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Revell LJ. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 2024; 12:e16505. [PMID: 38192598 PMCID: PMC10773453 DOI: 10.7717/peerj.16505] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 10/31/2023] [Indexed: 01/10/2024] Open
Abstract
Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.
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Affiliation(s)
- Liam J. Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA
- Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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Brignone NF, Pozner R, Denham SS. Macroevolutionary trends and diversification dynamics in Atripliceae (Amaranthaceae s.l., Chenopodioideae): a first approach. ANNALS OF BOTANY 2022; 130:199-214. [PMID: 35737947 PMCID: PMC9445597 DOI: 10.1093/aob/mcac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Atripliceae evolved and diversified by dispersals and radiations across continents in both hemispheres, colonizing similar semi-arid, saline-alkaline environments throughout the world. Meanwhile, its species developed different life forms, photosynthetic pathways, mono- or dioecy, and different morphological features in flowers, fruiting bracteoles and seeds. In this study, we introduce a first approach to the macroevolutionary patterns and diversification dynamics of the Atripliceae to understand how time, traits, speciation, extinction and new habitats influenced the evolution of this lineage. METHODS We performed molecular phylogenetic analyses and clade age estimation of Atripliceae to apply time-, trait- and geographic-dependent diversification analyses and ancestral state reconstructions to explore diversification patterns within the tribe. KEY RESULTS Opposite diversification dynamics within the two major clades of Atripliceae, the Archiatriplex and Atriplex clades, could explain the unbalanced species richness between them; we found low mean speciation rates in the Archiatriplex clade and one shift to higher speciation rates placed in the branch of the Atriplex core. This acceleration in diversification seems to have started before the transition between C3 and C4 metabolism and before the arrival of Atriplex in the Americas, and matches the Mid-Miocene Climatic Optimum. Besides, the American species of Atriplex exhibit slightly higher net diversification rates than the Australian and Eurasian ones. While time seems not to be associated with diversification, traits such as life form, photosynthetic pathway and plant sex may have played roles as diversification drivers. CONCLUSIONS Traits more than time played a key role in Atripliceae diversification, and we could speculate that climate changes could have triggered speciation. The extreme arid or saline environments where Atripliceae species prevail may explain its particular evolutionary trends and trait correlations compared with other angiosperms and highlight the importance of conservation efforts needed to preserve them as genetic resources to deal with climatic changes.
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Affiliation(s)
| | - Raúl Pozner
- Instituto de Botánica Darwinion (Consejo Nacional de Investigaciones Científicas y Técnicas, Academia Nacional de Ciencias Exactas, Físicas y Naturales), Labardén, Casilla de Correo, San Isidro, Buenos Aires, Argentina
| | - Silvia S Denham
- Instituto de Botánica Darwinion (Consejo Nacional de Investigaciones Científicas y Técnicas, Academia Nacional de Ciencias Exactas, Físicas y Naturales), Labardén, Casilla de Correo, San Isidro, Buenos Aires, Argentina
- Laboratorio de Investigaciones en Biotecnología Sustentable (LIBioS), Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña, Bernal, Buenos Aires, Argentina
- Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
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Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Recent accelerated diversification in rosids occurred outside the tropics. Nat Commun 2020; 11:3333. [PMID: 32620894 PMCID: PMC7335165 DOI: 10.1038/s41467-020-17116-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/05/2020] [Indexed: 01/28/2023] Open
Abstract
Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.
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Affiliation(s)
- Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. .,Department of Bioscience, Aarhus University, Aarhus, 8000C, Denmark. .,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. .,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.
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Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids. AMERICAN JOURNAL OF BOTANY 2020; 107:895-909. [PMID: 32519354 PMCID: PMC7384126 DOI: 10.1002/ajb2.1479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/03/2020] [Indexed: 05/03/2023]
Abstract
PREMISE Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. METHODS We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). RESULTS We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. CONCLUSIONS We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
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Affiliation(s)
- Miao Sun
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- Department of BioscienceAarhus UniversityAarhus8000Denmark
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
| | - Matthew A. Gitzendanner
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
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Nagy LG, Merényi Z, Hegedüs B, Bálint B. Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing. Nucleic Acids Res 2020; 48:2209-2219. [PMID: 31943056 PMCID: PMC7049691 DOI: 10.1093/nar/gkz1241] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/15/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022] Open
Abstract
Ongoing large-scale genome sequencing projects are forecasting a data deluge that will almost certainly overwhelm current analytical capabilities of evolutionary genomics. In contrast to population genomics, there are no standardized methods in evolutionary genomics for extracting evolutionary and functional (e.g. gene-trait association) signal from genomic data. Here, we examine how current practices of multi-species comparative genomics perform in this aspect and point out that many genomic datasets are under-utilized due to the lack of powerful methodologies. As a result, many current analyses emphasize gene families for which some functional data is already available, resulting in a growing gap between functionally well-characterized genes/organisms and the universe of unknowns. This leaves unknown genes on the 'dark side' of genomes, a problem that will not be mitigated by sequencing more and more genomes, unless we develop tools to infer functional hypotheses for unknown genes in a systematic manner. We provide an inventory of recently developed methods capable of predicting gene-gene and gene-trait associations based on comparative data, then argue that realizing the full potential of whole genome datasets requires the integration of phylogenetic comparative methods into genomics, a rich but underutilized toolbox for looking into the past.
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Affiliation(s)
- László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62. Szeged 6726, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62. Szeged 6726, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62. Szeged 6726, Hungary
| | - Balázs Bálint
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Temesvari krt 62. Szeged 6726, Hungary
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