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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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David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy long-standing macroecological patterns. Proc Natl Acad Sci U S A 2024; 121:e2316031121. [PMID: 38412132 DOI: 10.1073/pnas.2316031121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild. Here, we trained machine learning models on 12,816 terrestrial occurrence records and 96 environmental variables to infer global distribution maps at ~1 km2 resolution for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversity. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high-diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many long-standing macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and a positive relationship between latitude and range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.
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Affiliation(s)
- Kyle T David
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Department of Biology, Villanova University, Villanova, PA 19085
| | - Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223
| | - John F Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
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3
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Wacker KS, Winger BM. An Elevational Phylogeographic Diversity Gradient in Neotropical Birds Is Decoupled from Speciation Rates. Am Nat 2024; 203:362-381. [PMID: 38358813 DOI: 10.1086/728598] [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] [Indexed: 02/17/2024]
Abstract
AbstractA key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests that speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7,000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared with the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.
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Folk RA, Charboneau JLM, Belitz M, Singh T, Kates HR, Soltis DE, Soltis PS, Guralnick RP, Siniscalchi CM. Anatomy of a mega-radiation: Biogeography and niche evolution in Astragalus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16299. [PMID: 38419145 DOI: 10.1002/ajb2.16299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
PREMISE Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid-adapted clade and what sets it apart from close relatives with far less species richness. METHODS Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents. RESULTS Our results point to the importance of heterogeneity in the diversification of Astragalus, with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway. CONCLUSIONS Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging "mega-radiations." Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species-rich clades.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Michael Belitz
- Florida Museum, University of Florida, Gainesville, FL, USA
| | - Tajinder Singh
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | | | - Douglas E Soltis
- Florida Museum, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Robert P Guralnick
- Florida Museum, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
- General Libraries, Mississippi State University, Mississippi State, MS, USA
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5
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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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Haghighatnia M, Machac A, Schmickl R, Lafon Placette C. Darwin's 'mystery of mysteries': the role of sexual selection in plant speciation. Biol Rev Camb Philos Soc 2023; 98:1928-1944. [PMID: 37337476 DOI: 10.1111/brv.12991] [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: 12/14/2022] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
Sexual selection is considered one of the key processes that contribute to the emergence of new species. While the connection between sexual selection and speciation has been supported by comparative studies, the mechanisms that mediate this connection remain unresolved, especially in plants. Similarly, it is not clear how speciation processes within plant populations translate into large-scale speciation dynamics. Here, we review the mechanisms through which sexual selection, pollination, and mate choice unfold and interact, and how they may ultimately produce reproductive isolation in plants. We also overview reproductive strategies that might influence sexual selection in plants and illustrate how functional traits might connect speciation at the population level (population differentiation, evolution of reproductive barriers; i.e. microevolution) with evolution above the species level (macroevolution). We also identify outstanding questions in the field, and suitable data and tools for their resolution. Altogether, this effort motivates further research focused on plants, which might potentially broaden our general understanding of speciation by sexual selection, a major concept in evolutionary biology.
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Affiliation(s)
- Mohammadjavad Haghighatnia
- Department of Botany, Faculty of Science, Charles University, Benatska 2, Prague, CZ-128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Antonin Machac
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague, 14220, Czech Republic
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Benatska 2, Prague, CZ-128 01, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic
| | - Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University, Benatska 2, Prague, CZ-128 01, Czech Republic
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7
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Scott JE. The macroevolutionary dynamics of activity pattern in mammals: Primates in context. J Hum Evol 2023; 184:103436. [PMID: 37741141 DOI: 10.1016/j.jhevol.2023.103436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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8
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Cerezer FO, Dambros CS, Coelho MTP, Cassemiro FAS, Barreto E, Albert JS, Wüest RO, Graham CH. Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes. Nat Commun 2023; 14:6070. [PMID: 37770447 PMCID: PMC10539357 DOI: 10.1038/s41467-023-41812-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Speciation rates vary greatly among taxa and regions and are shaped by both biotic and abiotic factors. However, the relative importance and interactions of these factors are not well understood. Here we investigate the potential drivers of speciation rates in South American freshwater fishes, the most diverse continental vertebrate fauna, by examining the roles of multiple biotic and abiotic factors. We integrate a dataset on species geographic distribution, phylogenetic, morphological, climatic, and habitat data. We find that Late Neogene-Quaternary speciation events are strongly associated with body-size evolution, particularly in lineages with small body sizes that inhabit higher elevations near the continental periphery. Conversely, the effects of temperature, area, and diversity-dependence, often thought to facilitate speciation, are negligible. By evaluating multiple factors simultaneously, we demonstrate that habitat characteristics associated with elevation, as well as body size evolution, correlate with rapid speciation in South American freshwater fishes. Our study emphasizes the importance of integrative approaches that consider the interplay of biotic and abiotic factors in generating macroecological patterns of species diversity.
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Affiliation(s)
- Felipe O Cerezer
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland.
- Programa de Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Cristian S Dambros
- Programa de Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Marco T P Coelho
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - Fernanda A S Cassemiro
- Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, Brazil
| | - Elisa Barreto
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Rafael O Wüest
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - Catherine H Graham
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
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9
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García-Andrade AB, Tedesco PA, Carvajal-Quintero JD, Arango A, Villalobos F. Same process, different patterns: pervasive effect of evolutionary time on species richness in freshwater fishes. Proc Biol Sci 2023; 290:20231066. [PMID: 37700646 PMCID: PMC10498035 DOI: 10.1098/rspb.2023.1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023] Open
Abstract
Tropical lands harbour the highest number of species, resulting in the ubiquitous latitudinal diversity gradient (LDG). However, exceptions to this pattern have been observed in some taxa, explained by the interaction between the evolutionary histories and environmental factors that constrain species' physiological and ecological requirements. Here, we applied a deconstruction approach to map the detailed species richness patterns of Actinopterygian freshwater fishes at the class and order levels and to disentangle their drivers using geographical ranges and a phylogeny, comprising 77% (12 557) of all described species. We jointly evaluated seven evolutionary and ecological hypotheses posited to explain the LDG: diversification rate, time for speciation, species-area relationship, environmental heterogeneity, energy, temperature seasonality and past temperature stability. We found distinct diversity gradients across orders, including expected, bimodal and inverse LDGs. Despite these differences, the positive effect of evolutionary time explained patterns for all orders, where species-rich regions are inhabited by older species compared to species-poor regions. Overall, the LDG of each order has been shaped by a unique combination of factors, highlighting the importance of performing a joint evaluation of evolutionary, historical and ecological factors at different taxonomic levels to reach a comprehensive understanding on the causes driving global species richness patterns.
