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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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Rybnikov SR, Frenkel Z, Hübner S, Weissman DB, Korol AB. Modeling the evolution of recombination plasticity: A prospective review. Bioessays 2023; 45:e2200237. [PMID: 37246937 DOI: 10.1002/bies.202200237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 05/30/2023]
Abstract
Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains underexplored. In this review, we focus on the sensitivity of recombination rates to different extrinsic and intrinsic factors. We briefly present the empirical evidence for recombination plasticity in response to environmental perturbations and/or poor genetic background and discuss theoretical models developed to explain how such plasticity could have evolved and how it can affect important population characteristics. We highlight a gap between the evidence, which comes mostly from experiments with diploids, and theory, which typically assumes haploid selection. Finally, we formulate open questions whose solving would help to outline conditions favoring recombination plasticity. This will contribute to answering the long-standing question of why sexual recombination exists despite its costs, since plastic recombination may be evolutionary advantageous even in selection regimes rejecting any non-zero constant recombination.
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Affiliation(s)
- Sviatoslav R Rybnikov
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai College, Kiryat Shmona, Israel
| | | | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
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Barrera-Redondo J, Lotharukpong JS, Drost HG, Coelho SM. Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra. Genome Biol 2023; 24:54. [PMID: 36964572 PMCID: PMC10037820 DOI: 10.1186/s13059-023-02895-z] [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: 08/26/2022] [Accepted: 03/10/2023] [Indexed: 03/26/2023] Open
Abstract
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.
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Affiliation(s)
- Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Jaruwatana Sodai Lotharukpong
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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Cofre J, Saalfeld K. The first embryo, the origin of cancer and animal phylogeny. I. A presentation of the neoplastic process and its connection with cell fusion and germline formation. Front Cell Dev Biol 2023; 10:1067248. [PMID: 36684435 PMCID: PMC9846517 DOI: 10.3389/fcell.2022.1067248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 01/05/2023] Open
Abstract
The decisive role of Embryology in understanding the evolution of animal forms is founded and deeply rooted in the history of science. It is recognized that the emergence of multicellularity would not have been possible without the formation of the first embryo. We speculate that biophysical phenomena and the surrounding environment of the Ediacaran ocean were instrumental in co-opting a neoplastic functional module (NFM) within the nucleus of the first zygote. Thus, the neoplastic process, understood here as a biological phenomenon with profound embryologic implications, served as the evolutionary engine that favored the formation of the first embryo and cancerous diseases and allowed to coherently create and recreate body shapes in different animal groups during evolution. In this article, we provide a deep reflection on the Physics of the first embryogenesis and its contribution to the exaptation of additional NFM components, such as the extracellular matrix. Knowledge of NFM components, structure, dynamics, and origin advances our understanding of the numerous possibilities and different innovations that embryos have undergone to create animal forms via Neoplasia during evolutionary radiation. The developmental pathways of Neoplasia have their origins in ctenophores and were consolidated in mammals and other apical groups.
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Affiliation(s)
- Jaime Cofre
- Laboratório de Embriologia Molecular e Câncer, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil,*Correspondence: Jaime Cofre,
| | - Kay Saalfeld
- Laboratório de Filogenia Animal, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Metabolism as a screenwriter in the female-male coevolutionary play. Proc Natl Acad Sci U S A 2022; 119:e2213208119. [PMID: 36103573 PMCID: PMC9522325 DOI: 10.1073/pnas.2213208119] [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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Holding ML, Trevine VC, Zinenko O, Strickland JL, Rautsaw RM, Mason AJ, Hogan MP, Parkinson CL, Grazziotin FG, Santana SE, Davis MA, Rokyta DR. Evolutionary allometry and ecological correlates of fang length evolution in vipers. Proc Biol Sci 2022; 289:20221132. [PMID: 36300520 PMCID: PMC9449470 DOI: 10.1098/rspb.2022.1132] [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: 06/10/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022] Open
Abstract
Traits for prey acquisition form the phenotypic interface of predator-prey interactions. In venomous predators, morphological variation in venom delivery apparatus like fangs and stingers may be optimized for dispatching prey. Here, we determine how a single dimension of venom injection systems evolves in response to variation in the size, climatic conditions and dietary ecology of viperid snakes. We measured fang length in more than 1900 museum specimens representing 199 viper species (55% of recognized species). We find both phylogenetic signal and within-clade variation in relative fang length across vipers suggesting both general taxonomic trends and potential adaptive divergence in fang length. We recover positive evolutionary allometry and little static allometry in fang length. Proportionally longer fangs have evolved in larger species, which may facilitate venom injection in more voluminous prey. Finally, we leverage climatic and diet data to assess the global correlates of fang length. We find that models of fang length evolution are improved through the inclusion of both temperature and diet, particularly the extent to which diets are mammal-heavy diets. These findings demonstrate how adaptive variation can emerge among components of complex prey capture systems.
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Affiliation(s)
- Matthew L. Holding
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Vivian C. Trevine
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brazil, 1500, 05503-900 São Paulo, SP, Brazil
| | - Oleksandr Zinenko
- V. N. Karazin Kharkiv National University, 4 Svobody square, Kharkiv 61022, Ukraine
| | - Jason L. Strickland
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Rhett M. Rautsaw
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Andrew J. Mason
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Michael P. Hogan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher L. Parkinson
- Department of Biological Sciences, Clemson University, 190 Collings street, Clemson, SC 29634, USA
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, Av. Vital Brazil, 1500, 05503-900 São Paulo, SP, Brazil
| | - Sharlene E. Santana
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98105, USA
| | - Mark A. Davis
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820, USA
| | - Darin R. Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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