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Berbel-Filho WM, Pacheco G, Lira MG, Garcia de Leaniz C, Lima SMQ, Rodríguez-López CM, Zhou J, Consuegra S. Additive and non-additive epigenetic signatures of natural hybridisation between fish species with different mating systems. Epigenetics 2022; 17:2356-2365. [PMID: 36082413 PMCID: PMC9665120 DOI: 10.1080/15592294.2022.2123014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.
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Affiliation(s)
- Waldir M Berbel-Filho
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - George Pacheco
- Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Mateus G Lira
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Carlos Garcia de Leaniz
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Carlos M Rodríguez-López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Jia Zhou
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, Department of Biosciences, College of Science, Swansea University, Swansea, UK
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2
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Berbel-Filho WM, Pacheco G, Tatarenkov A, Lira MG, Garcia de Leaniz C, Rodríguez López CM, Lima SMQ, Consuegra S. Phylogenomics reveals extensive introgression and a case of mito-nuclear discordance in the killifish genus Kryptolebias. Mol Phylogenet Evol 2022; 177:107617. [PMID: 36038055 DOI: 10.1016/j.ympev.2022.107617] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/03/2022] [Accepted: 08/17/2022] [Indexed: 10/15/2022]
Abstract
Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on the evolutionary relationships within the killifish genus Kryptolebias. In addition, we tested for evidence of past introgression in the genus given the multiple reports of undergoing hybridization between its members. Our mtDNA phylogeny generally agreed with the relationships previously proposed for the genus. However, our reconstruction based on nuclear DNA revealed an unknown lineage - Kryptolebias sp. 'ESP' - as the sister group of the self-fertilizing mangrove killifishes, K. marmoratus and K. hermaphroditus. All individuals sequenced of Kryptolebias sp. 'ESP' had the same mtDNA haplotype commonly observed in K. hermaphroditus, demonstrating a clear case of mito-nuclear discordance. Our analysis further confirmed extensive history of introgression between Kryptolebias sp. 'ESP' and K. hermaphroditus. Population genomics analyses indicate no current gene flow between the two lineages, despite their current sympatry and history of introgression. We also confirmed introgression between other species pairs in the genus that have been recently reported to form hybrid zones. Overall, our study provides a phylogenomic reconstruction covering most of the Kryptolebias species, reveals a new lineage hidden in a case of mito-nuclear discordance, and provides evidence of multiple events of ancestral introgression in the genus. These findings underscore the importance of investigating different genomic information in a phylogenetic framework, particularly in taxa where introgression is common as in the sexually diverse mangrove killifishes.
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Affiliation(s)
- Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, USA(1); Department of Biosciences, College of Science, Swansea University, Swansea, UK.
| | - George Pacheco
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Mateus G Lira
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | | | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Sergio M Q Lima
- Laboratório de Ictiologia Sistemática e Evolutiva, Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande, Natal, Brazil
| | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
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3
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Against the Odds: Hybrid Zones between Mangrove Killifish Species with Different Mating Systems. Genes (Basel) 2021; 12:genes12101486. [PMID: 34680881 PMCID: PMC8535463 DOI: 10.3390/genes12101486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent hybridization between two mangrove killifish species with different mating systems, Kryptolebias ocellatus (obligately outcrossing) and K. hermaphroditus (predominantly self-fertilizing) in two hybrid zones in southeast Brazil. Hybridization rates were relatively high (~20%), representing the first example of natural hybridization between species with different mating systems in vertebrates. All F1 individuals were sired by the selfing species. Backcrossing was small, but mostly asymmetrical with the SI parental species, suggesting pattern commonly observed in plant hybrid zones with different mating systems. Our findings shed light on how contrasting mating systems may affect the direction and extent of gene flow between sympatric species, ultimately affecting the evolution and maintenance of hybrid zones.
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Yamaguchi S, Iwasa Y. Evolutionary game in an androdioecious population: Coupling of outcrossing and male production. J Theor Biol 2021; 513:110594. [PMID: 33460652 DOI: 10.1016/j.jtbi.2021.110594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Androdioecy, the coexistence of hermaphrodites and males, is very rare in vertebrates but occurs in mangrove killifish living in ephemeral or unstable habitats. Hermaphrodites reproduce both by outcrossing with males and by selfing. Outbreeding is advantageous because of inbreeding depression, but it requires encounters with males. The advantages of a propensity for outcrossing among hermaphrodites and the production of males affect each other very strongly. To study the evolutionary coupling of these two aspects, we here analyze a simple evolutionary game for a population composed of three phenotypes: outcrossing-oriented hermaphrodites, selfing-oriented hermaphrodites, and males. Outcrossing-oriented hermaphrodites first attempt to search for males and perform outcrossing if they encounter males. If they fail to encounter males, they reproduce via selfing. Selfing-oriented hermaphrodites simply reproduce by selfing. The replicator dynamics may show bistability, in which both the androdioecious population (with outcrossing-oriented hermaphrodites and males) and the pure hermaphroditic population are locally stable. The model shows the fraction of males is either zero or relatively high (more than 25%), which is not consistent with the observed low fraction of males (less than 5%). To explain this discrepancy, we studied several models including immigration and enforced copulation. We concluded that the observed pattern can be most likely explained by a population dominated by selfing-oriented hermaphrodites receiving immigration of males.
