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Urum A, Rice G, Glassford W, Yanku Y, Shklyar B, Rebeiz M, Preger-Ben Noon E. A developmental atlas of male terminalia across twelve species of Drosophila. Front Cell Dev Biol 2024; 12:1349275. [PMID: 38487271 PMCID: PMC10937369 DOI: 10.3389/fcell.2024.1349275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 03/17/2024] Open
Abstract
How complex morphologies evolve is one of the central questions in evolutionary biology. Observing the morphogenetic events that occur during development provides a unique perspective on the origins and diversification of morphological novelty. One can trace the tissue of origin, emergence, and even regression of structures to resolve murky homology relationships between species. Here, we trace the developmental events that shape some of the most diverse organs in the animal kingdom-the male terminalia (genitalia and analia) of Drosophilids. Male genitalia are known for their rapid evolution with closely related species of the Drosophila genus demonstrating vast variation in their reproductive morphology. We used confocal microscopy to monitor terminalia development during metamorphosis in twelve related species of Drosophila. From this comprehensive dataset, we propose a new staging scheme for pupal terminalia development based on shared developmental landmarks, which allows one to align developmental time points between species. We were able to trace the origin of different substructures, find new morphologies and suggest possible homology of certain substructures. Additionally, we demonstrate that posterior lobe is likely originated prior to the split between the Drosophila melanogaster and the Drosophila yakuba clade. Our dataset opens up many new directions of research and provides an entry point for future studies of the Drosophila male terminalia evolution and development.
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Affiliation(s)
- Anna Urum
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
| | - Gavin Rice
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - William Glassford
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yifat Yanku
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
| | - Boris Shklyar
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, Haifa, Israel
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2
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Rice GR, David JR, Gompel N, Yassin A, Rebeiz M. Resolving between novelty and homology in the rapidly evolving phallus of Drosophila. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:182-196. [PMID: 34958528 PMCID: PMC10155935 DOI: 10.1002/jez.b.23113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/24/2021] [Accepted: 10/10/2021] [Indexed: 11/11/2022]
Abstract
The genitalia present some of the most rapidly evolving anatomical structures in the animal kingdom, possessing a variety of parts that can distinguish recently diverged species. In the Drosophila melanogaster group, the phallus is adorned with several processes, pointed outgrowths, that are similar in size and shape between species. However, the complex three-dimensional nature of the phallus can obscure the exact connection points of each process. Previous descriptions based upon adult morphology have primarily assigned phallic processes by their approximate positions in the phallus and have remained largely agnostic regarding their homology relationships. In the absence of clearly identified homology, it can be challenging to model when each structure first evolved. Here, we employ a comparative developmental analysis of these processes in eight members of the melanogaster species group to precisely identify the tissue from which each process forms. Our results indicate that adult phallic processes arise from three pupal primordia in all species. We found that in some cases the same primordia generate homologous structures whereas in other cases, different primordia produce phenotypically similar but remarkably non-homologous structures. This suggests that the same gene regulatory network may have been redeployed to different primordia to induce phenotypically similar traits. Our results highlight how traits diversify and can be redeployed, even at short evolutionary scales.
