1
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Jiang C, Gu S, Pan T, Wang X, Qin W, Wang G, Gao X, Zhang J, Chen K, Warren A, Xiong J, Miao W. Dynamics and timing of diversification events of ciliated eukaryotes from a large phylogenomic perspective. Mol Phylogenet Evol 2024; 197:108110. [PMID: 38768875 DOI: 10.1016/j.ympev.2024.108110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Ciliophora, an exceptionally diverse lineage of unicellular eukaryotes, exhibits a remarkable range of species richness across classes in the ciliate Tree of Life. In this study, we have acquired transcriptome and genome data from 40 representative species in seven ciliate classes. Utilizing 247 genes and 105 taxa, we devised a comprehensive phylogenomic tree for Ciliophora, encompassing over 60 % of orders and constituting the most extensive dataset of ciliate species to date. We established a robust phylogenetic framework that encompasses ambiguous taxa and the major classes within the phylum. Our findings support the monophyly of each of two subphyla (Postciliodesmatophora and Intramacronucleata), along with three subclades (Protocruzia, CONTHREEP, and SAPML) nested within Intramacronucleata, and elucidate evolutionary positions among the major classes within the phylum. Drawing on the robust ciliate Tree of Life and three constraints, we estimated the radiation of Ciliophora around 1175 Ma during the middle of the Proterozoic Eon, and most of the ciliate classes diverged from their sister lineage during the latter half of this period. Additionally, based on the time-calibrated tree and species richness pattern, we investigated net diversification rates of Ciliophora and its classes. The global net diversification rate for Ciliophora was estimated at 0.004979 species/Ma. Heterogeneity in net diversification rates was evident at the class level, with faster rates observed in Oligohymenophorea and Spirotrichea than other classes within the subclades CONTHREEP and SAPML, respectively. Notably, our analysis suggests that variations in net diversification rates, rather than clade ages, appear to contribute to the differences in species richness in Ciliophora at the class level.
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Affiliation(s)
- Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Siyu Gu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Pan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xueyan Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weiwei Qin
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Guangying Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xinxin Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, UK
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
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2
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Yu D, Wiens JJ. The causes of species richness patterns among clades. Proc Biol Sci 2024; 291:20232436. [PMID: 38262607 PMCID: PMC10805600 DOI: 10.1098/rspb.2023.2436] [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: 10/30/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
Two major types of species richness patterns are spatial (e.g. the latitudinal diversity gradient) and clade-based (e.g. the dominance of angiosperms among plants). Studies have debated whether clade-based richness patterns are explained primarily by larger clades having faster rates of species accumulation (speciation minus extinction over time; diversification-rate hypothesis) or by simply being older (clade-age hypothesis). However, these studies typically compared named clades of the same taxonomic rank, such as phyla and families. This study design is potentially biased against the clade-age hypothesis, since clades of the same rank may be more similar in age than randomly selected clades. Here, we analyse the causes of clade-based richness patterns across the tree of life using a large-scale, time-calibrated, species-level phylogeny and random sampling of clades. We find that within major groups of organisms (animals, plants, fungi, bacteria, archaeans), richness patterns are most strongly related to clade age. Nevertheless, weaker relationships with diversification rates are present in animals and plants. These overall results contrast with similar large-scale analyses across life based on named clades, which showed little effect of clade age on richness. More broadly, these results help support the overall importance of time for explaining diverse types of species richness patterns.
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Affiliation(s)
- Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Science, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
| | - John J. Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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3
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Morinaga G, Wiens JJ, Moen DS. The radiation continuum and the evolution of frog diversity. Nat Commun 2023; 14:7100. [PMID: 37925440 PMCID: PMC10625520 DOI: 10.1038/s41467-023-42745-x] [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: 02/23/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Most of life's vast diversity of species and phenotypes is often attributed to adaptive radiation. Yet its contribution to species and phenotypic diversity of a major group has not been examined. Two key questions remain unresolved. First, what proportion of clades show macroevolutionary dynamics similar to adaptive radiations? Second, what proportion of overall species richness and phenotypic diversity do these adaptive-radiation-like clades contain? We address these questions with phylogenetic and morphological data for 1226 frog species across 43 families (which represent >99% of all species). Less than half of frog families resembled adaptive radiations (with rapid diversification and morphological evolution). Yet, these adaptive-radiation-like clades encompassed ~75% of both morphological and species diversity, despite rapid rates in other clades (e.g., non-adaptive radiations). Overall, we support the importance of adaptive-radiation-like evolution for explaining diversity patterns and provide a framework for characterizing macroevolutionary dynamics and diversity patterns in other groups.
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Affiliation(s)
- Gen Morinaga
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA.
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4
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Henao-Diaz LF, Pennell M. The Major Features of Macroevolution. Syst Biol 2023; 72:1188-1198. [PMID: 37248967 DOI: 10.1093/sysbio/syad032] [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: 12/23/2021] [Revised: 05/02/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the "major features of macroevolution." By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
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Affiliation(s)
- L Francisco Henao-Diaz
- Department of Ecology and Evolution, University of Chicago, Chicago, USA
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, USA
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5
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Sales-Oliveira V, Altmanová M, Gvoždík V, Kretschmer R, Ezaz T, Liehr T, Padutsch N, Badjedjea G, Utsunomia R, Tanomtong A, Cioffi M. Cross-species chromosome painting and repetitive DNA mapping illuminate the karyotype evolution in true crocodiles (Crocodylidae). Chromosoma 2023; 132:289-303. [PMID: 37493806 DOI: 10.1007/s00412-023-00806-6] [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: 04/17/2023] [Revised: 05/23/2023] [Accepted: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Crocodilians have maintained very similar karyotype structures and diploid chromosome numbers for around 100 million years, with only minor variations in collinearity. Why this karyotype structure has largely stayed unaltered for so long is unclear. In this study, we analyzed the karyotypes of six species belonging to the genera Crocodylus and Osteolaemus (Crocodylidae, true crocodiles), among which the Congolian endemic O. osborni was included and investigated. We utilized various techniques (differential staining, fluorescence in situ hybridization with repetitive DNA and rDNA probes, whole chromosome painting, and comparative genomic hybridization) to better understand how crocodile chromosomes evolved. We studied representatives of three of the four main diploid chromosome numbers found in crocodiles (2n = 30/32/38). Our data provided new information about the species studied, including the identification of four major chromosomal rearrangements that occurred during the karyotype diversification process in crocodiles. These changes led to the current diploid chromosome numbers of 2n = 30 (fusion) and 2n = 38 (fissions), derived from the ancestral state of 2n = 32. The conserved cytogenetic tendency in crocodilians, where extant species keep near-ancestral state, contrasts with the more dynamic karyotype evolution seen in other major reptile groups.
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Affiliation(s)
- Vanessa Sales-Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marie Altmanová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Rafael Kretschmer
- Departamento de Ecologia, Zoologia e Genética, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Niklas Padutsch
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Alongklod Tanomtong
- Department of Biology Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002, Thailand
| | - Marcelo Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil.