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Affiliation(s)
- Ana Berenice García-Andrade
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Pablo A. Tedesco
- UMR 5174 EDB—Evolution & Diversité Biologique, Institut de Recherche pour le Développement, Université Paul Sabatier - Bat. 4R1, 118 route de Narbonne, 31062 Toulouse cedex 4, France
| | - Juan D. Carvajal-Quintero
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstr. 4, D-04103 Leipzig, Germany
| | - Axel Arango
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
| | - Fabricio Villalobos
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, 91070 Xalapa, Veracruz, México
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David KT, Harrison MC, Opulente DA, LaBella AL, Wolters JF, Zhou X, Shen XX, Groenewald M, Pennell M, Hittinger CT, Rokas A. Saccharomycotina yeasts defy longstanding macroecological patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555417. [PMID: 37693602 PMCID: PMC10491267 DOI: 10.1101/2023.08.29.555417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The Saccharomycotina yeasts ("yeasts" hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth1; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild2. Here, we trained machine learning models on 12,221 occurrence records and 96 environmental variables to infer global distribution maps for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversification. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many longstanding macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and latitude-dependent range size (Rapoport's rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.
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Affiliation(s)
- Kyle T. David
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Marie-Claire Harrison
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana A. Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Department of Biology, Villanova University, Villanova PA 19085, USA
| | - Abigail L. LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC 28223, USA
| | - John F. Wolters
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Matt Pennell
- Department of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles CA 90089, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
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11
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Burbrink FT, Ruane S, Rabibisoa N, Raselimanana AP, Raxworthy CJ, Kuhn A. Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes. Ecol Evol 2023; 13:e10344. [PMID: 37529593 PMCID: PMC10375368 DOI: 10.1002/ece3.10344] [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: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single-island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.
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Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'EnvironnementUniversité de MahajangaMahajangaMadagascar
| | - Achille P. Raselimanana
- Zoologie et Biodiversité Animale, Faculté des SciencesUniversité d'AntananarivoAntananarivoMadagascar
| | | | - Arianna Kuhn
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
- Virginia Museum of Natural HistoryMartinsvilleVirginiaUSA
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12
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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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13
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Barreto E, Lim MCW, Rojas D, Dávalos LM, Wüest RO, Machac A, Graham CH. Morphology and niche evolution influence hummingbird speciation rates. Proc Biol Sci 2023; 290:20221793. [PMID: 37072043 PMCID: PMC10113027 DOI: 10.1098/rspb.2022.1793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/21/2023] [Indexed: 04/20/2023] Open
Abstract
How traits affect speciation is a long-standing question in evolution. We investigate whether speciation rates are affected by the traits themselves or by the rates of their evolution, in hummingbirds, a clade with great variation in speciation rates, morphology and ecological niches. Further, we test two opposing hypotheses, postulating that speciation rates are promoted by trait conservatism or, alternatively, by trait divergence. To address these questions, we analyse morphological (body mass and bill length) and niche traits (temperature and precipitation position and breadth, and mid-elevation), using a variety of methods to estimate speciation rates and correlate them with traits and their evolutionary rates. When it comes to the traits, we find faster speciation in smaller hummingbirds with shorter bills, living at higher elevations and experiencing greater temperature ranges. As for the trait evolutionary rates, we find that speciation increases with rates of divergence in the niche traits, but not in the morphological traits. Together, these results reveal the interplay of mechanisms through which different traits and their evolutionary rates (conservatism or divergence) influence the origination of hummingbird diversity.
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Affiliation(s)
- Elisa Barreto
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Departamento de Ecologia, Universidade Federal de Goiás, Campus Samambaia, Goiânia, Goiás, Brazil
| | - Marisa C. W. Lim
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cl. 18 #118-250, Cali, Valle del Cauca, Colombia
| | - Liliana M. Dávalos
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, 129 Dana Hall, Stony Brook, NY 11794, USA
| | - Rafael O. Wüest
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Antonin Machac
- Villum Center for Global Mountain Biodiversity and Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Center for Theoretical Study, Charles University and the Czech Academy of Science, Jilska 1, 11000 Prague, Czechia
- Department of Ecology, Charles University, Vinicna 7, 12844 Prague, Czechia
| | - Catherine H. Graham
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
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14
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Friedman ST, Muñoz MM. A latitudinal gradient of deep-sea invasions for marine fishes. Nat Commun 2023; 14:773. [PMID: 36774385 PMCID: PMC9922314 DOI: 10.1038/s41467-023-36501-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates - fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.
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Affiliation(s)
- Sarah T Friedman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA. .,Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06511, USA.
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
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15
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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16
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Lin HY, Sun M, Hao YJ, Li D, Gitzendanner MA, Fu CX, Soltis DE, Soltis PS, Zhao YP. Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time. PLANT DIVERSITY 2023; 45:27-35. [PMID: 36876316 PMCID: PMC9975473 DOI: 10.1016/j.pld.2022.09.008] [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: 06/24/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 06/18/2023]
Abstract
The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution. However, the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America (EA-ENA disjuncts) and their associated factors remain unknown. Here we investigated the standardized effect size of PD (SES-PD), PBD, and potentially associated factors in 11 natural mixed forest sites (five in EA and six in ENA) where abundant EA-ENA disjuncts occur. We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale (1.96 vs -1.12), even though the number of disjunct species in ENA is much lower than in EA (128 vs 263). SES-PD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites. The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites. Based on the unweighted unique fraction metric (UniFrac) distance and the phylogenetic community dissimilarity, PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites. Based on the standardized effect size of mean pairwise distances (SES-MPD), nine of eleven studied sites showed a neutral community structure (-1.96 ≤ SES-MPD ≤ 1.96). Both Pearson's r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time. Moreover, SES-PD of the EA-ENA disjuncts was positively correlated with temperature-related climatic factors, although negatively correlated with mean diversification rate and community structure. By applying approaches from phylogenetics and community ecology, our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.
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Affiliation(s)
- Han-Yang Lin
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- School of Advanced Study, Taizhou University, Taizhou 318000, China
| | - Miao Sun
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Ya-Jun Hao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Daijiang Li
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Matthew A. Gitzendanner
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Cheng-Xin Fu
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Yun-Peng Zhao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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17
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Tyler J, Younger JL. Diving into a dead-end: asymmetric evolution of diving drives diversity and disparity shifts in waterbirds. Proc Biol Sci 2022; 289:20222056. [PMID: 36515120 PMCID: PMC9748772 DOI: 10.1098/rspb.2022.2056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Diving is a relatively uncommon and highly specialized foraging strategy in birds, mostly observed within the Aequorlitornithes (waterbirds) by groups such as penguins, cormorants and alcids. Three key diving techniques are employed within waterbirds: wing-propelled pursuit diving (e.g. penguins), foot-propelled pursuit diving (e.g. cormorants) and plunge diving (e.g. gannets). How many times diving evolved within waterbirds, whether plunge diving is an intermediate state between aerial foraging and submarine diving, and whether the transition to a diving niche is reversible are not known. Here, we elucidate the evolutionary history of diving in waterbirds. We show that diving has been acquired independently at least 14 times within waterbirds, and this acquisition is apparently irreversible, in a striking example of asymmetric evolution. All three modes of diving have evolved independently, with no evidence for plunge diving as an intermediate evolutionary state. Net diversification rates differ significantly between diving versus non-diving lineages, with some diving clades apparently prone to extinction. We find that body mass is evolving under multiple macroevolutionary regimes, with unique optima for each diving type with varying degrees of constraint. Our findings highlight the vulnerability of highly specialized lineages during the ongoing sixth mass extinction.
