1
|
Soria E, Lu Q, Boswell W, Du K, Xing Y, Boswell M, Weldon KS, Lai Z, Savage M, Schartl M, Lu Y. Segregation Between an Ornamental and a Disease Driver Gene Provides Insights Into Pigment Cell Regulation. Pigment Cell Melanoma Res 2024. [PMID: 39289030 DOI: 10.1111/pcmr.13196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/18/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024]
Abstract
Genetic interactions are adaptive within a species. Hybridization can disrupt such species-specific genetic interactions and creates novel interactions that alter the hybrid progeny overall fitness. Hybrid incompatibility, which refers to degenerative genetic interactions that decrease the overall hybrid survival and sterility, is one of the results from combining two diverged genomes in hybrids. The discovery of spontaneous lethal tumorigenesis and underlying genetic interactions in select hybrids between diverged Xiphophorus species showed that lethal pathological process can result from degenerative genetic interactions. Such genetic interactions leading to lethal phenotype are thought to shield gene flow between diverged species. However, hybrids between certain Xiphophorus species do not develop such tumors. Here we report the identification of a locus residing in the genome of one Xiphophorus species that represses an oncogene from a different species. Our finding provides insights into normal and pathological pigment cell development, regulation and a molecular mechanism in hybrid incompatibility.
Collapse
Affiliation(s)
- Erika Soria
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | | | - Will Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Yanting Xing
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Korri S Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas, USA
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| |
Collapse
|
2
|
Du K, Ricci JMB, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge TO, Schumer M, Park H, Meyer A, Schartl M. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat Commun 2024; 15:6609. [PMID: 39098897 PMCID: PMC11298535 DOI: 10.1038/s41467-024-50852-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/16/2024] [Indexed: 08/06/2024] Open
Abstract
Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the genus Xiphophorus are proposed to have evolved with multiple ancient and ongoing hybridization events. They have served as an informative research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genomic resource including annotations for all described 26 Xiphophorus species and three undescribed taxa and resolve all uncertain phylogenetic relationships. We investigate the molecular evolution of genes related to cancers such as melanoma and for the genetic control of puberty timing, focusing on genes that are predicted to be involved in pre-and postzygotic isolation and thus affect hybridization. We discovered dramatic size-variation of some gene families. These persisted despite reticulate evolution, rapid speciation and short divergence time. Finally, we clarify the hybridization history in the entire genus settling disputed hybridization history of two Southern swordtails. Our comparative genomic analyses revealed hybridization ancestries that are manifested in the mosaic fused genomes and show that hybridization often preceded speciation.
Collapse
Affiliation(s)
- Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | | | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Mateo Garcia-Olazabal
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, MI, USA
| | - Tristram O Dodge
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Molly Schumer
- Department of Biology & Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Hyun Park
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, TX, USA.
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, Wuerzburg, Germany.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
| |
Collapse
|
3
|
Soria E, Lu Q, Boswell W, Du K, Xing Y, Boswell M, Weldon KS, Lai Z, Savage M, Schartl M, Lu Y. Segregation between an ornamental and a disease driver gene provides insights into pigment cell regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595041. [PMID: 38826429 PMCID: PMC11142077 DOI: 10.1101/2024.05.20.595041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Genetic interactions are adaptive within a species. Hybridization can disrupt such species-specific genetic interactions and creates novel interactions that alter the hybrid progeny overall fitness. Hybrid incompatibility, which refers to degenerative genetic interactions that decrease the overall hybrid survival, is one of the results from combining two diverged genomes in hybrids. The discovery of spontaneous lethal tumorigenesis and underlying genetic interactions in select hybrids between diverged Xiphophorus species showed that lethal pathological process can result from degenerative genetic interactions. Such genetic interactions leading to lethal phenotype are thought to shield gene flow between diverged species. However, hybrids between certain Xiphophorus species do not develop such tumors. Here we report the identification of a locus residing in the genome of one Xiphophorus species that represses an oncogene from a different species. Our finding provides insights into normal and pathological pigment cell development, regulation and molecular mechanism in hybrid incompatibility. Significance The Dobzhansky-Muller model states epistatic interactions occurred between genes in diverged species underlies hybrid incompatibility. There are a few vertebrate interspecies hybrid cases that support the Dobzhansky-Muller model. This study reports a fish hybrid system where incompatible genetic interactions are involved in neuronal regulation of pigment cell biology, and also identified a novel point of regulation for pigment cells.
Collapse
|
4
|
Rodríguez-Machado S, Elías DJ, McMahan CD, Gruszkiewicz-Tolli A, Piller KR, Chakrabarty P. Disentangling historical relationships within Poeciliidae (Teleostei: Cyprinodontiformes) using ultraconserved elements. Mol Phylogenet Evol 2024; 190:107965. [PMID: 37977500 DOI: 10.1016/j.ympev.2023.107965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/18/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Poeciliids (Cyprinodontiformes: Poeciliidae), commonly known as livebearers, are popular fishes in the aquarium trade (e.g., guppies, mollies, swordtails) that are widely distributed in the Americas, with 274 valid species in 27 genera. This group has undergone various taxonomic changes recently, spurred by investigations using traditional genetic markers. Here we used over 1,000 ultraconserved loci to infer the relationships within Poeciliidae in the first attempt at understanding their diversification based on genome-scale data. We explore gene tree discordance and investigate potential incongruence between concatenation and coalescent inference methods. Our aim is to examine the influence of incomplete lineage sorting and reticulate evolution on the poeciliids' evolutionary history and how these factors contribute to the observed gene tree discordace. Our concatenated and coalescent phylogenomic inferences recovered four major clades within Poeciliidae. Most supra-generic level relationships we inferred were congruent with previous molecular studies, but we found some disagreements; the Middle American taxa Phallichthys and Poecilia (Mollienesia) were recovered as non-monophyletic, and unlike other recent molecular studies, we recovered Brachyrhaphis as monophyletic. Our study is the first to provide signatures of reticulate evolution in Poeciliidae at the family level; however, continued finer-scale investigations are needed to understand the complex evolutionary history of the family along with a much-needed taxonomic re-evaluation.
Collapse
Affiliation(s)
- Sheila Rodríguez-Machado
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Diego J Elías
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States; Field Museum of Natural History, Chicago, IL 60605, United States
| | - Caleb D McMahan
- Field Museum of Natural History, Chicago, IL 60605, United States
| | - Anna Gruszkiewicz-Tolli
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402, United States
| | - Kyle R Piller
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA 70402, United States
| | - Prosanta Chakrabarty
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| |
Collapse
|
5
|
Liu R, Friedrich M, Hemmen K, Jansen K, Adolfi MC, Schartl M, Heinze KG. Dimerization of melanocortin 4 receptor controls puberty onset and body size polymorphism. Front Endocrinol (Lausanne) 2023; 14:1267590. [PMID: 38027153 PMCID: PMC10667928 DOI: 10.3389/fendo.2023.1267590] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Xiphophorus fish exhibit a clear phenotypic polymorphism in puberty onset and reproductive strategies of males. In X. nigrensis and X. multilineatus, puberty onset is genetically determined and linked to a melanocortin 4 receptor (Mc4r) polymorphism of wild-type and mutant alleles on the sex chromosomes. We hypothesized that Mc4r mutant alleles act on wild-type alleles by a dominant negative effect through receptor dimerization, leading to differential intracellular signaling and effector gene activation. Depending on signaling strength, the onset of puberty either occurs early or is delayed. Here, we show by Förster Resonance Energy Transfer (FRET) that wild-type Xiphophorus Mc4r monomers can form homodimers, but also heterodimers with mutant receptors resulting in compromised signaling which explains the reduced Mc4r signaling in large males. Thus, hetero- vs. homo- dimerization seems to be the key molecular mechanism for the polymorphism in puberty onset and body size in male fish.
