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Bessa MH, Gottschalk MS, Robe LJ. Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences. Mol Phylogenet Evol 2024; 199:108158. [PMID: 39025321 DOI: 10.1016/j.ympev.2024.108158] [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: 04/04/2024] [Revised: 06/28/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
Incomplete Lineage Sorting (ILS) and introgression are among the two main factors causing incongruence between gene and species trees. Advances in phylogenomic studies have allowed us to overcome most of these issues, providing reliable phylogenetic hypotheses while revealing the underlying evolutionary scenario. Across the last century, many incongruent phylogenetic reconstructions were recovered for Drosophilidae, employing a limited sampling of genetic markers or species. In these studies, the monophyly and the phylogenetic positioning of the Zygothrica genus group stood out as one of the most controversial questions. Thus, here, we addressed these issues using a phylogenomic approach, while accessing the influence of ILS and introgressions on the diversification of these species and addressing the spatio-temporal scenario associated with their evolution. For this task, the genomes of nine specimens from six Neotropical species belonging to the Zygothrica genus group were sequenced and evaluated in a phylogenetic framework encompassing other 39 species of Drosophilidae. Nucleotide and amino acid sequences recovered for a set of 2,534 single-copy genes by BUSCO were employed to reconstruct maximum likelihood (ML) concatenated and multi-species coalescent (MSC) trees. Likelihood mapping, quartet sampling, and reticulation tests were employed to infer the level and causes of incongruence. Lastly, a penalized-likelihood molecular clock strategy with fossil calibrations was performed to infer divergence times. Taken together, our results recovered the subdivision of Drosophila into six different lineages, one of which clusters species of the Zygothrica genus group (except for H. duncani). The divergence of this lineage was dated to Oligocene ∼ 31 Mya and seems to have occurred in the same timeframe as other key diversification within Drosophila. According to the concatenated and MSC strategies, this lineage is sister to the clade joining Drosophila (Siphlodora) with the Hawaiian Drosophila and Scaptomyza. Likelihood mapping, quartet sampling, reticulation reconstructions as well as introgression tests revealed that this lineage was the target of several hybridization events involving the ancestors of different Drosophila lineages. Thus, our results generally show introgression as a major source of previous incongruence. Nevertheless, the similar diversification times recovered for several of the Neotropical Drosophila lineages also support the scenario of multiple and simultaneous diversifications taking place at the base of Drosophilidae phylogeny, at least in the Neotropics.
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Affiliation(s)
- Maiara Hartwig Bessa
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Universidade Federal de Santa Maria (UFSM), Brazil
| | - Marco Silva Gottschalk
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBDiv), Instituto de Biologia, Universidade Federal de Pelotas (UFPel), Brazil
| | - Lizandra Jaqueline Robe
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Universidade Federal de Santa Maria (UFSM), Brazil.
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2
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Li F, Rane RV, Luria V, Xiong Z, Chen J, Li Z, Catullo RA, Griffin PC, Schiffer M, Pearce S, Lee SF, McElroy K, Stocker A, Shirriffs J, Cockerell F, Coppin C, Sgrò CM, Karger A, Cain JW, Weber JA, Santpere G, Kirschner MW, Hoffmann AA, Oakeshott JG, Zhang G. Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation. Mol Ecol Resour 2022; 22:1559-1581. [PMID: 34839580 PMCID: PMC9299920 DOI: 10.1111/1755-0998.13561] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/10/2021] [Indexed: 01/13/2023]
Abstract
Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high-quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome-wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert-adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate-continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics-restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large-scale and multifaceted genomic changes.