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Affiliation(s)
- Joshua Tyler
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Jane L. Younger
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK,Institute for Marine and Antarctic Studies, University of Tasmania, Battery Point, Hobart, Tasmania 7004, Australia
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18
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Hay EM, McGee MD, Chown SL. Geographic range size and speciation in honeyeaters. BMC Ecol Evol 2022; 22:86. [PMID: 35768772 PMCID: PMC9245323 DOI: 10.1186/s12862-022-02041-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Darwin and others proposed that a species’ geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin’s proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae).
Results
We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation.
Conclusions
Honeyeater speciation rate differs considerably between islands and the continental setting across the clade’s distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin’s original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.
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19
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Scott JE. Variation in macroevolutionary dynamics among extant primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:405-416. [PMCID: PMC9826261 DOI: 10.1002/ajpa.24622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 09/25/2023]
Abstract
Objectives This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity. Materials and methods Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification. Results Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages. Conclusions Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.
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Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the PacificWestern University of Health SciencesPomonaCaliforniaUSA
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20
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Gamboa S, Condamine FL, Cantalapiedra JL, Varela S, Pelegrín JS, Menéndez I, Blanco F, Hernández Fernández M. A phylogenetic study to assess the link between biome specialization and diversification in swallowtail butterflies. GLOBAL CHANGE BIOLOGY 2022; 28:5901-5913. [PMID: 35838418 PMCID: PMC9543414 DOI: 10.1111/gcb.16344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry) and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large Geographic Information System database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates (DRs). In this paper, we aim to answer the following questions: (1) Are there more biome-specialist swallowtail butterflies than biome generalists? (2) Is DR related to biome specialization? (3) If so, do swallowtail butterflies inhabiting extreme biomes show higher DRs? (4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher DRs compared to generalists. We also found that biome specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis, species climatic niche and biome fragmentation as key factors promoting isolation.
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Affiliation(s)
- Sara Gamboa
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, Edificio de Ciencias Campus Científico‐TecnológicoUniversidad de AlcaláAlcalá de HenaresSpain
| | - Sara Varela
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
| | - Jonathan S. Pelegrín
- Área de Biología y Ciencias Ambientales Facultades de Ciencias Básicas y EducaciónUniversidad Santiago de CaliSantiago de CaliValle del CaucaColombia
- Departamento de Biología, Facultad de Ciencias Naturales y ExactasUniversidad del Valle, Campus MeléndezSantiago de CaliValle del CaucaColombia
| | - Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
| | - Fernando Blanco
- Museum für Naturkunde, Leibniz‐Institut für Evolutions und BiodiversitätsforschungBerlinGermany
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
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21
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Giles SAW, Arbuckle K. Diversification dynamics of chameleons (Chamaeleonidae). J Zool (1987) 2022. [DOI: 10.1111/jzo.13019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. A. W. Giles
- Department of Biosciences, Faculty of Science and Engineering Swansea University Swansea UK
| | - K. Arbuckle
- Department of Biosciences, Faculty of Science and Engineering Swansea University Swansea UK
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22
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Skeels A, Bach W, Hagen O, Jetz W, Pellissier L. Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations. Syst Biol 2022:6637530. [PMID: 35809070 DOI: 10.1093/sysbio/syac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 06/21/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - W Bach
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
| | - O Hagen
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig 04103, Germany
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA.,Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Sciences, Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich 8092, Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf 8903, Switzerland
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23
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Ashokan A, Xavier A, Suksathan P, Ardiyani M, Leong-Škorničková J, Newman M, Kress WJ, Gowda V. Himalayan orogeny and monsoon intensification explain species diversification in an endemic ginger (Hedychium: Zingiberaceae) from the Indo-Malayan Realm. Mol Phylogenet Evol 2022; 170:107440. [PMID: 35192919 DOI: 10.1016/j.ympev.2022.107440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/26/2022]
Abstract
The Indo-Malayan Realm is a biogeographic realm that extends from the Indian Subcontinent to the islands of Southeast Asia (Malay Archipelago). Despite being megadiverse, evolutionary hypotheses explaining taxonomic diversity in this region have been rare. Here, we investigate the role of geoclimatic events such as Himalayan orogeny and monsoon intensification in the diversification of the ginger-lilies (Hedychium J.Koenig: Zingiberaceae). We first built a comprehensive, time-calibrated phylogeny of Hedychium with 75% taxonomic and geographic sampling. We found that Hedychium is a very young lineage that originated in Northern Indo-Burma, in the Late Miocene (c. 10.6 Ma). This was followed by a late Neogene and early Quaternary diversification, with multiple dispersal events to Southern Indo-Burma, Himalayas, Peninsular India, and the Malay Archipelago. The most speciose clade IV i.e., the predominantly Indo-Burmese clade also showed a higher diversification rate, suggesting its recent rapid radiation. Our divergence dating and GeoHiSSE results demonstrate that the diversification of Hedychium was shaped by both the intensifications in the Himalayan uplift as well as the Asian monsoon. Ancestral character-state reconstructions identified the occurrence of vegetative dormancy in both clades I and II, whereas the strictly epiphytic growth behavior, island dwarfism, lack of dormancy, and a distinct environmental niche were observed only in the predominantly island clade i.e., clade III. Finally, we show that the occurrence of epiphytism in clade III corresponds with submergence due to sea-level changes, suggesting it to be an adaptive trait. Our study highlights the role of recent geoclimatic events and environmental factors in the diversification of plants within the Indo-Malayan Realm and the need for collaborative work to understand biogeographic patterns within this understudied region. This study opens new perspectives for future biogeographic studies in this region and provides a framework to explain the taxonomic hyperdiversity of the Indo-Malayan Realm.
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Affiliation(s)
- Ajith Ashokan
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Madhya Pradesh 462066, India.
| | - Aleena Xavier
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Madhya Pradesh 462066, India
| | - Piyakaset Suksathan
- Herbarium (QBG), Queen Sirikit Botanic Garden, P.O. Box 7, Mae Rim, Chiang Mai 50180, Thailand
| | - Marlina Ardiyani
- Herbarium Bogoriense, Research Center for Biology, Indonesian Institute of Sciences/Lembaga Ilmu Pengetahuan Indonesia (LIPI), Cibinong Science Center, Jl Raya Bogor Km. 46, Cibinong 16912, Indonesia
| | - Jana Leong-Škorničková
- Research & Conservation Branch, Singapore Botanic Gardens, 1 Cluny Road, 259569, Singapore
| | - Mark Newman
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, United Kingdom
| | - W John Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P. O. Box 37012, Washington, DC 20013-7012, United States
| | - Vinita Gowda
- Tropical Ecology and Evolution (TrEE) Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Madhya Pradesh 462066, India.