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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6
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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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7
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Rolland J, Henao-Diaz LF, Doebeli M, Germain R, Harmon LJ, Knowles LL, Liow LH, Mank JE, Machac A, Otto SP, Pennell M, Salamin N, Silvestro D, Sugawara M, Uyeda J, Wagner CE, Schluter D. Conceptual and empirical bridges between micro- and macroevolution. Nat Ecol Evol 2023; 7:1181-1193. [PMID: 37429904 DOI: 10.1038/s41559-023-02116-7] [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: 12/08/2022] [Accepted: 06/13/2023] [Indexed: 07/12/2023]
Abstract
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| | - L Francisco Henao-Diaz
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Michael Doebeli
- Department of Zoology, and Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel Germain
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke J Harmon
- Dept. of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | - Judith E Mank
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonin Machac
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Sarah P Otto
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Pennell
- Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mauro Sugawara
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Mário Schenberg Institute, São Paulo, Brazil
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Catherine E Wagner
- Department of Botany, and Program in Ecology and Evolution, University of Wyoming, Laramie, WY, USA
| | - Dolph Schluter
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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8
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Wiens JJ. Trait-based species richness: ecology and macroevolution. Biol Rev Camb Philos Soc 2023; 98:1365-1387. [PMID: 37015839 DOI: 10.1111/brv.12957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2023]
Abstract
Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, USA
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9
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Belluardo F, Jesus Muñoz-Pajares A, Miralles A, Silvestro D, Cocca W, Mihaja Ratsoavina F, Villa A, Roberts SH, Mezzasalma M, Zizka A, Antonelli A, Crottini A. Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae). Mol Phylogenet Evol 2023; 178:107635. [PMID: 36208694 DOI: 10.1016/j.ympev.2022.107635] [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: 03/23/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
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Affiliation(s)
- Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
| | - A Jesus Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Genética, Universidad de Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
| | - Aurélien Miralles
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Ch. du Musée 10, 1700 Fribourg, Switzerland; Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Walter Cocca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Domaine Sciences et Technologies, Université d'Antananarivo, B.P. 906, 101 Antananarivo, Madagascar
| | - Andrea Villa
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Spain
| | - Sam Hyde Roberts
- SEED Madagascar, Unit 7, Beethoven Street 1A, W10 4LG London, UK; Oxford Brookes University, Headington Campus, 0X3 0BP Oxford, UK; Operation Wallacea, Wallace House, Old Bolingbroke, PE23 4EX Spilsby, UK
| | - Marcello Mezzasalma
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden; Royal Botanic Gardens, Kew, TW9 3AE Richmond, UK; Department of Biology, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
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10
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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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11
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Imfeld TS, Barker FK. Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification. J Evol Biol 2022; 35:1335-1351. [PMID: 36057939 DOI: 10.1111/jeb.14084] [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: 09/13/2021] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, Colorado, USA
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA.,Bell Museum, University of Minnesota, St. Paul, Minnesota, USA
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12
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Louca S, Henao-Diaz LF, Pennell M. The scaling of diversification rates with age is likely explained by sampling bias. Evolution 2022; 76:1625-1637. [PMID: 35567800 DOI: 10.1111/evo.14515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/07/2022] [Indexed: 01/22/2023]
Abstract
Numerous phylogenetic studies reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates. The causes of this age-rate-scaling (ARS), whether biological and/or artifactual, remain unresolved. Here we fit diversification models to thousands of eukaryotic time-calibrated phylogenies to explore multiple potential causes of the ARS including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and an important and ubiquitous form of sampling bias-preferentially analyzing larger extant clades. We distinguish between two mechanism by which such sampling biases can cause an ARS: First, by favoring clades that happen to be unusually large merely by chance (i.e., due to the stochastic nature of the cladogenic process), thus leading to rate overestimation, and second, by favoring clades that have truly higher diversification rates. We find that, of the proposed explanations, only sampling biases are likely to contribute to the observed ARS. We develop methods for fully correcting for sampling bias mechanism 1, and find that despite these corrections a substantial ARS remains. We then confirm using simulations that preferring trees with truly higher rates (mechanism 2) likely explains this residual ARS. Since we do not have a completely unbiased sample of clades, including extinct ones, for phylogenetic analyses, it is difficult to demonstrate unambiguously that sampling biases are the sole cause of the ARS. Sampling biases are, however, a parsimonious and plausible explanation for this widely observed macroevolutionary pattern, and this has implications for how we interpret the distribution of diversification rate estimates in extant clades.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - L Francisco Henao-Diaz
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
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13
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Davis KE, De Grave S, Delmer C, Payne ARD, Mitchell S, Wills MA. Ecological Transitions and the Shape of the Decapod Tree of Life. Integr Comp Biol 2022; 62:332-344. [PMID: 35612997 DOI: 10.1093/icb/icac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/14/2022] Open
Abstract
Understanding the processes that shaped the distribution of species richness across the Tree of Life is a central macroevolutionary research agenda. Major ecological innovations, including transitions between habitats, may help to explain the striking asymmetries of diversity that are often observed between sister clades. Here, we test the impact of such transitions on speciation rates across decapod crustaceans, modelling diversification dynamics within a phylogenetic framework. Our results show that, while terrestrial lineages have higher speciation rates than either marine or freshwater lineages, there is no difference between mean speciation rates in marine and freshwater lineages across Decapoda. Partitioning our data by infraorder reveals that those clades with habitat heterogeneity have higher speciation rates in freshwater and terrestrial lineages, with freshwater rates up to 1.5 times faster than marine rates, and terrestrial rates approximately four times faster. This averaging out of marine and freshwater speciation rates results from the varying contributions of different clades to average speciation rates. However, with the exception of Caridea, we find no evidence for any causal relationship between habitat and speciation rate. Our results demonstrate that while statistical generalisations about ecological traits and evolutionary rates are valuable, there are many exceptions. Hence, while freshwater and terrestrial lineages typically speciate faster than their marine relatives, there are many atypically slow freshwater lineages and fast marine lineages across Decapoda. Future work on diversification patterns will benefit from the inclusion of fossil data, as well as additional ecological factors.
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Affiliation(s)
- Katie E Davis
- University of York, Department of Biology York, North Yorkshire, UK
| | - Sammy De Grave
- Oxford University Museum of Natural History, Oxford, Oxfordshire, UK
| | - Cyrille Delmer
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
| | - Alexander R D Payne
- University of York, Leverhulme Centre for Anthropocene Biodiversity, York, North Yorkshire, UK
| | - Steve Mitchell
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
| | - Matthew A Wills
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
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14
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Ritchie AM, Hua X, Bromham L. Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary. BMC Ecol Evol 2022; 22:61. [PMID: 35538412 PMCID: PMC9088092 DOI: 10.1186/s12862-022-02015-8] [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: 06/29/2021] [Accepted: 04/14/2022] [Indexed: 11/17/2022] Open
Abstract
Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02015-8.
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15
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Ritchie AM, Hua X, Bromham L. Diversification Rate is Associated with Rate of Molecular Evolution in Ray-Finned Fish (Actinopterygii). J Mol Evol 2022; 90:200-214. [PMID: 35262772 PMCID: PMC8975766 DOI: 10.1007/s00239-022-10052-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 02/24/2022] [Indexed: 10/27/2022]
Abstract
Understanding the factors that drive diversification of taxa across the tree of life is a key focus of macroevolutionary research. While the effects of life history, ecology, climate and geography on diversity have been studied for many taxa, the relationship between molecular evolution and diversification has received less attention. However, correlations between rates of molecular evolution and diversification rate have been detected in a range of taxa, including reptiles, plants and birds. A correlation between rates of molecular evolution and diversification rate is a prediction of several evolutionary theories, including the evolutionary speed hypothesis which links variation in mutation rates to differences in speciation rates. If it is widespread, such correlations could also have significant practical impacts, if they are not adequately accounted for in phylogenetic inference of evolutionary rates and timescales. Ray-finned fish (Actinopterygii) offer a prime target to test for this relationship due to their extreme variation in clade size suggesting a wide range of diversification rates. We employ both a sister-pairs approach and a whole-tree approach to test for correlations between substitution rate and net diversification. We also collect life history and ecological trait data and account for potential confounding factors including body size, latitude, max depth and reef association. We find evidence to support a relationship between diversification and synonymous rates of nuclear evolution across two published backbone phylogenies, as well as weak evidence for a relationship between mitochondrial nonsynonymous rates and diversification at the genus level.
