1
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Mousavi SE, Patil JG. Stages of embryonic development in the live-bearing fish, Gambusia holbrooki. Dev Dyn 2021; 251:287-320. [PMID: 34139034 DOI: 10.1002/dvdy.388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Divergent morphology and placentation of Poeciliids make them suitable model for investigating how evolutionary selection has altered and conserved the developmental mechanisms. However, there is limited description of their embryonic staging, despite representing a key evolutionary node that shares developmental strategy with placental vertebrates. Here, we describe the embryonic developmental stages of Gambusia holbrooki from zygote to parturition using freshly harvested embryos. RESULTS We defined 40 embryonic stages using a numbered (stages 0-39; zygote to parturition, respectively) and named (grouped into seven periods, ie, zygote, cleavage, blastula, gastrula, segmentation, pharyngula, and parturition) staging system. Two sets of quantitative (ie, egg diameter, embryonic total length, otic vesicle closure index, heart rates, the number of caudal fin rays and elements) and qualitative (ie, three-dimensional analysis of images and key morphological criteria) data were acquired and used in combination to describe each stage. All 40 stages are separated by well-defined morphological traits, revealing developmental novelties that are influenced by narrow perivitelline space, placentation, internal gestation, and sex differentiation. CONCLUSIONS The principal diagnostic features described are quick, reliable, and easy to apply. This system will benefit researchers investigating molecular ontogeny, particularly sexual differentiation mechanisms in G. holbrooki.
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Affiliation(s)
- Seyed Ehsan Mousavi
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, Tasmania, Australia
| | - Jawahar G Patil
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, Tasmania, Australia.,Inland Fisheries Service, New Norfolk, Tasmania, Australia
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2
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Gammerdinger WJ, Conte MA, Sandkam BA, Ziegelbecker A, Koblmüller S, Kocher TD. Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika. J Hered 2019; 109:489-500. [PMID: 29444291 DOI: 10.1093/jhered/esy003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
African cichlids are well known for their adaptive radiations, but it is now apparent that they also harbor an extraordinary diversity of sex chromosome systems. In this study, we sequenced pools of males and females from species in 3 different genera of cichlids from Lake Tanganyika. We then searched for regions that were differentiated following the patterns expected for sex chromosomes. We report 2 novel sex chromosomes systems, an XY system on LG19 in Tropheus sp. "black" and a ZW system on LG7 in Hemibates stenosoma. We also identify a ZW system on LG5 in Cyprichromis leptosoma that may be convergent with a system previously described in Lake Malawi cichlids. Our data also identify candidate single nucleotide polymorphisms for the blue/yellow tail color polymorphism observed among male C. leptosoma.
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Affiliation(s)
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | | | | | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz, Graz, Austria
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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3
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Dayan DI, Du X, Baris TZ, Wagner DN, Crawford DL, Oleksiak MF. Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents. BMC Evol Biol 2019; 19:61. [PMID: 30808292 PMCID: PMC6390305 DOI: 10.1186/s12862-019-1392-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 02/14/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating. RESULTS We provide genome-wide analyses of rapid evolution in Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents using 5449 SNPs across two effluent-affected and four reference populations. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation. CONCLUSIONS While the ultimate trajectory of selection in these populations is unknown and we survey only a minority of genomic loci, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.