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24
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Si X, Cadotte MW, Davies TJ, Antonelli A, Ding P, Svenning JC, Faurby S. Phylogenetic and functional clustering illustrate the roles of adaptive radiation and dispersal filtering in jointly shaping late-Quaternary mammal assemblages on oceanic islands. Ecol Lett 2022; 25:1250-1262. [PMID: 35275608 DOI: 10.1111/ele.13997] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/29/2021] [Accepted: 02/11/2022] [Indexed: 12/15/2022]
Abstract
Islands frequently harbour unique assemblages of species, yet their ecological roles and differences are largely ignored in island biogeography studies. Here, we examine eco-evolutionary processes structuring mammal assemblages on oceanic islands worldwide, including all extant and extinct late-Quaternary mammal species. We find island mammal assemblages tend to be phylogenetically clustered (share more recent evolutionary histories), with clustering increasing with island area and isolation. We also observe that mammal assemblages often tend to be functionally clustered (share similar traits), but the strength of clustering is weak and generally independent from island area or isolation. These findings indicate the important roles of in situ speciation and dispersal filtering in shaping island mammal assemblages under pre-anthropogenic conditions, notably through adaptive radiation of a few clades (e.g. bats, with generally high dispersal abilities). Our study demonstrates that considering the functional and phylogenetic axes of diversity can better reveal the eco-evolutionary processes of island community assembly.
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Affiliation(s)
- Xingfeng Si
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China.,Institute of Eco-Chongming (IEC), Shanghai, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexandre Antonelli
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden.,Royal Botanic Gardens, Richmond, Surrey, UK.,Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ping Ding
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of Biology, Aarhus University, Aarhus C, Denmark.,Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus C, Denmark
| | - Søren Faurby
- Department of Biological & Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
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25
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Singhal S, Colli GR, Grundler MR, Costa GC, Prates I, Rabosky DL. No link between population isolation and speciation rate in squamate reptiles. Proc Natl Acad Sci U S A 2022; 119:e2113388119. [PMID: 35058358 PMCID: PMC8795558 DOI: 10.1073/pnas.2113388119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, California State University, Dominguez Hills, Carson, CA 90747;
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, Distrito Federal 70910-900, Brazil
| | - Maggie R Grundler
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL 36117
| | - Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109;
- Museum of Zoology, University of Michigan, Ann Arbor, MI 48109
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26
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Moreira MO, Fonseca C, Rojas D. ES-sim-GLM, a Multiple Regression Trait-Dependent Diversification Approach. Evol Biol 2022. [DOI: 10.1007/s11692-021-09557-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Freeman BG, Rolland J, Montgomery GA, Schluter D. Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds. Proc Biol Sci 2022; 289:20211514. [PMID: 34982949 PMCID: PMC8727149 DOI: 10.1098/rspb.2021.1514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 12/07/2021] [Indexed: 01/14/2023] Open
Abstract
Why are speciation rates so variable across the tree of life? One hypothesis is that this variation is explained by how rapidly reproductive barriers evolve. We tested this hypothesis by conducting a comparative study of the evolution of bird song, a premating barrier to reproduction. Speciation in birds is typically initiated when geographically isolated (allopatric) populations evolve reproductive barriers. We measured the strength of song as a premating barrier between closely related allopatric populations by conducting 2339 field experiments to measure song discrimination for 175 taxon pairs of allopatric or parapatric New World passerine birds, and estimated recent speciation rates from molecular phylogenies. We found evidence that song discrimination is indeed an important reproductive barrier: taxon pairs with high song discrimination in allopatry did not regularly interbreed in parapatry. However, evolutionary rates of song discrimination were not associated with recent speciation rates. Evolutionary rates of song discrimination were also unrelated to latitude or elevation, but species with innate song (suboscines) evolved song discrimination much faster than species with learned song (oscines). We conclude that song is a key premating reproductive barrier in birds, but faster evolution of this reproductive barrier between populations does not consistently result in faster diversification between species.
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Affiliation(s)
- Benjamin G. Freeman
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada V6T1Z4
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T1Z4
| | - Jonathan Rolland
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada V6T1Z4
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T1Z4
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Bâtiment 4R1, 118 Route de Narbonne, Toulouse 31062, France
| | - Graham A. Montgomery
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA 90095, USA
| | - Dolph Schluter
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada V6T1Z4
- Department of Zoology, University of British Columbia, Vancouver, Canada V6T1Z4
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28
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Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
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Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
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29
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Dale EE, Foest JJ, Hacket-Pain A, Bogdziewicz M, Tanentzap AJ. Macroevolutionary consequences of mast seeding. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200372. [PMID: 34657467 PMCID: PMC8520783 DOI: 10.1098/rstb.2020.0372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/05/2022] Open
Abstract
Masting characterizes large, intermittent and highly synchronous seeding events among individual plants and is found throughout the plant Tree of Life (ToL). Although masting can increase plant fitness, little is known about whether it results in evolutionary changes across entire clades, such as by promoting speciation or enhanced trait selection. Here, we tested if masting has macroevolutionary consequences by combining the largest existing dataset of population-level reproductive time series and time-calibrated phylogenetic tree of vascular plants. We found that the coefficient of variation (CVp) of reproductive output for 307 species covaried with evolutionary history, and more so within clades than expected by random. Speciation rates estimated at the species level were highest at intermediate values of CVp and regional-scale synchrony (Sr) in seed production, that is, there were unimodal correlations. There was no support for monotonic correlations between either CVp or Sr and rates of speciation or seed size evolution. These results were robust to different sampling decisions, and we found little bias in our dataset compared with the wider plant ToL. While masting is often adaptive and encompasses a rich diversity of reproductive behaviours, we suggest it may have few consequences beyond the species level. This article is part of the theme issue 'The ecology and evolution of synchronized seed production in plants'.