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Affiliation(s)
- Gavin R Rice
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jean R David
- Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE), UMR 9191, CNRS,IRD, Univ.Paris-Sud, Université Paris-Saclay, Orsay, Cedex, France
| | - Nicolas Gompel
- Fakultät für Biologie, Biozentrum, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
| | - Amir Yassin
- Laboratoire Evolution, Génomes, Comportement, Ecologie (EGCE), UMR 9191, CNRS,IRD, Univ.Paris-Sud, Université Paris-Saclay, Orsay, Cedex, France.,Institut de Systématique, Evolution et Biodiversité, UMR7205, Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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3
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Gibert JM. [Small scale evolution]. Biol Aujourdhui 2022; 216:41-47. [PMID: 35876520 DOI: 10.1051/jbio/2022008] [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: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Small-scale evolution or microevolution concerns evolution at the intra-specific level or between closely related species. At the intra-specific level, it allows the analysis of the evolutionary forces at work: mutation, genetic drift, migration and selection. Moreover, because of the short evolutionary time, it is easier to identify the genetic basis of observed phenotypic differences. Most studies focus on current populations but more and more analyses are performed on ancient DNA. This provides important information for tracing the history of populations and also allows the reconstruction of phenotypes of individuals that disappeared several thousand years ago. In this short review, I present studies showing how pre-zygotic or post-zygotic barriers involved in species formation are set up using the example of the geographical barrier due to the formation of the Isthmus of Panama and that of the heterochromatin divergence in Drosophilidae. I also describe the different approaches that have been used to identify the genetic basis of well known phenotypic variations: candidate gene approach (about melanism in felines), QTL mapping (variation in the number of lateral bone plates in sticklebacks), association study (pigmentation in the Asian ladybird). Finally, I illustrate the key impact of natural selection with the iconic example of the evolution of the beak of Galapagos finches, and the role of certain developmental genes in its morphological diversification.
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Affiliation(s)
- Jean-Michel Gibert
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire de Biologie du Développement, UMR 7622, 9 quai St-Bernard 75005 Paris, France
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4
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David JR, Ferreira EA, Jabaud L, Ogereau D, Bastide H, Yassin A. Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species. Ecol Evol 2022; 12:e8821. [PMID: 35432924 PMCID: PMC9006235 DOI: 10.1002/ece3.8821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
Adaptive introgression is ubiquitous in animals, but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during 1 year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after 4 years (~60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically distinct and reproductively isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step toward understanding the genome-wide dynamics of speciation-through-introgression.
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Affiliation(s)
- Jean R. David
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Laure Jabaud
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - David Ogereau
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Héloïse Bastide
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
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5
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Mendes MF, Gottschalk MS, Corrêa RC, Valente-Gaiesky VLS. Functional traits for ecological studies: a review of characteristics of Drosophilidae (Diptera). COMMUNITY ECOL 2021. [DOI: 10.1007/s42974-021-00060-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Finet C, Kassner VA, Carvalho AB, Chung H, Day JP, Day S, Delaney EK, De Ré FC, Dufour HD, Dupim E, Izumitani HF, Gautério TB, Justen J, Katoh T, Kopp A, Koshikawa S, Longdon B, Loreto EL, Nunes MDS, Raja KKB, Rebeiz M, Ritchie MG, Saakyan G, Sneddon T, Teramoto M, Tyukmaeva V, Vanderlinde T, Wey EE, Werner T, Williams TM, Robe LJ, Toda MJ, Marlétaz F. DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics. Genome Biol Evol 2021; 13:evab179. [PMID: 34343293 PMCID: PMC8382681 DOI: 10.1093/gbe/evab179] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2021] [Indexed: 02/06/2023] Open
Abstract
The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.