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Affiliation(s)
- David I. Dayan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Xiao Du
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Tara Z. Baris
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Dominique N. Wagner
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Douglas L. Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
| | - Marjorie F. Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL 33149 USA
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4
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Oguntuase BG, Ogunjemite BG, Meisel RP. Morphometric and genetic differentiation among populations of flat-headed cusimanse ( Crossarchus platycephalus) in Nigeria. Ecol Evol 2018; 8:7228-7235. [PMID: 30073081 PMCID: PMC6065274 DOI: 10.1002/ece3.4262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/27/2018] [Accepted: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
Geographic barriers can partition genetic diversity among populations and drive evolutionary divergence between populations, promoting the speciation process and affecting conservation goals. We integrated morphological and genomic data to assess the distribution of variation in the flat-headed cusimanse (Crossarchus platycephalus), a species of least conservation concern, on either side of the River Niger in Nigeria. Ecological disturbances affect the conservation status of many other animals in this region. The two populations were differentiated in the snout and fore limbs, with greater morphological diversity in the western population. We used Restriction site Associated DNA sequencing (RAD-seq) and identified two genotypic clusters in a STRUCTURE analysis. Individuals from the eastern population are almost entirely assigned to one cluster, whereas genotypes from the western population are a mixture of the two clusters. The population from west of the River Niger also had higher heterozygosity. The morphological and population genetic data are therefore in agreement that the population from west of the River Niger is more diverse than the eastern population, and the eastern population contains a subset of the genetic variation found in the western population. Our results demonstrate that combining morphological and genotypic measures of diversity can provide a congruent picture of the distribution of intraspecific variation. The results also suggest that future work should explore the role of the River Niger as a natural barrier to migration in Nigeria.
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Affiliation(s)
- Bukola G. Oguntuase
- Department of Ecotourism and Wildlife ManagementFederal University of TechnologyAkureNigeria
| | - Babafemi G. Ogunjemite
- Department of Ecotourism and Wildlife ManagementFederal University of TechnologyAkureNigeria
| | - Richard P. Meisel
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexas
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5
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The Colorful Sex Chromosomes of Teleost Fish. Genes (Basel) 2018; 9:genes9050233. [PMID: 29751562 PMCID: PMC5977173 DOI: 10.3390/genes9050233] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/14/2022] Open
Abstract
Teleost fish provide some of the most intriguing examples of sexually dimorphic coloration, which is often advantageous for only one of the sexes. Mapping studies demonstrated that the genetic loci underlying such color patterns are frequently in tight linkage to the sex-determining locus of a species, ensuring sex-specific expression of the corresponding trait. Several genes affecting color synthesis and pigment cell development have been previously described, but the color loci on the sex chromosomes have mostly remained elusive as yet. Here, we summarize the current knowledge about the genetics of such color loci in teleosts, mainly from studies on poeciliids and cichlids. Further studies on these color loci will certainly provide important insights into the evolution of sex chromosomes.
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6
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Morin PA, Foote AD, Hill CM, Simon-Bouhet B, Lang AR, Louis M. SNP Discovery from Single and Multiplex Genome Assemblies of Non-model Organisms. Methods Mol Biol 2018; 1712:113-144. [PMID: 29224072 DOI: 10.1007/978-1-4939-7514-3_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population genetic studies of non-model organisms often rely on initial ascertainment of genetic markers from a single individual or a small pool of individuals. This initial screening has been a significant barrier to beginning population studies on non-model organisms (Aitken et al., Mol Ecol 13:1423-1431, 2004; Morin et al., Trends Ecol Evol 19:208-216, 2004). As genomic data become increasingly available for non-model species, SNP ascertainment from across the genome can be performed directly from published genome contigs and short-read archive data. Alternatively, low to medium genome coverage from shotgun NGS library sequencing of single or pooled samples, or from reduced-representation libraries (e.g., capture enrichment; see Ref. "Hancock-Hanser et al., Mol Ecol Resour 13:254-268, 2013") can produce sufficient new data for SNP discovery with limited investment. We describe protocols for assembly of short read data to reference or related species genome contig sequences, followed by SNP discovery and filtering to obtain an optimal set of SNPs for population genotyping using a variety of downstream high-throughput genotyping methods.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA.