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Affiliation(s)
- Esther E. Dale
- Manaaki Whenua - Landcare Research, Dunedin, New Zealand
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Jessie J. Foest
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Andrew Hacket-Pain
- Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Michał Bogdziewicz
- Department of Systematic Zoology, Faculty of Biology, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 6, Poznań 61-614, Poland
- INRAE, LESSEM, University Grenoble Alpes, Saint-Martin-d'Heres, France
| | - Andrew J. Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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30
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Luza AL, Maestri R, Debastiani VJ, Patterson BD, Hartz SM, Duarte LDS. Is evolution faster at ecotones? A test using rates and tempo of diet transitions in Neotropical Sigmodontinae (Rodentia, Cricetidae). Ecol Evol 2021; 11:18676-18690. [PMID: 35003701 PMCID: PMC8717272 DOI: 10.1002/ece3.8476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/27/2021] [Accepted: 12/03/2021] [Indexed: 11/20/2022] Open
Abstract
We evaluated whether evolution is faster at ecotones as niche shifts may be needed to persist under unstable environment. We mapped diet evolution along the evolutionary history of 350 sigmodontine species. Mapping was used in three new tip-based metrics of trait evolution - Transition Rates, Stasis Time, and Last Transition Time - which were spatialized at the assemblage level (aTR, aST, aTL). Assemblages were obtained by superimposing range maps on points located at core and ecotone of the 93 South American ecoregions. Using Linear Mixed Models, we tested whether ecotones have species with more changes from the ancestral diet (higher aTR), have maintained the current diet for a shorter time (lower aST), and have more recent transitions to the current diet (lower aLT) than cores. We found lower aTR, and higher aST and aLT at ecotones than at cores. Although ecotones are more heterogeneous, both environmentally and in relation to selection pressures they exert on organisms, ecotone species change little from the ancestral diet as generalist habits are necessary toward feeding in ephemeral environments. The need to incorporate phylogenetic uncertainty in tip-based metrics was evident from large uncertainty detected. Our study integrates ecology and evolution by analyzing how fast trait evolution is across space.
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Affiliation(s)
- André Luís Luza
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
- Departamento de Ecologia e EvoluçãoUniversidade Federal de Santa MariaSanta MariaRio Grande do SulCEP 97105‐900Brazil
| | - Renan Maestri
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Vanderlei Júlio Debastiani
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
| | - Bruce D. Patterson
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Sandra Maria Hartz
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
| | - Leandro D. S. Duarte
- Programa de Pós‐Graduação em EcologiaDepartamento de EcologiaInstituto de BiociênciasUniversidade Federal do Rio Grande do SulBairro AgronomiaRio Grande do SulCEP 91501‐970Brazil
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31
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Rapid increase in snake dietary diversity and complexity following the end-Cretaceous mass extinction. PLoS Biol 2021; 19:e3001414. [PMID: 34648487 PMCID: PMC8516226 DOI: 10.1371/journal.pbio.3001414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/16/2021] [Indexed: 11/19/2022] Open
Abstract
The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs as well as to long-term physiographic changes that created new biogeographic theaters and new habitats. Snakes underwent massive ecological diversification during this period, repeatedly evolving novel dietary adaptations and prey preferences. The evolutionary tempo and mode of these trophic ecological changes remain virtually unknown, especially compared with co-radiating lineages of birds and mammals that are simultaneously predators and prey of snakes. Here, we assemble a dataset on snake diets (34,060 observations on the diets of 882 species) to investigate the history and dynamics of the multidimensional trophic niche during the global radiation of snakes. Our results show that per-lineage dietary niche breadths remained remarkably constant even as snakes diversified to occupy disparate outposts of dietary ecospace. Rapid increases in dietary diversity and complexity occurred in the early Cenozoic, and the overall rate of ecospace expansion has slowed through time, suggesting a potential response to ecological opportunity in the wake of the end-Cretaceous mass extinction. Explosive bursts of trophic innovation followed colonization of the Nearctic and Neotropical realms by a group of snakes that today comprises a majority of living snake diversity. Our results indicate that repeated transformational shifts in dietary ecology are important drivers of adaptive radiation in snakes and provide a framework for analyzing and visualizing the evolution of complex ecological phenotypes on phylogenetic trees. The Cenozoic marked a period of dramatic ecological opportunity in Earth history due to the extinction of non-avian dinosaurs and long-term physiographic changes. This phylogenetic natural history study offers new insights into the evolution of snake ecological diversity after the end-Cretaceous mass extinction, as they took advantage of these new opportunities.
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32
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Upham NS, Esselstyn JA, Jetz W. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Curr Biol 2021; 31:4195-4206.e3. [PMID: 34329589 DOI: 10.1016/j.cub.2021.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022]
Abstract
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to "pull" speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or "push" the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66-56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific "tip" rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade's extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
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Affiliation(s)
- Nathan S Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA.
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33
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van Els P, Herrera-Alsina L, Pigot AL, Etienne RS. Evolutionary dynamics of the elevational diversity gradient in passerine birds. Nat Ecol Evol 2021; 5:1259-1265. [PMID: 34294897 DOI: 10.1038/s41559-021-01515-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
Low-elevation regions harbour the majority of the world's species diversity compared to high-elevation areas. This global gradient suggests that lowland species have had more time to diversify, or that net diversification rates have been higher in the lowlands. However, highlands seem to be cradles of diversity as they contain many young endemics, suggesting that their rates of speciation are exceptionally fast. Here we use a phylogenetic diversification model that accounts for the dispersal of species between different elevations to examine the evolutionary dynamics of the elevational diversity gradient in passerine birds, a group that has radiated globally to occupy almost all elevations and latitudes. We find strong support for a model in which passerines diversify at the same rate in the highlands and the lowlands but in which the per-capita rate of dispersal from high to low elevations is more than twice as fast as that in the reverse direction. This suggests that while there is no consistent trend in diversification across elevations, part of the diversity generated by highland regions migrates into the lowlands, thus setting up the observed gradient in passerine diversity. We find that this process drives tropical regions but for temperate areas, the analysis could be hampered by their lower richness. Despite their lower diversity, highland regions are disproportionally important for maintaining diversity in the adjacent lowlands.
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Affiliation(s)
- Paul van Els
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.,Sovon Dutch Centre for Field Ornithology, Nijmegen, The Netherlands
| | - Leonel Herrera-Alsina
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands. .,School of Biological Sciences, University of Aberdeen, Aberdeen, UK.
| | - Alex L Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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34
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Pie MR, Divieso R, Caron FS. The evolution of climatic niche breadth in terrestrial vertebrates. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Marcio R. Pie
- Departamento de Zoologia Universidade Federal do Paraná Curitiba Brazil
| | - Raquel Divieso
- Departamento de Zoologia Universidade Federal do Paraná Curitiba Brazil
| | - Fernanda S. Caron
- Departamento de Zoologia Universidade Federal do Paraná Curitiba Brazil
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35
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García-Rodríguez A, Martínez PA, Oliveira BF, Velasco JA, Pyron RA, Costa GC. Amphibian Speciation Rates Support a General Role of Mountains as Biodiversity Pumps. Am Nat 2021; 198:E68-E79. [PMID: 34403310 DOI: 10.1086/715500] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractContinental mountain areas cover <15% of global land surface, yet these regions concentrate >80% of global terrestrial diversity. One prominent hypothesis to explain this pattern proposes that high mountain diversities could be explained by higher diversification rates in regions of high topographic complexity (HTC). While high speciation in mountains has been detected for particular clades and regions, the global extent to which lineages experience faster speciation in mountains remains unknown. Here we addressed this issue using amphibians as a model system (>7,000 species), and we found that families showing high speciation rates contain a high proportion of species distributed in mountains. Moreover, we found that lineages inhabiting areas of HTC speciate faster than lineages occupying areas that are topographically less complex. When comparing across regions, we identified the same pattern in five biogeographical realms where higher speciation rates are associated with higher levels of complex topography. Low-magnitude differences in speciation rates between some low and high complex topographies suggest that high mountain diversity is also affected by low extinction and/or high colonization rates. Nevertheless, our results bolster the importance of mountains as engines of speciation at different geographical scales and highlight their importance for the conservation of global biodiversity.