Collapse
Affiliation(s)
- Ruiqi Liu
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
- Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Mike Friedrich
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Katherina Hemmen
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Kerstin Jansen
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Mateus C. Adolfi
- Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States
| | - Katrin G. Heinze
- Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, Julius-Maximilians-Universität Würzburg (JMU), Wuerzburg, Germany
| |
Collapse
|
6
|
Lu Y, Rice E, Du K, Kneitz S, Naville M, Dechaud C, Volff JN, Boswell M, Boswell W, Hillier L, Tomlinson C, Milin K, Walter RB, Schartl M, Warren WC. High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis. Genome Res 2023; 33:557-571. [PMID: 37147111 PMCID: PMC10234306 DOI: 10.1101/gr.277434.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
Because of diverged adaptative phenotypes, fish species of the genus Xiphophorus have contributed to a wide range of research for a century. Existing Xiphophorus genome assemblies are not at the chromosomal level and are prone to sequence gaps, thus hindering advancement of the intra- and inter-species differences for evolutionary, comparative, and translational biomedical studies. Herein, we assembled high-quality chromosome-level genome assemblies for three distantly related Xiphophorus species, namely, X. maculatus, X. couchianus, and X. hellerii Our overall goal is to precisely assess microevolutionary processes in the clade to ascertain molecular events that led to the divergence of the Xiphophorus species and to progress understanding of genetic incompatibility to disease. In particular, we measured intra- and inter-species divergence and assessed gene expression dysregulation in reciprocal interspecies hybrids among the three species. We found expanded gene families and positively selected genes associated with live bearing, a special mode of reproduction. We also found positively selected gene families are significantly enriched in nonpolymorphic transposable elements, suggesting the dispersal of these nonpolymorphic transposable elements has accompanied the evolution of the genes, possibly by incorporating new regulatory elements in support of the Britten-Davidson hypothesis. We characterized inter-specific polymorphisms, structural variants, and polymorphic transposable element insertions and assessed their association to interspecies hybridization-induced gene expression dysregulation related to specific disease states in humans.
Collapse
Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA;
| | - Edward Rice
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon, France
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Kremitzki Milin
- McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA
| | - Ronald B Walter
- Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas 78666, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, 97074 Würzburg, Germany
| | - Wesley C Warren
- Department of Animal Sciences, Department of Surgery, Institute for Data Science and Informatics, University of Missouri, Bond Life Sciences Center, Columbia, Missouri 65201, USA
| |
Collapse
|
7
|
Fast KM, Rakestraw AW, Sandel MW. Complete mitochondrial genome of a livebearing freshwater fish (Cyprinodontiformes: Poeciliidae): Poecilia parae. Mitochondrial DNA B Resour 2023; 8:215-219. [PMID: 36761101 PMCID: PMC9904314 DOI: 10.1080/23802359.2023.2171246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Members of the fish family Poeciliidae (livebearing 'tooth-carps') have historically been used as models in medical research, behavior ecology, and biological control. This group of primarily freshwater fishes is highly tolerant to environmental factors such as salinity and warm temperatures and includes some invasive species. Here, we present the mitochondrial genome of Poecilia parae. A representative of this species was obtained from Suriname. The complete mitochondrial genome was sequenced using Oxford Nanopore technology and is 16,559 bp long. The genome contains 13 protein-coding genes, two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one control region (D-loop). Phylogenetic analysis yielded topologies similar to those previously published. The data generated here will be useful in future studies of comparative biology and those utilizing environmental DNA (eDNA).
Collapse
Affiliation(s)
- Kayla M. Fast
- Department of Biological and Environmental Sciences, The University of West Alabama, Livingston, AL, USA,CONTACT Kayla M. Fast Department of Biological and Environmental Sciences, The University of West Alabama, Livingston, AL, USA
| | - Alex W. Rakestraw
- Department of Biological and Environmental Sciences, The University of West Alabama, Livingston, AL, USA
| | - Michael W. Sandel
- Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, Mississippi State, MS, USA,Michael W. Sandel Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University, Mississippi State, MS, USA
| |
Collapse
|
8
|
Russo C, Drewery M, Chang CT, Savage M, Sanchez L, Varga Z, Kent ML, Walter R, Lu Y. Assessment of Various Standard Fish Diets on Growth and Fecundity of Platyfish ( Xiphophorus maculatus) and Medaka ( Oryzias latipes). Zebrafish 2022; 19:181-189. [PMID: 35862011 PMCID: PMC9595639 DOI: 10.1089/zeb.2022.0004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Several small freshwater fish species are utilized as models for human conditions and disease in biomedical research. Research animal diets are generally tailored to optimize growth, fecundity, and produce healthy research animals. However, a lack of reference diets presents a barrier in comparative studies between aquatic animal models and even among laboratories using the same species. Therefore, the objective of this study was to determine feeding regime and dietary effects on growth and fecundity in two commonly used freshwater fish, platyfish and medaka. From 1 through 6 months of age, platyfish and medaka were fed one of three feeding regime/diets: (1) our custom feeding regime consists of commercial flake food, beef liver paste, and live brine shrimp (CON); (2) a commercially available zebrafish diet, Gemma (GEM); and (3) a laboratory defined reference feeding regime (WAT). Weight, size, brood numbers, and survival rates for both species were measured monthly. Numbers of platyfish fry and hatch rate of medaka embryos were also determined. We observed that custom feeding regime (CON) fed platyfish and medaka grew larger, exhibited a higher survival rate, and had higher fecundity than WAT or GEM fed fish. These observations suggest that diets and regimes designed for zebrafish are not optimal to maintain platyfish or medaka. Thus, base diets, with clearly defined components and regimes, need to be developed with compositions that can be adjusted in a species-specific manner.
Collapse
Affiliation(s)
- Crystal Russo
- Department of Agricultural Sciences and Texas State University, San Marcos, Texas, USA
| | - Merritt Drewery
- Department of Agricultural Sciences and Texas State University, San Marcos, Texas, USA
| | - Carolyn T. Chang
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Markita Savage
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Lindsey Sanchez
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Zoltan Varga
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon, USA
| | - Michael L. Kent
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Ronald Walter
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| | - Yuan Lu
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, Texas, USA
| |
Collapse
|
9
|
Gao JJ, Barmina O, Thompson A, Kim BY, Suvorov A, Tanaka K, Watabe H, Toda MJ, Chen JM, Katoh TK, Kopp A. Secondary reversion to sexual monomorphism associated with tissue-specific loss of doublesex expression. Evolution 2022; 76:2089-2104. [PMID: 35841603 DOI: 10.1111/evo.14564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 01/22/2023]
Abstract
Animal evolution is characterized by frequent turnover of sexually dimorphic traits-new sex-specific characters are gained, and some ancestral sex-specific characters are lost, in many lineages. In insects, sexual differentiation is predominantly cell autonomous and depends on the expression of the doublesex (dsx) transcription factor. In most cases, cells that transcribe dsx have the potential to undergo sex-specific differentiation, while those that lack dsx expression do not. Consistent with this mode of development, comparative research has shown that the origin of new sex-specific traits can be associated with the origin of new spatial domains of dsx expression. In this report, we examine the opposite situation-a secondary loss of the sex comb, a male-specific grasping structure that develops on the front legs of some drosophilid species. We show that while the origin of the sex comb is linked to an evolutionary gain of dsx expression in the leg, sex comb loss in a newly identified species of Lordiphosa (Drosophilidae) is associated with a secondary loss of dsx expression. We discuss how the developmental control of sexual dimorphism affects the mechanisms by which sex-specific traits can evolve.
Collapse
Affiliation(s)
- Jian-Jun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, China.,State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, China
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, USA
| | - Ammon Thompson
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Anton Suvorov
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kohtaro Tanaka
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, USA
| | - Hideaki Watabe
- The Hokkaido University Museum, Kita-10, Nishi-8, Kitaku, Sapporo, 060-0810, Japan
| | - Masanori J Toda
- The Hokkaido University Museum, Kita-10, Nishi-8, Kitaku, Sapporo, 060-0810, Japan
| | - Ji-Min Chen
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, China
| | - Takehiro K Katoh
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, China
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, Davis, CA, 95616, USA
| |
Collapse
|
10
|
Thacker CE, Geiger DL, Unmack PJ. Species delineation and systematics of a hemiclonal hybrid complex in Australian freshwaters (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris). ROYAL SOCIETY OPEN SCIENCE 2022; 9:220201. [PMID: 35911191 PMCID: PMC9326278 DOI: 10.1098/rsos.220201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
The rivers of southeastern Australia host a species complex within the carp gudgeon genus Hypseleotris that includes parental species and hemiclonal hybrid lineages. These hemiclones can be difficult to distinguish from their parent taxa, making delineation of species unusually difficult. We approach this historical taxonomic problem by using single nucleotide polymorphism (SNP) genotyping to distinguish individuals of each species and hemiclones, enabling us to quantify the variation among evolutionary lineages and assign names to the species. Hypseleotris klunzingeri remains valid and does not have any hemiclones. We describe Hypseleotris bucephala and Hypseleotris gymnocephala from the Murray-Darling Basin and Hypseleotris acropinna from the Murray-Darling as well as eastern coastal streams north of the Mary River, part of the range attributed to H. galii. We further split H. galii to distinguish a species from the Mary River, Hypseleotris moolooboolaensis. We designate a neotype and redescribe H. galii due to uncertainty about the source and species identity of specimens used in the original description. We reconcile previous taxonomies, provide new common names for parental species, and advocate using the scientific names of both parents when referring to the hemiclone hybrids to avoid confusion with previous common names that did not distinguish parental taxa and hemiclones.
