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Richardson JML, Alexander HJ, Anholt BR. Variance components of sex determination in the copepod Tigriopus californicus estimated from a pedigree analysis. Ecol Evol 2023; 13:e9997. [PMID: 37153021 PMCID: PMC10154854 DOI: 10.1002/ece3.9997] [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: 12/20/2022] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 05/09/2023] Open
Abstract
Extensive theory exists regarding population sex ratio evolution that predicts equal sex ratio (when parental investment is equal). In most animals, sex chromosomes determine the sex of offspring, and this fixed genotype for sex has made theory difficult to test since genotypic variance for the trait (sex) is lacking. It has long been argued that the genotype has become fixed in most animals due to the strong selection for equal sex ratios. The marine copepod Tigriopus californicus has no sex chromosomes, multiple genes affecting female brood sex ratio, and a brood sex ratio that responds to selection. The species thus provides an opportune system in which to test established sex ratio theory. In this paper, we further our exploration of polygenic sex determination in T. californicus using an incomplete diallel crossing design for analysis of the variance components of sex determination in the species. Our data confirm the presence of extra-binomial variance for sex, further confirming that sex is not determined through simple Mendelian trait inheritance. In addition, our crosses and backcrosses of isofemale lines selected for biased brood sex ratios show intermediate phenotypic means, as expected if sex is a threshold trait determined by an underlying "liability" trait controlled by many genes of small effects. Furthermore, crosses between families from the same selection line had similar increases in phenotypic variance as crosses between families from different selection lines, suggesting families from artificial selection lines responded to selection pressure through different underlying genetic bases. Finally, we estimate heritability of an individual to be male or female on the observed binary scale as 0.09 (95% CI: 0.034-0.14). This work furthers our accumulating evidence for polygenic sex determination in T. californicus laying the foundation for this as a model species in future studies of sex ratio evolution theory.
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Affiliation(s)
- Jean M. L. Richardson
- Bamfield Marine Sciences CentreBamfieldBritish ColumbiaCanadaV0R 1B0
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | | | - Bradley R. Anholt
- Bamfield Marine Sciences CentreBamfieldBritish ColumbiaCanadaV0R 1B0
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
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Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. Nat Commun 2022; 13:4024. [PMID: 35821220 PMCID: PMC9276764 DOI: 10.1038/s41467-022-31622-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/27/2022] [Indexed: 01/01/2023] Open
Abstract
The role of epistasis in driving adaptation has remained an unresolved problem dating back to the Evolutionary Synthesis. In particular, whether epistatic interactions among genes could promote parallel evolution remains unexplored. To address this problem, we employ an Evolve and Resequence (E&R) experiment, using the copepod Eurytemora affinis, to elucidate the evolutionary genomic response to rapid salinity decline. Rapid declines in coastal salinity at high latitudes are a predicted consequence of global climate change. Based on time-resolved pooled whole-genome sequencing, we uncover a remarkably parallel, polygenic response across ten replicate selection lines, with 79.4% of selected alleles shared between lines by the tenth generation of natural selection. Using extensive computer simulations of our experiment conditions, we find that this polygenic parallelism is consistent with positive synergistic epistasis among alleles, far more so than other mechanisms tested. Our study provides experimental and theoretical support for a novel mechanism promoting repeatable polygenic adaptation, a phenomenon that may be common for selection on complex physiological traits. Using time-series whole-genome sequencing data from a laboratory evolution experiment, along with extensive computer simulations, the authors show that synergistic epistasis could drive rapid parallel freshwater adaptation in a saline copepod.
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3
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Evolutionary origins of genomic adaptations in an invasive copepod. Nat Ecol Evol 2020; 4:1084-1094. [DOI: 10.1038/s41559-020-1201-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022]
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4
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Jeong CB, Lee BY, Choi BS, Kim MS, Park JC, Kim DH, Wang M, Park HG, Lee JS. The genome of the harpacticoid copepod Tigriopus japonicus: Potential for its use in marine molecular ecotoxicology. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105462. [PMID: 32169740 DOI: 10.1016/j.aquatox.2020.105462] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
The copepod Tigriopus japonicus has been widely used as an experimental species in the field of ecotoxicology. We have sequenced and assembled the whole genome of T. japonicus with comparative analysis of gene families that represent detoxification phases in two additional public genomes of Tigriopus spp., namely, T. californicus and T. kingsejongensis. The total length of the T. japonicus assembled genome was 196.6 Mb with an N50 value of 10.65 Mb and consisted of 339 scaffolds and 25,143 annotated genes. The detoxification gene families encoding cytochrome P450s (CYP450s), glutathione S-transferases (GSTs), and ATP-binding cassette (ABC) proteins in Tigriopus spp. have shown species-dependent diversity in several gene sets, suggesting that these genes have undergone a species-specific expansion to increase their fitness to different marine habitats and environmental pressures. Our study will provide a better understanding of the detoxification system in Tigriopus spp. and will contribute to various areas of research, including ecotoxicology.
