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Duvernell DD, Remex NS, Miller JT, Schaefer JF. Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus. Ecol Evol 2023; 13:e10399. [PMID: 37560181 PMCID: PMC10408002 DOI: 10.1002/ece3.10399] [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: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Pairs of species that exhibit broadly overlapping distributions, and multiple geographically isolated contact zones, provide opportunities to investigate the mechanisms of reproductive isolation. Such naturally replicated systems have demonstrated that hybridization rates can vary substantially among populations, raising important questions about the genetic basis of reproductive isolation. The topminnows, Fundulus notatus and F. olivaceus, are reciprocally monophyletic, and co-occur in drainages throughout much of the central and southern United States. Hybridization rates vary substantially among populations in isolated drainage systems. We employed genome-wide sampling to investigate geographic variation in hybridization, and to assess the possible importance of chromosome fusions to reproductive isolation among nine separate contact zones. The species differ by chromosomal rearrangements resulting from Robertsonian (Rb) fusions, so we hypothesized that Rb fusion chromosomes would serve as reproductive barriers, exhibiting steeper genomic clines than the rest of the genome. We observed variation in hybridization dynamics among drainages that ranged from nearly random mating to complete absence of hybridization. Contrary to predictions, our use of genomic cline analyses on mapped species-diagnostic SNP markers did not indicate consistent patterns of variable introgression across linkage groups, or an association between Rb fusions and genomic clines that would be indicative of reproductive isolation. We did observe a relationship between hybridization rates and population phylogeography, with the lowest rates of hybridization tending to be found in populations inferred to have had the longest histories of drainage sympatry. Our results, combined with previous studies of contact zones between the species, support population history as an important factor in explaining variation in hybridization rates.
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Affiliation(s)
- David D. Duvernell
- Department of Biological SciencesMissouri University of Science and TechnologyRollaMissouriUSA
| | - Naznin S. Remex
- Department of Biological SciencesMissouri University of Science and TechnologyRollaMissouriUSA
- Present address:
Department of Molecular and Cellular PhysiologyLouisiana State University Health Sciences CenterShreveportLouisianaUSA
| | - Jeffrey T. Miller
- Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Jacob F. Schaefer
- Department of Biological SciencesUniversity of Southern MississippiHattiesburgMississippiUSA
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Evolutionary Toxicogenomics of the Striped Killifish ( Fundulus majalis) in the New Bedford Harbor (Massachusetts, USA). Int J Mol Sci 2019; 20:ijms20051129. [PMID: 30841640 PMCID: PMC6429206 DOI: 10.3390/ijms20051129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 12/27/2022] Open
Abstract
In this paper, we used a Genotyping-by-Sequencing (GBS) approach to find and genotype more than 4000 genome-wide SNPs (Single Nucleotide Polymorphisms) from striped killifish exposed to a variety of polychlorinated biphenyls (PCBs) and other aromatic pollutants in New Bedford Harbor (NBH, Massachusetts, USA). The aims of this study were to identify the genetic consequences of exposure to aquatic pollutants and detect genes that may be under selection. Low genetic diversity (HE and π) was found in the site exposed to the highest pollution level, but the pattern of genetic diversity did not match the pollution levels. Extensive connectivity was detected among sampling sites, which suggests that balanced gene flow may explain the lack of genetic variation in response to pollution levels. Tests for selection identified 539 candidate outliers, but many of the candidate outliers were not shared among tests. Differences among test results likely reflect different test assumptions and the complex pollutant mixture. Potentially, selectively important loci are associated with 151 SNPs, and enrichment analysis suggests a likely involvement of these genes with pollutants that occur in NBH. This result suggests that selective processes at genes targeted by pollutants may be occurring, even at a small geographical scale, and may allow the local striped killifish to resist the high pollution levels.
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Adaptation Without Boundaries: Population Genomics in Marine Systems. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Nunez JCB, Elyanow RG, Ferranti DA, Rand DM. Population Genomics and Biogeography of the Northern Acorn Barnacle (Semibalanus balanoides) Using Pooled Sequencing Approaches. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_58] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Xu S, Song N, Zhao L, Cai S, Han Z, Gao T. Genomic evidence for local adaptation in the ovoviviparous marine fish Sebastiscus marmoratus with a background of population homogeneity. Sci Rep 2017; 7:1562. [PMID: 28484228 PMCID: PMC5431535 DOI: 10.1038/s41598-017-01742-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Advances in next-generation sequencing techniques have allowed for the generation of genome-wide sequence data, to gain insight into the dynamics influencing genetic structure and the local adaptation of marine fish. Here, using genotyping-by-sequencing (GBS) technique, we identified 31,119 single nucleotide polymorphisms (SNPs) for Sebastiscus marmoratus in 59 individuals from three populations in Chinese coastal waters. Based on all SNPs, there was little evidence of genetic differentiation among populations. However, outlier tests revealed 329 SNPs putatively under divergent selection across populations. Structural and phylogenetic topology analyses based on the outliers showed clear genetic differentiation among populations. Gene Ontology (GO) annotation results revealed that most of these outliers are known or hypothesized to be involved in metabolic process. Together with previous work using mitochondrial cytochrome b sequences, the present results further suggest that the population structure is strongly influenced by locally adaptive pressure. Overall, adaptive evolution in a heterogeneous environment plays an important role in inducing genetic differentiation among local populations. This study increases understanding of the factors (including gene flow and local adaptation) promoting and constraining population genetic differentiation in marine organisms.