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Affiliation(s)
- Fang Li
- BGI‐ShenzhenShenzhenChina
- Section for Ecology and EvolutionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Rahul V. Rane
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Victor Luria
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Zijun Xiong
- BGI‐ShenzhenShenzhenChina
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of Sciences (CAS)KunmingYunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Renee A. Catullo
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Division of Ecology and EvolutionCentre for Biodiversity AnalysisThe Australian National UniversityActonACTAustralia
| | - Philippa C. Griffin
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Michele Schiffer
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
- Daintree Rainforest ObservatoryJames Cook UniversityCape TribulationQldAustralia
| | - Stephen Pearce
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
| | - Siu Fai Lee
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Applied BioSciencesMacquarie UniversityNorth RydeNSWAustralia
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
| | - Ann Stocker
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Jennifer Shirriffs
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - Fiona Cockerell
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Chris Coppin
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
| | - Carla M. Sgrò
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Amir Karger
- IT ‐ Research ComputingHarvard Medical SchoolBostonMassachusettsUSA
| | - John W. Cain
- Department of MathematicsHarvard UniversityCambridgeMassachusettsUSA
| | - Jessica A. Weber
- Department of GeneticsHarvard Medical SchoolBostonMassachusettsUSA
| | - Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB)Department of Experimental and Health Sciences (DCEXS)Hospital del Mar Medical Research Institute (IMIM)Universitat Pompeu FabraBarcelonaCataloniaSpain
| | - Marc W. Kirschner
- Department of Systems BiologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Ary A. Hoffmann
- Bio21 InstituteSchool of BioSciencesUniversity of MelbourneParkvilleVic.Australia
| | - John G. Oakeshott
- Commonwealth Scientific and Industrial Research OrganisationActonACTAustralia
- Applied BioSciencesMacquarie UniversityNorth RydeNSWAustralia
| | - Guojie Zhang
- BGI‐ShenzhenShenzhenChina
- Section for Ecology and EvolutionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of Sciences (CAS)KunmingYunnanChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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3
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Rane RV, Clarke DF, Pearce SL, Zhang G, Hoffmann AA, Oakeshott JG. Detoxification Genes Differ Between Cactus-, Fruit-, and Flower-Feeding Drosophila. J Hered 2020; 110:80-91. [PMID: 30445496 DOI: 10.1093/jhered/esy058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
We use annotated genomes of 14 Drosophila species covering diverse host use phenotypes to test whether 4 gene families that often have detoxification functions are associated with host shifts among species. Bark, slime flux, flower, and generalist necrotic fruit-feeding species all have similar numbers of carboxyl/cholinesterase, glutathione S-transferase, cytochrome P450, and UDP-glucuronosyltransferase genes. However, species feeding on toxic Morinda citrifolia fruit and the fresh fruit-feeding Drosophila suzukii have about 30 and 60 more, respectively. ABC transporters show a different pattern, with the flower-feeding D. elegans and the generalist necrotic fruit and cactus feeder D. hydei having about 20 and >100 more than the other species, respectively. Surprisingly, despite the complex secondary chemistry we find that 3 cactophilic specialists in the mojavensis species cluster have variably fewer genes than any of the other species across all 4 families. We also find 82 positive selection events across the 4 families, with the terminal D. suzukii and M. citrifolia-feeding D. sechellia branches again having the highest number of such events in proportion to their respective branch lengths. Many of the genes involved in these host-use-specific gene number differences or positive selection events lie in specific clades of the gene families that have been recurrently associated with detoxification. Several genes are also found to be involved in multiple duplication and/or positive selection events across the species studied regardless of their host use phenotypes; the most frequently involved are the ABC transporter CG1718, which is not in a specific clade associated with detoxification, and the α-esterase gene cluster, which is.
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Affiliation(s)
- Rahul V Rane
- CSIRO, Acton, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - David F Clarke
- CSIRO, Acton, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, København, Denmark
| | - Ary A Hoffmann
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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Abstract
Understanding phylogenetic relationships among taxa is key to designing and implementing comparative analyses. The genus Drosophila, which contains over 1600 species, is one of the most important model systems in the biological sciences. For over a century, one species in this group, Drosophila melanogaster, has been key to studies of animal development and genetics, genome organization and evolution, and human disease. As whole-genome sequencing becomes more cost-effective, there is increasing interest in other members of this morphologically, ecologically, and behaviorally diverse genus. Phylogenetic relationships within Drosophila are complicated, and the goal of this paper is to provide a review of the recent taxonomic changes and phylogenetic relationships in this genus to aid in further comparative studies.