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Affiliation(s)
- Cédric Finet
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, USA
| | - Victoria A Kassner
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, USA
| | - Antonio B Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Henry Chung
- Department of Entomology, Michigan State University, USA
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, United Kingdom
| | - Stephanie Day
- Department of Biological Sciences, University of Pittsburgh, USA
| | - Emily K Delaney
- Department of Evolution and Ecology, University of California-Davis, USA
| | - Francine C De Ré
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Héloïse D Dufour
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, USA
| | - Eduardo Dupim
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Hiroyuki F Izumitani
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Thaísa B Gautério
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Jessa Justen
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison, USA
| | - Toru Katoh
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California-Davis, USA
| | - Shigeyuki Koshikawa
- The Hakubi Center for Advanced Research and Graduate School of Science, Kyoto University, Japan
| | - Ben Longdon
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Elgion L Loreto
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, United Kingdom
- Centre for Functional Genomics, Oxford Brookes University, United Kingdom
| | - Komal K B Raja
- Department of Biological Sciences, Michigan Technological University, USA
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, USA
| | | | - Gayane Saakyan
- Department of Evolution and Ecology, University of California-Davis, USA
| | - Tanya Sneddon
- School of Biology, University of St Andrews, United Kingdom
| | - Machiko Teramoto
- The Hakubi Center for Advanced Research and Graduate School of Science, Kyoto University, Japan
| | | | - Thyago Vanderlinde
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Emily E Wey
- Department of Biology, University of Dayton, USA
| | - Thomas Werner
- Department of Biological Sciences, Michigan Technological University, USA
| | | | - Lizandra J Robe
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Programa de Pós-Graduação em Biologia de Ambientes Aquáticos Continentais, Universidade Federal do Rio Grande, Rio Grande do Sul, Brazil
| | - Masanori J Toda
- Hokkaido University Museum, Hokkaido University, Sapporo, Japan
| | - Ferdinand Marlétaz
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, United Kingdom
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7
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Peluffo AE, Hamdani M, Vargas‐Valderrama A, David JR, Mallard F, Graner F, Courtier‐Orgogozo V. A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature. Ecol Evol 2021; 11:7492-7506. [PMID: 34188829 PMCID: PMC8216934 DOI: 10.1002/ece3.7580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 11/18/2022] Open
Abstract
Male genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister species Drosophila santomea and Drosophila yakuba. We designed a semi-automatic measurement machine learning pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that temperature does not affect ventral branches in D. yakuba but that in D. santomea ventral branches tend to morph into a D. yakuba-like shape at lower temperature. We found that male genitalia structures involved in reproductive isolation can be relatively variable within one species and can resemble the shape of closely related species' genitalia through plasticity to temperature. Our results suggest that reproductive isolation mechanisms can be dependent on the environmental context.
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Affiliation(s)
| | | | | | - Jean R. David
- Institut Systématique Evolution Biodiversité (ISYEB)CNRSMNHNSorbonne UniversitéEPHEParisFrance
- Laboratoire Evolution, Génomes, Comportement, Biodiversité (EGCE)CNRSIRDUniv. Paris‐sudUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - François Mallard
- Institut de Biologie de l’École Normale SupérieureCNRS UMR 8197PSL Research UniversityParisFrance
| | - François Graner
- Matière et Systèmes ComplexesCNRS UMR 7057Univ. de ParisParisFrance
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8
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Smith SJ, Davidson LA, Rebeiz M. Evolutionary expansion of apical extracellular matrix is required for the elongation of cells in a novel structure. eLife 2020; 9:55965. [PMID: 32338602 PMCID: PMC7266619 DOI: 10.7554/elife.55965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
One of the fundamental gaps in our knowledge of how novel anatomical structures evolve is understanding the origins of the morphogenetic processes that form these features. Here, we traced the cellular development of a recently evolved morphological novelty, the posterior lobe of D. melanogaster. We found that this genital outgrowth forms through extreme increases in epithelial cell height. By examining the apical extracellular matrix (aECM), we also uncovered a vast matrix associated with the developing genitalia of lobed and non-lobed species. Expression of the aECM protein Dumpy is spatially expanded in lobe-forming species, connecting the posterior lobe to the ancestrally derived aECM network. Further analysis demonstrated that Dumpy attachments are necessary for cell height increases during posterior lobe development. We propose that the aECM presents a rich reservoir for generating morphological novelty and highlights a yet unseen role for aECM in regulating extreme cell height.
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Affiliation(s)
- Sarah Jacquelyn Smith
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Lance A Davidson
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, United States
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
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9
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An Atlas of Transcription Factors Expressed in Male Pupal Terminalia of Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:3961-3972. [PMID: 31619460 PMCID: PMC6893207 DOI: 10.1534/g3.119.400788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have identified network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in whole Drosophila melanogaster male terminalia followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the male terminalia are highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (https://flyterminalia.pitt.edu/) as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.