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Affiliation(s)
- Andrew M Ritchie
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia. .,Research School of Biological Sciences, Australian National University, Robertson Building, 134 Linnaeus Way, Canberra, ACT 2600, Australia.
| | - Xia Hua
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia.,Mathematical Sciences Institute, Australian National University, Canberra, ACT 2600, Australia
| | - Lindell Bromham
- Research School of Biological Sciences, Australian National University, Canberra, ACT 2600, Australia
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16
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Harmon LJ, Pennell MW, Henao-Diaz LF, Rolland J, Sipley BN, Uyeda JC. Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-011921-023644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.
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Affiliation(s)
- Luke J. Harmon
- Institute for Bioinformatics and Evolutionary Studies (IBEST) and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - L. Francisco Henao-Diaz
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jonathan Rolland
- Laboratoire Evolution et Diversité Biologique, CNRS, UMR5174, Université Toulouse III–Paul Sabatier, 31062 Toulouse, France
| | - Breanna N. Sipley
- Program for Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho 83844, USA
| | - Josef C. Uyeda
- Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA
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17
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Arbuckle K, Harris RJ. Radiating pain: venom has contributed to the diversification of the largest radiations of vertebrate and invertebrate animals. BMC Ecol Evol 2021; 21:150. [PMID: 34344322 PMCID: PMC8336261 DOI: 10.1186/s12862-021-01880-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 07/09/2021] [Indexed: 01/04/2023] Open
Abstract
Background Understanding drivers of animal biodiversity has been a longstanding aim in evolutionary biology. Insects and fishes represent the largest lineages of invertebrates and vertebrates respectively, and consequently many ideas have been proposed to explain this diversity. Natural enemy interactions are often important in diversification dynamics, and key traits that mediate such interactions may therefore have an important role in explaining organismal diversity. Venom is one such trait which is intricately bound in antagonistic coevolution and has recently been shown to be associated with increased diversification rates in tetrapods. Despite ~ 10% of fish families and ~ 16% of insect families containing venomous species, the role that venom may play in these two superradiations remains unknown. Results In this paper we take a broad family-level phylogenetic perspective and show that variation in diversification rates are the main cause of variations in species richness in both insects and fishes, and that venomous families have diversification rates twice as high as non-venomous families. Furthermore, we estimate that venom was present in ~ 10% and ~ 14% of the evolutionary history of fishes and insects respectively. Conclusions Consequently, we provide evidence that venom has played a role in generating the remarkable diversity in the largest vertebrate and invertebrate radiations. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01880-z.
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Affiliation(s)
- Kevin Arbuckle
- Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK.
| | - Richard J Harris
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, Saint Lucia, QLD, 4072, Australia
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18
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Prušáková D, Peska V, Pekár S, Bubeník M, Čížek L, Bezděk A, Čapková Frydrychová R. Telomeric DNA sequences in beetle taxa vary with species richness. Sci Rep 2021; 11:13319. [PMID: 34172809 PMCID: PMC8233369 DOI: 10.1038/s41598-021-92705-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Telomeres are protective structures at the ends of eukaryotic chromosomes, and disruption of their nucleoprotein composition usually results in genome instability and cell death. Telomeric DNA sequences have generally been found to be exceptionally conserved in evolution, and the most common pattern of telomeric sequences across eukaryotes is (TxAyGz)n maintained by telomerase. However, telomerase-added DNA repeats in some insect taxa frequently vary, show unusual features, and can even be absent. It has been speculated about factors that might allow frequent changes in telomere composition in Insecta. Coleoptera (beetles) is the largest of all insect orders and based on previously available data, it seemed that the telomeric sequence of beetles varies to a great extent. We performed an extensive mapping of the (TTAGG)n sequence, the ancestral telomeric sequence in Insects, across the main branches of Coleoptera. Our study indicates that the (TTAGG)n sequence has been repeatedly or completely lost in more than half of the tested beetle superfamilies. Although the exact telomeric motif in most of the (TTAGG)n-negative beetles is unknown, we found that the (TTAGG)n sequence has been replaced by two alternative telomeric motifs, the (TCAGG)n and (TTAGGG)n, in at least three superfamilies of Coleoptera. The diversity of the telomeric motifs was positively related to the species richness of taxa, regardless of the age of the taxa. The presence/absence of the (TTAGG)n sequence highly varied within the Curculionoidea, Chrysomeloidea, and Staphylinoidea, which are the three most diverse superfamilies within Metazoa. Our data supports the hypothesis that telomere dysfunctions can initiate rapid genomic changes that lead to reproductive isolation and speciation.
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Affiliation(s)
- Daniela Prušáková
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Michal Bubeník
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Lukáš Čížek
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Aleš Bezděk
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Radmila Čapková Frydrychová
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 31, 370 05, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
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19
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Beavan AJS, Pisani D, Donoghue PCJ. Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times. SCIENCE ADVANCES 2021; 7:eabf2257. [PMID: 34117058 PMCID: PMC8195484 DOI: 10.1126/sciadv.abf2257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/28/2021] [Indexed: 05/05/2023]
Abstract
Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.
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Affiliation(s)
- Alan J S Beavan
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Davide Pisani
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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20
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Sánchez-García M, Ryberg M, Khan FK, Varga T, Nagy LG, Hibbett DS. Fruiting body form, not nutritional mode, is the major driver of diversification in mushroom-forming fungi. Proc Natl Acad Sci U S A 2020; 117:32528-32534. [PMID: 33257574 PMCID: PMC7768725 DOI: 10.1073/pnas.1922539117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With ∼36,000 described species, Agaricomycetes are among the most successful groups of Fungi. Agaricomycetes display great diversity in fruiting body forms and nutritional modes. Most have pileate-stipitate fruiting bodies (with a cap and stalk), but the group also contains crust-like resupinate fungi, polypores, coral fungi, and gasteroid forms (e.g., puffballs and stinkhorns). Some Agaricomycetes enter into ectomycorrhizal symbioses with plants, while others are decayers (saprotrophs) or pathogens. We constructed a megaphylogeny of 8,400 species and used it to test the following five hypotheses regarding the evolution of morphological and ecological traits in Agaricomycetes and their impact on diversification: 1) resupinate forms are plesiomorphic, 2) pileate-stipitate forms promote diversification, 3) the evolution of gasteroid forms is irreversible, 4) the ectomycorrhizal (ECM) symbiosis promotes diversification, and 5) the evolution of ECM symbiosis is irreversible. The ancestor of Agaricomycetes was a saprotroph with a resupinate fruiting body. There have been 462 transitions in the examined morphologies, including 123 origins of gasteroid forms. Reversals of gasteroid forms are highly unlikely but cannot be rejected. Pileate-stipitate forms are correlated with elevated diversification rates, suggesting that this morphological trait is a key to the success of Agaricomycetes. ECM symbioses have evolved 36 times in Agaricomycetes, with several transformations to parasitism. Across the entire 8,400-species phylogeny, diversification rates of ectomycorrhizal lineages are no greater than those of saprotrophic lineages. However, some ECM lineages have elevated diversification rates compared to their non-ECM sister clades, suggesting that the evolution of symbioses may act as a key innovation at local phylogenetic scales.
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Affiliation(s)
- Marisol Sánchez-García
- Biology Department, Clark University, Worcester, MA 01610
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75005 Uppsala, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
| | - Faheema Kalsoom Khan
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, Sweden
| | - Torda Varga
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, 6726 Szeged, Hungary
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, 6726 Szeged, Hungary
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21
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Machine learning approaches identify male body size as the most accurate predictor of species richness. BMC Biol 2020; 18:105. [PMID: 32854698 PMCID: PMC7453550 DOI: 10.1186/s12915-020-00835-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera. RESULTS We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness. CONCLUSIONS We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.