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Affiliation(s)
- Sachi Yamaguchi
- Division of Mathematical Sciences, Tokyo Woman's Christian University, Tokyo, Japan.
| | - Yoh Iwasa
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Hyogo, Japan
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5
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Qu M, Ding S, Schartl M, Adolfi MC. Spatial and temporal expression pattern of sex-related genes in ovo-testis of the self-fertilizing mangrove killifish (Kryptolebias marmoratus). Gene 2020; 742:144581. [PMID: 32173540 DOI: 10.1016/j.gene.2020.144581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/23/2023]
Abstract
In vertebrates, sex determination and differentiation comprehend a fine balance between female and male factors, leading the bipotential anlage to develop towards ovary or testis, respectively. Nevertheless, the mangrove killifish, (Kryptolebias marmoratus) a simultaneous hermaphroditic species, could overcome those antagonistic pathways and evolved to develop and maintain reproductively active ovarian and testicular tissues in the same organ. Morphological and mRNA localization analyzes of developing and adult gonads demonstrate that genes related to testis (dmrt1 and amh) and ovary differentiation (foxl2 and sox9a) follow the same expression pattern observed in gonochoristic species, thus functioning as two independent organs. In addition, Amh expression patterns make it a strong candidate for initiation of the formation and maintenance of the testicular tissue in the hermaphroditic gonad. Differently from described so far, foxl3 seems to have an important role in oogenesis as well as spermatogenesis and gonadal structure.
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Affiliation(s)
- Meng Qu
- University of Wuerzburg, Physiological Chemistry, Biocenter, Am Hubland, D-97074 Wuerzburg, Germany; State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, China; CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Guangzhou 510220, China
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, China
| | - Manfred Schartl
- University of Wuerzburg, Physiological Chemistry, Biocenter, Am Hubland, D-97074 Wuerzburg, Germany; University of Wuerzburg, Developmental Biochemistry, Biocenter, Am Hubland, D-97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Mateus Contar Adolfi
- University of Wuerzburg, Physiological Chemistry, Biocenter, Am Hubland, D-97074 Wuerzburg, Germany; University of Wuerzburg, Developmental Biochemistry, Biocenter, Am Hubland, D-97074 Wuerzburg, Germany.
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7
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Fellous A, Earley RL, Silvestre F. Identification and expression of mangrove rivulus (Kryptolebias marmoratus) histone deacetylase (HDAC) and lysine acetyltransferase (KAT) genes. Gene 2019; 691:56-69. [DOI: 10.1016/j.gene.2018.12.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/14/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022]
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8
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Marson KM, Taylor DS, Earley RL. Cryptic Male Phenotypes in the Mangrove Rivulus Fish, Kryptolebias marmoratus. THE BIOLOGICAL BULLETIN 2019; 236:13-28. [PMID: 30707609 DOI: 10.1086/700697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alternative male phenotypes exist in many species and impact mating system dynamics, population genetics, and mechanisms of natural and sexual selection that operate within a population. We report on the discovery of a cryptic male phenotype in the mangrove rivulus fish (Kryptolebias marmoratus), one of only two self-fertilizing hermaphroditic vertebrates. In this androdiecious species, males are infrequent, often making up less than 5% of a population; and they have historically been described as having an orange color and lacking or having a very faded outline of the well-defined caudal eyespot (ocellus) that is obvious in hermaphrodites. The cryptic male we describe varies subtly from the hermaphrodite phenotype, without visible orange pigmentation on the body and retention or only minor fading of the ocellus. This male morph was identified by a loss of a defined melanistic "fingerprinting" on the caudal fin seen in hermaphrodites, not previously used as diagnostic for hermaphrodites, and replaced by a diffuse deposition of pigment across the fin. Individuals were identified as male with 85.7% accuracy when using these criteria. We report that in nine populations, spanning three geographically distinct regions in Florida, across two and a half years, 0.3% of the 6057 mangrove rivulus collected exhibited this cryptic male phenotype and were confirmed to have testes via dissection. Overall, 2.3% of the animals were male (normal and cryptic phenotypes), and cryptic males represented 12.9% of all males collected. Even a minor increase in individuals identified as male in a species where males make up such a small portion of the population can have important implications for population genetics. Opportunities for outbreeding are likely enhanced, which has significant evolutionary ramifications.