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Affiliation(s)
- Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, South Korea
| | - Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Min-Sub Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Minghua Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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5
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Danzmann RG, Norman JD, Rondeau EB, Messmer AM, Kent MP, Lien S, Igboeli O, Fast MD, Koop BF. A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Mol Genet Genomics 2018; 294:343-363. [PMID: 30460550 DOI: 10.1007/s00438-018-1513-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 01/28/2023]
Abstract
A salmon louse (Lepeophtheirus salmonis salmonis) genetic linkage map was constructed to serve as a genomic resource for future investigations into the biology of this important marine parasitic copepod species, and to provide insights into the inheritance patterns of genetic markers in this species. SNP genotyping of 8 families confirmed the presence of 15 linkage groups based upon the assignment of 93,773 markers. Progeny sample size weight adjusted map sizes in males (with the exception of SL12 and SL15) ranged in size from 96.50 cM (SL11) to 134.61 cM (SL06), and total combined map steps or bins ranged from 143 (SL09) to 203 (SL13). The SL12 male map was the smallest linkage group with a weight-averaged size of 3.05 cM with 6 recombination bins. Male:female specific recombination rate differences are 10.49:1 and represent one of the largest reported sex-specific differences for any animal species. Recombination ratio differences (M:F) ranged from 1.0 (SL12) to 29:1 (SL15). The number of markers exhibiting normal Mendelian segregation within the sex linkage group SL15 was extremely low (N = 80) in comparison to other linkage groups genotyped [range: 1459 (SL12)-10206 markers (SL05)]. Re-evaluation of Mendelian inheritance patterns of markers unassigned to any mapping parent according to hemizygous segregation patterns (models presented) identified matches for many of these markers to hemizygous patterns. The greatest proportion of these markers assigned to SL15 (N increased to 574). Inclusion of the hemizygous markers revised SL15 sex-specific recombination rate differences to 28:1. Recombination hot- and coldspots were identified across all linkage groups with all linkage groups possessing multiple peaks. Nine of 13 linkage groups evaluated possessed adjacent domains with hot-coldspot transitional zones. The most common pattern was for one end of the linkage to show elevated recombination in addition to internal regions. For SL01 and SL06, however, a terminal region with high recombination was not evident while a central domain possessing extremely high-recombination levels was present. High levels of recombination were weakly coupled to higher levels of SNP variation within domains, but this association was very strong for the central domains of SL01 and SL06. From the pooled paternal half-sib lots (several virgin females placed with 1 male), only 1 or two surviving family lots were obtained. Surviving families possessed parents where both the male and female possessed either inherently low or high recombination rates. This study provides insight into the organization of the sea louse genome, and describes large differences in recombination rate that exist among individuals of the same sex, and between the sexes. These differences in recombination rate may be coupled to the capabilities of this species to adapt to environmental and pharmaceutical treatments, given that family survivorship appears to be enhanced when parents have similar recombination levels.