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22
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Modica MV, Gorson J, Fedosov AE, Malcolm G, Terryn Y, Puillandre N, Holford M. Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification. Syst Biol 2020; 69:413-430. [PMID: 31504987 PMCID: PMC7164365 DOI: 10.1093/sysbio/syz059] [Citation(s) in RCA: 8] [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] [Received: 11/09/2018] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- UMR5247, Université de Montpellier CC 1703, Place Eugène Bataillon 34095 Montpellier, France
| | - Juliette Gorson
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
| | - Alexander E Fedosov
- Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, 33, Moscow 119071, Russia
| | - Gavin Malcolm
- Bird Hill, Barnes Lane, Milford on Sea, Hampshire, UK
| | - Yves Terryn
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
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Musher LJ, Ferreira M, Auerbach AL, McKay J, Cracraft J. Why is Amazonia a 'source' of biodiversity? Climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae). Proc Biol Sci 2020; 286:20182343. [PMID: 30940057 DOI: 10.1098/rspb.2018.2343] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Amazonia is a 'source' of biodiversity for other Neotropical ecosystems, but which conditions trigger in situ speciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally mediated corridors facilitated emigration and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.
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Affiliation(s)
- Lukas J Musher
- 1 Department of Ornithology, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA.,2 The Richard Gilder Graduate School, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA
| | - Mateus Ferreira
- 3 Programa Pós-Graduação em Genética, Conservação e Biologia Evolutiva, INPA , Manaus, AM , Brazil
| | - Anya L Auerbach
- 4 Department of Biological Sciences Collegiate Division, University of Chicago , 1101 East 57th Street, Chicago, IL 60637 , USA
| | - Jessica McKay
- 1 Department of Ornithology, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA
| | - Joel Cracraft
- 1 Department of Ornithology, American Museum of Natural History , Central Park West @ 79th Street, New York, NY 10024 , USA
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Phillips AG, Töpfer T, Böhning-Gaese K, Fritz SA. Rates of ecomorphological trait evolution in passerine bird clades are independent of age. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Although the links between species richness and diversification rates with clade age have been studied extensively, few studies have investigated the relationship between the rates of trait evolution and clade age. The rate of morphological trait evolution has repeatedly been shown to vary through time, as expected, for example, for adaptive radiations, but the strength and sources of this variation are not well understood. We compare the relationship between the rates of trait evolution and clade age across eight monophyletic clades of passerine birds by investigating ecomorphological traits, i.e. morphological traits that influence the ecology of the species directly. We study the ecomorphological divergence pattern using analyses of the disparity through time and determine the best-fitting model of evolution for each trait in each clade. We find no support for a consistent dependence of evolutionary rates on clade age across wing, tail, tarsus and beak shape in our eight clades and also show that early burst models of trait evolution are rarely the best-fitting models within these clades. These results suggest that key innovations or adaptive radiations might be less common evolutionary patterns and processes than generally thought or might depend on the taxonomic level investigated.
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Affiliation(s)
- Anna G Phillips
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Till Töpfer
- Zoological Research Museum Alexander Koenig (ZFMK), Section Ornithology, Bonn, Germany
| | - Katrin Böhning-Gaese
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
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25
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Huang XC, German DA, Koch MA. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. ANNALS OF BOTANY 2020; 125:29-47. [PMID: 31314080 PMCID: PMC6948214 DOI: 10.1093/aob/mcz123] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/16/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. METHODS We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. KEY RESULTS Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. CONCLUSIONS The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
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Affiliation(s)
- Xiao-Chen Huang
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
- For correspondence. E-mail
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26
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Reply to Wiens and Scholl: The time dependency of diversification rates is a widely observed phenomenon. Proc Natl Acad Sci U S A 2019; 116:24401. [PMID: 31719200 DOI: 10.1073/pnas.1917189116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Janicke T, Marie-Orleach L, Aubier TG, Perrier C, Morrow EH. Assortative Mating in Animals and Its Role for Speciation. Am Nat 2019; 194:865-875. [PMID: 31738105 DOI: 10.1086/705825] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Evolutionary theory predicts that positive assortative mating-the tendency of similar individuals to mate with each other-plays a key role for speciation by generating reproductive isolation between diverging populations. However, comprehensive tests for an effect of assortative mating on species richness at the macroevolutionary scale are lacking. We used a meta-analytic approach to test the hypothesis that the strength of assortative mating within populations is positively related to species richness across a broad range of animal taxa. Specifically, we ran a phylogenetically independent meta-analysis using an extensive database of 1,447 effect sizes for the strength of assortative mating, encompassing 307 species from 130 families and 14 classes. Our results suggest that there is no relationship between the strength of assortative mating and species richness across and within major taxonomic groups and trait categories. Moreover, our analysis confirms an earlier finding that animals typically mate assortatively (global Pearson correlation coefficient: r=0.36; 95% confidence interval: 0.19-0.52) when accounting for phylogenetic nonindependence. We argue that future advances will rely on a better understanding of the evolutionary causes and consequences of the observed intra- and interspecific variation in the strength of assortative mating.
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28
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Li H, Wiens JJ. Time Explains Regional Richness Patterns within Clades More Often than Diversification Rates or Area. Am Nat 2019; 193:514-529. [DOI: 10.1086/702253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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29
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Soltis PS, Folk RA, Soltis DE. Darwin review: angiosperm phylogeny and evolutionary radiations. Proc Biol Sci 2019; 286:20190099. [PMCID: PMC6452062 DOI: 10.1098/rspb.2019.0099] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/05/2019] [Indexed: 08/17/2023] Open
Abstract
Darwin's dual interests in evolution and plants formed the basis of evolutionary botany, a field that developed following his publications on both topics. Here, we review his many contributions to plant biology—from the evolutionary origins of angiosperms to plant reproduction, carnivory, and movement—and note that he expected one day there would be a ‘true’ genealogical tree for plants. This view fuelled the field of plant phylogenetics. With perhaps nearly 400 000 species, the angiosperms have diversified rapidly since their origin in the Early Cretaceous, often through what appear to be rapid radiations. We describe these evolutionary patterns, evaluate possible drivers of radiations, consider how new approaches to studies of diversification can contribute to our understanding of angiosperm diversity, and suggest new directions for further insight into plant evolution.
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Affiliation(s)
- Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Ryan A. Folk
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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30
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Abstract
For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and describe a hidden generality among these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law in which both depend on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time dependency is unlikely to be a result of simple statistical artifacts. As such, this time scaling is likely a genuine feature of the tree of life, hinting that the dynamics of biodiversity over deep time may be driven in part by surprisingly simple and general principles.
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31
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Crouch NMA, Ricklefs RE. Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds. Am Nat 2019; 193:E78-E91. [PMID: 30912971 DOI: 10.1086/701630] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, then lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades but that rates of morphological evolution are decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space and not just overall ecological opportunity.