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5
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Franco FF, Silva ECC, Barrios-Leal DY, Sene FM, Manfrin MH. The Calibrated Phylogeny of the Drosophila fasciola Subgroup (D. repleta Group Wasserman) Indicates Neogene Diversification of Its Internal Branches. NEOTROPICAL ENTOMOLOGY 2017; 46:537-545. [PMID: 28144910 DOI: 10.1007/s13744-017-0484-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/06/2017] [Indexed: 06/06/2023]
Abstract
The species of the Drosophila fasciola subgroup Wasserman represent the dominant section of the Drosophila repleta group Wasserman in the American rainforests and have a broad geographical distribution in the New World. However, despite of its wide range, the D. fasciola subgroup is one of the most overlooked D. repleta subgroups. Here, we report a molecular phylogenetic analysis focused on the D. fasciola subgroup using two mitochondrial [cytochrome oxidase subunit I (COI), cytochrome oxidase subunit II (COII)] and two nuclear [elongation factor-1alpha F1 (EF-alphaF1) and transformer (tra)] genes. Overall, we found that this subgroup is a monophyletic taxon, subdivided into two main internal branches: named Fas1 and Fas2 clades. The diversification of these clades is estimated to have begun in the middle Miocene, around 12 Ma [95% high posterior density (HPD) 9.0-15 Ma], and might be associated with the colonization of South America by Central America populations after the closure of Isthmus of Panama due to the temporal congruence between these events. The terminal branches had their origins estimated to be in the Pliocene or the Plio-Pleistocene transition. For the later estimates, both the geomorphological influences and the climatic oscillations of the Pleistocene may have played a role in shaping the diversification of the D. fasciola group.
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Affiliation(s)
- F F Franco
- Depto de Biologia, Centro de Ciências Humanas e Biológicas, Univ Federal de São Carlos, Rodovia João Leme dos Santos, Km 110, SP264, Sorocaba, 18052-780, Brasil.
| | - E C C Silva
- Secretaria do Meio Ambiente do Estado de São Paulo, São Paulo, Brasil
| | - D Y Barrios-Leal
- Pós-Graduação do Depto de Genética-Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, São Paulo, Brasil
| | - F M Sene
- Pós-Graduação do Depto de Genética-Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, São Paulo, Brasil
- Depto de Biologia-Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brasil
| | - M H Manfrin
- Pós-Graduação do Depto de Genética-Faculdade de Medicina de Ribeirão Preto, Univ de São Paulo, São Paulo, Brasil
- Depto de Biologia-Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Univ de São Paulo, Ribeirão Preto, Brasil
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6
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Izumitani HF, Kusaka Y, Koshikawa S, Toda MJ, Katoh T. Phylogeography of the Subgenus Drosophila (Diptera: Drosophilidae): Evolutionary History of Faunal Divergence between the Old and the New Worlds. PLoS One 2016; 11:e0160051. [PMID: 27462734 PMCID: PMC4962979 DOI: 10.1371/journal.pone.0160051] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/13/2016] [Indexed: 11/19/2022] Open
Abstract
The current subgenus Drosophila (the traditional immigrans-tripunctata radiation) includes major elements of temperate drosophilid faunas in the northern hemisphere. Despite previous molecular phylogenetic analyses, the phylogeny of the subgenus Drosophila has not fully been resolved: the resulting trees have more or less varied in topology. One possible factor for such ambiguous results is taxon-sampling that has been biased towards New World species in previous studies. In this study, taxon sampling was balanced between Old and New World species, and phylogenetic relationships among 45 ingroup species selected from ten core species groups of the subgenus Drosophila were analyzed using nucleotide sequences of three nuclear and two mitochondrial genes. Based on the resulting phylogenetic tree, ancestral distributions and divergence times were estimated for each clade to test Throckmorton’s hypothesis that there was a primary, early-Oligocene disjunction of tropical faunas and a subsequent mid-Miocene disjunction of temperate faunas between the Old and the New Worlds that occurred in parallel in separate lineages of the Drosophilidae. Our results substantially support Throckmorton’s hypothesis of ancestral migrations via the Bering Land Bridge mainly from the Old to the New World, and subsequent vicariant divergence of descendants between the two Worlds occurred in parallel among different lineages of the subgenus Drosophila. However, our results also indicate that these events took place multiple times over a wider time range than Throckmorton proposed, from the late Oligocene to the Pliocene.