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Christopher M Hill
- Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Benoit Simon-Bouhet
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, 79360, Villiers-en-Bois, France
| | - Aimee R Lang
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 8901 La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Marie Louis
- Scottish Oceans Institute, University of St Andrews, East Sands, KY16 8LB, St Andrews, UK
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7
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Fu Z, Epstein B, Kelley JL, Zheng Q, Bergland AO, Castillo Carrillo CI, Jensen AS, Dahan J, Karasev AV, Snyder WE. Using NextRAD sequencing to infer movement of herbivores among host plants. PLoS One 2017; 12:e0177742. [PMID: 28505182 PMCID: PMC5432177 DOI: 10.1371/journal.pone.0177742] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 05/02/2017] [Indexed: 12/29/2022] Open
Abstract
Herbivores often move among spatially interspersed host plants, tracking high-quality resources through space and time. This dispersal is of particular interest for vectors of plant pathogens. Existing molecular tools to track such movement have yielded important insights, but often provide insufficient genetic resolution to infer spread at finer spatiotemporal scales. Here, we explore the use of Nextera-tagmented reductively-amplified DNA (NextRAD) sequencing to infer movement of a highly-mobile winged insect, the potato psyllid (Bactericera cockerelli), among host plants. The psyllid vectors the pathogen that causes zebra chip disease in potato (Solanum tuberosum), but understanding and managing the spread of this pathogen is limited by uncertainty about the insect's host plant(s) outside of the growing season. We identified 1,978 polymorphic loci among psyllids separated spatiotemporally on potato or in patches of bittersweet nightshade (S. dulcumara), a weedy plant proposed to be the source of potato-colonizing psyllids. A subset of the psyllids on potato exhibited genetic similarity to insects on nightshade, consistent with regular movement between these two host plants. However, a second subset of potato-collected psyllids was genetically distinct from those collected on bittersweet nightshade; this suggests that a currently unrecognized source, i.e., other nightshade patches or a third host-plant species, could be contributing to psyllid populations in potato. Oftentimes, dispersal of vectors of pathogens must be tracked at a fine scale in order to understand, predict, and manage disease spread. We demonstrate that emerging sequencing technologies that detect genome-wide SNPs of a vector can be used to infer such localized movement.
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Affiliation(s)
- Zhen Fu
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
| | - Brendan Epstein
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Qi Zheng
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
| | - Alan O. Bergland
- Department of Biology, Stanford University, Stanford, California, United States of America
| | | | - Andrew S. Jensen
- Northwest Potato Research Consortium, Lakeview, Oregon, United States of America
| | - Jennifer Dahan
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Alexander V. Karasev
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - William E. Snyder
- Department of Entomology, Washington State University, Pullman, Washington, United States of America
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8
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Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops. PLoS One 2016; 11:e0161876. [PMID: 27563719 PMCID: PMC5001709 DOI: 10.1371/journal.pone.0161876] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/12/2016] [Indexed: 12/05/2022] Open
Abstract
The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture.
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9
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Carlson JE, Holsinger KE. Extrapolating from local ecological processes to genus-wide patterns in colour polymorphism in South African Protea. Proc Biol Sci 2015; 282:20150583. [PMID: 25876847 PMCID: PMC4426637 DOI: 10.1098/rspb.2015.0583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022] Open
Abstract
Polymorphic traits are central to many fundamental discoveries in evolution, yet why they are found in some species and not others remains poorly understood. We use the African genus Protea-within which more than 40% of species have co-occurring pink and white floral colour morphs-to ask whether convergent evolution and ecological similarity could explain the genus-wide pattern of polymorphism. First, we identified environmental correlates of pink morph frequency across 28 populations of four species. Second, we determined whether the same correlates could predict species-level polymorphism and monomorphism across 31 species. We found that pink morph frequency increased with elevation in Protea repens and three section Exsertae species, increased eastward in P. repens, and increased with seed predation intensity in section Exsertae. For cross-species comparisons, populations of monomorphic pink species occurred at higher elevations than populations of monomorphic white species, and 18 polymorphic species spanned broader elevational gradients than 13 monomorphic species. These results suggest that divergent selection along elevational clines has repeatedly favoured polymorphism, and that more uniform selection in altitudinally restricted species may promote colour monomorphism. Our findings are, to our knowledge, the first to link selection acting within species to the presence and absence of colour polymorphism at broader phylogenetic scales.