Collapse
Affiliation(s)
- Christine E. Thacker
- Department of Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
- Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007, USA
| | - Daniel L. Geiger
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Peter J. Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia
| |
Collapse
|
11
|
Eastis AN, Fast KM, Sandel MW. The complete mitochondrial genome of the Variable Platyfish Xiphophorus variatus. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2640-2642. [PMID: 34409164 PMCID: PMC8366644 DOI: 10.1080/23802359.2021.1963339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We present the complete mitochondrial genome sequence of the Variable Platyfish, Xiphophorus variatus (Meek 1904) (Cyprinodontiformes: Poeciliidae). The genome consists of 16,624 bp which encodes 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 control region. Genome-wide nucleotide composition is 27.79% adenine, 31.11% cytosine, 15.63% guanine, and 25.48% thymine. The X. variatus mitochondrial genome shares similar GC content and identical gene order and gene strand location with other members of Poeciliidae. The sequence presented herein will be of utility for future phylogenetic and biomedical research and for designing primers for species detection from environmental DNA samples.
Collapse
Affiliation(s)
- Anna Nicole Eastis
- Department of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, USA
| | - Kayla Marie Fast
- Department of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, USA
| | - Michael Warren Sandel
- Department of Biological and Environmental Sciences, University of West Alabama, Livingston, AL, USA
| |
Collapse
|
12
|
Kozak KM, Joron M, McMillan WO, Jiggins CD. Rampant Genome-Wide Admixture across the Heliconius Radiation. Genome Biol Evol 2021; 13:evab099. [PMID: 33944917 PMCID: PMC8283734 DOI: 10.1093/gbe/evab099] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a genomic representation of 40 out of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of Heliconius erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of Heliconius melpomene and relatives. We identify Heliconius hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.
Collapse
Affiliation(s)
- Krzysztof M Kozak
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| | - Mathieu Joron
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, EPHE, IRD, France
| | | | - Chris D Jiggins
- Smithsonian Tropical Research Institute, Panamá, Panamá
- Department of Zoology, University of Cambridge, United Kingdom
| |
Collapse
|
13
|
Safian D, Wiegertjes GF, Pollux BJA. The Fish Family Poeciliidae as a Model to Study the Evolution and Diversification of Regenerative Capacity in Vertebrates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The capacity of regenerating a new structure after losing an old one is a major challenge in the animal kingdom. Fish have emerged as an interesting model to study regeneration due to their high and diverse regenerative capacity. To date, most efforts have focused on revealing the mechanisms underlying fin regeneration, but information on why and how this capacity evolves remains incomplete. Here, we propose the livebearing fish family Poeciliidae as a promising new model system to study the evolution of fin regeneration. First, we review the current state of knowledge on the evolution of regeneration in the animal kingdom, with a special emphasis on fish fins. Second, we summarize recent advances in our understanding of the mechanisms behind fin regeneration in fish. Third, we discuss potential evolutionary pressures that may modulate the regenerative capacity of fish fins and propose three new theories for how natural and sexual selection can lead to the evolution of fin regeneration: (1) signaling-driven fin regeneration, (2) predation-driven fin regeneration, and (3) matrotrophy-suppressed fin regeneration. Finally, we argue that fish from the family Poeciliidae are an excellent model system to test these theories, because they comprise of a large variety of species in a well-defined phylogenetic framework that inhabit very different environments and display remarkable variation in reproductive traits, allowing for comparative studies of fin regeneration among closely related species, among populations within species or among individuals within populations. This new model system has the potential to shed new light on the underlying genetic and molecular mechanisms driving the evolution and diversification of regeneration in vertebrates.
Collapse
|
14
|
Schartl M, Kneitz S, Ormanns J, Schmidt C, Anderson JL, Amores A, Catchen J, Wilson C, Geiger D, Du K, Garcia-Olazábal M, Sudaram S, Winkler C, Hedrich R, Warren WC, Walter R, Meyer A, Postlethwait JH. The Developmental and Genetic Architecture of the Sexually Selected Male Ornament of Swordtails. Curr Biol 2021; 31:911-922.e4. [PMID: 33275891 PMCID: PMC8580132 DOI: 10.1016/j.cub.2020.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 11/11/2020] [Indexed: 12/21/2022]
Abstract
Sexual selection results in sex-specific characters like the conspicuously pigmented extension of the ventral tip of the caudal fin-the "sword"-in males of several species of Xiphophorus fishes. To uncover the genetic architecture underlying sword formation and to identify genes that are associated with its development, we characterized the sword transcriptional profile and combined it with genetic mapping approaches. Results showed that the male ornament of swordtails develops from a sexually non-dimorphic prepattern of transcription factors in the caudal fin. Among genes that constitute the exclusive sword transcriptome and are located in the genomic region associated with this trait we identify the potassium channel, Kcnh8, as a sword development gene. In addition to its neural function kcnh8 performs a known role in fin growth. These findings indicate that during evolution of swordtails a brain gene has been co-opted for an additional novel function in establishing a male ornament.
Collapse
Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA.
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jenny Ormanns
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Cornelia Schmidt
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Jennifer L Anderson
- Systematic Biology, Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Julian Catchen
- Department of Animal Biology, University of Illinois, Urbana, IL 6812, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA
| | - Dietmar Geiger
- Julius-von-Sachs-Institute for Biosciences, Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | | | - Sudha Sudaram
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Rainer Hedrich
- Julius-von-Sachs-Institute for Biosciences, Molecular Plant Physiology and Biophysics, Biocenter, University Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Wesley C Warren
- 440G Bond Life Sciences Center, 1201 Rollins Street, University of Missouri, Columbia, MO 65211, USA
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
| | | |
Collapse
|
15
|
Liu R, Du K, Ormanns J, Adolfi MC, Schartl M. Melanocortin 4 receptor signaling and puberty onset regulation in Xiphophorus swordtails. Gen Comp Endocrinol 2020; 295:113521. [PMID: 32470471 DOI: 10.1016/j.ygcen.2020.113521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/15/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023]
Abstract
Fish of the genus Xiphophorus provide a prominent example of genetic control of male body size and reproductive tactics. In X.nigrensis and X.multilineatus, puberty onset and body length are determined by melanocortin 4 receptor (Mc4r) allelic and copy number variations which were proposed to fine-tune the signaling output of the system. Accessory protein Mrap2 is required for growth across species by affecting Mc4r signaling. The molecular mechanism how Mc4r signaling controls puberty regulation in Xiphophorus and whether the interaction with Mrap2 is also involved was so far unclear. Hence, we examined Mc4r and Mrap2 in X.nigrensis and X.multilineatus, in comparison to a more distantly related species, X.hellerii. mc4r and mrap2 transcripts co-localized in the hypothalamus and preoptic regions in large males, small males and females of X.nigrensis, with similar signal strength for mrap2 but higher expression of mc4r in large males. This overexpression is constituted by wild-type and one subtype of mutant alleles. In vitro studies revealed that Mrap2 co-expressed with Mc4r increased cAMP production but did not change EC50. Cells co-expressing the wild-type and one mutant allele showed lower cAMP signaling than Mc4r wild-type cells. This indicates a role of Mc4r alleles, but not Mrap2, in puberty signaling. Different from X.nigrensis and X.multilineatus, X.hellerii has only wild-type alleles, but also shows a puberty onset and body length polymorphism, despite the absence of mutant alleles. Like in the two other species, mc4r and mrap2 transcripts colocalized and mc4r is expressed at substantially higher levels in large males. This demonstrates that puberty and growth regulation mechanism may not be identical even within same genus.
Collapse
MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Alleles
- Amino Acid Sequence
- Animals
- Cyprinodontiformes/genetics
- Cyprinodontiformes/metabolism
- DNA Copy Number Variations/genetics
- Female
- Gene Expression Regulation, Developmental
- Male
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, Melanocortin, Type 4/chemistry
- Receptor, Melanocortin, Type 4/genetics
- Receptor, Melanocortin, Type 4/metabolism
- Sexual Maturation/physiology
- Signal Transduction
Collapse
Affiliation(s)
- Ruiqi Liu
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Kang Du
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Jenny Ormanns
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mateus C Adolfi
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA.
| |
Collapse
|
16
|
Huang J. Is population subdivision different from speciation? From phylogeography to species delimitation. Ecol Evol 2020; 10:6890-6896. [PMID: 32760499 PMCID: PMC7391551 DOI: 10.1002/ece3.6524] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Species-level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model-based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.
