107287. [PMID: 34365014 DOI: 10.1016/j.ympev.2021.107287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
Lamiales is one of the most intractable orders of flowering plants, with several changes in family composition, and circumscription throughout history. The order is worldwide distributed, occurring in tropical forests and frozen habitats. In this study, a comprehensive phylogeny of Lamiales was reconstructed using DNA sequences. The tree was used to infer dispersal patterns, focusing on the tropics and extratropics. Molecular and species geographic data available from public repositories were combined to address both objectives. A total of 6,910 species, and 842 genera of Lamiales were sampled using the Python tool PyPHLAWD. The tree was inferred using RAxML, and recovered a monophyletic Lamiales. All 26 families were recovered as monophyletic with high support. The families Bignoniaceae, and Plantaginaceae are remarkable examples. The first emerged as monophyletic and included tribe Jacarandeae, while the later emerged as monophyletic in its sensu lato and included both the tribes Angelonieae, and Gratioleae. Distribution points for all species were retrieved from GBIF. After filtering, 1,136,425 records were retained. Species were coded as present in extratropical or tropical environments. The in and out of the tropics dispersal patterns were inferred using a maximum likelihood approach that identifies hidden rate changes. The model recovered higher rates of transition from extratropics to tropics, estimating two rates of state transitions. When ancestral states are considered, more discrete transitions from extratropics to tropics were observed. The extratropical state was also inferred for the crown node of Lamiales and old nested nodes, revealing a rare pattern of transitions to the tropics throughout the upper Cretaceous and Tertiary. A significant phylogenetic signal was recovered for the in and out of the tropics dispersal patterns, showing that state transitions are not frequent enough to erase the effect of tree structure on the data.
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11
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Stull GW, Qu XJ, Parins-Fukuchi C, Yang YY, Yang JB, Yang ZY, Hu Y, Ma H, Soltis PS, Soltis DE, Li DZ, Smith SA, Yi TS. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. NATURE PLANTS 2021; 7:1015-1025. [PMID: 34282286 DOI: 10.1038/s41477-021-00964-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/10/2021] [Indexed: 05/15/2023]
Abstract
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution-including gene and genome duplication, genome size, and chromosome number-with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | | | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Yun Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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12
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Primack RB, Ellwood ER, Gallinat AS, Miller-Rushing AJ. The growing and vital role of botanical gardens in climate change research. THE NEW PHYTOLOGIST 2021; 231:917-932. [PMID: 33890323 DOI: 10.1111/nph.17410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Botanical gardens make unique contributions to climate change research, conservation, and public engagement. They host unique resources, including diverse collections of plant species growing in natural conditions, historical records, and expert staff, and attract large numbers of visitors and volunteers. Networks of botanical gardens spanning biomes and continents can expand the value of these resources. Over the past decade, research at botanical gardens has advanced our understanding of climate change impacts on plant phenology, physiology, anatomy, and conservation. For example, researchers have utilized botanical garden networks to assess anatomical and functional traits associated with phenological responses to climate change. New methods have enhanced the pace and impact of this research, including phylogenetic and comparative methods, and online databases of herbarium specimens and photographs that allow studies to expand geographically, temporally, and taxonomically in scope. Botanical gardens have grown their community and citizen science programs, informing the public about climate change and monitoring plants more intensively than is possible with garden staff alone. Despite these advances, botanical gardens are still underutilized in climate change research. To address this, we review recent progress and describe promising future directions for research and public engagement at botanical gardens.
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Affiliation(s)
| | - Elizabeth R Ellwood
- iDigBio, Florida Museum of Natural History, University of Florida, Gainesville, FL, 33430, USA
- La Brea Tar Pits and Museum, Natural History Museum of Los Angeles County, Los Angeles, CA, 90036, USA
| | - Amanda S Gallinat
- Department of Biology and Ecology Center, Utah State University, Logan, UT, 84322, USA
- Department of Geography, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
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13
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Thomas AE, Igea J, Meudt HM, Albach DC, Lee WG, Tanentzap AJ. Using target sequence capture to improve the phylogenetic resolution of a rapid radiation in New Zealand Veronica. AMERICAN JOURNAL OF BOTANY 2021; 108:1289-1306. [PMID: 34173225 DOI: 10.1002/ajb2.1678] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/10/2021] [Indexed: 05/08/2023]
Abstract
PREMISE Recent, rapid radiations present a challenge for phylogenetic reconstruction. Fast successive speciation events typically lead to low sequence divergence and poorly resolved relationships with standard phylogenetic markers. Target sequence capture of many independent nuclear loci has the potential to improve phylogenetic resolution for rapid radiations. METHODS Here we applied target sequence capture with 353 protein-coding genes (Angiosperms353 bait kit) to Veronica sect. Hebe (common name hebe) to determine its utility for improving the phylogenetic resolution of rapid radiations. Veronica section Hebe originated 5-10 million years ago in New Zealand, forming a monophyletic radiation of ca 130 extant species. RESULTS We obtained approximately 150 kbp of 353 protein-coding exons and an additional 200 kbp of flanking noncoding sequences for each of 77 hebe and two outgroup species. When comparing coding, noncoding, and combined data sets, we found that the latter provided the best overall phylogenetic resolution. While some deep nodes in the radiation remained unresolved, our phylogeny provided broad and often improved support for subclades identified by both morphology and standard markers in previous studies. Gene-tree discordance was nonetheless widespread, indicating that additional methods are needed to disentangle fully the history of the radiation. CONCLUSIONS Phylogenomic target capture data sets both increase phylogenetic signal and deliver new insights into the complex evolutionary history of rapid radiations as compared with traditional markers. Improving methods to resolve remaining discordance among loci from target sequence capture is now important to facilitate the further study of rapid radiations.