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Affiliation(s)
- Roy G Danzmann
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Amber M Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Okechukwu Igboeli
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
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Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W, Burton RS. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat Ecol Evol 2018; 2:1250-1257. [DOI: 10.1038/s41559-018-0588-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
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8
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Haag CR, Theodosiou L, Zahab R, Lenormand T. Low recombination rates in sexual species and sex-asex transitions. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160461. [PMID: 29109224 PMCID: PMC5698623 DOI: 10.1098/rstb.2016.0461] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
In most sexual, diploid eukaryotes, at least one crossover occurs between each pair of homologous chromosomes during meiosis, presumably in order to ensure proper segregation. Well-known exceptions to this rule are species in which one sex does not recombine and specific chromosomes lacking crossover. We review other possible exceptions, including species with chromosome maps of less than 50 cM in one or both sexes. We discuss the idea that low recombination rates may favour sex-asex transitions, or, alternatively may be a consequence of it. We then show that a yet undescribed species of brine shrimp Artemia from Kazakhstan (A sp. Kazakhstan), the closest known relative of the asexual Artemia parthenogenetica, has one of the shortest genetic linkage maps known. Based on a family of 42 individuals and 589 RAD markers, we find that many linkage groups are considerably shorter than 50 cM, suggesting either no obligate crossover or crossovers concentrated at terminal positions with little effect on recombination. We contrast these findings with the published map of the more distantly related sexual congener, A. franciscana, and conclude that the study of recombination in non-model systems is important to understand the evolutionary causes and consequences of recombination.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Loukas Theodosiou
- Research Group for Community Dynamics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany
| | - Roula Zahab
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
| | - Thomas Lenormand
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE)-Unité Mixte de Recherche 5175, Centre National de la Recherche Scientifique (CNRS), Université de Montpellier-Université Paul-Valéry Montpellier-École Pratique des Hautes Études, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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9
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Han J, Won EJ, Kang HM, Lee MC, Jeong CB, Kim HS, Hwang DS, Lee JS. Marine copepod cytochrome P450 genes and their applications for molecular ecotoxicological studies in response to oil pollution. MARINE POLLUTION BULLETIN 2017; 124:953-961. [PMID: 27686823 DOI: 10.1016/j.marpolbul.2016.09.048] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/20/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
Recently, accidental spills of heavy oil have caused adverse effects in marine organisms. Oil pollution can induce damages on development and reproduction, linking with detrimental effects on diverse molecular levels of genes and proteins in plankton and fish. However, most information was mainly focused on marine vertebrates and consequently, limited information was available in marine invertebrates. Furthermore, there is still a lack of knowledge bridging in vivo endpoints with the functional regulation of cytochrome P450 (CYP) genes in response to oil spill pollution in marine invertebrates. In this paper, adverse effects of oil spill pollution in marine invertebrates are summarized with the importance of CYP genes as a potential biomarker, applying for environmental monitoring to detect oil spill using marine copepods.
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Affiliation(s)
- Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Eun-Ji Won
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Marine Chemistry and Geochemistry Research Center, Korea Institute of Ocean Science and Technology, Ansan 15627, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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10
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Dukić M, Berner D, Roesti M, Haag CR, Ebert D. A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna. BMC Genet 2016; 17:137. [PMID: 27737627 PMCID: PMC5064971 DOI: 10.1186/s12863-016-0445-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. RESULTS A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. CONCLUSIONS Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.
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Affiliation(s)
- Marinela Dukić
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.
| | - Daniel Berner
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
| | - Marius Roesti
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland.,Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive - CEFE UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, campus CNRS, 1919, route de Mende, 34293, Montpellier Cedex 5, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Chemin du Muśee 10, 1700, Fribourg, Switzerland
| | - Dieter Ebert
- University of Basel, Zoological Institute, Vesalgasse 1, Basel, CH-4051, Switzerland
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Hwang AS, Pritchard VL, Edmands S. Recovery from hybrid breakdown in a marine invertebrate is faster, stronger and more repeatable under environmental stress. J Evol Biol 2016; 29:1793-803. [DOI: 10.1111/jeb.12913] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/30/2016] [Indexed: 11/26/2022]
Affiliation(s)
- A. S. Hwang
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - V. L. Pritchard
- Department of Biological Sciences University of Southern California Los Angeles CA USA
| | - S. Edmands
- Department of Biological Sciences University of Southern California Los Angeles CA USA
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12
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Willett CS, Lima TG, Kovaleva I, Hatfield L. Chromosome-Wide Impacts on the Expression of Incompatibilities in Hybrids of Tigriopus californicus. G3 (BETHESDA, MD.) 2016; 6:1739-49. [PMID: 27172190 PMCID: PMC4889669 DOI: 10.1534/g3.116.028050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/06/2016] [Indexed: 11/18/2022]
Abstract
Chromosome rearrangements such as inversions have been recognized previously as contributing to reproductive isolation by maintaining alleles together that jointly contribute to deleterious genetic interactions and postzygotic reproductive isolation. In this study, an impact of potential incompatibilities merely residing on the same chromosome was found in crosses of populations of the copepod Tigriopus californicus When genetically divergent populations of this copepod are crossed, hybrids show reduced fitness, and deviations from expected genotypic ratios can be used to determine regions of the genome involved in deleterious interactions. In this study, a set of markers was genotyped for a cross of two populations of T. californicus, and these markers show widespread deviations from Mendelian expectations, with entire chromosomes showing marked skew. Despite the importance of mtDNA/nuclear interactions in incompatibilities in this system in previous studies, in these crosses the expected patterns stemming from these interactions are not widely apparent. Females lack recombination in this species, and a striking difference is observed between male and female backcrosses. This suggests that the maintenance of multiple loci on individual chromosomes can enable some incompatibilities, perhaps playing a similar role in the initial rounds of hybridization to chromosomal rearrangements in preserving sets of alleles together that contribute to incompatibilities. Finally, it was observed that candidate pairs of incompatibility regions are not consistently interacting across replicates or subsets of these crosses, despite the repeatability of the deviations at many of the single loci themselves, suggesting that more complicated models of Dobzhansky-Muller incompatibilities may need to be considered.