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Key Words
- EPP, Emerson Point Preserve
- FDS, Fort De Soto State Preserve
- HAM, Curry Hammock State Park
- LK, Long Key State Park
- MES, New Smyrna Beach
- MRT, New Smyrna Beach
- PC, Pepper Cove, Brevard County Environmentally Endangered Lands
- UM, Upper Matecumbe Key
- WEED, Weedon Island Preserve
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9
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Turko AJ, Doherty JE, Yin-Liao I, Levesque K, Kruth P, Holden JM, Earley RL, Wright PA. Prolonged survival out of water is linked to a slow pace of life in a selfing amphibious fish. J Exp Biol 2019; 222:jeb.209270. [DOI: 10.1242/jeb.209270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/25/2019] [Indexed: 12/25/2022]
Abstract
Metabolic rate and life history traits vary widely both among and within species reflecting trade-offs in energy allocation, but the proximate and ultimate causes of variation are not well understood. We tested the hypothesis that these trade-offs are mediated by environmental heterogeneity, using isogenic strains of the amphibious fish Kryptolebias marmoratus that vary in the amount of time each can survive out of water. Consistent with pace of life theory, the strain that survived air exposure the longest generally exhibited a “slow” phenotype including the lowest metabolic rate, largest scope for metabolic depression, slowest consumption of energy stores, and least investment in reproduction under standard conditions. Growth rates were fastest in the otherwise “slow” strain, however. We then tested for fitness trade-offs between “fast” and “slow” strains using microcosms where fish were held with either constant water availability or under fluctuating conditions where water was absent for half of the experiment. Under both conditions the “slow” strain grew larger and was in better condition, and under fluctuating conditions the “slow” strain produced more embryos. However, the “fast” strain had larger adult population sizes under both conditions, indicating that fecundity is not the sole determinant of population size in this species. We conclude that genetically based differences in pace of life of amphibious fish determine survival duration out of water. Relatively “slow” fish tended to perform better under conditions of limited water availability, but there was no detectable cost under control conditions. Thus, pace of life differences may reflect a conditionally neutral instead of antagonistic trade-off.
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Affiliation(s)
- Andy J. Turko
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Justine E. Doherty
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Irene Yin-Liao
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Kelly Levesque
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Perryn Kruth
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Joseph M. Holden
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA, 35487
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA, 35487
| | - Patricia A. Wright
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1
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10
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Lins LS, Trojahn S, Sockell A, Yee MC, Tatarenkov A, Bustamante CD, Earley RL, Kelley JL. Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate. Genome 2018; 61:241-247. [DOI: 10.1139/gen-2017-0188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.
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Affiliation(s)
- Luana S.F. Lins
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
| | - Shawn Trojahn
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford University, 300 Pasteur Dr., Stanford, CA 94305, USA
| | - Muh-Ching Yee
- Stanford Functional Genomics Facility, Stanford University, CCSR 0120, 269 Campus Drive, Stanford, CA 94305, USA
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University, 300 Pasteur Dr., Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, 365 Lasuen Street, Littlefield Center, Room 303, Stanford, CA 94305, USA
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Joanna L. Kelley
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, 100 Dairy Road, Pullman, WA 99164, USA
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11
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Scarsella GE, Gresham JD, Earley RL. Relationships between external sexually dimorphic characteristics and internal gonadal morphology in a sex-changing fish. J Zool (1987) 2018. [DOI: 10.1111/jzo.12546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- G. E. Scarsella
- Department of Biological Sciences; The University of Alabama; Tuscaloosa AL USA
| | - J. D. Gresham
- Department of Biological Sciences; The University of Alabama; Tuscaloosa AL USA
| | - R. L. Earley
- Department of Biological Sciences; The University of Alabama; Tuscaloosa AL USA
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12
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Uyenoyama MK, Takebayashi N. Evolution of the sex ratio and effective number under gynodioecy and androdioecy. Theor Popul Biol 2017; 118:27-45. [PMID: 28911800 DOI: 10.1016/j.tpb.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/05/2017] [Accepted: 08/21/2017] [Indexed: 11/24/2022]
Abstract
We address the evolution of effective number of individuals under androdioecy and gynodioecy. We analyze dynamic models of autosomal modifiers of weak effect on sex expression. In our zygote control models, the sex expressed by a zygote depends on its own genotype, while in our maternal control models, it depends on the genotype of its maternal parent. Our analysis unifies full multi-dimensional local stability analysis with the Li-Price equation, which for all its heuristic appeal, describes evolutionary change over a single generation. We define a point in the neighborhood of a fixation state from which a single-generation step indicates the asymptotic behavior of the frequency of a modifier allele initiated at an arbitrary point near the fixation state. A concept of heritability appropriate for the evolutionary modification of sex emerges from the Li-Priceframework. We incorporate our theoretical analysis into our previously-developed Bayesian inference framework to develop a new method for inferring the viability of gonochores (males or females) relative to hermaphrodites. Applying this approach to microsatellite data derived from natural populations of the gynodioecious plant Schiedea salicaria and the androdioecious killifish Kryptolebias marmoratus, we find that while female and hermaphrodite S. salicaria appear to have similar viabilities, male K. marmoratus appear to survive to reproductive age at less than half the rate of hermaphrodites.