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Affiliation(s)
- Jane E Carlson
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT 06269, USA
| | - Kent E Holsinger
- Department of Ecology and Evolutionary Biology, University of Connecticut, U-3043, Storrs, CT 06269, USA
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10
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Ding B, Daugherty DW, Husemann M, Chen M, Howe AE, Danley PD. Quantitative Genetic Analyses of Male Color Pattern and Female Mate Choice in a Pair of Cichlid Fishes of Lake Malawi, East Africa. PLoS One 2014; 9:e114798. [PMID: 25494046 PMCID: PMC4262453 DOI: 10.1371/journal.pone.0114798] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/29/2014] [Indexed: 12/28/2022] Open
Abstract
The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1-2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish.
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Affiliation(s)
- Baoqing Ding
- Biology Department, Baylor University, One Bear Place #97388, Waco, Texas, 76798, United States of America
| | - Daniel W. Daugherty
- Biology Department, Baylor University, One Bear Place #97388, Waco, Texas, 76798, United States of America
| | - Martin Husemann
- Biology Department, Baylor University, One Bear Place #97388, Waco, Texas, 76798, United States of America
| | - Ming Chen
- Biology Department, Baylor University, One Bear Place #97388, Waco, Texas, 76798, United States of America
| | - Aimee E. Howe
- Biology Department, Baylor University, One Bear Place #97388, Waco, Texas, 76798, United States of America
| | - Patrick D. Danley
- Biology Department, Baylor University, One Bear Place #97388, Waco, Texas, 76798, United States of America
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11
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Takahashi T, Nagata N, Sota T. Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol Phylogenet Evol 2014; 80:137-44. [DOI: 10.1016/j.ympev.2014.07.016] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022]
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12
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Sefc KM, Brown AC, Clotfelter ED. Carotenoid-based coloration in cichlid fishes. Comp Biochem Physiol A Mol Integr Physiol 2014; 173C:42-51. [PMID: 24667558 PMCID: PMC4003536 DOI: 10.1016/j.cbpa.2014.03.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/03/2014] [Accepted: 03/14/2014] [Indexed: 02/04/2023]
Abstract
Animal colors play important roles in communication, ecological interactions and speciation. Carotenoid pigments are responsible for many yellow, orange and red hues in animals. Whereas extensive knowledge on the proximate mechanisms underlying carotenoid coloration in birds has led to testable hypotheses on avian color evolution and signaling, much less is known about the expression of carotenoid coloration in fishes. Here, we promote cichlid fishes (Perciformes: Cichlidae) as a system in which to study the physiological and evolutionary significance of carotenoids. Cichlids include some of the best examples of adaptive radiation and color pattern diversification in vertebrates. In this paper, we examine fitness correlates of carotenoid pigmentation in cichlids and review hypotheses regarding the signal content of carotenoid-based ornaments. Carotenoid-based coloration is influenced by diet and body condition and is positively related to mating success and social dominance. Gaps in our knowledge are discussed in the last part of this review, particularly in the understanding of carotenoid metabolism pathways and the genetics of carotenoid coloration. We suggest that carotenoid metabolism and transport are important proximate mechanisms responsible for individual and population-differences in cichlid coloration that may ultimately contribute to diversification and speciation.