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Affiliation(s)
- Hiroyuki F. Izumitani
- Department of Natural History Science, Graduate school of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yohei Kusaka
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Shigeyuki Koshikawa
- The Hakubi Center for Advanced Research and Graduate School of Science, Kyoto University, Kyoto, Kyoto, Japan
| | - Masanori J. Toda
- Hokkaido University Museum, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Toru Katoh
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
- * E-mail:
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7
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Machado S, Gottschalk MS, Robe LJ. Historical patterns of niche dynamics in Neotropical species of the Drosophila subgenus (Drosophilidae, Diptera). Evol Ecol 2015. [DOI: 10.1007/s10682-015-9805-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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8
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Morales-Hojas R, Vieira J. Phylogenetic patterns of geographical and ecological diversification in the subgenus Drosophila. PLoS One 2012; 7:e49552. [PMID: 23152919 PMCID: PMC3495880 DOI: 10.1371/journal.pone.0049552] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 10/15/2012] [Indexed: 11/18/2022] Open
Abstract
Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.
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Affiliation(s)
- Ramiro Morales-Hojas
- Molecular Evolution Lab, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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9
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Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group. Mol Phylogenet Evol 2012; 64:533-44. [DOI: 10.1016/j.ympev.2012.05.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 05/12/2012] [Accepted: 05/14/2012] [Indexed: 11/20/2022]
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Abstract
SummaryThe genus Drosophila is diverse and heterogeneous and contains a large number of easy-to-rear species, so it is an attractive subject for comparative studies. The ability to perform such studies is currently compromised by the lack of a comprehensive phylogeny for Drosophila and related genera. The genus Drosophila as currently defined is known to be paraphyletic with respect to several other genera, but considerable uncertainty remains about other aspects of the phylogeny. Here, we estimate a phylogeny for 176 drosophilid (12 genera) and four non-drosophilid species, using gene sequences for up to 13 different genes per species (average: 4333 bp, five genes per species). This is the most extensive set of molecular data on drosophilids yet analysed. Phylogenetic analyses were conducted with maximum-likelihood (ML) and Bayesian approaches. Our analysis confirms that the genus Drosophila is paraphyletic with 100% support in the Bayesian analysis and 90% bootstrap support in the ML analysis. The subgenus Sophophora, which includes Drosophila melanogaster, is the sister clade of all the other subgenera as well as of most species of six other genera. This sister clade contains two large, well-supported subclades. The first subclade contains the Hawaiian Drosophila, the genus Scaptomyza, and the virilis-repleta radiation. The second contains the immigrans-tripunctata radiation as well as the genera Hirtodrosophila (except Hirtodrosophila duncani), Mycodrosophila, Zaprionus and Liodrosophila. We argue that these results support a taxonomic revision of the genus Drosophila.
