1
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Du K, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge T, Schumer M, Park H, Meyer A, Schartl M. Phylogenomics analyses of all species of Swordtails (Genus Xiphophorus ) highlights hybridization precedes speciation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573732. [PMID: 38260540 PMCID: PMC10802237 DOI: 10.1101/2023.12.30.573732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to the lack of appropriate experimental systems. Fish of the central American genus Xiphophorus were proposed to have evolved with multiple ancient and ongoing hybridization events, and served as a valuable research model in evolutionary biology and in biomedical research on human disease for more than a century. Here, we provide the complete genome resource and its annotation of all 26 Xiphophorus species. On this dataset we resolved the so far conflicting phylogeny. Through comparative genomic analyses we investigated the molecular evolution of genes related to melanoma, for a main sexually selected trait and for the genetic control of puberty timing, which are predicted to be involved in pre-and postzygotic isolation and thus to influence the probability of interspecific hybridization in Xiphophorus . We demonstrate dramatic size-variation of some gene families across species, despite the reticulate evolution and short divergence time. Finally, we clarify the hybridization history in the genus Xiphophorus genus, settle the long dispute on the hybridization origin of two Southern swordtails, highlight hybridizations precedes speciation, and reveal the distribution of hybridization ancestry remaining in the fused genome.
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2
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Valdesalici S. A new annual killifish, Moema beltramonorum (Cyprinodontiformes: Rivulidae) from the Amazon basin, Bolivia. Zootaxa 2023; 5383:594-600. [PMID: 38221230 DOI: 10.11646/zootaxa.5383.4.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Indexed: 01/16/2024]
Abstract
A new annual killifish species, Moema beltramonorum, is described from a seasonal swamp next to arroyo Crespo, belonging to Ro San Martin, a tributary of Ro Itnez, Amazon River basin, Bolivia. The new taxon presents an unique combination of male colour pattern characters not present in any congener, and an unique caudal fin coloration.
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3
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Darolti I, Mank JE. Sex-biased gene expression at single-cell resolution: cause and consequence of sexual dimorphism. Evol Lett 2023; 7:148-156. [PMID: 37251587 PMCID: PMC10210449 DOI: 10.1093/evlett/qrad013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/31/2023] Open
Abstract
Gene expression differences between males and females are thought to be key for the evolution of sexual dimorphism, and sex-biased genes are often used to study the molecular footprint of sex-specific selection. However, gene expression is often measured from complex aggregations of diverse cell types, making it difficult to distinguish between sex differences in expression that are due to regulatory rewiring within similar cell types and those that are simply a consequence of developmental differences in cell-type abundance. To determine the role of regulatory versus developmental differences underlying sex-biased gene expression, we use single-cell transcriptomic data from multiple somatic and reproductive tissues of male and female guppies, a species that exhibits extensive phenotypic sexual dimorphism. Our analysis of gene expression at single-cell resolution demonstrates that nonisometric scaling between the cell populations within each tissue and heterogeneity in cell-type abundance between the sexes can influence inferred patterns of sex-biased gene expression by increasing both the false-positive and false-negative rates. Moreover, we show that, at the bulk level, the subset of sex-biased genes that are the product of sex differences in cell-type abundance can significantly confound patterns of coding-sequence evolution. Taken together, our results offer a unique insight into the effects of allometry and cellular heterogeneity on perceived patterns of sex-biased gene expression and highlight the power of single-cell RNA-sequencing in distinguishing between sex-biased genes that are the result of regulatory change and those that stem from sex differences in cell-type abundance, and hence are a consequence rather than a cause of sexual dimorphism.
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Affiliation(s)
- Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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4
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Price PD, Parkus SM, Wright AE. Recent progress in understanding the genomic architecture of sexual conflict. Curr Opin Genet Dev 2023; 80:102047. [PMID: 37163877 DOI: 10.1016/j.gde.2023.102047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/02/2023] [Accepted: 04/02/2023] [Indexed: 05/12/2023]
Abstract
Genomic conflict between the sexes over shared traits is widely assumed to be resolved through the evolution of sex-biased expression and the subsequent emergence of sexually dimorphic phenotypes. However, while there is support for a broad relationship between genome-wide patterns of expression level and sexual conflict, recent studies suggest that sex differences in the nature and strength of interactions between loci are instead key to conflict resolution. Furthermore, the advent of new technologies for measuring and perturbing expression means we now have much more power to detect genomic signatures of sexual conflict. Here, we review our current understanding of the genomic architecture of sexual conflict in the light of these new studies and highlight the potential for novel approaches to address outstanding knowledge gaps.