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Affiliation(s)
- Marcy K Uyenoyama
- Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338, USA.
| | - Naoki Takebayashi
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska, Fairbanks, Fairbanks, AK 99775, USA.
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13
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Tatarenkov A, Lima SMQ, Earley RL, Berbel-Filho WM, Vermeulen FBM, Taylor DS, Marson K, Turner BJ, Avise JC. Deep and concordant subdivisions in the self-fertilizing mangrove killifishes (Kryptolebias) revealed by nuclear and mtDNA markers. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx103] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Lomax JL, Carlson RE, Wells JW, Crawford PM, Earley RL. Factors affecting egg production in the selfing mangrove rivulus (Kryptolebias marmoratus). ZOOLOGY 2017; 122:38-45. [PMID: 28268048 DOI: 10.1016/j.zool.2017.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 02/03/2023]
Abstract
The mangrove rivulus, Kryptolebias marmoratus, is one of two known vertebrate species with preferentially self-fertilizing hermaphrodites. Males also exist, and can outcross with hermaphrodites. Outcrossing events vary across wild populations and occur infrequently in laboratory settings. This study sought to add dimension to our understanding of mangrove rivulus reproductive habits by probing the effects of male presence on hermaphroditic unfertilized egg production. Specifically, we quantified egg production of solitary hermaphrodites compared to hermaphrodites exposed to males and exposed to other hermaphrodites. Hermaphrodites tended to produce more fertilized eggs in the presence of males but unfertilized eggs were produced relatively rarely and did not vary significantly among treatments. The probability that hermaphrodites would produce eggs changed as a function of genetic dissimilarity with their partner and in a season-dependent manner. In the fall, the probability of laying eggs decreased as a function of increased genetic dissimilarity, regardless of the sex of the partner. In the winter/spring, however, the probability of laying eggs increased markedly with increased genetic dissimilarity, regardless of the sex of the partner. Our findings indicate that reproductive decisions are modulated by factors beyond male presence, and we discuss a number of alternative hypotheses that should be tested in future studies.
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Affiliation(s)
- Justin L Lomax
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Box 870344, Tuscaloosa, AL 35487, USA
| | - Rachel E Carlson
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Box 870344, Tuscaloosa, AL 35487, USA
| | - Judson W Wells
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Box 870344, Tuscaloosa, AL 35487, USA
| | - Patrice M Crawford
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Box 870344, Tuscaloosa, AL 35487, USA
| | - Ryan L Earley
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Box 870344, Tuscaloosa, AL 35487, USA.
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15
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Garcia MJ, Ferro JM, Mattox T, Kopelic S, Marson K, Jones R, Svendsen JC, Earley RL. Phenotypic differences between the sexes in the sexually plastic mangrove rivulus fish (Kryptolebias marmoratus). ACTA ACUST UNITED AC 2016; 219:988-97. [PMID: 27030777 DOI: 10.1242/jeb.124040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 01/18/2016] [Indexed: 01/23/2023]
Abstract
To maximize reproductive success, many animal species have evolved functional sex change. Theory predicts that transitions between sexes should occur when the fitness payoff of the current sex is exceeded by the fitness payoff of the opposite sex. We examined phenotypic differences between the sexes in a sex-changing vertebrate, the mangrove rivulus fish (Kryptolebias marmoratus), to elucidate potential factors that might drive the 'decision' to switch sex. Rivulus populations consist of self-fertilizing hermaphrodites and males. Hermaphrodites transition into males under certain environmental conditions, affording us the opportunity to generate 40 hermaphrodite-male pairs where, within a pair, individuals possessed identical genotypes despite being different sexes. We quantified steroid hormone levels, behavior (aggression and risk taking), metabolism and morphology (organ masses). We found that hermaphrodites were more aggressive and risk averse, and had higher maximum metabolic rates and larger gonadosomatic indices. Males had higher steroid hormone levels and showed correlations among hormones that hermaphrodites lacked. Males also had greater total mass and somatic body mass and possessed considerable fat stores. Our findings suggest that there are major differences between the sexes in energy allocation, with hermaphrodites exhibiting elevated maximum metabolic rates, and showing evidence of favoring investments in reproductive tissues over somatic growth. Our study serves as the foundation for future research investigating how environmental challenges affect both physiology and reproductive investment and, ultimately, how these changes dictate the transition between sexes.