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Affiliation(s)
- Anne E Thomas
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Javier Igea
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Heidi M Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Dirk C Albach
- Carl von Ossietzky-University, Oldenburg, D-26111, Germany
| | - William G Lee
- Manaaki Whenua - Landcare Research Otago, Dunedin, New Zealand
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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14
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Sánchez-Reyes LL, Kandziora M, McTavish EJ. Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. BMC Bioinformatics 2021; 22:355. [PMID: 34187366 PMCID: PMC8244228 DOI: 10.1186/s12859-021-04274-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and non-specialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. RESULTS Physcraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. The program can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). CONCLUSION The Physcraper workflow showcases the benefits of doing open science for phylogenetics, encouraging researchers to strive for better scientific sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and usage are available at https://physcraper.readthedocs.io.
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Affiliation(s)
| | - Martha Kandziora
- School of Natural Sciences, University of California, Merced, USA.,Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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15
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Repeated evolution of a reproductive polyphenism in plants is strongly associated with bilateral flower symmetry. Curr Biol 2021; 31:1515-1520.e3. [PMID: 33539770 DOI: 10.1016/j.cub.2021.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/03/2020] [Accepted: 01/06/2021] [Indexed: 11/20/2022]
Abstract
Polyphenisms are a special type of phenotypic plasticity in which the products of development are not continuous but instead are separate and distinct phenotypes produced in the same genetic background. One of the most widespread polyphenisms in the flowering plants is cleistogamy, in which the same individual plant produces both open, cross-pollinated flowers as well as highly reduced and closed, self-pollinated (cleistogamous) flowers.1-5 Cleistogamy is not a rare evolutionary phenomenon. It has evolved independently at least 41 times.1 But what favors the evolution of cleistogamy is still largely unknown.1 Darwin6 proposed a hypothesis that has never been properly tested. He observed that cleistogamy is more common in taxa with bilaterally symmetric (zygomorphic) flowers than in those with radially symmetric (actinomorphic) flowers. Moreover, Darwin suggested that cleistogamous flowers help to ensure pollination, which he postulated is less certain in zygomorphic taxa that rely on more specialized groups of pollinators. Here, we combined the largest datasets on floral symmetry and cleistogamy and used phylogenetic approaches to show that cleistogamy is indeed disproportionately associated with zygomorphic flowers and that zygomorphic species are more likely to evolve cleistogamy than actinomorphic species. We also show that zygomorphic species are less capable of autonomous open-flower self-pollination (lower autofertility), suggesting that selection of cleistogamy via reproductive assurance in zygomorphic taxa could help account for Darwin's observation. Our results provide support for the hypothesis that polyphenisms are favored when organisms encounter contrasting environments.
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16
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Gallinat AS, Pearse WD. Phylogenetic generalized linear mixed modeling presents novel opportunities for eco‐evolutionary synthesis. OIKOS 2021. [DOI: 10.1111/oik.08048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Amanda S. Gallinat
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Geography, Univ. of Wisconsin‐Milwaukee Milwaukee WI USA
| | - William D. Pearse
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
- Dept of Life Sciences, Imperial College London Silwood Park Campus Ascot Berkshire UK
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17
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Bradshaw M, Goolsby E, Mason C, Tobin PC. Evolution of Disease Severity and Susceptibility in the Asteraceae to the Powdery Mildew Golovinomyces latisporus: Major Phylogenetic Structure Coupled With Highly Variable Disease Severity at Fine Scales. PLANT DISEASE 2021; 105:268-275. [PMID: 32787655 DOI: 10.1094/pdis-06-20-1375-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pathogen host range and pathogen severity are dependent on interactions with their hosts and are hypothesized to have evolved as products of a coevolutionary arms race. An understanding of the factors that affect host range and pathogen severity is especially crucial in introduced pathogens that infect evolutionarily naïve hosts and cause substantial damage to ecosystems. Powdery mildews are detrimental pathogens found worldwide in managed and natural systems. Golovinomyces latisporus is a powdery mildew species that is especially damaging to plants within Asteraceae and to plants within the genus Helianthus in particular. In this study, we evaluated 126 species within Asteraceae to measure the role of host plant morphophysiological traits and evolutionary history on susceptibility to G. latisporus and disease severity. We observed phylogenetic signal in both susceptibility and severity within and among major clades of the Asteraceae. In general, there was a major phylogenetic structure of host severity to G. latisporus; however, there was some fine-scale phylogenetic variability. Phylogenetic statistical methods showed that chlorophyll content, biomass, stomatal index, and trichome density were not associated with disease severity, thus providing evidence that phylogenetic structure, rather than observed plant morphophysiological traits, is the most reliable predictor of pathogen severity. This work sheds light on the role that evolutionary history plays in plant susceptibility and severity to disease and underscores the relative unimportance of commonly assessed host plant traits in powdery mildew severity.