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Affiliation(s)
- Shengyong Xu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5th Yushan Road, Qingdao, 266003, P.R. China
| | - Na Song
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5th Yushan Road, Qingdao, 266003, P.R. China
| | - Linlin Zhao
- The First Institute of Oceanography, State Oceanic Administration, 6th Xianxialing Road, Qingdao, 266061, P.R. China
| | - Shanshan Cai
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China.
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, 1st Haidanan Road, Zhoushan, 316022, P.R. China.
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Baris TZ, Wagner DN, Dayan DI, Du X, Blier PU, Pichaud N, Oleksiak MF, Crawford DL. Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions. PLoS Genet 2017; 13:e1006517. [PMID: 28362806 PMCID: PMC5375140 DOI: 10.1371/journal.pgen.1006517] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 12/01/2016] [Indexed: 02/05/2023] Open
Abstract
The oxidative phosphorylation (OxPhos) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins. The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects and how they may affect human health and disease. In many different organisms, healthy nuclear and mitochondrial genome hybrids between species or among distant populations within a species affect fitness and OxPhos functions. However, what is less understood is whether these interactions impact individuals within a single natural population. The significance of this impact depends on the strength of selection for mito-nuclear interactions. We examined whether mito-nuclear interactions alter allele frequencies for ~11,000 nuclear SNPs within a single, natural Fundulus heteroclitus population containing two divergent mitochondrial haplotypes (mt-haplotypes). Between the two mt-haplotypes, there are significant nuclear allele frequency differences for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of the genome, these 349 outlier SNPs form two groups associated with each mt-haplotype, with a minority of individuals having mixed ancestry. We use this mixed ancestry in combination with mt-haplotype as a polygenic factor to explain a significant fraction of the individual OxPhos variation. These data suggest that mito-nuclear interactions affect cardiac OxPhos function. The 349 outlier SNPs occur in genes involved in regulating metabolic processes but are not directly associated with the 79 nuclear OxPhos proteins. Therefore, we postulate that the evolution of mito-nuclear interactions affects OxPhos function by acting upstream of OxPhos.
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Affiliation(s)
- Tara Z. Baris
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
- * E-mail:
| | - Dominique N. Wagner
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - David I. Dayan
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - Xiao Du
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - Pierre U. Blier
- Dept de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Quebec, Canada
| | - Nicolas Pichaud
- Dept de Biologie, Université du Québec à Rimouski, 300 Allée des Ursulines, Rimouski, Quebec, Canada
| | - Marjorie F. Oleksiak
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
| | - Douglas L. Crawford
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, Rickenbacker Causeway, Miami, FL, United States of America
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Fine-scale genetic structure due to adaptive divergence among microhabitats. Heredity (Edinb) 2017; 118:594-604. [PMID: 28295034 DOI: 10.1038/hdy.2017.6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 01/20/2016] [Accepted: 01/22/2017] [Indexed: 02/03/2023] Open
Abstract
It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic-does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3-2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate ⩽1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.
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Schaefer J, Duvernell D, Campbell DC. Hybridization and introgression in two ecologically dissimilarFundulushybrid zones. Evolution 2016; 70:1051-63. [DOI: 10.1111/evo.12920] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 03/25/2016] [Accepted: 03/26/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Jacob Schaefer
- Department of Biological Sciences; The University of Southern Mississippi; Hattiesburg Mississippi 39406
| | - David Duvernell
- Department of Biological Sciences; Southern Illinois University Edwardsville; Edwardsville Illinois 62026
| | - Dave Cooper Campbell
- Department of Biological Sciences; The University of Southern Mississippi; Hattiesburg Mississippi 39406
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Crawford DL, Oleksiak MF. Ecological population genomics in the marine environment. Brief Funct Genomics 2016; 15:342-51. [DOI: 10.1093/bfgp/elw008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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