Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
| Autor: | Bonnie A. Fraser, Detlef Weigel, Josephine R. Paris, Mijke J. van der Zee, Paul J. Parsons, James R. Whiting |
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| Rok vydání: | 2021 |
| Předmět: |
Convergent Evolution
0106 biological sciences Cancer Research Heredity Introgression Single Nucleotide Polymorphisms Marine and Aquatic Sciences QH426-470 01 natural sciences Convergent evolution Genetics (clinical) Data Management 0303 health sciences Genome Natural selection biology Phylogenetic Analysis Genomics Guppy Phylogenetics Genetic Mapping Trait Research Article Freshwater Environments Computer and Information Sciences Evolutionary Processes Genetic Introgression 010603 evolutionary biology Chromosomes Evolution Molecular 03 medical and health sciences Rivers Genetics Animals Evolutionary Systematics Molecular Biology Alleles Ecology Evolution Behavior and Systematics Selection (genetic algorithm) Taxonomy 030304 developmental biology Evolutionary Biology Poecilia Population Biology Ecology and Environmental Sciences Haplotype Aquatic Environments Biology and Life Sciences Genetic Variation Bodies of Water 15. Life on land biology.organism_classification Genetics Population Haplotypes Evolutionary biology Predatory Behavior Earth Sciences Genetic Polymorphism Adaptation Population Genetics |
| Zdroj: | PLoS Genetics PLoS Genetics, Vol 17, Iss 5, p e1009566 (2021) |
| ISSN: | 1553-7404 |
| DOI: | 10.1371/journal.pgen.1009566 |
| Popis: | Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage. Author summary Convergent evolution is the process whereby similar phenotypes evolve in response to common selection in independent lineages, providing strong evidence of adaptation in response to natural selection. This process can involve changes at the same regions of the genome, known as genomic convergence. We explore this in the replicated evolution of high- and low-predation Trinidadian guppies, an important model system for studies of phenotypic evolution, but where little is known about the underlying genetics. Our findings highlight that limitations on how genetic variation is distributed have restricted the same mutations or genes being involved in the convergent evolution of high- and low-predation guppies, but different genes of similar function are likely involved. We also highlight and examine a large candidate region associated with three rivers from the same drainage. Our results demonstrate constraints on genomic convergence at certain levels, but suggest there is some repeatability in the genetic basis of convergent phenotypic evolution in this important model system. Genomic convergence in the guppy system is therefore more limited than in other prominent study systems, suggesting the pervasiveness of this process in nature is highly context-dependent. |
| Databáze: | OpenAIRE |
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