Collapse
Affiliation(s)
- Jen‐Pan Huang
- Biodiversity Research CenterAcademia SinicaTaipeiTaiwan
| |
Collapse
|
17
|
Ichthyological Differentiation and Homogenization in the Pánuco Basin, Mexico. DIVERSITY 2020. [DOI: 10.3390/d12050187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Species introductions and extirpations are key aspects of aquatic ecosystem change that need to be examined at large geographic and temporal scales. The Pánuco Basin (Eastern Mexico) has high ichthyological diversity and ecological heterogeneity. However, freshwater fish (FWF) introductions and extirpations since the mid-1900s have modified species range and distribution. We examine changes in FWF species composition in and among four sub-basins of the Pánuco by comparing fish collection records pre-1980 to 2018. Currently, the FWF of the Pánuco includes 95 species. Fishes in the Poeciliidae, Cyprinidae, and Cichlidae, respectively, comprised most records over time. Significant differences in species composition were found between the first (pre-1980) and last (2011–2018) study periods, but not for periods in-between. Eight independent species groups were key for explaining changes in Pánuco river ichthyofauna; one group was dominated by invasive species, and saw increases in the number of records across study periods (faunal homogenization). Another group was formed by species with conservation concern with a declining number of records over time. Thirteen (2 native and 11 non-native) species were responsible for temporal turnover. These results strongly suggest high rates of differentiation over time (via native species loss) following widespread non-native species introductions.
Collapse
|
18
|
Kottler VA, Feron R, Nanda I, Klopp C, Du K, Kneitz S, Helmprobst F, Lamatsch DK, Lopez-Roques C, Lluch J, Journot L, Parrinello H, Guiguen Y, Schartl M. Independent Origin of XY and ZW Sex Determination Mechanisms in Mosquitofish Sister Species. Genetics 2020; 214:193-209. [PMID: 31704715 PMCID: PMC6944411 DOI: 10.1534/genetics.119.302698] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Fish are known for the outstanding variety of their sex determination mechanisms and sex chromosome systems. The western (Gambusia affinis) and eastern mosquitofish (G. holbrooki) are sister species for which different sex determination mechanisms have been described: ZZ/ZW for G. affinis and XX/XY for G. holbrooki Here, we carried out restriction-site associated DNA (RAD-) and pool sequencing (Pool-seq) to characterize the sex chromosomes of both species. We found that the ZW chromosomes of G. affinis females and the XY chromosomes of G. holbrooki males correspond to different linkage groups, and thus evolved independently from separate autosomes. In interspecific hybrids, the Y chromosome is dominant over the W chromosome, and X is dominant over Z. In G. holbrooki, we identified a candidate region for the Y-linked melanic pigmentation locus, a rare male phenotype that constitutes a potentially sexually antagonistic trait and is associated with other such characteristics, e.g., large body size and aggressive behavior. We developed a SNP-based marker in the Y-linked allele of GIPC PDZ domain containing family member 1 (gipc1), which was linked to melanism in all tested G. holbrooki populations. This locus represents an example for a color locus that is located in close proximity to a putative sex determiner, and most likely substantially contributed to the evolution of the Y.
Collapse
Affiliation(s)
- Verena A Kottler
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
| | - Romain Feron
- INRA, UR1037 Fish Physiology and Genomics, 35000 Rennes, France
- University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Indrajit Nanda
- Institute for Human Genetics, Biocenter, University of Wuerzburg, 97074, Germany
| | - Christophe Klopp
- Sigenae, Mathématiques et Informatique Appliquées de Toulouse, INRA, 31326 Castanet Tolosan, France
| | - Kang Du
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
| | | | - Dunja K Lamatsch
- University of Innsbruck, Research Department for Limnology, Mondsee, 5310 Mondsee, Austria
| | | | - Jerôme Lluch
- INRA, US 1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France
| | - Laurent Journot
- Montpellier GenomiX (MGX), University Montpellier, CNRS, INSERM, 34094 France
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), University Montpellier, CNRS, INSERM, 34094 France
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, 35000 Rennes, France
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg, 97074, Germany
- Developmental Biochemistry, Biocenter, University of Wuerzburg, 97074, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas 77843
| |
Collapse
|
19
|
Maxwell SJ, Bordon AV, Rymer TL, Congdon BC. The birth of a species and the validity of hybrid nomenclature demonstrated with a revision of hybrid taxa within Strombidae (Neostromboidae). P BIOL SOC WASH 2019. [DOI: 10.2988/19-00007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Stephen J. Maxwell
- (SJM, TLR, BCC) College of Science and Engineering, James Cook University, Cairns Qld 4870 Australia
| | - Anton V. Bordon
- (AVB) Snezhnaya, 17-2-459, Moscow, 129323, The Russian Federation
| | - Tasmin L. Rymer
- (SJM, TLR, BCC) College of Science and Engineering, James Cook University, Cairns Qld 4870 Australia
| | - Bradley C. Congdon
- (SJM, TLR, BCC) College of Science and Engineering, James Cook University, Cairns Qld 4870 Australia
| |
Collapse
|
20
|
DiSciullo RA, Basolo AL. Body size, but not age‐at‐maturation or context, affects the expression of predator‐induced behavioural plasticity in female green swordtails (
Xiphophorus hellerii
). Ethology 2019. [DOI: 10.1111/eth.12974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
21
|
Parker E, Dornburg A, Domínguez-Domínguez O, Piller KR. Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae). Mol Phylogenet Evol 2019; 134:282-290. [DOI: 10.1016/j.ympev.2019.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 01/18/2023]
|
22
|
Liotta MN, Abbott JK, Rios-Cardenas O, Morris MR. Tactical dimorphism: the interplay between body shape and mating behaviour in the swordtail Xiphophorus multilineatus (Cyprinodontiformes: Poeciliidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Melissa N Liotta
- Department of Biological Sciences, The Ohio Center for Ecological and Evolutionary Studies, Ohio University, Athens, OH, USA
| | | | - Oscar Rios-Cardenas
- Instituto de Ecología A.C., Red de Biología Evolutiva, Xalapa, Veracruz, México
| | - Molly R Morris
- Department of Biological Sciences, The Ohio Center for Ecological and Evolutionary Studies, Ohio University, Athens, OH, USA
| |
Collapse
|
23
|
Intergeneric hybrids inform reproductive isolating barriers in the Antarctic icefish radiation. Sci Rep 2019; 9:5989. [PMID: 30979924 PMCID: PMC6461676 DOI: 10.1038/s41598-019-42354-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 03/29/2019] [Indexed: 12/02/2022] Open
Abstract
Interspecific hybridization or barriers to hybridization may have contributed to the diversification of Antarctic icefishes (Channichthyidae), but data supporting these hypotheses is scarce. To understand the potential for hybridization and to investigate reproductive isolating mechanisms among icefish species, we performed in vitro fertilization experiments using eggs from a female blackfin icefish Chaenocephalus aceratus and sperm from a male of another genera, the ocellated icefish Chionodraco rastrospinosus. Sequencing of genomic and mitochondrial DNA confirmed the intergeneric hybrid nature of resulting embryos which successfully developed and hatched as active larvae at about four and a half months during the Antarctic winter. This result demonstrates the compatibility of gametes of these two species and the viability of resulting zygotes and larvae. Due to logistic constraints and the slow developmental rate of icefishes, we could not test for long-term hybrid viability, fertility, fitness, or hybrid breakdown. Analysis of our fishing records and available literature, however, suggests that the strongest barriers to hybridization among parapatric icefish species are likely to be behavioral and characterized by assortative mating and species-specific courtship and nesting behaviors. This conclusion suggests that, in long-lived fish species with late sexual maturity and high energetic investment in reproduction like icefishes, pre-mating barriers are energetically more efficient than post-mating barriers to prevent hybridization.