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Affiliation(s)
- Kristina M Sefc
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Alexandria C Brown
- Department of Biology, Amherst College, Amherst, MA 01002, USA; Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003 USA
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13
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Lancaster LT, McAdam AG, Hipsley CA, Sinervo BR. Frequency-dependent and correlational selection pressures have conflicting consequences for assortative mating in a color-polymorphic lizard, Uta stansburiana. Am Nat 2014; 184:188-97. [PMID: 25058279 DOI: 10.1086/676645] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Genetically determined polymorphisms incorporating multiple traits can persist in nature under chronic, fluctuating, and sometimes conflicting selection pressures. Balancing selection among morphs preserves equilibrium frequencies, while correlational selection maintains favorable trait combinations within each morph. Under negative frequency-dependent selection, females should mate (often disassortatively) with rare male morphotypes to produce conditionally fit offspring. Conversely, under correlational selection, females should mate assortatively to preserve coadapted gene complexes and avoid ontogenetic conflict. Using controlled breeding designs, we evaluated consequences of assortative mating patterns in color-polymorphic side-blotched lizards (Uta stansburiana), to identify conflict between these sources of selection. Females who mated disassortatively, and to conditionally high-quality males in the context of frequency-dependent selection, experienced highest fertility rates. In contrast, assortatively mated females experienced higher fetal viability rates. The trade-off between fertility and egg viability resulted in no overall fitness benefit to either assortative or disassortative mating patterns. These results suggest that ongoing conflict between correlational and frequency dependent selection in polymorphic populations may generate a trade-off between rare-morph advantage and phenotypic integration and between assortative and disassortative mating decisions. More generally, interactions among multiple sources of diversity-promoting selection can alter adaptations and dynamics predicted to arise under any of these regimes alone.
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Affiliation(s)
- Lesley T Lancaster
- Institute of Biological and Environmental Sciences, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, United Kingdom
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14
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Rieseberg L, Vines T, Gow J, Kane N. Molecular Ecology continues to perform well according to the major publication metrics. Introduction. Mol Ecol 2014; 23:1-15. [PMID: 24372750 DOI: 10.1111/mec.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
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15
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Bourgeois YXC, Lhuillier E, Cézard T, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Bouchez O, Milá B, Thébaud C. Mass production of
SNP
markers in a nonmodel passerine bird through
RAD
sequencing and contig mapping to the zebra finch genome. Mol Ecol Resour 2013; 13:899-907. [DOI: 10.1111/1755-0998.12137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Emeline Lhuillier
- INRA UAR 1209 Département de Génétique Animale INRA Auzeville F‐31326 Castanet‐Tolosan France
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Timothée Cézard
- The GenePool Ashworth Laboratories The University of Edinburgh The King's Building Edinburgh EH9 3JT UK
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Thomas Duval
- Société Calédonienne d'Ornithologie Nord BP 236 F‐98822 Poindimié Nouvelle Calédonie France
| | - Olivier Bouchez
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
- INRA UMR 444 Laboratoire de Génétique Cellulaire INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Borja Milá
- Museo Nacional de Ciencias Naturales CSIC José Gutiérrez Abascal 2 Madrid 28006 Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
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Maan ME, Sefc KM. Colour variation in cichlid fish: developmental mechanisms, selective pressures and evolutionary consequences. Semin Cell Dev Biol 2013; 24:516-28. [PMID: 23665150 PMCID: PMC3778878 DOI: 10.1016/j.semcdb.2013.05.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 04/15/2013] [Accepted: 05/01/2013] [Indexed: 12/17/2022]
Abstract
Cichlid fishes constitute one of the most species-rich families of vertebrates. In addition to complex social behaviour and morphological versatility, they are characterised by extensive diversity in colouration, both within and between species. Here, we review the cellular and molecular mechanisms underlying colour variation in this group and the selective pressures responsible for the observed variation. We specifically address the evidence for the hypothesis that divergence in colouration is associated with the evolution of reproductive isolation between lineages. While we conclude that cichlid colours are excellent models for understanding the role of animal communication in species divergence, we also identify taxonomic and methodological biases in the current research effort. We suggest that the integration of genomic approaches with ecological and behavioural studies, across the entire cichlid family and beyond it, will contribute to the utility of the cichlid model system for understanding the evolution of biological diversity.