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Affiliation(s)
- Christopher S Willett
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
| | - Thiago G Lima
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
| | - Inna Kovaleva
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
| | - Lydia Hatfield
- Department of Biology, University of North Carolina at Chapel Hill, North Carolina 27599-3280
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13
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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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14
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Alexander HJ, Richardson JML, Edmands S, Anholt BR. Sex without sex chromosomes: genetic architecture of multiple loci independently segregating to determine sex ratios in the copepod Tigriopus californicus. J Evol Biol 2015; 28:2196-207. [DOI: 10.1111/jeb.12743] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 08/19/2015] [Accepted: 08/25/2015] [Indexed: 11/27/2022]
Affiliation(s)
- H. J. Alexander
- Bamfield Marine Sciences Centre; Bamfield BC Canada
- Department of Biology; University of Victoria; Victoria BC Canada
| | - J. M. L. Richardson
- Bamfield Marine Sciences Centre; Bamfield BC Canada
- Department of Biology; University of Victoria; Victoria BC Canada
| | - S. Edmands
- Department of Biological Sciences; University of Southern California; Los Angeles CA USA
| | - B. R. Anholt
- Bamfield Marine Sciences Centre; Bamfield BC Canada
- Department of Biology; University of Victoria; Victoria BC Canada
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15
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Zhang N, Zhang L, Tao Y, Guo L, Sun J, Li X, Zhao N, Peng J, Li X, Zeng L, Chen J, Yang G. Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus. BMC Genomics 2015; 16:189. [PMID: 25887315 PMCID: PMC4369078 DOI: 10.1186/s12864-015-1371-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. RESULTS We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. CONCLUSIONS A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
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Affiliation(s)
- Ning Zhang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Linan Zhang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Ye Tao
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Li Guo
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xia Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Nan Zhao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Jie Peng
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Liang Zeng
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Jinsa Chen
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Guanpin Yang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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16
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Alexander HJ, Richardson JML, Anholt BR. Multigenerational response to artificial selection for biased clutch sex ratios in Tigriopus californicus
populations. J Evol Biol 2014; 27:1921-9. [DOI: 10.1111/jeb.12449] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/16/2014] [Indexed: 01/02/2023]
Affiliation(s)
| | | | - B. R. Anholt
- Bamfield Marine Sciences Centre; Bamfield BC Canada
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17
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Berdan EL, Kozak GM, Ming R, Rayburn AL, Kiehart R, Fuller RC. Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion. G3 (BETHESDA, MD.) 2014; 4:1363-72. [PMID: 24898707 PMCID: PMC4132168 DOI: 10.1534/g3.114.012096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/20/2014] [Indexed: 01/31/2023]
Abstract
Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and L. goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) whereas L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density single-nucleotide polymorphism-based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania LG had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae.