Collapse
|
24
|
Romero‐Diaz C, Rivera JA, Ossip‐Drahos AG, Zúñiga‐Vega JJ, Vital‐García C, Hews DK, Martins EP. Losing the trait without losing the signal: Evolutionary shifts in communicative colour signalling. J Evol Biol 2019; 32:320-330. [DOI: 10.1111/jeb.13416] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 11/28/2022]
Affiliation(s)
| | - Julio A. Rivera
- School of Life Sciences Arizona State University Tempe Arizona
| | | | - José Jaime Zúñiga‐Vega
- Departamento de Ecología y Recursos Naturales Facultad de Ciencias Universidad Nacional Autónoma de México Mexico City Mexico
| | - Cuauhcihuatl Vital‐García
- Departamento de Ciencias Veterinarias Instituto de Ciencias Biomédicas Universidad Autónoma de Ciudad Juárez Ciudad Juárez Mexico
| | - Diana K. Hews
- Department of Biology Indiana State University Terre Haute Indiana
| | | |
Collapse
|
25
|
Goldberg DL, Landy JA, Travis J, Springer MS, Reznick DN. In love and war: The morphometric and phylogenetic basis of ornamentation, and the evolution of male display behavior, in the livebearer genus
Poecilia. Evolution 2019; 73:360-377. [DOI: 10.1111/evo.13671] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 12/06/2018] [Accepted: 12/09/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel L. Goldberg
- Behavior, Ecology, Evolution, and Systematics Section, School of Biological Sciences Illinois State University Normal Illinois 61761
- Department of Biology University of California Riverside California 92521
| | - Joseph A. Landy
- Department of Biological Science Florida State University Tallahassee Florida 32306
| | - Joseph Travis
- Department of Biological Science Florida State University Tallahassee Florida 32306
| | - Mark S. Springer
- Department of Biology University of California Riverside California 92521
| | - David N. Reznick
- Department of Biology University of California Riverside California 92521
| |
Collapse
|
26
|
Doellman MM, Egan SP, Ragland GJ, Meyers PJ, Hood GR, Powell THQ, Lazorchak P, Hahn DA, Berlocher SH, Nosil P, Feder JL. Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies. Ecol Evol 2019; 9:393-409. [PMID: 30680122 PMCID: PMC6342182 DOI: 10.1002/ece3.4758] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/30/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022] Open
Abstract
Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer whether standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency differences associated with early vs. late eclosion time within each host race were significantly related to geographic genetic variation and host race differentiation across four sites, arrayed from north to south along a 430-km transect, where the host races co-occur in sympatry in the Midwest United States. Host fruiting phenology is clinal, with both apple and hawthorn trees fruiting earlier in the North and later in the South. Thus, we expected alleles associated with earlier eclosion to be at higher frequencies in northern populations. This pattern was observed in the hawthorn race across all four populations; however, allele frequency patterns in the apple race were more complex. Despite the generally earlier eclosion timing of apple flies and corresponding apple fruiting phenology, alleles on chromosomes 2 and 3 associated with earlier emergence were paradoxically at lower frequency in the apple than hawthorn host race across all four sympatric sites. However, loci on chromosome 1 did show higher frequencies of early eclosion-associated alleles in the apple than hawthorn host race at the two southern sites, potentially accounting for their earlier eclosion phenotype. Thus, although extensive clinal genetic variation in the ancestral hawthorn race exists and contributed to the host shift to apple, further study is needed to resolve details of how this standing variation was selected to generate earlier eclosing apple fly populations in the North.
Collapse
Affiliation(s)
| | - Scott P. Egan
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Advanced Diagnostics and Therapeutics InitiativeUniversity of Notre DameNotre DameIndiana
- Department of BiosciencesRice UniversityHoustonTexas
| | - Gregory J. Ragland
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana
- Department of Integrative BiologyUniversity of Colorado–DenverDenverColorado
| | - Peter J. Meyers
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
| | - Glen R. Hood
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Department of Biological SciencesWayne State UniversityDetroitMichigan
| | - Thomas H. Q. Powell
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Department of Biological SciencesState University of New York–BinghamtonBinghamtonNew York
| | - Peter Lazorchak
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Department of Computer ScienceJohns Hopkins UniversityBaltimoreMaryland
| | - Daniel A. Hahn
- Department of Entomology and NematologyUniversity of FloridaGainesvilleFlorida
| | - Stewart H. Berlocher
- Department of EntomologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois
| | - Patrik Nosil
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Jeffrey L. Feder
- Department of Biological SciencesUniversity of Notre DameNotre DameIndiana
- Advanced Diagnostics and Therapeutics InitiativeUniversity of Notre DameNotre DameIndiana
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndiana
| |
Collapse
|
27
|
Franchini P, Jones JC, Xiong P, Kneitz S, Gompert Z, Warren WC, Walter RB, Meyer A, Schartl M. Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish. Nat Commun 2018; 9:5136. [PMID: 30510159 PMCID: PMC6277394 DOI: 10.1038/s41467-018-07648-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/13/2018] [Indexed: 01/13/2023] Open
Abstract
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome. Fish have a high diversity of sex-determining systems, but the mechanisms responsible for this are not well understood. Here, Franchini et al. show how hybridization and backcrossing have led to the evolution of a new sex chromosome in swordtail fish during 30 years of experimental evolution.
Collapse
Affiliation(s)
- Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Julia C Jones
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 75123, Sweden
| | - Peiwen Xiong
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | | | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63108, MO, USA
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, 78666-4616, TX, USA
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany. .,Radcliffe Institute for Advanced Study, Harvard University, 9 Garden Street, Cambridge, MA, 02139, USA.
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Am Hubland, 97074, Würzburg, Germany. .,Comprehensive Cancer Centre, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
28
|
In search of the Goldilocks zone for hybrid speciation. PLoS Genet 2018; 14:e1007613. [PMID: 30192761 PMCID: PMC6145587 DOI: 10.1371/journal.pgen.1007613] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/19/2018] [Accepted: 08/07/2018] [Indexed: 12/16/2022] Open
Abstract
Hybridization has recently gained considerable interest both as a unique opportunity for observing speciation mechanisms and as a potential engine for speciation. The latter remains a controversial topic. It was recently hypothesized that the reciprocal sorting of genetic incompatibilities from parental species could result in hybrid speciation, when the hybrid population maintains a mixed combination of the parental incompatibilities that prevents further gene exchange with both parental populations. However, the specifics of the purging/sorting process of multiple incompatibilities have not been examined theoretically. We here investigate the allele-frequency dynamics of an isolated hybrid population that results from a single hybridization event. Using models of two or four loci, we investigate the fate of one or two genetic incompatibilities of the Dobzhansky-Muller type (DMIs). We study how various parameters affect both the sorting/purging of the DMIs and the probability of observing hybrid speciation by reciprocal sorting. We find that the probability of hybrid speciation is strongly dependent on the linkage architecture (i.e. the order and recombination rate between loci along chromosomes), the population size of the hybrid population, and the initial relative contributions of the parental populations to the hybrid population. We identify a Goldilocks zone for specific linkage architectures and intermediate recombination rates, in which hybrid speciation becomes highly probable. Whereas an equal contribution of parental populations to the hybrid population maximizes the hybrid speciation probability in the Goldilocks zone, other linkage architectures yield unintuitive asymmetric maxima. We provide an explanation for this pattern, and discuss our results both with respect to the best conditions for observing hybrid speciation in nature and their implications regarding patterns of introgression in hybrid zones. Hybridization is observed ubiquitously in nature. Its outcome can range from extinction to the creation of new species. With respect to the latter, the probability of homoploid hybrid speciation, i.e. the formation of a new species as a result of a hybridization event without changes in the ploidy of the organism, is a hotly debated topic. Here, we analyze a minimal model for homoploid hybrid speciation, in which reproductive isolation is achieved by means of (postzygotic) Dobzhansky-Muller incompatibilities. When these postzygotic genetic incompatibilities are resolved in the hybrid population, their reciprocal sorting can result in reproductive isolation from both parental populations, thus creating a hybrid species. We show that, in accordance with the current literature, hybrid speciation tends to be rare. However, specific arrangements of the genes responsible for reproductive isolation can make reciprocal sorting almost unavoidable and thus create barriers to the parental population in an almost deterministic matter. We discuss the implications of these results for hybrid speciation and patterns of introgression in nature.