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Affiliation(s)
- Peter D Price
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, United Kingdom. https://twitter.com/@PeterDPrice
| | - Sylvie M Parkus
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, United Kingdom
| | - Alison E Wright
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, United Kingdom.
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5
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Silic MR, Zhang G. Bioelectricity in Developmental Patterning and Size Control: Evidence and Genetically Encoded Tools in the Zebrafish Model. Cells 2023; 12:cells12081148. [PMID: 37190057 DOI: 10.3390/cells12081148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Developmental patterning is essential for regulating cellular events such as axial patterning, segmentation, tissue formation, and organ size determination during embryogenesis. Understanding the patterning mechanisms remains a central challenge and fundamental interest in developmental biology. Ion-channel-regulated bioelectric signals have emerged as a player of the patterning mechanism, which may interact with morphogens. Evidence from multiple model organisms reveals the roles of bioelectricity in embryonic development, regeneration, and cancers. The Zebrafish model is the second most used vertebrate model, next to the mouse model. The zebrafish model has great potential for elucidating the functions of bioelectricity due to many advantages such as external development, transparent early embryogenesis, and tractable genetics. Here, we review genetic evidence from zebrafish mutants with fin-size and pigment changes related to ion channels and bioelectricity. In addition, we review the cell membrane voltage reporting and chemogenetic tools that have already been used or have great potential to be implemented in zebrafish models. Finally, new perspectives and opportunities for bioelectricity research with zebrafish are discussed.
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Affiliation(s)
- Martin R Silic
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - GuangJun Zhang
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Inflammation, Immunology and Infectious Diseases (PI4D), Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, 625 Harrison Street, West Lafayette, IN 47907, USA
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6
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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.
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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
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7
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Rees L, König D, Jaźwińska A. Platyfish bypass the constraint of the caudal fin ventral identity in teleosts. Dev Dyn 2022; 251:1862-1879. [PMID: 35803741 PMCID: PMC9796532 DOI: 10.1002/dvdy.518] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The caudal fin of teleosts is characterized by dorsoventral symmetry. Despite this external morphology, the principal rays of this appendage connect to bones below the notochord, indicating the ventral (hypochordal) identity of this organ. RESULTS Here, we report that this typical architecture of the caudal fin is not fully conserved in the platyfish (Xiphophorus maculatus) and the guppy (Poecilia reticulata), representatives of the Poeciliidae family. We show that in these species, 3-4 principal rays connect to bones above the notochord, suggesting an epichordal contribution. Consistently, as examined in platyfish, dorsal identity genes zic1/4 were highly expressed in these rays, providing molecular evidence of their epichordal origin. Developmental analysis revealed that the earliest rays above the notochord emerge at the 10-ray stage of fin morphogenesis. In contrast to zebrafish and medaka, platyfish and guppies display a mirrored shape of dorsal and ventral processes of the caudal endoskeleton. Our study suggests that an ancestral bauplan expanded in poeciliids by advancing its symmetrical pattern. CONCLUSION The platyfish evolved a fin architecture with the epichordal origin of its upper principal rays and a high level of symmetry in the caudal endoskeleton. This innovative architecture highlights the adaptation of the teleost skeleton.
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Affiliation(s)
- Lana Rees
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Désirée König
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Anna Jaźwińska
- Department of BiologyUniversity of FribourgFribourgSwitzerland
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8
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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: 0] [Impact Index Per Article: 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.