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32
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Moharrek F, Sanmartín I, Kazempour-Osaloo S, Nieto Feliner G. Morphological Innovations and Vast Extensions of Mountain Habitats Triggered Rapid Diversification Within the Species-Rich Irano-Turanian Genus Acantholimon (Plumbaginaceae). Front Genet 2019; 9:698. [PMID: 30745908 PMCID: PMC6360523 DOI: 10.3389/fgene.2018.00698] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/12/2018] [Indexed: 01/24/2023] Open
Abstract
The Irano-Turanian floristic region spans a topographically complex and climatically continental territory, which has served as a source of xerophytic taxa for neighboring regions and is represented by a high percent of endemics. Yet, a comprehensive picture of the abiotic and biotic factors that have driven diversification within this biota remains to be established due to the scarcity of phylogenetic studies. Acantholimon is an important component of the subalpine steppe flora of the Irano-Turanian region, containing c. 200 cushion-forming sub-shrubby pungent-leaved species. Our recent molecular phylogenetic study has led to enlarging the circumscription of this genus to include eight mono- or oligospecific genera lacking the characteristic life-form and leaves. Using the same molecular phylogeny, here we investigate the tempo and mode of diversification as well as the biogeographic patterns in this genus, to test the hypothesis that a combination of key morphological innovations and abiotic factors is behind Acantholimon high species diversity. Molecular dating analysis indicates that Acantholimon s.l. started to diversify between the Late Miocene and the Pliocene and the biogeographic analysis points to an Eastern Iran-Afghanistan origin. Macroevolutionary models support the hypothesis that the high diversity of the genus is explained by accelerated diversification rates in two clades associated with the appearance of morphological key innovations such as a cushion life-form and pungent leaves; this would have favored the colonization of water-stressed, substrate-poor mountainous habitats along the newly uplifted IT mountains during the Mio-Pliocene. Given the apparent similarity of mountain habitats for most species of Acantholimon, we hypothesize that its current high species diversity responds to a scenario of non-adaptive radiation fueled by allopatric speciation rather than evolutionary radiation driven by ecological opportunity. Similar scenarios might underlie the high diversity of other speciose genera in the topographically complex Irano-Turanian landscape, though this remains to be tested with fine-grained distribution and climatic data.
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Affiliation(s)
- Farideh Moharrek
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Isabel Sanmartín
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Madrid, Spain
| | - Shahrokh Kazempour-Osaloo
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Madrid, Spain
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33
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Sclavi B, Herrick J. Genome size variation and species diversity in salamanders. J Evol Biol 2019; 32:278-286. [DOI: 10.1111/jeb.13412] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/14/2018] [Accepted: 12/20/2018] [Indexed: 12/13/2022]
Affiliation(s)
| | - John Herrick
- Department of Physics; Simon Fraser University; Burnaby British Columbia Canada
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34
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Lu HP, Yeh YC, Shiah FK, Gong GC, Hsieh CH. Evolutionary constraints on species diversity in marine bacterioplankton communities. ISME JOURNAL 2019; 13:1032-1041. [PMID: 30607025 DOI: 10.1038/s41396-018-0336-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 07/23/2018] [Accepted: 12/11/2018] [Indexed: 01/14/2023]
Abstract
Variation in microbial species diversity has typically been explained as the outcome of local ecological factors driving species coexistence, overlooking the roles of evolutionary constraints. Here, we argue that macro-evolutionary niche conservatism and unequal diversification rates among phylum-level lineages are strong determinants of diversity-environment relationships in bacterial systems. That is, apart from stochasticity, environmental effects operate most strongly on phylum composition, which in turn dictates the species diversity of bacterial communities. This concept is demonstrated using bacterioplankton in the surface seawaters of the East China Sea. Furthermore, we show that the species richness of a local bacterioplankton community can generally be estimated based on the relative abundances of phyla and their contributions of species numbers in the global seawater pool-highlighting the important influence of evolutionary constraints on local community diversity.
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Affiliation(s)
- Hsiao-Pei Lu
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Yi-Chun Yeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Fuh-Kwo Shiah
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.,Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Gwo-Ching Gong
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan. .,Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan. .,Department of Life Science, Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan. .,National Center for Theoretical Sciences, Taipei, Taiwan.
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35
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Marin J, Rapacciuolo G, Costa GC, Graham CH, Brooks TM, Young BE, Radeloff VC, Behm JE, Helmus MR, Hedges SB. Evolutionary time drives global tetrapod diversity. Proc Biol Sci 2019; 285:rspb.2017.2378. [PMID: 29436494 DOI: 10.1098/rspb.2017.2378] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/17/2018] [Indexed: 11/12/2022] Open
Abstract
Global variation in species richness is widely recognized, but the explanation for what drives it continues to be debated. Previous efforts have focused on a subset of potential drivers, including evolutionary rate, evolutionary time (maximum clade age of species restricted to a region), dispersal (migration from one region to another), ecological factors and climatic stability. However, no study has evaluated these competing hypotheses simultaneously at a broad spatial scale. Here, we examine their relative contribution in determining the richness of the most comprehensive dataset of tetrapods to our knowledge (84% of the described species), distinguishing between the direct influences of evolutionary rate, evolutionary time and dispersal, and the indirect influences of ecological factors and climatic stability through their effect on direct factors. We found that evolutionary time exerted a primary influence on species richness, with evolutionary rate being of secondary importance. By contrast, dispersal did not significantly affect richness patterns. Ecological and climatic stability factors influenced species richness indirectly by modifying evolutionary time (i.e. persistence time) and rate. Overall, our findings suggest that global heterogeneity in tetrapod richness is explained primarily by the length of time species have had to diversify.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA .,Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum national d'Histoire naturelle, Sorbonne-Universités, 75231 Paris Cedex 05, France
| | - Giovanni Rapacciuolo
- Life and Environmental Sciences, University of California Merced, 5200 N Lake Road, Merced, CA 95340, USA.,NatureServe, 4600 N. Fairfax Drive, 7th Floor, Arlington, VA 22203, USA
| | - Gabriel C Costa
- Department of Biology, Auburn University at Montgomery, Montgomery, AL 36124, USA
| | - Catherine H Graham
- Swiss Federal Institute for Forest Snow and Landscape, Birmensdorf, Switzerland
| | - Thomas M Brooks
- International Union for Conservation of Nature, Gland, Switzerland.,World Agroforestry Center (ICRAF), University of the Philippines Los Baños, Laguna 4031, Philippines.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Bruce E Young
- NatureServe, 4600 N. Fairfax Drive, 7th Floor, Arlington, VA 22203, USA
| | - Volker C Radeloff
- SILVIS Lab, Department of Forestry and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jocelyn E Behm
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA.,Department of Animal Ecology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Matthew R Helmus
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA
| | - S Blair Hedges
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA
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36
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Eberle J, Dimitrov D, Valdez-Mondragón A, Huber BA. Microhabitat change drives diversification in pholcid spiders. BMC Evol Biol 2018; 18:141. [PMID: 30231864 PMCID: PMC6145181 DOI: 10.1186/s12862-018-1244-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/16/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera. RESULTS Assessments of ancestral microhabitat revealed frequent evolutionary change. In particular, within the largest subfamily Pholcinae, numerous changes from near-ground habitats towards leaves and back were found. In general, taxa occupying leaves and large sheltered spaces had higher diversification rates than ground-dwelling taxa. Shifts in speciation rate were found in leaf- and space-dwelling taxa. CONCLUSIONS Our analyses result in one of the most comprehensive phylogenies available for a major spider family and provide a framework for any subsequent studies of pholcid spider biology. Diversification analyses strongly suggest that microhabitat is an important factor influencing diversification patterns in pholcid spiders.