Collapse
|
29
|
Zimmer C, Riesch R, Jourdan J, Bierbach D, Arias-Rodriguez L, Plath M. Female Choice Undermines the Emergence of Strong Sexual Isolation between Locally Adapted Populations of Atlantic Mollies ( Poecilia mexicana). Genes (Basel) 2018; 9:E232. [PMID: 29724050 PMCID: PMC5977172 DOI: 10.3390/genes9050232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 11/16/2022] Open
Abstract
Divergent selection between ecologically dissimilar habitats promotes local adaptation, which can lead to reproductive isolation (RI). Populations in the Poecilia mexicana species complex have independently adapted to toxic hydrogen sulfide and show varying degrees of RI. Here, we examined the variation in the mate choice component of prezygotic RI. Mate choice tests across drainages (with stimulus males from another drainage) suggest that specific features of the males coupled with a general female preference for yellow color patterns explain the observed variation. Analyses of male body coloration identified the intensity of yellow fin coloration as a strong candidate to explain this pattern, and common-garden rearing suggested heritable population differences. Male sexual ornamentation apparently evolved differently across sulfide-adapted populations, for example because of differences in natural counterselection via predation. The ubiquitous preference for yellow color ornaments in poeciliid females likely undermines the emergence of strong RI, as female discrimination in favor of own males becomes weaker when yellow fin coloration in the respective sulfide ecotype increases. Our study illustrates the complexity of the (partly non-parallel) pathways to divergence among replicated ecological gradients. We suggest that future work should identify the genomic loci involved in the pattern reported here, making use of the increasing genomic and transcriptomic datasets available for our study system.
Collapse
Affiliation(s)
- Claudia Zimmer
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, China.
- Department of Ecology and Evolution, Goethe University of Frankfurt, Max-von-Laue-Straße 13, D-60438 Frankfurt am Main, Germany.
| | - Rüdiger Riesch
- Centre for Ecology, Evolution and Behaviour, School of Biological Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK.
| | - Jonas Jourdan
- Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, D-63571 Gelnhausen, Germany.
| | - David Bierbach
- Department of Biology and Ecology of Fishes, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, D-12587 Berlin, Germany.
| | - Lenin Arias-Rodriguez
- División Académica de Ciencias Biológicas, Universidad Juárez Autónoma de Tabasco (UJAT), 86150 Villahermosa, Tabasco, Mexico.
| | - Martin Plath
- College of Animal Science & Technology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling 712100, China.
| |
Collapse
|
30
|
Culumber ZW, Tobler M. Correlated evolution of thermal niches and functional physiology in tropical freshwater fishes. J Evol Biol 2018; 31:722-734. [DOI: 10.1111/jeb.13260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/13/2018] [Accepted: 02/23/2018] [Indexed: 11/30/2022]
Affiliation(s)
| | - Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| |
Collapse
|
31
|
Lamichhaney S, Han F, Webster MT, Andersson L, Grant BR, Grant PR. Rapid hybrid speciation in Darwin’s finches. Science 2018; 359:224-228. [DOI: 10.1126/science.aao4593] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Rapid hybrid speciation in Darwin's finches
Galapagos finches have driven hypotheses of how speciation occurs. Most commonly, it is assumed that natural selection separates species originating from a single population on the basis of variation in traits that confer advantages for survival and reproduction. Lamichhaney
et al.
document a case where cross-species hybridization established a reproductively isolated lineage, which demonstrates a process known as homoploid hybrid speciation in action (see the Perspective by Wagner). The authors used genetic markers and phenotypic analyses to create a pedigree that revealed how a cross-island migrant bred with a native species to form a self-perpetuating hybrid population that was reproductively isolated from both parental species.
Science
, this issue p.
224
; see also p.
157
Collapse
Affiliation(s)
- Sangeet Lamichhaney
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fan Han
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Matthew T. Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Peter R. Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| |
Collapse
|
32
|
Jimenez M, Goodchild SC, Stockwell CA, Lema SC. Characterization and phylogenetic analysis of complete mitochondrial genomes for two desert cyprinodontoid fishes, Empetrichthys latos and Crenichthys baileyi. Gene 2017; 626:163-172. [PMID: 28512060 DOI: 10.1016/j.gene.2017.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 04/04/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
Abstract
The Pahrump poolfish (Empetrichthys latos) and White River springfish (Crenichthys baileyi) are small-bodied teleost fishes (order Cyprinodontiformes) endemic to the arid Great Basin and Mojave Desert regions of western North America. These taxa survive as small, isolated populations in remote streams and springs and evolved to tolerate extreme conditions of high temperature and low dissolved oxygen. Both species have experienced severe population declines over the last 50-60years that led to some subspecies being categorized with protected status under the U.S. Endangered Species Act. Here we report the first sequencing of the complete mitochondrial DNA genomes for both E. l. latos and the moapae subspecies of C. baileyi. Complete mitogenomes of 16,546bp nucleotides were obtained from two E. l. latos individuals collected from introduced populations at Spring Mountain Ranch State Park and Shoshone Ponds Natural Area, Nevada, USA, while a single mitogenome of 16,537bp was sequenced for C. b. moapae. The mitogenomes of both species contain 13 protein-encoding genes, twenty-two tRNAs, and two rRNAs (12S and 18S) following the syntenic arrangement typical of Actinopterygiian fish mitogenomes, as well as D-loop control regions of 858bp for E. latos and 842bp for C. baileyi moapae. The two E. latos individuals exhibited only 0.0181% nucleotide sequence divergence across the entire mitogenome, implying little intraspecific mtDNA genetic variation. Comparative phylogenetic analysis of the poolfish and springfish mitochondrial genomes to available mitogenomes of other Cyprinodontoid fishes confirmed the close relationship of these oviparous Empetrichthys and Crenichthys genera to the viviparous goodeid fishes of central Mexico, and showed the combined clade of these fishes to be a sister group to the Profundulidae killifishes. Despite several significant life history and morphological differences between the Empetrichthyinae and Goodienae, estimates of evolutionary genetic distances using two partial regions of mtDNA point to inclusion of the Empetrichthys and Crenichthys genera within the family Goodeidae along with the goodeid fishes of central Mexico.
Collapse
Affiliation(s)
- Miguel Jimenez
- Alan Hancock College, Santa Maria, CA, USA; Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Shawn C Goodchild
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA; Environmental & Conservation Sciences Graduate Program, North Dakota State University, Fargo, ND, USA
| | - Craig A Stockwell
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Sean C Lema
- Biological Sciences Department, Center for Coastal Marine Sciences, California Polytechnic State University, San Luis Obispo, CA, USA.
| |
Collapse
|
33
|
Pitts PM, Volkoff H. Characterization of appetite-regulating factors in platyfish, Xiphophorus maculatus (Cyprinodontiformes Poeciliidae). Comp Biochem Physiol A Mol Integr Physiol 2017; 208:80-88. [PMID: 28377124 DOI: 10.1016/j.cbpa.2017.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022]
Abstract
The regulation of energy in fish, like most vertebrates, is a complex process that involves a number of brain and peripheral hormones. These signals include anorexigenic (e.g. cholecystokinin (CCK) and cocaine- and amphetamine-regulated transcript (CART)) as well as orexigenic (e.g. orexin and neuropeptide Y (NPY)) peptides. Platyfish, Xiphophorus maculatus, are freshwater viviparous fish for which little is known about the endocrine mechanisms regulating feeding. In order to elucidate the role of these peptides in the regulation of feeding of platyfish, we examined the effects of peripheral injections of CCK and orexin on feeding behavior and food intake. Injections of CCK decreased both food intake and searching behavior, while injections of orexin increased searching behavior but did not affect food consumption. In order to better characterize these peptides, we examined their mRNA tissue distribution and assessed the effects of a 10-day fast on their brain and intestine expressions in both males and females. CCK, CART, NPY and orexin all show widespread distributions in brain and several peripheral tissues, including intestine and gonads. Fasting induced decreases in both CCK and CART and an increase in orexin mRNA expressions in the brain and a decrease in CCK expression in the intestine, but did not affect either expressions of NPY. There were no significant sex-specific differences in either the behavioral responses to injections or the expression responses to fasting. The widespread distribution and the fasting-induced changes in expression of these peptides suggest that they might have several physiological roles in platyfish, including the regulation of feeding.