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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
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9
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Desvignes T, Robbins AE, Carey AZ, Bailon-Zambrano R, Nichols JT, Postlethwait JH, Stankunas K. Coordinated patterning of zebrafish caudal fin symmetry by a central and two peripheral organizers. Dev Dyn 2022; 251:1306-1321. [PMID: 35403297 PMCID: PMC9357109 DOI: 10.1002/dvdy.475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 04/03/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Caudal fin symmetry characterizes teleosts and likely contributes to their evolutionary success. However, the coordinated development and patterning of skeletal elements establishing external symmetry remains incompletely understood. We explore the spatiotemporal emergence of caudal skeletal elements in zebrafish to consider evolutionary and developmental origins of caudal fin symmetry. RESULTS Transgenic reporters and skeletal staining reveal that the hypural diastema-defining gap between hypurals 2 and 3 forms early and separates progenitors of two plates of connective tissue. Two sets of central principal rays (CPRs) synchronously, sequentially, and symmetrically emerge around the diastema. The two dorsal- and ventral-most rays (peripheral principal rays, PPRs) arise independently and earlier than adjacent CPRs. Muscle and tendon markers reveal that different muscles attach to CPR and PPR sets. CONCLUSIONS We propose that caudal fin symmetry originates from a central organizer that establishes the hypural diastema and bidirectionally patterns surrounding tissue into two plates of connective tissue and two mirrored sets of CPRs. Further, two peripheral organizers unidirectionally specify PPRs, forming a symmetric "composite" fin derived from three fields. Distinct CPR and PPR ontogenies may represent developmental modules conferring ray identities, muscle connections, and biomechanical properties. Our model contextualizes mechanistic studies of teleost fin morphological variation.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
| | - Andrew Z. Carey
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Raisa Bailon-Zambrano
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045, USA
| | - James T. Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045, USA
| | | | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
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10
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Maderspacher F. Evolution and development: From the pet shop to the pelagic zone. Curr Biol 2021; 31:R1469-R1471. [PMID: 34813749 DOI: 10.1016/j.cub.2021.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Flying fish and some of their relatives have evolved the ability to elegantly escape predators by gliding through air. A new study - involving a pet shop zebrafish mutant - offers glimpses into how fins might have been modified to enable this stunt.
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11
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Powell DL, Moran B, Kim B, Banerjee SM, Aguillon SM, Fascinetto-Zago P, Langdon Q, Schumer M. Two new hybrid populations expand the swordtail hybridization model system. Evolution 2021; 75:2524-2539. [PMID: 34460102 PMCID: PMC8659863 DOI: 10.1111/evo.14337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 12/25/2022]
Abstract
Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here, we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and Xiphophorus birchmanni from collection sites on two rivers. We use simulations and new genetic reference panels to develop sensitive and accurate local ancestry calling in this novel system. Strikingly, we find that hybrid populations on both rivers consist of two genetically distinct subpopulations: a cluster of pure X. birchmanni individuals and one of phenotypically intermediate hybrids that derive ∼85-90% of their genome from X. cortezi. Simulations suggest that initial hybridization occurred ∼150 generations ago at both sites, with little evidence for contemporary gene flow between subpopulations. This population structure is consistent with strong assortative mating between individuals of similar ancestry. The patterns of population structure uncovered here mirror those seen in hybridization between X. birchmanni and its sister species, Xiphophorus malinche, indicating an important role for assortative mating in the evolution of hybrid populations. Future comparisons will provide a window into the shared mechanisms driving the outcomes of hybridization not only among independent hybridization events between the same species but also across distinct species pairs.
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Affiliation(s)
- Daniel L. Powell
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C.,Correspondence to: and
| | - Ben Moran
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Shreya M. Banerjee
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University,Department of Ecology and Evolutionary Biology, Cornell University
| | - Paola Fascinetto-Zago
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C.,Department of Biology, Texas A&M University
| | - Quinn Langdon
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Molly Schumer
- Department of Biology, Stanford University,Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C.,Hanna H. Gray Fellow, Howard Hughes Medical Institutes,Correspondence to: and
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12
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Mank JE, Rideout EJ. Developmental mechanisms of sex differences: from cells to organisms. Development 2021; 148:272484. [PMID: 34647574 DOI: 10.1242/dev.199750] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Male-female differences in many developmental mechanisms lead to the formation of two morphologically and physiologically distinct sexes. Although this is expected for traits with prominent differences between the sexes, such as the gonads, sex-specific processes also contribute to traits without obvious male-female differences, such as the intestine. Here, we review sex differences in developmental mechanisms that operate at several levels of biological complexity - molecular, cellular, organ and organismal - and discuss how these differences influence organ formation, function and whole-body physiology. Together, the examples we highlight show that one simple way to gain a more accurate and comprehensive understanding of animal development is to include both sexes.