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Affiliation(s)
- Martine E. Maan
- University of Groningen, Behavioural Biology, PO Box 11103, 9700 CC Groningen, The Netherlands
| | - Kristina M. Sefc
- Institute of Zoology, University of Graz, Universitätsplatz 2, A-8010 Graz, Austria
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17
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Narum SR, Buerkle CA, Davey JW, Miller MR, Hohenlohe PA. Genotyping-by-sequencing in ecological and conservation genomics. Mol Ecol 2013; 22:2841-7. [PMID: 23711105 DOI: 10.1111/mec.12350] [Citation(s) in RCA: 343] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 12/12/2022]
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O'Quin CT, Drilea AC, Conte MA, Kocher TD. Mapping of pigmentation QTL on an anchored genome assembly of the cichlid fish, Metriaclima zebra. BMC Genomics 2013; 14:287. [PMID: 23622422 PMCID: PMC3691601 DOI: 10.1186/1471-2164-14-287] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/25/2013] [Indexed: 12/28/2022] Open
Abstract
Background Pigmentation patterns are one of the most recognizable phenotypes across the animal kingdom. They play an important role in camouflage, communication, mate recognition and mate choice. Most progress on understanding the genetics of pigmentation has been achieved via mutational analysis, with relatively little work done to understand variation in natural populations. Pigment patterns vary dramatically among species of cichlid fish from Lake Malawi, and are thought to be important in speciation. In this study, we crossed two species, Metriaclima zebra and M. mbenjii, that differ in several aspects of their body and fin color. We genotyped 798 SNPs in 160 F2 male individuals to construct a linkage map that was used to identify quantitative trait loci (QTL) associated with the pigmentation traits of interest. We also used the linkage map to anchor portions of the M. zebra genome assembly. Results We constructed a linkage map consisting of 834 markers in 22 linkage groups that spanned over 1,933 cM. QTL analysis detected one QTL each for dorsal fin xanthophores, caudal fin xanthophores, and pelvic fin melanophores. Dorsal fin and caudal fin xanthophores share a QTL on LG12, while pelvic fin melanophores have a QTL on LG11. We used the mapped markers to anchor 66.5% of the M. zebra genome assembly. Within each QTL interval we identified several candidate genes that might play a role in pigment cell development. Conclusion This is one of a few studies to identify QTL for natural variation in fish pigmentation. The QTL intervals we identified did not contain any pigmentation genes previously identified by mutagenesis studies in other species. We expect that further work on these intervals will identify new genes involved in pigment cell development in natural populations.
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Richards PM, Liu MM, Lowe N, Davey JW, Blaxter ML, Davison A. RAD-Seq derived markers flank the shell colour and banding loci of the Cepaea nemoralis supergene. Mol Ecol 2013; 22:3077-89. [PMID: 23496771 PMCID: PMC3712483 DOI: 10.1111/mec.12262] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 01/11/2013] [Accepted: 01/15/2013] [Indexed: 01/24/2023]
Abstract
Studies on the classic shell colour and banding polymorphism of the land snail Cepaea played a crucial role in establishing the importance of natural selection in maintaining morphological variation. Cepaea is also a pre-eminent model for ecological genetics because the outward colour and banding phenotype is entirely genetically determined, primarily by a 'supergene' of at least five loci. Unfortunately, progress in understanding the evolution and maintenance of the Cepaea polymorphism stalled, partly because of a lack of genetic markers. With a view to re-establish Cepaea as a prominent model of molecular ecology, we made six laboratory crosses of Cepaea nemoralis, five of which segregated for shell ground colour (C) and the presence or absence of bands (B). First, scoring of colour and banding in 323 individuals found no recombination between the C and B loci of the supergene. Second, using restriction site-associated DNA sequencing (RAD-Seq) of two parents and 22 offspring, we identified 44 anonymous markers putatively linked to the colour (C) and banding (B) loci. The genotype of eleven of the most promising RAD-Seq markers was independently validated in the same 22 offspring, then up to a further 146 offspring were genotyped. The closest RAD-Seq markers scored are within ~0.6 centimorgan (cM) of the C-B supergene linkage group, with the combined loci together forming a 35.8 cM linkage map of markers that flank both sides of the Cepaea C-B supergene.
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Affiliation(s)
- Paul M Richards
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Nottingham, NG7 2RD, UK
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