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Affiliation(s)
- Mark J Garcia
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
| | - Jack M Ferro
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
| | - Tyler Mattox
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
| | - Sydney Kopelic
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
| | - Kristine Marson
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
| | - Ryan Jones
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
| | - Jon C Svendsen
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, 4050-123 Porto, Portugal Section for Ecosystem based Marine Management, National Institute of Aquatic Resources (DTU Aqua), Technical University of Denmark, 2920 Charlottenlund, Denmark
| | - Ryan L Earley
- Department of Biological Sciences, University of Alabama, Box 870344, Tuscaloosa, AL 35473, USA
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16
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Kelley JL, Yee MC, Brown AP, Richardson RR, Tatarenkov A, Lee CC, Harkins TT, Bustamante CD, Earley RL. The Genome of the Self-Fertilizing Mangrove Rivulus Fish, Kryptolebias marmoratus: A Model for Studying Phenotypic Plasticity and Adaptations to Extreme Environments. Genome Biol Evol 2016; 8:2145-54. [PMID: 27324916 PMCID: PMC4987111 DOI: 10.1093/gbe/evw145] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages without significant limitations associated with inbreeding depression. Over 400 isogenic lineages currently held in laboratories across the globe show considerable among-lineage variation in physiology, behavior, and life history traits that is maintained under common garden conditions. Temperature mediates the development of primary males and also sex change between hermaphrodites and secondary males, which makes the system ideal for the study of sex determination and sexual plasticity. Mangrove rivulus also exhibit remarkable adaptations to living in extreme environments, and the system has great promise to shed light on the evolution of terrestrial locomotion, aerial respiration, and broad tolerances to hypoxia, salinity, temperature, and environmental pollutants. Genome assembly of the mangrove rivulus allows the study of genes and gene families associated with the traits described above. Here we present a de novo assembled reference genome for the mangrove rivulus, with an approximately 900 Mb genome, including 27,328 annotated, predicted, protein-coding genes. Moreover, we are able to place more than 50% of the assembled genome onto a recently published linkage map. The genome provides an important addition to the linkage map and transcriptomic tools recently developed for this species that together provide critical resources for epigenetic, transcriptomic, and proteomic analyses. Moreover, the genome will serve as the foundation for addressing key questions in behavior, physiology, toxicology, and evolutionary biology.
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Affiliation(s)
- Joanna L Kelley
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California
| | - Anthony P Brown
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, Washington
| | | | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | | | | | | | - Ryan L Earley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama
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17
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Redelings BD, Kumagai S, Tatarenkov A, Wang L, Sakai AK, Weller SG, Culley TM, Avise JC, Uyenoyama MK. A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation. Genetics 2015; 201:1171-88. [PMID: 26374460 PMCID: PMC4649643 DOI: 10.1534/genetics.115.179093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/04/2015] [Indexed: 11/18/2022] Open
Abstract
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens sampling formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet process prior model. Our sampler is designed to accommodate additional information, including observations pertaining to the sex ratio, the intensity of inbreeding depression, and other aspects of reproduction. It can provide joint posterior distributions for the population-wide proportion of uniparental individuals, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual. Further, estimation of all basic parameters of a given model permits estimation of functions of those parameters, including the proportion of the gene pool contributed by each sex and relative effective numbers.
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Affiliation(s)
| | - Seiji Kumagai
- Department of Biology, Duke University, Durham, North Carolina 27708-0338
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525
| | - Liuyang Wang
- Department of Biology, Duke University, Durham, North Carolina 27708-0338
| | - Ann K Sakai
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525
| | - Stephen G Weller
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525
| | - Theresa M Culley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio 45220
| | - John C Avise
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525
| | - Marcy K Uyenoyama
- Department of Biology, Duke University, Durham, North Carolina 27708-0338
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