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36
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Miller EC. Comparing diversification rates in lakes, rivers, and the sea. Evolution 2021; 75:2055-2073. [PMID: 34181244 DOI: 10.1111/evo.14295] [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: 05/28/2020] [Revised: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 12/23/2022]
Abstract
The diversity of species inhabiting freshwater relative to marine habitats is striking, given that freshwater habitats encompass <1% of Earth's water. The most commonly proposed explanation for this pattern is that freshwater habitats are more fragmented than marine habitats, allowing more opportunities for allopatric speciation and thus increased diversification rates in freshwater. However, speciation may be generally faster in sympatry than in allopatry, as illustrated by lacustrine radiations such as African cichlids. Such differences between rivers and lakes may be important to consider when comparing diversification broadly among freshwater and marine groups. Here I compared diversification rates of teleost fishes in marine, riverine and lacustrine habitats. I found that lakes had faster speciation and net diversification rates than other aquatic habitats. However, most freshwater diversity arose in rivers. Surprisingly, riverine and marine habitats had similar rates of net diversification on average. Biogeographic models suggest that lacustrine habitats are evolutionarily unstable, explaining the dearth of lacustrine species in spite of their rapid diversification. Collectively, these results suggest that strong diversification rate differences are unlikely to explain the freshwater paradox. Instead, this pattern may be attributable to the comparable amount of time spent in riverine and marine habitats over the 200-million-year history of teleosts.
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37
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Maliet O, Morlon H. Fast and accurate estimation of species-specific diversification rates using data augmentation. Syst Biol 2021; 71:353-366. [PMID: 34228799 DOI: 10.1093/sysbio/syab055] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 06/10/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Diversification rates vary across species as a response to various factors, including environmental conditions and species-specific features. Phylogenetic models that allow accounting for and quantifying this heterogeneity in diversification rates have proven particularly useful for understanding clades diversification. Recently, we introduced the cladogenetic diversification rate shift model (ClaDS), which allows inferring multiple rate changes of small magnitude across lineages. Here we present a new inference technique for this model that considerably reduces computation time through the use of data augmentation and provide an implementation of this method in Julia. In addition to drastically reducing computation time, this new inference approach provides a posterior distribution of the augmented data, that is the tree with extinct and unsampled lineages as well as associated diversification rates. In particular, this allows extracting the distribution through time of both the mean rate and the number of lineages. We assess the statistical performances of our approach using simulations and illustrate its application on the entire bird radiation.
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Affiliation(s)
- Odile Maliet
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Hélène Morlon
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
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38
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Fenker J, Tedeschi LG, Melville J, Moritz C. Predictors of phylogeographic structure among codistributed taxa across the complex Australian monsoonal tropics. Mol Ecol 2021; 30:4276-4291. [PMID: 34216506 DOI: 10.1111/mec.16057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 11/28/2022]
Abstract
Differences in the geographic scale and depth of phylogeographic structure across codistributed taxa can reveal how microevolutionary processes such as population isolation and persistence drive diversification. In turn, environmental heterogeneity, species' traits, and historical biogeographic barriers may influence the potential for isolation and persistence. Using extensive SNP data and a combination of population genetic summary statistics and landscape genomic analyses, we explored predictors of the scale and depth of phylogeographic structure in codistributed lizard taxa from the topographically and climatically complex monsoonal tropics (AMT) of Australia. We first resolved intraspecific lineages and then tested whether genetic divergence across space within lineages is related to isolation by distance, resistance and/or environment and whether these factors differ across genera or between rock-related versus habitat generalist taxa. We then tested whether microevolutionary processes within lineages explain differences in the geographic scale and depth of intraspecific phylogeographic lineages. The results indicated that landscape predictors of phylogeographic structure differ between taxa. Within lineages, there was prevalent isolation by distance, but the strength of isolation by distance is independent of the taxonomic family, habitat specialization, and climate. Isolation by environment is the strongest predictor of landscape-scale genetic divergence for all taxa, with both temperature and precipitation acting as limiting factors. The strength of isolation by distance does not predict the geographic scale of the phylogeographic structure. However, more localized lineages had higher mean individual heterozygosity and less negative Tajima's D. This result implies that finer-scale phylogeographic structuring within species is associated with larger and more stable populations and, hence, persistence.
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Affiliation(s)
- Jessica Fenker
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Leonardo G Tedeschi
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jane Melville
- Department of Sciences, Museums Victoria, Melbourne, VIC, Australia.,School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
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39
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Mitchell N, Whitney KD. Limited evidence for a positive relationship between hybridization and diversification across seed plant families. Evolution 2021; 75:1966-1982. [PMID: 34156712 DOI: 10.1111/evo.14291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 01/09/2023]
Abstract
Hybridization has experimental and observational ties to evolutionary processes and outcomes such as adaptation, speciation, and radiation. Although it has been hypothesized that hybridization and diversification are positively correlated, this idea remains largely untested empirically, and hybridization can also potentially reduce diversity. Here, we use a hybridization database on 170 seed plant families, life history information, and a time-calibrated phylogeny to test for phylogenetically-corrected associations between hybridization and diversification rates, while also taking into account life-history traits that may be correlated with both processes. We use three methods to estimate diversification rates and two metrics of hybridization. Although hybridization explains only a small amount of overall variation in diversification rates, we show that diversification and hybridization are sometimes positively correlated, although the effect sizes are very small. Moreover, the relationship remains detectable when incorporating the correlations between diversification and two other life history characteristics, perenniality and woodiness. We discuss potential mechanisms for this association under four different scenarios: hybridization may drive diversification, diversification may drive hybridization, both hybridization and diversification may jointly be driven by other factors, or, as an alternative, that there is in fact no relationship between the two. We suggest future studies to disentangle the causal structure.
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Affiliation(s)
- Nora Mitchell
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131.,Department of Biology, University of Wisconsin - Eau Claire, Eau Claire, Wisconsin, 54701
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131
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40
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Melo BF, Sidlauskas BL, Near TJ, Roxo FF, Ghezelayagh A, Ochoa LE, Stiassny MLJ, Arroyave J, Chang J, Faircloth BC, MacGuigan DJ, Harrington RC, Benine RC, Burns MD, Hoekzema K, Sanches NC, Maldonado-Ocampo JA, Castro RMC, Foresti F, Alfaro ME, Oliveira C. Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes. Syst Biol 2021; 71:78-92. [PMID: 34097063 DOI: 10.1093/sysbio/syab040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 11/12/2022] Open
Abstract
The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1,288 ultraconserved element loci (UCE) spanning 293 species, 211 genera and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 million years ago (Ma) during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2,150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity.