Collapse
Affiliation(s)
- Paul M Pitts
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Hélène Volkoff
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada; Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| |
Collapse
|
34
|
Pilakouta N, Correa MA, Alonzo SH. Predation Risk Reduces a Female Preference for Heterospecific Males in the Green Swordtail. Ethology 2016. [DOI: 10.1111/eth.12573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Natalie Pilakouta
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT USA
- Institute of Evolutionary Biology; University of Edinburgh; Edinburgh UK
- Institute of Biodiversity, Animal Health, and Comparative Medicine; University of Glasgow; Glasgow UK
| | - Maria A. Correa
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT USA
| | - Suzanne H. Alonzo
- Department of Ecology and Evolutionary Biology; Yale University; New Haven CT USA
- Department of Ecology and Evolutionary Biology; University of California Santa Cruz; Santa Cruz CA USA
| |
Collapse
|
35
|
Zhang K, Liu S, Chen DY, Chen X, Zhang GY. The complete mitochondrial genome of the Monterrey platyfish ( Xiphophorus couchianus). Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:4453-4454. [DOI: 10.3109/19401736.2015.1089567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kai Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China and
- BGI-Shenzhen, Shenzhen, China
| | - Sheng Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China and
- BGI-Shenzhen, Shenzhen, China
| | - Da-Yang Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China and
- BGI-Shenzhen, Shenzhen, China
| | - Xi Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China and
- BGI-Shenzhen, Shenzhen, China
| | | |
Collapse
|
36
|
Hulsey CD, Bell KL, García-de-León FJ, Nice CC, Meyer A. Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish? Ecol Evol 2016; 6:3684-3698. [PMID: 27186367 PMCID: PMC4853310 DOI: 10.1002/ece3.2121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/14/2016] [Accepted: 03/21/2016] [Indexed: 12/19/2022] Open
Abstract
Introgression might be exceptionally common during the evolution of narrowly endemic species. For instance, in the springs of the small and isolated Cuatro Ciénegas Valley, the mitogenome of the cichlid fish Herichthys cyanoguttatus could be rapidly introgressing into populations of the trophically polymorphic H. minckleyi. We used a combination of genetic and environmental data to examine the factors associated with this mitochondrial introgression. A reduced representation library of over 6220 single nucleotide polymorphisms (SNPs) from the nuclear genome showed that mitochondrial introgression into H. minckleyi is biased relative to the amount of nuclear introgression. SNP assignment probabilities also indicated that cichlids with more hybrid ancestry are not more commonly female providing no support for asymmetric backcrossing or hybrid‐induced sex‐ratio distortion in generating the bias in mitochondrial introgression. Smaller effective population size in H. minckleyi inferred from the SNPs coupled with sequences of all 13 mitochondrial proteins suggests that relaxed selection on the mitogenome could be facilitating the introgression of “H. cyanoguttatus” haplotypes. Additionally, we showed that springs with colder temperatures had greater amounts of mitochondrial introgression from H. cyanoguttatus. Relaxed selection in H. minckleyi coupled with temperature‐related molecular adaptation could be facilitating mitogenomic introgression into H. minckleyi.
Collapse
Affiliation(s)
| | - Katherine L Bell
- Department of Biology Texas State University, San Marcos 601 University Drive 78666 San Marcos Texas
| | - Francisco J García-de-León
- Laboratorio de Genética para la Conservación Centro de Investigaciones Biológicas del Noroeste PO Box 128 La Paz B.C.S. Mexico
| | - Chris C Nice
- Department of Biology Texas State University, San Marcos 601 University Drive 78666 San Marcos Texas
| | - Axel Meyer
- Department of Biology University of Konstanz Universitätstraße 10 78457 Konstanz Germany
| |
Collapse
|
37
|
Schumer M, Cui R, Powell DL, Rosenthal GG, Andolfatto P. Ancient hybridization and genomic stabilization in a swordtail fish. Mol Ecol 2016; 25:2661-79. [DOI: 10.1111/mec.13602] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/06/2016] [Accepted: 01/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
- Max Planck Institute for the Biology of Aging D‐50931 Cologne Germany
| | - Daniel L. Powell
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Gil G. Rosenthal
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca” 16 de Septiembre 392 Calnali Hidalgo 43230 Mexico
- Department of Biology Texas A&M University TAMU College Station TX 77843 USA
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology Princeton University Princeton NJ 08544 USA
- Lewis‐Sigler Institute for Integrative Genomics Princeton University Princeton NJ 08544 USA
| |
Collapse
|
38
|
Culumber ZW, Tobler M. Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus). BMC Evol Biol 2016; 16:44. [PMID: 26895994 PMCID: PMC4761163 DOI: 10.1186/s12862-016-0593-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/13/2016] [Indexed: 01/23/2023] Open
Abstract
Background Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested. Results By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species’ geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence. Conclusion The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0593-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zachary W Culumber
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| | - Michael Tobler
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
39
|
Shen Y, Chalopin D, Garcia T, Boswell M, Boswell W, Shiryev SA, Agarwala R, Volff JN, Postlethwait JH, Schartl M, Minx P, Warren WC, Walter RB. X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species. BMC Genomics 2016; 17:37. [PMID: 26742787 PMCID: PMC4705583 DOI: 10.1186/s12864-015-2361-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/30/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. RESULTS We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. CONCLUSIONS Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.
Collapse
Affiliation(s)
- Yingjia Shen
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
- Key Laboratory of Coastal and Wetland Ecosystems, Ministry of Education, A316 Environment and Ecology Bldg., Xiamen, Fujian, 361102, China.
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Tzintzuni Garcia
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Sergey A Shiryev
- The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Richa Agarwala
- The National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA.
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Unité Mixte de Recherche 5242, Centre National de la Recherche Scientifique, Université de Lyon I, Ecole Normale Supérieure de Lyon, Lyon, France.
| | - John H Postlethwait
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR, 97403, USA.
| | - Manfred Schartl
- Universität Würzburg, Physiologische Chemie I, Biozentrum, Am Hubland, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany.
| | - Patrick Minx
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA.
| | - Wesley C Warren
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA.
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| |
Collapse
|
40
|
|
41
|
Dall SRX, McNamara JM, Leimar O. Genes as cues: phenotypic integration of genetic and epigenetic information from a Darwinian perspective. Trends Ecol Evol 2015; 30:327-33. [PMID: 25944666 DOI: 10.1016/j.tree.2015.04.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
The development of multicellular organisms involves a delicate interplay between genetic and environmental influences. It is often useful to think of developmental systems as integrating available sources of information about current conditions to produce organisms. Genes and inherited physiology provide cues, as does the state of the environment during development. The integration systems themselves are under genetic control and subject to Darwinian selection, so we expect them to evolve to produce organisms that fit well with current ecological (including social) conditions. We argue for the scientific value of this explicitly informational perspective by providing detailed examples of how it can elucidate taxonomically diverse phenomena. We also present a general framework for linking genetic and phenotypic variation from an informational perspective. This application of Darwinian logic at the organismal level can elucidate genetic influences on phenotypic variation in novel and counterintuitive ways.
Collapse
Affiliation(s)
- Sasha R X Dall
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Tremough, Penryn TR10 9EZ, UK.
| | - John M McNamara
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, Tremough, Penryn TR10 9EZ, UK; School of Mathematics, University of Bristol, University Walk, Bristol BS8 1TW, UK
| | - Olof Leimar
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|
42
|
Frandsen PB, Calcott B, Mayer C, Lanfear R. Automatic selection of partitioning schemes for phylogenetic analyses using iterative k-means clustering of site rates. BMC Evol Biol 2015; 15:13. [PMID: 25887041 PMCID: PMC4327964 DOI: 10.1186/s12862-015-0283-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 01/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Model selection is a vital part of most phylogenetic analyses, and accounting for the heterogeneity in evolutionary patterns across sites is particularly important. Mixture models and partitioning are commonly used to account for this variation, and partitioning is the most popular approach. Most current partitioning methods require some a priori partitioning scheme to be defined, typically guided by known structural features of the sequences, such as gene boundaries or codon positions. Recent evidence suggests that these a priori boundaries often fail to adequately account for variation in rates and patterns of evolution among sites. Furthermore, new phylogenomic datasets such as those assembled from ultra-conserved elements lack obvious structural features on which to define a priori partitioning schemes. The upshot is that, for many phylogenetic datasets, partitioned models of molecular evolution may be inadequate, thus limiting the accuracy of downstream phylogenetic analyses. RESULTS We present a new algorithm that automatically selects a partitioning scheme via the iterative division of the alignment into subsets of similar sites based on their rates of evolution. We compare this method to existing approaches using a wide range of empirical datasets, and show that it consistently leads to large increases in the fit of partitioned models of molecular evolution when measured using AICc and BIC scores. In doing so, we demonstrate that some related approaches to solving this problem may have been associated with a small but important bias. CONCLUSIONS Our method provides an alternative to traditional approaches to partitioning, such as dividing alignments by gene and codon position. Because our method is data-driven, it can be used to estimate partitioned models for all types of alignments, including those that are not amenable to traditional approaches to partitioning.
Collapse
Affiliation(s)
- Paul B Frandsen
- Office of Research Information Services, Office of the CIO, Smithsonian Institution, Washington, D.C., USA. .,Department of Entomology, Rutgers University, New Brunswick, New Jersey, USA.
| | - Brett Calcott
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.
| | - Christoph Mayer
- Zoologisches Forschungsmuseum Alexander Koenig (ZFMK)/Zentrum für Molekulare Biodiversitätsforschung (ZMB), Bonn, Germany.
| | - Robert Lanfear
- Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia. .,National Evolutionary Synthesis Center, Durham, NC, USA. .,Department of Biological Sciences, Macquarie University, Sydney, Australia.
| |
Collapse
|
43
|
Abstract
Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice.