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10
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Al Sayad S, Yassin A. Quantifying the extent of morphological homoplasy: A phylogenetic analysis of 490 characters in Drosophila. Evol Lett 2019; 3:286-298. [PMID: 31171984 PMCID: PMC6546384 DOI: 10.1002/evl3.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/28/2019] [Accepted: 04/05/2019] [Indexed: 12/31/2022] Open
Abstract
Homoplasy is a fundamental phenomenon in evolutionary biology but an appraisal of its extent at the morphological level is still lacking. Here, we analyzed the evolution of 490 morphological characters conceptualized among 56 drosophilid species. We found that two thirds of morphological changes were homoplastic and that the level of homoplasy depended on the stage of development and the type of the organ, with the adult terminalia being the least homoplastic. In spite of its predominance at the character change level, homoplasy accounts for only ∼13% of between species similarities in pairwise comparisons. These results provide empirical insights on the limits of morphological changes and the frequency of recurrent evolution.
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Affiliation(s)
- Sinan Al Sayad
- Institut Systématique Evolution Biodiversité (ISYEB)Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE57 rue Cuvier, CP 50,75005ParisFrance
| | - Amir Yassin
- Institut Systématique Evolution Biodiversité (ISYEB)Centre National de la Recherche Scientifique, MNHN, Sorbonne Université, EPHE57 rue Cuvier, CP 50,75005ParisFrance
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11
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Fujisawa T, Sasabe M, Nagata N, Takami Y, Sota T. Genetic basis of species-specific genitalia reveals role in species diversification. SCIENCE ADVANCES 2019; 5:eaav9939. [PMID: 31249868 PMCID: PMC6594765 DOI: 10.1126/sciadv.aav9939] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
The diversity of genital morphology among closely related animals with internal fertilization is well known, but the genetic backgrounds are unclear. Here, we show that, in Carabus (Ohomopterus) beetles showing correlated evolution of male and female genital parts, only a few major quantitative trait loci (QTLs) determine differences in genital dimensions between sister species, and sequence divergence is pronounced in the genomic regions containing genital QTLs. The major QTLs for male and female genital dimensions reside in different locations within the same linkage group, implying that coevolution between the sexes is only loosely constrained and can respond to sexually antagonistic selection. The same genomic regions containing the major QTLs show elevated divergence between three pairs of parapatric species with marked differences in genital parts. Our study demonstrates that species diversification can follow coevolution of genitalia between the sexes, even without tight linkage of loci affecting male and female genital dimensions.
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Affiliation(s)
- Tomochika Fujisawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Masataka Sasabe
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Nobuaki Nagata
- Division of Collections Conservation, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Yasuoki Takami
- Graduate School of Human Development and Environment, Kobe University, Kobe 657-8501, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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12
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Meiklejohn CD, Landeen EL, Gordon KE, Rzatkiewicz T, Kingan SB, Geneva AJ, Vedanayagam JP, Muirhead CA, Garrigan D, Stern DL, Presgraves DC. Gene flow mediates the role of sex chromosome meiotic drive during complex speciation. eLife 2018; 7:e35468. [PMID: 30543325 PMCID: PMC6292695 DOI: 10.7554/elife.35468] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022] Open
Abstract
During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation.
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Affiliation(s)
| | - Emily L Landeen
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - Kathleen E Gordon
- School of Biological SciencesUniversity of NebraskaLincolnUnited States
| | | | - Sarah B Kingan
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - Anthony J Geneva
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | | | | | - Daniel Garrigan
- Department of BiologyUniversity of RochesterNew YorkUnited States
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical InstituteVirginiaUnited States
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13
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Outomuro D, Johansson F. A potential pitfall in studies of biological shape: Does size matter? J Anim Ecol 2017; 86:1447-1457. [PMID: 28699246 DOI: 10.1111/1365-2656.12732] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/21/2017] [Indexed: 01/26/2023]
Abstract
The number of published studies using geometric morphometrics (GM) for analysing biological shape has increased steadily since the beginning of the 1990s, covering multiple research areas such as ecology, evolution, development, taxonomy and palaeontology. Unfortunately, we have observed that many published studies using GM do not evaluate the potential allometric effects of size on shape, which normally require consideration or assessment. This might lead to misinterpretations and flawed conclusions in certain cases, especially when size effects explain a large part of the shape variation. We assessed, for the first time and in a systematic manner, how often published studies that have applied GM consider the potential effects of allometry on shape. We reviewed the 300 most recent published papers that used GM for studying biological shape. We also estimated how much of the shape variation was explained by allometric effects in the reviewed papers. More than one-third (38%) of the reviewed studies did not consider the allometric component of shape variation. In studies where the allometric component was taken into account, it was significant in 88% of the cases, explaining up to 87.3% of total shape variation. We believe that one reason that may cause the observed results is a misunderstanding of the process that superimposes landmark configurations, i.e. the Generalized Procrustes Analysis, which removes isometric effects of size on shape, but not allometric effects. Allometry can be a crucial component of shape variation. We urge authors to address, and report, size effects in studies of biological shape. However, we do not propose to always remove size effects, but rather to evaluate the research question with and without the allometric component of shape variation. This approach can certainly provide a thorough understanding of how much size contributes to the observed shaped variation.