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Affiliation(s)
- Bruno F Melo
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Brian L Sidlauskas
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Thomas J Near
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Fabio F Roxo
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Ava Ghezelayagh
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Luz E Ochoa
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil.,Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Palmira, Valle del Cauca, 763547, Colombia
| | - Melanie L J Stiassny
- Dept of Ichthyology, American Museum of Natural History, New York, NY, 10024, USA
| | - Jairo Arroyave
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, 04510, México
| | - Jonathan Chang
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Brant C Faircloth
- Dept of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Daniel J MacGuigan
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Richard C Harrington
- Dept of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Ricardo C Benine
- Sector of Zoology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 18618-689, Brazil
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell University Museum of Vertebrates, Ithaca, NY, 14850, USA
| | - Kendra Hoekzema
- Dept of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Natalia C Sanches
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Javier A Maldonado-Ocampo
- Dept de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, DC, Colombia (in memoriam)
| | - Ricardo M C Castro
- Faculdade de Filosofia, Ciências e Letras, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Fausto Foresti
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
| | - Michael E Alfaro
- Dept of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudio Oliveira
- Dept of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, SP, 16818-689, Brazil
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41
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Burress ED, Muñoz MM. Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation. Syst Biol 2021; 71:93-104. [PMID: 33956152 DOI: 10.1093/sysbio/syab031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists ('ecomorphs') evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in stimulating diversification. Here, we assess the proposed "island effect" on anole diversification using Bayesian phylogenetic comparative methods that explicitly incorporate rate heterogeneity across the tree and demonstrate two cases of would-be false positives. We discovered that rates of speciation and morphological evolution of island and mainland anoles are equivalent, implying that islands provide no special context for exceptionally rapid diversification. Likewise, rates of evolution were equivalent between island anoles that arose via in situ versus dispersal-based mechanisms, and we found no evidence for island-specific rates of speciation or morphological evolution. Nonetheless, the origin of Anolis is characterized by a speciation pulse that slowed over time - a classic signature of waning ecological opportunity. Our findings cast doubt on the notion that islands catalyzed the anole adaptive radiation and instead point to a key innovation, adhesive toe pads, which facilitated the exploitation of many arboreal niches sparsely utilized by other iguanian lizards. The selective pressures responsible for arboreal niche diversification differ between islands and the mainland, but the tempo of diversification driven by these discordant processes is indistinguishable.
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Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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42
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Odom KJ, Araya-Salas M, Morano JL, Ligon RA, Leighton GM, Taff CC, Dalziell AH, Billings AC, Germain RR, Pardo M, de Andrade LG, Hedwig D, Keen SC, Shiu Y, Charif RA, Webster MS, Rice AN. Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa. Biol Rev Camb Philos Soc 2021; 96:1135-1159. [PMID: 33652499 DOI: 10.1111/brv.12695] [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: 12/17/2019] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.
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Affiliation(s)
- Karan J Odom
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Marcelo Araya-Salas
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Sede del Sur, Universidad de Costa Rica, Golfito, 60701, Costa Rica
| | - Janelle L Morano
- Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Russell A Ligon
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Gavin M Leighton
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Department of Biology, SUNY Buffalo State, Buffalo, NY, 14222, U.S.A
| | - Conor C Taff
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Anastasia H Dalziell
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Centre for Sustainable Ecosystem Solutions, University of Wollongong, Northfields Ave, Wollongong, NSW, 2522, Australia
| | - Alexis C Billings
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, U.S.A.,Department of Environmental, Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94709, U.S.A
| | - Ryan R Germain
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Michael Pardo
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, U.S.A
| | - Luciana Guimarães de Andrade
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, U.S.A.,Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Daniela Hedwig
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Sara C Keen
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Geological Sciences, Stanford University, Stanford, CA, 94305, U.S.A
| | - Yu Shiu
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Russell A Charif
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Michael S Webster
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Aaron N Rice
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
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43
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Laudanno G, Haegeman B, Rabosky DL, Etienne RS. Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach. Syst Biol 2021; 70:389-407. [PMID: 32617585 PMCID: PMC7875465 DOI: 10.1093/sysbio/syaa048] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Abstract
The branching patterns of molecular phylogenies are generally assumed to contain information on rates of the underlying speciation and extinction processes. Simple birth-death models with constant, time-varying, or diversity-dependent rates have been invoked to explain these patterns. They have one assumption in common: all lineages have the same set of diversification rates at a given point in time. It seems likely, however, that there is variability in diversification rates across subclades in a phylogenetic tree. This has inspired the construction of models that allow multiple rate regimes across the phylogeny, with instantaneous shifts between these regimes. Several methods exist for calculating the likelihood of a phylogeny under a specified mapping of diversification regimes and for performing inference on the most likely diversification history that gave rise to a particular phylogenetic tree. Here, we show that the likelihood computation of these methods is not correct. We provide a new framework to compute the likelihood correctly and show, with simulations of a single shift, that the correct likelihood indeed leads to parameter estimates that are on average in much better agreement with the generating parameters than the incorrect likelihood. Moreover, we show that our corrected likelihood can be extended to multiple rate shifts in time-dependent and diversity-dependent models. We argue that identifying shifts in diversification rates is a nontrivial model selection exercise where one has to choose whether shifts in now-extinct lineages are taken into account or not. Hence, our framework also resolves the recent debate on such unobserved shifts. [Diversification; macroevolution; phylogeny; speciation].
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Affiliation(s)
- Giovanni Laudanno
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC, Groningen, The Netherlands
| | - Bart Haegeman
- Centre for Biodiversity Theory and Modelling, Theoretical and Experimental Ecology Station, CNRS and Paul Sabatier University, 09200, Moulis, France
| | - Daniel L Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC, Groningen, The Netherlands
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44
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Igea J, Tanentzap AJ. Global topographic uplift has elevated speciation in mammals and birds over the last 3 million years. Nat Ecol Evol 2021; 5:1530-1535. [PMID: 34475571 PMCID: PMC8560637 DOI: 10.1038/s41559-021-01545-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Topographic change shapes the evolution of biodiversity by influencing both habitat connectivity and habitat diversity as well as abiotic factors like climate. However, its role in creating global biodiversity gradients remains poorly characterized because geology, climate and evolutionary data have rarely been integrated across concordant timescales. Here we show that topographic uplift over the last 3 million years explains more spatial variation in the speciation of all mammals and birds than do the direct effects of palaeoclimate change and both present-day elevation and present-day temperature. By contrast, the effects of topographic changes are much smaller than those of present-day temperatures in eroded areas. Together, our results stress that historical geological processes rather than traditionally studied macroecological gradients may ultimately generate much of the world's biodiversity. More broadly, as the Earth's surface continues to rise and fall, topography will remain an important driver of evolutionary change and novelty.