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Affiliation(s)
- Michael Bradshaw
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195
| | - Eric Goolsby
- Department of Biology, University of Central Florida, Orlando, FL 32816
| | - Chase Mason
- Department of Biology, University of Central Florida, Orlando, FL 32816
| | - Patrick C Tobin
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA 98195
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18
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Mander L, Parins‐Fukuchi C, Dick CW, Punyasena SW, Jaramillo C. Phylogenetic and ecological correlates of pollen morphological diversity in a Neotropical rainforest. Biotropica 2020. [DOI: 10.1111/btp.12847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luke Mander
- School of Environment, Earth and Ecosystem Sciences The Open University Milton Keynes UK
| | | | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan, MI USA
- Smithsonian Tropical Research Institute Balboa, Ancon Republic of Panama
| | | | - Carlos Jaramillo
- Smithsonian Tropical Research Institute Balboa, Ancon Republic of Panama
- ISEM, U. Montpellier CNRS EPHE Montpellier France
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19
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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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20
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Sheehan H, Feng T, Walker‐Hale N, Lopez‐Nieves S, Pucker B, Guo R, Yim WC, Badgami R, Timoneda A, Zhao L, Tiley H, Copetti D, Sanderson MJ, Cushman JC, Moore MJ, Smith SA, Brockington SF. Evolution of l-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales. THE NEW PHYTOLOGIST 2020; 227:914-929. [PMID: 31369159 PMCID: PMC7384185 DOI: 10.1111/nph.16089] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/22/2019] [Indexed: 05/03/2023]
Abstract
The evolution of l-DOPA 4,5-dioxygenase activity, encoded by the gene DODA, was a key step in the origin of betalain biosynthesis in Caryophyllales. We previously proposed that l-DOPA 4,5-dioxygenase activity evolved via a single Caryophyllales-specific neofunctionalisation event within the DODA gene lineage. However, this neofunctionalisation event has not been confirmed and the DODA gene lineage exhibits numerous gene duplication events, whose evolutionary significance is unclear. To address this, we functionally characterised 23 distinct DODA proteins for l-DOPA 4,5-dioxygenase activity, from four betalain-pigmented and five anthocyanin-pigmented species, representing key evolutionary transitions across Caryophyllales. By mapping these functional data to an updated DODA phylogeny, we then explored the evolution of l-DOPA 4,5-dioxygenase activity. We find that low l-DOPA 4,5-dioxygenase activity is distributed across the DODA gene lineage. In this context, repeated gene duplication events within the DODA gene lineage give rise to polyphyletic occurrences of elevated l-DOPA 4,5-dioxygenase activity, accompanied by convergent shifts in key functional residues and distinct genomic patterns of micro-synteny. In the context of an updated organismal phylogeny and newly inferred pigment reconstructions, we argue that repeated convergent acquisition of elevated l-DOPA 4,5-dioxygenase activity is consistent with recurrent specialisation to betalain synthesis in Caryophyllales.
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Affiliation(s)
- Hester Sheehan
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
| | - Tao Feng
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhan430074China
| | - Nathanael Walker‐Hale
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
| | - Samuel Lopez‐Nieves
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
| | - Boas Pucker
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
- CeBiTec & Faculty of BiologyBielefeld UniversityUniversitaetsstrasseBielefeld33615Germany
| | - Rui Guo
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhan430074China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Won C. Yim
- Department of Biochemistry and Molecular BiologyUniversity of NevadaRenoNV89577USA
| | - Roshani Badgami
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
| | - Alfonso Timoneda
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
| | - Lijun Zhao
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Helene Tiley
- Department of BiologyOberlin CollegeScience Center K111OberlinOH44074USA
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of ArizonaTucsonAZ85721USA
- Molecular Plant BreedingInstitute of Agricultural SciencesETH Zurich, Universitaetstrasse 28092ZurichSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Michael J. Sanderson
- Department of Ecology and Evolutionary BiologyUniversity of Arizona1041 E. Lowell St.TucsonAZ85721USA
| | - John C. Cushman
- Department of Biochemistry and Molecular BiologyUniversity of NevadaRenoNV89577USA
| | - Michael J. Moore
- Department of BiologyOberlin CollegeScience Center K111OberlinOH44074USA
| | - Stephen A. Smith
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Samuel F. Brockington
- Department of Plant SciencesUniversity of CambridgeTennis Court RoadCambridgeCB2 3EAUK
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21
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Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research. DIVERSITY 2020. [DOI: 10.3390/d12080288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.
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Portik DM, Wiens JJ. SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Daniel M. Portik
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
- California Academy of Sciences San Francisco CA USA
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
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