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Affiliation(s)
- Jonas Eberle
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
| | - Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
- Department of Natural History, University Museum of Bergen, University of Bergen, PO Box 7800, NO-5020 Bergen, Norway
| | - Alejandro Valdez-Mondragón
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
- Instituto de Biologia UNAM, sede Tlaxcala. Contiguo FES-Zaragoza Campus III, Ex Fábrica San Manuel de Morcom s/n, San Miguel Contla, Municipio de Santa Cruz Tlaxcala, C.P, 90640 Tlaxcala, Mexico
| | - Bernhard A. Huber
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
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37
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Foster KL, Piller KR. Disentangling the drivers of diversification in an imperiled group of freshwater fishes (Cyprinodontiformes: Goodeidae). BMC Evol Biol 2018; 18:116. [PMID: 30021522 PMCID: PMC6052539 DOI: 10.1186/s12862-018-1220-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/20/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND One of the most perplexing questions in evolutionary biology is why some lineages diversify into many species, and others do not. In many cases, ecological opportunity has played an important role, leading to diversification along trophic or habitat-based axes. The Goodeidae (Teleostomi: Cyprinodontiformes) are a family of freshwater fishes with two subfamilies: Goodeinae (42 species, viviparous, heterogeneous habitats, Mesa Central of Mexico) and Empetrichthyinae (4 species, oviparous, homogeneous habitats, Great Basin of the United States). These discrepant sets of characteristics and their sister-group relationship make the goodeids amenable to a comparative study of diversification. We gathered lateral body images from more than 1600 specimens of all extant species in the family. Geometric morphometric, and phylogenetic comparative analyses were used to address whether higher species diversity correlates with higher rates of morphological shape evolution and whether there are differences in functional/habitat modules between the two subfamilies. RESULTS This study recovered a higher rate of overall body shape evolution in the Goodeinae that is nearly double in magnitude compared to the Empetrichthyinae. A modularity test indicated that the Goodeinae displayed elevated rates of morphological evolution in comparison to the Empetrichthyinae when only trunk (locomotor) regions were compared between subfamilies. No significant differences in evolutionary shape rates were recovered when the trophic (head) regions were compared between subfamilies. DISCUSSION These results support the hypothesis that Mexican goodeids radiated via an ecological opportunity scenario into a wide-array of novel habitats in the island-like Mesa Central as evidenced by their high rate of shape evolution, relative to the Empetrichthyinae. This study quantitatively unraveled the drivers of evolution and eliminated trophic specialization as a driving force within the Goodeidae. CONCLUSIONS A combination of phylogenetic and morphometric data, and phylogenetic comparative analyses were used to examine body shape rate evolution within the Goodeidae. Results support the hypothesis that species in the subfamily Goodeinae on the central Mexican plateau had a higher rate of body shape evolution relative to its sister subfamily Empetrichthyinae in the Great Basin suggesting that the Goodeinae diversified via an ecological opportunity scenario along habitat, rather than trophic axes.
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Affiliation(s)
- Kimberly L. Foster
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402 USA
- Present Address: Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008-5410 USA
| | - Kyle R. Piller
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402 USA
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Ricci M, Peona V, Guichard E, Taccioli C, Boattini A. Transposable Elements Activity is Positively Related to Rate of Speciation in Mammals. J Mol Evol 2018; 86:303-310. [PMID: 29855654 PMCID: PMC6028844 DOI: 10.1007/s00239-018-9847-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 05/24/2018] [Indexed: 02/05/2023]
Abstract
Transposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Speciation and TE activity bursts could be strongly related in mammals, in which simple gradualistic models of differentiation do not account for the currently observed species variability. In order to test this hypothesis, we designed two parameters: the Density of insertion (DI) and the Relative rate of speciation (RRS). DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts. Thus, by analyzing TE insertions in mammals, we defined the genomes as “hot” (high DI) and “cold” (low DI). Then, comparing TE activity among 29 taxonomical families of the whole Mammalia class, 16 intra-order pairs of mammalian species, and four superorders of Eutheria, we showed that taxa with high rates of speciation are associated with “hot” genomes, whereas taxa with low ones are associated with “cold” genomes. These results suggest a remarkable correlation between TE activity and speciation, also being consistent with patterns describing variable rates of differentiation and accounting for the different time frames of the speciation bursts.
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Affiliation(s)
- Marco Ricci
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
| | - Valentina Peona
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Ecology and Genetics, University of Uppsala, Uppsala, Sweden
| | - Etienne Guichard
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
| | - Cristian Taccioli
- Department of Animal Medicine, Health and Production, University of Padova, Padova, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
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Rajeh A, Lv J, Lin Z. Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota. BMC Genomics 2018; 19:282. [PMID: 29690866 PMCID: PMC5937819 DOI: 10.1186/s12864-018-4683-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 01/06/2023] Open
Abstract
Background Chromosomal rearrangements have been shown to facilitate speciation through creating a barrier of gene flow. However, it is not known whether heterogeneous rates of chromosomal rearrangement at the genome scale contributed to the huge disparity of species richness among different groups of organisms, which is one of the most remarkable and pervasive patterns on Earth. The largest fungal phylum Ascomycota is an ideal study system to address this question because it comprises three subphyla (Saccharomycotina, Taphrinomycotina, and Pezizomycotina) whose species numbers differ by two orders of magnitude (59,000, 1000, and 150 respectively). Results We quantified rates of genome rearrangement for 71 Ascomycota species that have well-assembled genomes. The rates of inter-species genome rearrangement, which were inferred based on the divergence rates of gene order, are positively correlated with species richness at both ranks of subphylum and class in Ascomycota. This finding is further supported by our quantification of intra-species rearrangement rates based on paired-end genome sequencing data of 216 strains from three representative species, suggesting a difference of intrinsic genome instability among Ascomycota lineages. Our data also show that different rates of imbalanced rearrangements, such as deletions, are a major contributor to the heterogenous rearrangement rates. Conclusions Various lines of evidence in this study support that a higher rate of rearrangement at the genome scale might have accelerated the speciation process and increased species richness during the evolution of Ascomycota species. Our findings provide a plausible explanation for the species disparity among Ascomycota lineages, which will be valuable to unravel the underlying causes for the huge disparity of species richness in various taxonomic groups. Electronic supplementary material The online version of this article (10.1186/s12864-018-4683-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahmad Rajeh
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.,Department of Computer Science, Saint Louis University, St. Louis, MO, 63103, USA
| | - Jie Lv
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.
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Ecological opportunity may facilitate diversification in Palearctic freshwater organisms: a case study on hydrobiid gastropods. BMC Evol Biol 2018; 18:55. [PMID: 29673313 PMCID: PMC5907725 DOI: 10.1186/s12862-018-1169-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/27/2018] [Indexed: 11/23/2022] Open
Abstract
Background Differences in species richness among phylogenetic clades are attributed to clade age and/or variation in diversification rates. Access to ecological opportunity may trigger a temporary increase in diversification rates and ecomorphological variation. In addition, lower body temperatures in poikilothermic animals may result in decreasing speciation rates as proposed by the metabolic theory of ecology. For strictly freshwater organisms, environmental gradients within a river continuum, linked to elevation and temperature, might promote access to ecological opportunity and alter metabolic rates, eventually influencing speciation and extinction processes. To test these hypotheses, we investigated the influence of environmental temperature and elevation, as proxies for body temperature and ecological opportunity, respectively, on speciation rates and ecomorphological divergence. As model systems served two closely related gastropod genera with unequal species richness and habitat preferences – Pseudamnicola and Corrosella. Results Lineage-through-time plots and Bayesian macroevolutionary modeling evidenced that Pseudamnicola species, which typically live in lower reaches of rivers, displayed significantly elevated speciation rates in comparison to the ‘headwater genus’ Corrosella. Moreover, state-dependent speciation models suggested that the speciation rate increased with decreasing elevation, supporting the ecological opportunity hypothesis. In contrast, a significant effect of environmental temperature, as proposed by the metabolic theory of ecology, could not be observed. Disparity-through-time plots, models of ecomorphological evolution, and ancestral habitat estimation showed for Pseudamnicola species rapid morphological divergence shortly after periods of elevational and habitat divergence. In contrast, Corrosella species did not deviate from null models of drift-like evolution. Conclusion Our finding that speciation rates are correlated with elevation and ecomorphological disparity but not with environmental temperatures suggests that differences in ecological opportunity may have played a key role in Corrosella and Pseudamnicola diversifications. We propose that Pseudamnicola lineages experienced higher ecological opportunity through dispersal to new locations or habitats in lowlands, which may explain the increase in speciation rates and morphological change. In contrast, the evolution of Corrosella in headwaters is likely less facilitated by the environment and more by non-ecological processes. Electronic supplementary material The online version of this article (10.1186/s12862-018-1169-2) contains supplementary material, which is available to authorized users.