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Affiliation(s)
- David Outomuro
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Frank Johansson
- Section for Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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14
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Genetic and Transgenic Reagents for Drosophila simulans, D. mauritiana, D. yakuba, D. santomea, and D. virilis. G3-GENES GENOMES GENETICS 2017; 7:1339-1347. [PMID: 28280212 PMCID: PMC5386881 DOI: 10.1534/g3.116.038885] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Species of the Drosophila melanogaster species subgroup, including the species D. simulans, D. mauritiana, D. yakuba, and D. santomea, have long served as model systems for studying evolution. However, studies in these species have been limited by a paucity of genetic and transgenic reagents. Here, we describe a collection of transgenic and genetic strains generated to facilitate genetic studies within and between these species. We have generated many strains of each species containing mapped piggyBac transposons including an enhanced yellow fluorescent protein (EYFP) gene expressed in the eyes and a ϕC31 attP site-specific integration site. We have tested a subset of these lines for integration efficiency and reporter gene expression levels. We have also generated a smaller collection of other lines expressing other genetically encoded fluorescent molecules in the eyes and a number of other transgenic reagents that will be useful for functional studies in these species. In addition, we have mapped the insertion locations of 58 transposable elements in D. virilis that will be useful for genetic mapping studies.
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15
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Yassin A. Drosophila yakuba mayottensis, a new model for the study of incipient ecological speciation. Fly (Austin) 2017; 11:37-45. [PMID: 27560369 DOI: 10.1080/19336934.2016.1221550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
A full understanding of how ecological factors drive the fixation of genetic changes during speciation is obscured by the lack of appropriate models with clear natural history and powerful genetic toolkits. In a recent study, we described an early stage of ecological speciation in a population of the generalist species Drosophila yakuba (melanogaster subgroup) on the island of Mayotte (Indian Ocean). On this island, flies are strongly associated with the toxic fruits of noni (Morinda citrifolia) and show a partial degree of pre-zygotic reproductive isolation. Here, I mine the nuclear and mitochondrial genomes and provide a full morphological description of this population. Only 29 nuclear sites (< 4 × 10-7 of the genome) are fixed in this population and absent from 3 mainland populations and the closest relative D. santomea, but no mitochondrial or morphological character distinguish Mayotte flies from the mainland. This result indicates that physiological and behavioral traits may evolve faster than morphology at the early stages of speciation. Based on these differences, the Mayotte population is designated as a new subspecies, Drosophila yakuba mayottensis subsp. nov., and its strong potential in understanding the genetics of speciation and plant-insect interactions is discussed.
