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Murray CS, Karram M, Bass DJ, Doceti M, Becker D, Nunez JCB, Ratan A, Bergland AO. Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589693. [PMID: 38659826 PMCID: PMC11042267 DOI: 10.1101/2024.04.16.589693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The patterns of genetic variation within and between related taxa represent the genetic history of a species. Shared polymorphisms, loci with identical alleles across species, are of unique interest as they may represent cases of ancient selection maintaining functional variation post-speciation. In this study, we investigate the abundance of shared polymorphism in the Daphnia pulex species complex. We test whether shared mutations are consistent with the action of balancing selection or alternative hypotheses such as hybridization, incomplete lineage sorting, or convergent evolution. We analyzed over 2,000 genomes from North American and European D. pulex and several outgroup species to examine the prevalence and distribution of shared alleles between the focal species pair, North American and European D. pulex. We show that while North American and European D. pulex diverged over ten million years ago, they retained tens of thousands of shared alleles. We found that the number of shared polymorphisms between North American and European D. pulex cannot be explained by hybridization or incomplete lineage sorting alone. Instead, we show that most shared polymorphisms could be the product of convergent evolution, that a limited number appear to be old trans-specific polymorphisms, and that balancing selection is affecting young and ancient mutations alike. Finally, we provide evidence that a blue wavelength opsin gene with trans-specific polymorphisms has functional effects on behavior and fitness in the wild. Ultimately, our findings provide insights into the genetic basis of adaptation and the maintenance of genetic diversity between species.
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Affiliation(s)
- Connor S. Murray
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Madison Karram
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - David J. Bass
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Madison Doceti
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | | | - Aakrosh Ratan
- Center of Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Alan O. Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
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Ye Z, Wei W, Pfrender ME, Lynch M. Evolutionary Insights from a Large-Scale Survey of Population-Genomic Variation. Mol Biol Evol 2023; 40:msad233. [PMID: 37863047 PMCID: PMC10630549 DOI: 10.1093/molbev/msad233] [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: 05/03/2023] [Revised: 09/11/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
The field of genomics has ushered in new methods for studying molecular-genetic variation in natural populations. However, most population-genomic studies still rely on small sample sizes (typically, <100 individuals) from single time points, leaving considerable uncertainties with respect to the behavior of relatively young (and rare) alleles and, owing to the large sampling variance of measures of variation, to the specific gene targets of unusually strong selection. Genomic sequences of ∼1,700 haplotypes distributed over a 10-year period from a natural population of the microcrustacean Daphnia pulex reveal evolutionary-genomic features at a refined scale, including previously hidden information on the behavior of rare alleles predicted by recent theory. Background selection, resulting from the recurrent introduction of deleterious alleles, appears to strongly influence the dynamics of neutral alleles, inducing indirect negative selection on rare variants and positive selection on common variants. Temporally fluctuating selection increases the persistence of nonsynonymous alleles with intermediate frequencies, while reducing standing levels of variation at linked silent sites. Combined with the results from an equally large metapopulation survey of the study species, classes of genes that are under strong positive selection can now be confidently identified in this key model organism. Most notable among rapidly evolving Daphnia genes are those associated with ribosomes, mitochondrial functions, sensory systems, and lifespan determination.
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Affiliation(s)
- Zhiqiang Ye
- Hubei Key Laboratory of Genetic Regulation & Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Wen Wei
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
| | - Michael E Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287, USA
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Becker D, Barnard-Kubow K, Porter R, Edwards A, Voss E, Beckerman AP, Bergland AO. Adaptive phenotypic plasticity is under stabilizing selection in Daphnia. Nat Ecol Evol 2022; 6:1449-1457. [PMID: 35982224 DOI: 10.1038/s41559-022-01837-5] [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: 07/12/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
The adaptive nature of phenotypic plasticity is widely documented. However, little is known about the evolutionary forces that shape genetic variation of plasticity within populations. Whether genetic variation in plasticity is driven by stabilizing or diversifying selection and whether the strength of such forces remains constant through time, remain open questions. Here, we address this issue by assessing the evolutionary forces that shape genetic variation in antipredator developmental plasticity of Daphnia pulex. Antipredator plasticity in D. pulex is characterized by the growth of a pedestal and spikes in the dorsal head region upon exposure to predator cue. We characterized genetic variation in plasticity using a method that describes the entire dorsal shape amongst >100 D. pulex strains recently derived from the wild. We observed the strongest reduction in genetic variation in dorsal areas where plastic responses were greatest, consistent with stabilizing selection. We compared mutational variation (Vm) to standing variation (Vg) and found that Vg/Vm is lowest in areas of greatest plasticity, again consistent with stabilizing selection. Our results suggest that stabilizing selection operates directly on phenotypic plasticity in Daphnia and provide a rare glimpse into the evolution of fitness-related traits in natural populations.
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Affiliation(s)
- Dörthe Becker
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK.
- Department of Biology, University of Marburg, Marburg, Germany.
| | - Karen Barnard-Kubow
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | - Robert Porter
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Austin Edwards
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Biological Imaging Development CoLab, University of California San Francisco, San Francisco, CA, USA
| | - Erin Voss
- Department of Biology, University of Virginia, Charlottesville, VA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Andrew P Beckerman
- School of Biosciences, Ecology and Evolutionary Biology, University of Sheffield, Sheffield, UK
| | - Alan O Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
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