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41
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Maliet O, Gascuel F, Lambert A. Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity. Syst Biol 2018; 67:1025-1040. [DOI: 10.1093/sysbio/syy030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/08/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Odile Maliet
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
| | - Fanny Gascuel
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS, Paris, France
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Cyriac VP, Kodandaramaiah U. Digging their own macroevolutionary grave: fossoriality as an evolutionary dead end in snakes. J Evol Biol 2018; 31:587-598. [DOI: 10.1111/jeb.13248] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023]
Affiliation(s)
- V. P. Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology; Indian Institute of Science Education and Research Thiruvananthapuram; Thiruvananthapuram India
| | - U. Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology; Indian Institute of Science Education and Research Thiruvananthapuram; Thiruvananthapuram India
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Goldenberg J, Cipriani V, Jackson TNW, Arbuckle K, Debono J, Dashevsky D, Panagides N, Ikonomopoulou MP, Koludarov I, Li B, Santana RC, Nouwens A, Jones A, Hay C, Dunstan N, Allen L, Bush B, Miles JJ, Ge L, Kwok HF, Fry BG. Proteomic and functional variation within black snake venoms (Elapidae: Pseudechis). Comp Biochem Physiol C Toxicol Pharmacol 2018; 205:53-61. [PMID: 29353015 DOI: 10.1016/j.cbpc.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/03/2018] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
Abstract
Pseudechis (black snakes) is an Australasian elapid snake genus that inhabits much of mainland Australia, with two representatives confined to Papua New Guinea. The present study is the first to analyse the venom of all 9 described Pseudechis species (plus one undescribed species) to investigate the evolution of venom composition and functional activity. Proteomic results demonstrated that the typical Pseudechis venom profile is dominated by phospholipase A2 toxins. Strong cytotoxicity was the dominant function for most species. P. porphyriacus, the most basal member of the genus, also exhibited the most divergent venom composition, being the only species with appreciable amounts of procoagulant toxins. The relatively high presence of factor Xa recovered in P. porphyriacus venom may be related to a predominantly amphibian diet. Results of this study provide important insights to guide future ecological and toxinological investigations.
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Affiliation(s)
- Jonathan Goldenberg
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia; Evolution and Optics of Nanostructures Group, Department of Biology, University of Ghent, Ledeganckstraat 35, Ghent 9000, Belgium
| | - Vittoria Cipriani
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Timothy N W Jackson
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia; Australian Venom Research Unit, Department of Pharmacology, University of Melbourne, Parkville, VIC 3000, Australia
| | - Kevin Arbuckle
- Department of Biosciences, College of Science, Swansea University, Swansea SA2, 8PP, UK
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Daniel Dashevsky
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Nadya Panagides
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Maria P Ikonomopoulou
- QIMR Berghofer Institute of Medical Research, Herston, QLD 4049, Australia; School of Medicine, The University of Queensland, Herston, QLD 4002, Australia; Madrid Institute for Advanced Studies (IMDEA) in Food, CEI UAM+CSIC, Madrid 28049, Spain
| | - Ivan Koludarov
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Bin Li
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China
| | - Renan Castro Santana
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - Alun Jones
- Institute for Molecular Biosciences, University of Queensland, Slt Lucia, QLD 4072, Australia
| | - Chris Hay
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia
| | | | - Luke Allen
- Venom Supplies, Tanunda, SA 5352, Australia
| | - Brian Bush
- Snakes Harmful & Harmless, 9 Birch Place, Stoneville, WA 6081, Australia
| | - John J Miles
- QIMR Berghofer Institute of Medical Research, Herston, QLD 4049, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Lilin Ge
- School of Pharmacy, Nanjing University of Chinese Medicine, Qixia District, Nanjing, China
| | - Hang Fai Kwok
- Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, China.
| | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St Lucia, QLD 4072, Australia.
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Title PO, Rabosky DL. Do Macrophylogenies Yield Stable Macroevolutionary Inferences? An Example from Squamate Reptiles. Syst Biol 2018; 66:843-856. [PMID: 27821703 DOI: 10.1093/sysbio/syw102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 10/27/2016] [Indexed: 01/03/2023] Open
Abstract
Advances in the generation, retrieval, and analysis of phylogenetic data have enabled researchers to create phylogenies that contain many thousands of taxa. These "macrophylogenies"-large trees that typically derive from megaphylogeny, supermatrix, or supertree approaches-provide researchers with an unprecedented ability to conduct evolutionary analyses across broad phylogenetic scales. Many studies have now used these phylogenies to explore the dynamics of speciation, extinction, and phenotypic evolution across large swaths of the tree of life. These trees are characterized by substantial phylogenetic uncertainty on multiple levels, and the stability of macroevolutionary inferences from these data sets has not been rigorously explored. As a case study, we tested whether five recently published phylogenies for squamate reptiles-each consisting of more than 4000 species-yield congruent inferences about the processes that underlie variation in species richness across replicate evolutionary radiations of Australian snakes and lizards. We find discordance across the five focal phylogenies with respect to clade age and several diversification rate metrics, and in the effects of clade age on species richness. We also find that crown clade ages reported in the literature on these Australian groups are in conflict with all of the large phylogenies examined. Macrophylogenies offer an unprecedented opportunity to address evolutionary and ecological questions at broad phylogenetic scales, but accurately representing the uncertainty that is inherent to such analyses remains a critical challenge to our field. [Australia; macroevolution; macrophylogeny; squamates; time calibration.].
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Affiliation(s)
- Pascal O Title
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI 48109, USA
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Sánchez-Reyes LL, Morlon H, Magallón S. Uncovering Higher-Taxon Diversification Dynamics from Clade Age and Species-Richness Data. Syst Biol 2018; 66:367-378. [PMID: 28003532 DOI: 10.1093/sysbio/syw088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
Abstract
The relationship between clade age and species richness has been increasingly used in macroevolutionary studies as evidence for ecologically versus time-dependent diversification processes. However, theory suggests that phylogenetic structure, age type (crown or stem age), and taxonomic delimitation can affect estimates of the age-richness correlation (ARC) considerably. We currently lack an integrative understanding of how these different factors affect ARCs, which in turn, obscures further interpretations. To assess its informative breadth, we characterize ARC behavior with simulated and empirical phylogenies, considering phylogenetic structure and both crown and stem ages. First, we develop a two-state birth-death model to simulate phylogenies including the origin of higher taxa and a hierarchical taxonomy to determine ARC expectations under ecologically and time-dependent diversification processes. Then, we estimate ARCs across various taxonomic ranks of extant amphibians, squamate reptiles, mammals, birds, and flowering plants. We find that our model reproduces the general ARC trends of a wide range of biological systems despite the particularities of taxonomic practice within each, suggesting that the model is adequate to establish a framework of ARC null expectations for different diversification processes when taxa are defined with a hierarchical taxonomy. ARCs estimated with crown ages were positive in all the scenarios we studied, including ecologically dependent processes. Negative ARCs were only found at less inclusive taxonomic ranks, when considering stem age, and when rates varied among clades. This was the case both in ecologically and time-dependent processes. Together, our results warn against direct interpretations of single ARC estimates and advocate for a more integrative use of ARCs across age types and taxonomic ranks in diversification studies. [Birth-Death models; crown age; diversity dependence; extinction; phylogenetic structure; speciation; stem age; taxonomy; time dependence; tree simulations.].
