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De-Kayne R, Perry BW, McGowan KL, Landers J, Arias-Rodriguez L, Greenway R, Rodríguez Peña CM, Tobler M, Kelley JL. Evolutionary Rate Shifts in Coding and Regulatory Regions Underpin Repeated Adaptation to Sulfidic Streams in Poeciliid Fishes. Genome Biol Evol 2024; 16:evae087. [PMID: 38788745 PMCID: PMC11126329 DOI: 10.1093/gbe/evae087] [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] [Accepted: 04/13/2024] [Indexed: 05/26/2024] Open
Abstract
Adaptation to extreme environments often involves the evolution of dramatic physiological changes. To better understand how organisms evolve these complex phenotypic changes, the repeatability and predictability of evolution, and possible constraints on adapting to an extreme environment, it is important to understand how adaptive variation has evolved. Poeciliid fishes represent a particularly fruitful study system for investigations of adaptation to extreme environments due to their repeated colonization of toxic hydrogen sulfide-rich springs across multiple species within the clade. Previous investigations have highlighted changes in the physiology and gene expression in specific species that are thought to facilitate adaptation to hydrogen sulfide-rich springs. However, the presence of adaptive nucleotide variation in coding and regulatory regions and the degree to which convergent evolution has shaped the genomic regions underpinning sulfide tolerance across taxa are unknown. By sampling across seven independent lineages in which nonsulfidic lineages have colonized and adapted to sulfide springs, we reveal signatures of shared evolutionary rate shifts across the genome. We found evidence of genes, promoters, and putative enhancer regions associated with both increased and decreased convergent evolutionary rate shifts in hydrogen sulfide-adapted lineages. Our analysis highlights convergent evolutionary rate shifts in sulfidic lineages associated with the modulation of endogenous hydrogen sulfide production and hydrogen sulfide detoxification. We also found that regions with shifted evolutionary rates in sulfide spring fishes more often exhibited convergent shifts in either the coding region or the regulatory sequence of a given gene, rather than both.
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Affiliation(s)
- Rishi De-Kayne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Blair W Perry
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Kerry L McGowan
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Jake Landers
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), Villahermosa, México
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Carlos M Rodríguez Peña
- Instituto de Investigaciones Botánicas y Zoológicas, Universidad Autónoma de Santo Domingo, Santo Domingo 10105, Dominican Republic
| | - Michael Tobler
- Department of Biology, University of Missouri–St. Louis, St. Louis, MO 63131, USA
- Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, MO 63121, USA
- WildCare Institute, Saint Louis Zoo, St. Louis, MO 63110, USA
| | - Joanna L Kelley
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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Sherpa S, Paris JR, Silva‐Rocha I, Di Canio V, Carretero MA, Ficetola GF, Salvi D. Genetic depletion does not prevent rapid evolution in island-introduced lizards. Ecol Evol 2023; 13:e10721. [PMID: 38034325 PMCID: PMC10682264 DOI: 10.1002/ece3.10721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.
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Affiliation(s)
- Stéphanie Sherpa
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Josephine R. Paris
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
| | - Iolanda Silva‐Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Viola Di Canio
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Miguel Angel Carretero
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
- Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPortoPortugal
| | | | - Daniele Salvi
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
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Travis J, Bassar RD, Coulson T, Lopez-Sepulcre A, Reznick D. Population Regulation and Density-Dependent Demography in the Trinidadian Guppy. Am Nat 2023; 202:413-432. [PMID: 37792920 DOI: 10.1086/725796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
AbstractClassic theory for density-dependent selection for delayed maturation requires that a population be regulated through some combination of adult fecundity and/or juvenile survival. We tested whether those demographic conditions were met in four experimental populations of Trinidadian guppies in which delayed maturation of males evolved when the densities of those populations became high. We used monthly mark-recapture data to examine population dynamics and demography in these populations. Three of the four populations displayed clear evidence of regulation. In all four populations, monthly adult survival rates were independent of biomass density or actually increased with increased biomass density. Juvenile recruitment, which is a combination of adult fecundity and juvenile survival, decreased as biomass density increased in all four populations. Demography showed marked seasonality, with greater survival and higher recruitment in the dry season than the wet season. Population regulation via juvenile recruitment supports the hypothesis that density-dependent selection was responsible for the evolution of delayed maturity in males. This body of work represents one of the few complete tests of density-dependent selection theory.
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Lin Y, Darolti I, van der Bijl W, Morris J, Mank JE. Extensive variation in germline de novo mutations in Poecilia reticulata. Genome Res 2023; 33:1317-1324. [PMID: 37442578 PMCID: PMC10547258 DOI: 10.1101/gr.277936.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023]
Abstract
The rate of germline mutation is fundamental to evolutionary processes, as it generates the variation upon which selection acts. The guppy, Poecilia reticulata, is a model of rapid adaptation, however the relative contribution of standing genetic variation versus de novo mutation (DNM) to evolution in this species remains unclear. Here, we use pedigree-based approaches to quantify and characterize germline DNMs in three large guppy families. Our results suggest germline mutation rate in the guppy varies substantially across individuals and families. Most DNMs are shared across multiple siblings, suggesting they arose during early embryonic development. DNMs are randomly distributed throughout the genome, and male-biased mutation rate is low, as would be expected from the short guppy generation time. Overall, our study shows remarkable variation in germline mutation rate and provides insights into rapid evolution of guppies.
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Affiliation(s)
- Yuying Lin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada;
| | - Iulia Darolti
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Wouter van der Bijl
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jake Morris
- School of Biological Science, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Whiting JR, Paris JR, van der Zee MJ, Fraser BA. AF‐vapeR
: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James R. Whiting
- Department of Biosciences University of Exeter Exeter UK
- Department of Biological Sciences University of Calgary Calgary Alberta Canada
| | - Josephine R. Paris
- Department of Biosciences University of Exeter Exeter UK
- Department of Health, Life and Environmental Sciences University of L'Aquila L'Aquila Italy
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Bruce J, Hoskisson PA. Editorial overview: Eco-evolutionary dynamics in microbiology comes of age. Curr Opin Microbiol 2022; 68:102171. [PMID: 35709553 DOI: 10.1016/j.mib.2022.102171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intimate linkage of ecology and evolution is central to our understanding of biodiversity. The traditional perspective was to separate these fields based on timescales, but rapid, contemporary evolution is widely accepted and perhaps even more so in microbial systems. The study of eco-evolutionary dynamics is advancing at great pace and microorganisms are at the forefront of emerging paradigms, driven by conceptual and technological advances, such that we can move beyond the widely studied eco to evo aspects of the field and develop our understanding of how microorganisms shape virtually all processes on the planet (evo to eco).
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Affiliation(s)
- John Bruce
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK.
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