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Affiliation(s)
- Emma L Berdan
- Department of Animal Biology, University of Illinois, Champaign, Illinois 61820
| | - Genevieve M Kozak
- Department of Animal Biology, University of Illinois, Champaign, Illinois 61820
| | - Ray Ming
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - A Lane Rayburn
- Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801
| | - Ryan Kiehart
- Department of Biology, Ursinus College, Collegeville, Pennsylvania 19426
| | - Rebecca C Fuller
- Department of Animal Biology, University of Illinois, Champaign, Illinois 61820
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18
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Foley BR, Rose CG, Rundle DE, Leong W, Edmands S. Postzygotic isolation involves strong mitochondrial and sex-specific effects in Tigriopus californicus, a species lacking heteromorphic sex chromosomes. Heredity (Edinb) 2013; 111:391-401. [PMID: 23860232 DOI: 10.1038/hdy.2013.61] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 05/08/2013] [Accepted: 05/13/2013] [Indexed: 11/09/2022] Open
Abstract
Detailed studies of the genetics of speciation have focused on a few model systems, particularly Drosophila. The copepod Tigriopus californicus offers an alternative that differs from standard animal models in that it lacks heteromorphic chromosomes (instead, sex determination is polygenic) and has reduced opportunities for sexual conflict, because females mate only once. Quantitative trait loci (QTL) mapping was conducted on reciprocal F2 hybrids between two strongly differentiated populations, using a saturated linkage map spanning all 12 autosomes and the mitochondrion. By comparing sexes, a possible sex ratio distorter was found but no sex chromosomes. Although studies of standard models often find an excess of hybrid male sterility factors, we found no QTL for sterility and multiple QTL for hybrid viability (indicated by non-Mendelian adult ratios) and other characters. Viability problems were found to be stronger in males, but the usual explanations for weaker hybrid males (sex chromosomes, sensitivity of spermatogenesis, sexual selection) cannot fully account for these male viability problems. Instead, higher metabolic rates may amplify deleterious effects in males. Although many studies of standard speciation models find the strongest genetic incompatibilities to be nuclear-nuclear (specifically X chromosome-autosome), we found the strongest deleterious interaction in this system was mito-nuclear. Consistent with the snowball theory of incompatibility accumulation, we found that trigenic interactions in this highly divergent cross were substantially more frequent (>6×) than digenic interactions. This alternative system thus allows important comparisons to studies of the genetics of reproductive isolation in more standard model systems.
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Affiliation(s)
- B R Foley
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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19
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De Vos S, Bossier P, Van Stappen G, Vercauteren I, Sorgeloos P, Vuylsteke M. A first AFLP-based genetic linkage map for brine shrimp Artemia franciscana and its application in mapping the sex locus. PLoS One 2013; 8:e57585. [PMID: 23469207 PMCID: PMC3587612 DOI: 10.1371/journal.pone.0057585] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/22/2013] [Indexed: 12/26/2022] Open
Abstract
We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ-ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species.
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Affiliation(s)
- Stephanie De Vos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- * E-mail:
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20
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Nie H, Li Q, Zhao X, Kong L. Genetic positioning of centromeres through half-tetrad analysis in gynogenetic diploid families of the Zhikong scallop (Chlamys farreri). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:1-15. [PMID: 22538933 DOI: 10.1007/s10126-012-9454-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 04/03/2012] [Indexed: 05/10/2023]
Abstract
Centromere mapping is a powerful tool for improving linkage maps, investigating crossover events, and understanding chiasma interference during meiosis. Ninety microsatellite markers selected across all linkage groups (LGs) from a previous Chlamys farreri genetic map were studied in three artificially induced meiogynogenetic families for centromere mapping by half-tetrad analysis. Inheritance analyses showed that all 90 microsatellite loci conformed to Mendelian inheritance in the control crosses, while 4.4 % of the microsatellite loci showed segregation departures from an expected 1:1 ratio of two homozygote classes in meiogynogenetic progeny. The second division segregation frequency (y) of the microsatellites ranged from 0.033 to 0.778 with a mean of 0.332, confirming the occurrence of partial chiasma interference in this species. Heterogeneity of y is observed in one of 42 cases in which markers were typed in more than one family, suggesting variation in gene-centromere recombination among families. Centromere location was mostly in accordance with the C. farreri karyotype, but differences in marker order between linkage and centromere maps occurred. Overall, this study makes the genetic linkage map a more complete and informative tool for genomic studies and it will also facilitate future research of the structure and function of the scallop centromeres.
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Affiliation(s)
- Hongtao Nie
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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21
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Pritchard VL, Edmands S. THE GENOMIC TRAJECTORY OF HYBRID SWARMS: OUTCOMES OF REPEATED CROSSES BETWEEN POPULATIONS OFTIGRIOPUS CALIFORNICUS. Evolution 2012; 67:774-91. [DOI: 10.1111/j.1558-5646.2012.01814.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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22
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Long-term experimental hybrid swarms between nearly incompatible Tigriopus californicus populations: persistent fitness problems and assimilation by the superior population. CONSERV GENET 2012. [DOI: 10.1007/s10592-011-0308-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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