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Affiliation(s)
- Luna L Sánchez-Reyes
- Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México.,Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, Ciudad de México 04510, México
| | - Hélène Morlon
- École Normale Supérieure, UMR 8197 CNRS, 46 rue d'Ulm, 75005, Paris, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito de Ciudad Universitaria, Coyoacán, Ciudad de México 04510, México
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46
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Scholl JP, Wiens JJ. Diversification rates and species richness across the Tree of Life. Proc Biol Sci 2017; 283:rspb.2016.1334. [PMID: 27605507 DOI: 10.1098/rspb.2016.1334] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/12/2016] [Indexed: 11/12/2022] Open
Abstract
Species richness varies dramatically among clades across the Tree of Life, by over a million-fold in some cases (e.g. placozoans versus arthropods). Two major explanations for differences in richness among clades are the clade-age hypothesis (i.e. species-rich clades are older) and the diversification-rate hypothesis (i.e. species-rich clades diversify more rapidly, where diversification rate is the net balance of speciation and extinction over time). Here, we examine patterns of variation in diversification rates across the Tree of Life. We address how rates vary across higher taxa, whether rates within higher taxa are related to the subclades within them, and how diversification rates of clades are related to their species richness. We find substantial variation in diversification rates, with rates in plants nearly twice as high as in animals, and rates in some eukaryotes approximately 10-fold faster than prokaryotes. Rates for each kingdom-level clade are then significantly related to the subclades within them. Although caution is needed when interpreting relationships between diversification rates and richness, a positive relationship between the two is not inevitable. We find that variation in diversification rates seems to explain most variation in richness among clades across the Tree of Life, in contrast to the conclusions of previous studies.
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Affiliation(s)
- Joshua P Scholl
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721-0088, USA
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47
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Cunha RL, Patrão C, Castilho R. Different diversity-dependent declines in speciation rate unbalances species richness in terrestrial slugs. Sci Rep 2017; 7:16198. [PMID: 29170460 PMCID: PMC5700933 DOI: 10.1038/s41598-017-16417-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/09/2017] [Indexed: 11/14/2022] Open
Abstract
Two genera of terrestrial slugs (Arion and Geomalacus) display a striking disproportion in species richness in the Iberian Peninsula. While there are 17 Iberian endemic species in Arion, morphological criteria only recognize four species within Geomalacus. Sequence data were used to test whether these differences could result from: (1) cryptic diversity within Geomalacus; (2) an earlier origin for Arion (older clades are expected to accumulate more species); (3) distinct patterns of diversification rates (higher initial speciation rates in Arion), and (4) some combination of the above factors (e.g., an older clade with higher speciation rates). Species delimitation tests based on mitochondrial and nuclear data revealed eight cryptic lineages within Geomalacus that lessened the asymmetry; nevertheless, the disparity required further investigation. No meaningful differences in crown group ages of each recovered clade were found. Regardless the different premises of the two equally plausible diversification models (similar initial speciation rates vs. higher initial speciation rates in Geomalacus), both coincide on diversity-dependent diversification for the two groups but weaker rate declines in Arion best explains the observed asymmetry in species richness. Also, the broader environmental tolerance combined with a faster dispersal and wider distribution may have represented an evolutionary advantage for Arion.
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Affiliation(s)
- Regina L Cunha
- CCMAR (Centre of Marine Sciences) - Campus de Gambelas, Universidade do Algarve, 8005-139, Faro, Portugal.
| | - Cláudia Patrão
- CCMAR (Centre of Marine Sciences) - Campus de Gambelas, Universidade do Algarve, 8005-139, Faro, Portugal
| | - Rita Castilho
- CCMAR (Centre of Marine Sciences) - Campus de Gambelas, Universidade do Algarve, 8005-139, Faro, Portugal
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48
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Jønsson KA, Borregaard MK, Carstensen DW, Hansen LA, Kennedy JD, Machac A, Marki PZ, Fjeldså J, Rahbek C. Biogeography and Biotic Assembly of Indo-Pacific Corvoid Passerine Birds. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022813] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Knud Andreas Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Michael Krabbe Borregaard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Daniel Wisbech Carstensen
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Louis A. Hansen
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Jonathan D. Kennedy
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Antonin Machac
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Petter Zahl Marki
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
- Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;, ,
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
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49
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Burress ED, Tan M. Ecological opportunity alters the timing and shape of adaptive radiation. Evolution 2017; 71:2650-2660. [PMID: 28895124 DOI: 10.1111/evo.13362] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/18/2017] [Accepted: 08/27/2017] [Indexed: 12/14/2022]
Abstract
The uneven distribution of diversity is a conspicuous phenomenon across the tree of life. Ecological opportunity is a prominent catalyst of adaptive radiation and therefore may alter patterns of diversification. We evaluated the distribution of shifts in diversification rates across the cichlid phylogeny and the distribution of major clades across phylogenetic space. We also tested if ecological opportunity influenced these patterns. Colonization-associated ecological opportunity altered the tempo and mode of diversification during the adaptive radiation of cichlid fishes. Clades that arose following colonization events diversified faster than other clades. Speciation rate shifts were nonrandomly distributed across the phylogeny such that they were disproportionally concentrated around nodes that corresponded with colonization events (i.e., of continents, river basins, or lakes). Young clades tend to expand faster than older clades; however, colonization-associated ecological opportunity accentuated this pattern. There was an interaction between clade age and ecological opportunity that explained the trajectory of clades through phylogenetic space over time. Our results indicate that ecological opportunities afforded by continental and ecosystem-scale colonization events explain the dramatic speciation rate heterogeneity and phylogenetic imbalance that arose during the evolutionary history of cichlid fishes.
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Affiliation(s)
- Edward D Burress
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama
| | - Milton Tan
- Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia
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50
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Herrera JP. Primate diversification inferred from phylogenies and fossils. Evolution 2017; 71:2845-2857. [PMID: 28913907 DOI: 10.1111/evo.13366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/07/2017] [Accepted: 09/10/2017] [Indexed: 02/06/2023]
Abstract
Biodiversity arises from the balance between speciation and extinction. Fossils record the origins and disappearance of organisms, and the branching patterns of molecular phylogenies allow estimation of speciation and extinction rates, but the patterns of diversification are frequently incongruent between these two data sources. I tested two hypotheses about the diversification of primates based on ∼600 fossil species and 90% complete phylogenies of living species: (1) diversification rates increased through time; (2) a significant extinction event occurred in the Oligocene. Consistent with the first hypothesis, analyses of phylogenies supported increasing speciation rates and negligible extinction rates. In contrast, fossils showed that while speciation rates increased, speciation and extinction rates tended to be nearly equal, resulting in zero net diversification. Partially supporting the second hypothesis, the fossil data recorded a clear pattern of diversity decline in the Oligocene, although diversification rates were near zero. The phylogeny supported increased extinction ∼34 Ma, but also elevated extinction ∼10 Ma, coinciding with diversity declines in some fossil clades. The results demonstrated that estimates of speciation and extinction ignoring fossils are insufficient to infer diversification and information on extinct lineages should be incorporated into phylogenetic analyses.
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Affiliation(s)
- James P Herrera
- Richard Gilder Graduate School, Department of Mammalogy and Division of Vertebrate Paleontology, American Museum of Natural History, New York, New York 10024.,Department of Mammalogy, American Museum of Natural History, New York, New York 10024
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