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Affiliation(s)
- Judith E Mank
- Department of Zoology, Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Biosciences, University of Exeter, Penryn Campus, Penryn TR10 9FE, UK
| | - Elizabeth J Rideout
- Department of Cellular and Physiological Sciences, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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13
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Modulation of bioelectric cues in the evolution of flying fishes. Curr Biol 2021; 31:5052-5061.e8. [PMID: 34534441 DOI: 10.1016/j.cub.2021.08.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/09/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023]
Abstract
Changes to allometry, or the relative proportions of organs and tissues within organisms, is a common means for adaptive character change in evolution. However, little is understood about how relative size is specified during development and shaped during evolution. Here, through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors. To refine our analysis, we intersected convergent phylogenomic signatures with mutants with altered fin size identified in distantly related zebrafish. Through these paired approaches, we identify a surprising role for an L-type amino acid transporter, lat4a, and the potassium channel, kcnh2a, in the regulation of fin proportion. We show that interaction between these genetic loci in zebrafish closely phenocopies the observed fin proportions of flying fishes. The congruence of experimental and phylogenomic findings point to conserved, non-canonical signaling integrating bioelectric cues and amino acid transport in the establishment of relative size in development and evolution.
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14
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Wang L, Sun F, Wan ZY, Ye B, Wen Y, Liu H, Yang Z, Pang H, Meng Z, Fan B, Alfiko Y, Shen Y, Bai B, Lee MSQ, Piferrer F, Schartl M, Meyer A, Yue GH. Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish. Mol Biol Evol 2021; 38:3383-3396. [PMID: 33871625 PMCID: PMC8321530 DOI: 10.1093/molbev/msab110] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long-fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole-genome sequencing, quantitative trait loci mapping, genome-wide association studies, and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino, and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double-tail mutant was suggested to be caused by a deletion in a zic1/zic4 coenhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Fei Sun
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Baoqing Ye
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Yanfei Wen
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Huiming Liu
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zituo Yang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Hongyan Pang
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Fan
- Department of Food and Environmental Engineering, Yangjiang Polytechnic, Yangjiang, China
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Yubang Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China
| | - Bin Bai
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - May Shu Qing Lee
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Francesc Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Manfred Schartl
- 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
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gen Hua Yue
- Molecular Population Genetics & Breeding Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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15
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Stewart S, Le Bleu HK, Yette GA, Henner AL, Robbins AE, Braunstein JA, Stankunas K. longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth. Development 2021; 148:dev199384. [PMID: 34061172 PMCID: PMC8217709 DOI: 10.1242/dev.199384] [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: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Organs stop growing to achieve a characteristic size and shape in scale with the body of an animal. Likewise, regenerating organs sense injury extents to instruct appropriate replacement growth. Fish fins exemplify both phenomena through their tremendous diversity of form and remarkably robust regeneration. The classic zebrafish mutant longfint2 develops and regenerates dramatically elongated fins and underlying ray skeleton. We show longfint2 chromosome 2 overexpresses the ether-a-go-go-related voltage-gated potassium channel kcnh2a. Genetic disruption of kcnh2a in cis rescues longfint2, indicating longfint2 is a regulatory kcnh2a allele. We find longfint2 fin overgrowth originates from prolonged outgrowth periods by showing Kcnh2a chemical inhibition during late stage regeneration fully suppresses overgrowth. Cell transplantations demonstrate longfint2-ectopic kcnh2a acts tissue autonomously within the fin intra-ray mesenchymal lineage. Temporal inhibition of the Ca2+-dependent phosphatase calcineurin indicates it likewise entirely acts late in regeneration to attenuate fin outgrowth. Epistasis experiments suggest longfint2-expressed Kcnh2a inhibits calcineurin output to supersede growth cessation signals. We conclude ion signaling within the growth-determining mesenchyme lineage controls fin size by tuning outgrowth periods rather than altering positional information or cell-level growth potency.