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Affiliation(s)
- Javier Igea
- grid.5335.00000000121885934Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Andrew J. Tanentzap
- grid.5335.00000000121885934Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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45
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Heterogeneous relationships between rates of speciation and body size evolution across vertebrate clades. Nat Ecol Evol 2020; 5:101-110. [PMID: 33106601 DOI: 10.1038/s41559-020-01321-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 09/04/2020] [Indexed: 01/09/2023]
Abstract
Several theories predict that rates of phenotypic evolution should be related to the rate at which new lineages arise. However, drawing general conclusions regarding the coupling between these fundamental evolutionary rates has been difficult due to the inconsistent nature of previous results combined with uncertainty over the most appropriate methodology with which to investigate such relationships. Here we propose and compare the performance of several different approaches for testing associations between lineage-specific rates of speciation and phenotypic evolution using phylogenetic data. We then use the best-performing method to test relationships between rates of speciation and body size evolution in five major vertebrate clades (amphibians, birds, mammals, ray-finned fish and squamate reptiles) at two phylogenetic scales. Our results provide support for the long-standing view that rates of speciation and morphological evolution are generally positively related at broad macroevolutionary scales, but they also reveal a substantial degree of heterogeneity in the strength and direction of these associations at finer scales across the vertebrate tree of life.
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46
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Román-Palacios C, Molina-Henao YF, Barker MS. Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae. Proc Biol Sci 2020; 287:20200962. [PMID: 32873209 PMCID: PMC7542780 DOI: 10.1098/rspb.2020.0962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022] Open
Abstract
Although polyploidy is widespread across the plant Tree of Life, its long-term evolutionary significance is still poorly understood. Here, we examine the effects of polyploidy in explaining the large-scale evolutionary patterns within angiosperms by focusing on a single family exhibiting extensive interspecific variation in chromosome numbers. We inferred ploidy from haploid chromosome numbers for 80% of species in the most comprehensive species-level chronogram for the Brassicaceae. After evaluating a total of 94 phylogenetic models of diversification, we found that ploidy influences diversification rates across the Brassicaceae. We also found that despite diversifying at a similar rate to diploids, polyploids have played a significant role in driving present-day differences in species richness among clades. Overall, in addition to highlighting the complexity in the evolutionary consequences of polyploidy, our results suggest that rare successful polyploids persist while significantly contributing to the long-term evolution of clades. Our findings further indicate that polyploidy has played a major role in driving the long-term evolution of the Brassicaceae and highlight the potential of polyploidy in shaping present-day diversity patterns across the plant Tree of Life.
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Affiliation(s)
- Cristian Román-Palacios
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Y. Franchesco Molina-Henao
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA 02131, USA
- Departamento de Biología, Universidad del Valle, Cali, Valle 760032, Colombia
| | - Michael S. Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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47
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Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Recent accelerated diversification in rosids occurred outside the tropics. Nat Commun 2020; 11:3333. [PMID: 32620894 PMCID: PMC7335165 DOI: 10.1038/s41467-020-17116-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/05/2020] [Indexed: 01/28/2023] Open
Abstract
Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.
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Affiliation(s)
- Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. .,Department of Bioscience, Aarhus University, Aarhus, 8000C, Denmark. .,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. .,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.
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48
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Nürk NM, Linder HP, Onstein RE, Larcombe MJ, Hughes CE, Piñeiro Fernández L, Schlüter PM, Valente L, Beierkuhnlein C, Cutts V, Donoghue MJ, Edwards EJ, Field R, Flantua SGA, Higgins SI, Jentsch A, Liede‐Schumann S, Pirie MD. Diversification in evolutionary arenas-Assessment and synthesis. Ecol Evol 2020; 10:6163-6182. [PMID: 32607221 PMCID: PMC7319112 DOI: 10.1002/ece3.6313] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/30/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b), and clade-specific phenotypes or traits (c); thus, d ~ a,b,c. We refer to the four components (a-d) and their interactions collectively as the "Evolutionary Arena." We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.
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Affiliation(s)
- Nicolai M. Nürk
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - H. Peter Linder
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Renske E. Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | | | - Colin E. Hughes
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - Laura Piñeiro Fernández
- Department of Systematic & Evolutionary BotanyUniversity of ZurichZurichSwitzerland
- Department of BotanyUniversity of HohenheimStuttgartGermany
| | | | - Luis Valente
- Naturalis Biodiversity CenterUnderstanding Evolution GroupLeidenThe Netherlands
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Carl Beierkuhnlein
- Department of BiogeographyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Vanessa Cutts
- School of GeographyUniversity of NottinghamNottinghamUK
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Erika J. Edwards
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Richard Field
- School of GeographyUniversity of NottinghamNottinghamUK
| | | | | | - Anke Jentsch
- Department of Disturbance EcologyBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Sigrid Liede‐Schumann
- Department of Plant SystematicsBayreuth Center of Ecology and Environmental Research (BayCEER)University of BayreuthBayreuthGermany
| | - Michael D. Pirie
- Johannes Gutenberg‐UniversitätMainzGermany
- University MuseumUniversity of BergenBergenNorway
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49
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Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids. AMERICAN JOURNAL OF BOTANY 2020; 107:895-909. [PMID: 32519354 PMCID: PMC7384126 DOI: 10.1002/ajb2.1479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/03/2020] [Indexed: 05/03/2023]
Abstract
PREMISE Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. METHODS We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). RESULTS We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. CONCLUSIONS We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
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Affiliation(s)
- Miao Sun
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- Department of BioscienceAarhus UniversityAarhus8000Denmark
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
| | - Matthew A. Gitzendanner
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
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50
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Siqueira AC, Morais RA, Bellwood DR, Cowman PF. Trophic innovations fuel reef fish diversification. Nat Commun 2020; 11:2669. [PMID: 32472063 PMCID: PMC7260216 DOI: 10.1038/s41467-020-16498-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/01/2020] [Indexed: 12/29/2022] Open
Abstract
Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their diversification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage diversification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to assess the importance of ecological and geographical factors in explaining lineage origination patterns. We reveal that reef fish diversification is strongly associated with species' trophic identity and body size. Large-bodied herbivorous fishes outpace all other trophic groups in recent diversification rates, a pattern that is consistent through time. Additionally, we show that omnivory acts as an intermediate evolutionary step between higher and lower trophic levels, while planktivory represents a common transition destination. Overall, these results suggest that Miocene changes in reef configurations were likely driven by, and subsequently promoted, trophic innovations. This highlights trophic evolution as a key element in enhancing reef fish diversification.
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Affiliation(s)
- Alexandre C Siqueira
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia.
| | - Renato A Morais
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - David R Bellwood
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Peter F Cowman
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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