Collapse
Affiliation(s)
- David Kainer
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Robert Lanfear
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia National Evolutionary Synthesis Center, Durham, NC Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| |
Collapse
|
44
|
Kang JH, Manousaki T, Franchini P, Kneitz S, Schartl M, Meyer A. Transcriptomics of two evolutionary novelties: how to make a sperm-transfer organ out of an anal fin and a sexually selected "sword" out of a caudal fin. Ecol Evol 2015; 5:848-64. [PMID: 25750712 PMCID: PMC4338968 DOI: 10.1002/ece3.1390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 01/09/2023] Open
Abstract
Swords are exaggerated male ornaments of swordtail fishes that have been of great interest to evolutionary biologists ever since Darwin described them in the Descent of Man (1871). They are a novel sexually selected trait derived from modified ventral caudal fin rays and are only found in the genus Xiphophorus. Another phylogenetically more widespread and older male trait is the gonopodium, an intromittent organ found in all poeciliid fishes, that is derived from a modified anal fin. Despite many evolutionary and behavioral studies on both traits, little is known so far about the molecular mechanisms underlying their development. By investigating transcriptomic changes (utilizing a RNA-Seq approach) in response to testosterone treatment in the swordtail fish, Xiphophorus hellerii, we aimed to better understand the architecture of the gene regulatory networks underpinning the development of these two evolutionary novelties. Large numbers of genes with tissue-specific expression patterns were identified. Among the "sword genes" those involved in embryonic organ development, sexual character development and coloration were highly expressed, while in the gonopodium rather more morphogenesis-related genes were found. Interestingly, many genes and genetic pathways are shared between both developing novel traits derived from median fins: the sword and the gonopodium. Our analyses show that a larger set of gene networks was co-opted during the development and evolution of the "older" gonopodium than in the "younger," and morphologically less complex trait, the sword. We provide a catalog of candidate genes for future efforts to dissect the development of those sexually selected exaggerated male traits in swordtails.
Collapse
Affiliation(s)
- Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| | - Tereza Manousaki
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine ResearchHeraklion, Greece
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of WürzburgAm Hubland, Würzburg, Germany
- Comprehensive Cancer Center, University Clinic WürzburgJosef Schneider Straβe 6, 97074, Würzburg, Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of KonstanzUniversitätsstraβe 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of KonstanzKonstanz, Germany
| |
Collapse
|
45
|
Tinghitella RM, Lehto WR, Minter R. The evolutionary loss of a badge of status alters male competition in three-spine stickleback. Behav Ecol 2015. [DOI: 10.1093/beheco/aru242] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
46
|
Mitchell D, Paniker L, Lin K, Fernandez A. Interspecific variation in the repair of UV damaged DNA in the genus Xiphophorus as a factor in the decline of the Rio Grande Platyfish. Photochem Photobiol 2014; 91:486-92. [PMID: 25298266 DOI: 10.1111/php.12358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Abstract
The fish genus Xiphophorus consists of 26 species distributed along the eastern slopes of mountain ranges extending from northern Mexico to Belize and Nicaragua. We analyzed light-dependent repair of UV-induced DNA damage in at least two species from each of the four monophyletic Xiphophorus groups. We found that the northern platyfish had significantly reduced photoenzymatic repair compared to the other three groups, including the northern swordtails, southern platyfish and southern swordtails. All of the species of the northern platyfish, including the Marbled (meyeri), Northern (gordoni) and Monterrey Platyfish (couchianus) are the northernmost species in the genus and are the only three species in the genus that are currently found on the IUCN Red List of Threatened Species. Satellite data from the past 30 years (1979-2008) correlate greater increases in shorter wavelength UVB with higher latitudes within the Xiphophorus range. We suggest that, combined with other consequences of human population growth, anthropogenic deozonation resulting in a disproportionate increase in UVB in temperate latitudes may be a contributing factor in the decline and extirpation of the northern platyfish.
Collapse
Affiliation(s)
- David Mitchell
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | | | | | | |
Collapse
|
47
|
Kolluru GR, Bertram SM, Chin EH, Dunmeyer CV, Graves JS. Mating behavior and its morphological correlates in two color morphs of Girardinus metallicus (Pisces: Poeciliidae), a species previously thought not to exhibit courtship display. Behav Processes 2014; 106:44-52. [DOI: 10.1016/j.beproc.2014.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 02/24/2014] [Accepted: 04/07/2014] [Indexed: 02/03/2023]
|
48
|
Walter DJ, Boswell M, Volk de García SM, Walter SM, Breitenfeldt EW, Boswell W, Walter RB. Characterization and differential expression of CPD and 6-4 DNA photolyases in Xiphophorus species and interspecies hybrids. Comp Biochem Physiol C Toxicol Pharmacol 2014; 163:77-85. [PMID: 24496042 PMCID: PMC4032606 DOI: 10.1016/j.cbpc.2014.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 11/25/2022]
Abstract
Among the many Xiphophorus interspecies hybrid tumor models are those that exhibit ultraviolet light (UVB) induced melanoma. In previous studies, assessment of UVB induced DNA damage and nucleotide excision DNA repair has been performed in parental lines and interspecies hybrids. Species and hybrid specific differences in the levels of DNA damage induced and the dark repair rates for cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine pyrimidine photoproducts (6-4PPs) have been reported. However, UVB induced DNA lesions in Xiphophorus fishes are thought to primarily be repaired via light dependent CPD and 6-4PP specific photolyases. Photolyases are of evolutionary interest since they are ancient and presumably function solely to ameliorate the deleterious effects of UVB exposure. Herein, we report results from detailed studies of CPD and 6-4PP photolyase gene expression within several Xiphophorus tissues. We determined photolyase gene expression patterns before and after exposure to fluorescent light in X. maculatus, X. couchianus, and for F1 interspecies hybrids produced from crossing these two parental lines (X. maculatus Jp 163 B×X. couchianus). We present novel results showing these two photolyase genes exhibit species, tissue, and hybrid-specific differences in basal and light induced gene expression.
Collapse
Affiliation(s)
- Dylan J Walter
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Mikki Boswell
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Sara M Volk de García
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Sean M Walter
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Erik W Breitenfeldt
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - William Boswell
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Ronald B Walter
- Department of Chemistry and Biochemistry, Molecular Biosciences Research Group, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| |
Collapse
|
49
|
Schumer M, Rosenthal GG, Andolfatto P. HOW COMMON IS HOMOPLOID HYBRID SPECIATION? Evolution 2014; 68:1553-60. [DOI: 10.1111/evo.12399] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 02/28/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Molly Schumer
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
| | - Gil G. Rosenthal
- Department of Biology; Texas A&M University (TAMU); College Station Texas 77843
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca,” Calnali; Hidalgo 43230 Mexico
| | - Peter Andolfatto
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton New Jersey 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University; Princeton New Jersey 08544
| |
Collapse
|
50
|
Oufiero CE, Meredith RW, Jugo KN, Tran P, Chappell MA, Springer MS, Reznick DN, Garland T. The evolution of the sexually selected sword in Xiphophorus does not compromise aerobic locomotor performance. Evolution 2014; 68:1806-23. [PMID: 24571289 DOI: 10.1111/evo.12391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 02/17/2014] [Indexed: 11/28/2022]
Abstract
Sexual selection can increase morphological diversity within and among species. Little is known regarding how interspecific variation produced through sexual selection affects other functional systems. Here, we examine how morphological diversity resulting from sexual selection impacts aerobic locomotor performance. Using Xiphophorus (swordtail fish) and their close relatives (N = 19 species), we examined whether the evolution of a longer sexually selected sword affects critical swimming speed. We also examined the effect of other suborganismal, physiological, and morphological traits on critical swimming speed, as well as their relationship with sword length. In correlation analyses, we found no significant relationship between sword length and critical swimming speed. Unexpectedly, we found that critical swimming speed was higher in species with longer swords, after controlling for body size in multiple regression analyses. We also found several suborganismal and morphological predictors of critical swimming speed, as well as a significant negative relationship between sword length and heart and gill mass. Our results suggest that interspecific variation in sword length is not costly for this aspect of swimming performance, but further studies should examine potential costs for other types of locomotion and other components of Darwinian fitness (e.g., survivorship, life span).
Collapse
|