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Affiliation(s)
- Scott Stewart
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Heather K. Le Bleu
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Gabriel A. Yette
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Astra L. Henner
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Joshua A. Braunstein
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
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16
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Abstract
It is well known that electrical signals are deeply associated with living entities. Much of our understanding of excitable tissues is derived from studies of specialized cells of neurons or myocytes. However, electric potential is present in all cell types and results from the differential partitioning of ions across membranes. This electrical potential correlates with cell behavior and tissue organization. In recent years, there has been exciting, and broadly unexpected, evidence linking the regulation of development to bioelectric signals. However, experimental modulation of electrical potential can have multifaceted and pleiotropic effects, which makes dissecting the role of electrical signals in development difficult. Here, I review evidence that bioelectric cues play defined instructional roles in orchestrating development and regeneration, and further outline key areas in which to refine our understanding of this signaling mechanism.
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Affiliation(s)
- Matthew P. Harris
- Department of Genetics, Harvard Medical School, Department of Orthopaedics, Boston Children's Hospital, 300 Longwood Avenue Enders 260, Boston MA 02115, USA
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17
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Powell DL, Payne C, Banerjee SM, Keegan M, Bashkirova E, Cui R, Andolfatto P, Rosenthal GG, Schumer M. The Genetic Architecture of Variation in the Sexually Selected Sword Ornament and Its Evolution in Hybrid Populations. Curr Biol 2021; 31:923-935.e11. [PMID: 33513352 DOI: 10.1016/j.cub.2020.12.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 12/25/2020] [Indexed: 10/22/2022]
Abstract
Biologists since Darwin have been fascinated by the evolution of sexually selected ornaments, particularly those that reduce viability. Uncovering the genetic architecture of these traits is key to understanding how they evolve and are maintained. Here, we investigate the genetic architecture and evolutionary loss of a sexually selected ornament, the "sword" fin extension that characterizes many species of swordtail fish (Xiphophorus). Using sworded and swordless sister species of Xiphophorus, we generated a mapping population and show that the sword ornament is polygenic-with ancestry across the genome explaining substantial variation in the trait. After accounting for the impacts of genome-wide ancestry, we identify one major-effect quantitative trait locus (QTL) that explains ~5% of the overall variation in the trait. Using a series of approaches, we narrow this large QTL interval to several likely candidate genes, including genes involved in fin regeneration and growth. Furthermore, we find evidence of selection on ancestry at one of these candidates in four natural hybrid populations, consistent with selection against the sword in these populations.
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Affiliation(s)
- Daniel L Powell
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA.
| | - Cheyenne Payne
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Shreya M Banerjee
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México
| | - Mackenzie Keegan
- Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Elizaveta Bashkirova
- Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, New York, NY 10032, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, 622 West 168th Street, New York, NY 10032, USA
| | - Rongfeng Cui
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA; Max Planck Institute for the Biology of Aging, Postfach 41 06 23, 50931 Cologne, Germany; School of Ecology, Sun Yat-sen University, 135 Xingang West Road, Binjiang Road, Haizhu District, Guangdong Province, China
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
| | - Gil G Rosenthal
- Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX 77843, USA
| | - Molly Schumer
- Department of Biology, Stanford University, 327 Campus Drive, Stanford, CA 94305, USA; Centro de Investigaciones Científicas de las Huastecas "Aguazarca," A.C., 16 de Septiembre, 392 Barrio Aguazarca, Calnali, Hidalgo 43240, México; Howard Hughes Medical Institute, 327 Campus Drive, Stanford, CA 94305, USA.
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18
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Sexual Selection: A Cross-Sword Puzzle. Curr Biol 2021; 31:R243-R246. [PMID: 33689721 DOI: 10.1016/j.cub.2021.01.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Swordtail fish with their eponymous male ornament have long been a paradigm for how sexual selection works. Two studies now aim to dissect the genetic and developmental basis of the sword. They home in on similar regions of the swordtail genome but arrive at different candidate genes.
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