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Affiliation(s)
- Amir Yassin
- a Laboratory of Genetics , University of Wisconsin-Madison , Madison , WI , USA
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16
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Schmidt-Ott U, Lynch JA. Emerging developmental genetic model systems in holometabolous insects. Curr Opin Genet Dev 2016; 39:116-128. [PMID: 27399647 DOI: 10.1016/j.gde.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 01/08/2023]
Abstract
The number of insect species that are amenable to functional genetic studies is growing rapidly and provides many new research opportunities in developmental and evolutionary biology. The holometabolous insects represent a disproportionate percentage of animal diversity and are thus well positioned to provide model species for a wide variety of developmental processes. Here we discuss emerging holometabolous models, and review some recent breakthroughs. For example, flies and midges were found to use structurally unrelated long-range pattern organizers, butterflies and moths revealed extensive pattern formation during oogenesis, new imaging possibilities in the flour beetle Tribolium castaneum showed how embryos break free of their extraembryonic membranes, and the complex genetics governing interspecies difference in head shape were revealed in Nasonia wasps.
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Affiliation(s)
- Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, United States.
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, United States.
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17
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Schultz NG, Ingels J, Hillhouse A, Wardwell K, Chang PL, Cheverud JM, Lutz C, Lu L, Williams RW, Dean MD. The Genetic Basis of Baculum Size and Shape Variation in Mice. G3 (BETHESDA, MD.) 2016; 6:1141-51. [PMID: 26935419 PMCID: PMC4856068 DOI: 10.1534/g3.116.027888] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/05/2016] [Indexed: 01/01/2023]
Abstract
The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL) that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.
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Affiliation(s)
- Nicholas G Schultz
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Jesse Ingels
- University of Tennessee, Health Science Center, Memphis, Tennessee 38163
| | - Andrew Hillhouse
- Texas A & M, Veterinary Medicine and Biomedical Sciences, College Station, Texas 77845
| | | | - Peter L Chang
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - James M Cheverud
- Loyola University, Department of Biology, Chicago, Illinois 60626
| | | | - Lu Lu
- University of Tennessee, Health Science Center, Memphis, Tennessee 38163
| | - Robert W Williams
- University of Tennessee, Health Science Center, Memphis, Tennessee 38163
| | - Matthew D Dean
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
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18
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Lang M, Nagy O, Lang C, Orgogozo V. High throughput preparation of fly genomic DNA in 96-well format using a paint-shaker. Fly (Austin) 2016; 9:138-44. [PMID: 26818699 PMCID: PMC4862422 DOI: 10.1080/19336934.2015.1137401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Sample homogenization is an essential step for genomic DNA extraction, with multiple downstream applications in Molecular Biology. Genotyping hundreds or thousands of samples requires an automation of this homogenization step, and high throughput homogenizer equipment currently costs 7000 euros or more. We present an apparatus for homogenization of individual Drosophila adult flies in 96-well micro-titer dishes, which was built from a small portable paint-shaker (F5 portable paint-shaker, Ushake). Single flies are disrupted in each well that contains extraction buffer and a 4-mm metal ball. Our apparatus can hold up to five 96-well micro-titer plates. Construction of the homogenizer apparatus takes about 3–4 days, and all equipment can be obtained from a home improvement store. The total material cost is approximately 700 euros including the paint-shaker. We tested the performance of our apparatus using the ZR-96 Quick-gDNA™ kit (Zymo Research) homogenization buffer and achieved nearly complete tissue homogenization after 15 minutes of shaking. PCR tests did not detect any cross contamination between samples of neighboring wells. We obtained on average 138 ng of genomic DNA per fly, and DNA quality was adequate for standard PCR applications. In principle, our tissue homogenizer can be used for isolation of DNA suitable for library production and high throughput genotyping by Multiplexed Shotgun Genotyping (MSG), as well as RNA isolation from single flies. The sample adapter can also hold and shake other items, such as centrifuge tubes (15–50 mL) or small bottles.
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Affiliation(s)
- Michael Lang
- a Institut Jacques Monod; CNRS; UMR 7592; Universite Paris Diderot ; Sorbonne Paris , France
| | - Olga Nagy
- a Institut Jacques Monod; CNRS; UMR 7592; Universite Paris Diderot ; Sorbonne Paris , France
| | | | - Virginie Orgogozo
- a Institut Jacques Monod; CNRS; UMR 7592; Universite Paris Diderot ; Sorbonne Paris , France
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