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Robe LJ, Loreto ELS, Valente VLS. Radiation of the ,,Drosophila“ subgenus (Drosophilidae, Diptera) in the Neotropics. J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2009.00563.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Mota NR, Robe LJ, Valente VLS, Budnik M, Loreto ELS. Phylogeny of the Drosophila mesophragmatica group (Diptera, Drosophilidae): an example of Andean evolution. Zoolog Sci 2008; 25:526-32. [PMID: 18558806 DOI: 10.2108/zsj.25.526] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 03/12/2008] [Indexed: 11/17/2022]
Abstract
The mesophragmatica group of Drosophila belongs to the virilis-repleta radiation of the Drosophila subgenus. This group comprises 13 Neotropical species that are endemic to the South-American continent and seem to be fundamentally Andean in their distribution. The mesophragmatica-group phylogeny has been inferred previously by other authors based on morphological, cytological, and isozyme analyses. However, the relationships within the group have not yet been completely resolved, although its monophyletic origin has already been confirmed by molecular data. This work attempts to enhance the molecular approach to the relationships among the species of the mesophragmatica group, using both nuclear and mitochondrial markers. Phylogenetic analyses were performed using fragments of the nuclear alcohol dehydrogenase (Adh; 631 bp), alpha-methyldopa (Amd; 1211 bp), dopa-decarboxylase (Ddc; 1105 bp), and hunchback (Hb; 687 bp) genes and the mitochondrial cytochrome oxidase subunit II (COII; 672 bp) gene, and included a total of 4306 bp. The sequences obtained for eight representatives of the mesophragmatica group were analyzed both individually and in combination by distance methods, maximum parsimony, and maximum likelihood. Our results support subdivision of the mesophragmatica group into three main lineages: the first is composed of D. viracochi; the second comprises a clade grouping the sibling species D. pavani and D. gaucha; and the third encompasses D. gasici, D. brncici, and D. mesophragmatica. The best supported scenario suggests that D. viracochi is an early offshoot in the mesophragmatica group, with this and other early branchings occuring in the Pliocene/Pleistocene Epochs, possibly associated with Andean glacial refuges. Also based on the phylogenies obtained, we present a genealogical view of the evolution of previously described characters within the group.
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Affiliation(s)
- Nina R Mota
- Programa de Pos-Graduacao em Genetica e Biologia Molecular, Departamento de Genetica, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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13
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Joly D, Luck N, Dejonghe B. Adaptation to long sperm in Drosophila: correlated development of the sperm roller and sperm packaging. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2008; 310:167-78. [PMID: 17377954 DOI: 10.1002/jez.b.21167] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Sperm are generally small and produced in huge numbers, but some species combine exaggerated sperm length with extremely limited numbers of sperm, an evolutionary trend that deviates from the theory of anisogamy. Sperm gigantism has arisen recurrently in various species, but insects exhibit the longest sperm, with some species of the Drosophilidae family producing sperm up to 6 cm in length. The anatomical, cytological, and physiological requirements for males to cope with these giant sperm were hitherto poorly understood. In this paper, we investigate the internal morphology of the male reproductive tract, and highlight specific features that may be linked to this increase in sperm size. We focus on species in the repleta group, within which sperm length varies by a factor of 35. An associated development of the sperm roller, a special twisting device inserted between the testis and the seminal vesicle, is demonstrated. Its length and the number of coils involved increase with sperm size, and it allows individual sperm to swell and roll into a spermatic pellet before reaching the seminal vesicle. This process occurs independently of and in addition to the sperm bundle coiling that takes place at the base of the testis. It is suggested that the emergence and development of the sperm roller may be a male adaptation to sperm gigantism.
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Affiliation(s)
- Dominique Joly
- Laboratoire Evolution, Génomes et Spéciation, Gif sur Yvette Cedex, France.
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14
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Independent origins of new sex-linked chromosomes in the melanica and robusta species groups of Drosophila. BMC Evol Biol 2008; 8:33. [PMID: 18230153 PMCID: PMC2268673 DOI: 10.1186/1471-2148-8-33] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Accepted: 01/29/2008] [Indexed: 01/03/2023] Open
Abstract
Background Recent translocations of autosomal regions to the sex chromosomes represent important systems for identifying the evolutionary forces affecting convergent patterns of sex-chromosome heteromorphism. Additions to the sex chromosomes have been reported in the melanica and robusta species groups, two sister clades of Drosophila. The close relationship between these two species groups and the similarity of their rearranged karyotypes motivates this test of alternative hypotheses; the rearranged sex chromosomes in both groups are derived through a common origin, or the rearrangements are derived through at least two independent origins. Here we examine chromosomal arrangement in representatives of the melanica and the robusta species groups and test these alternative hypotheses using a phylogenetic approach. Results Two mitochondrial and two nuclear gene sequences were used to reconstruct phylogenetic relationships of a set of nine ingroup species having fused and unfused sex chromosomes and representing a broad sample of both species groups. Different methods of phylogenetic inference, coupled with concurrent cytogenetic analysis, indicate that the hypothesis of independent origins of rearranged sex chromosomes within each species group is significantly more likely than the alternative hypothesis of a single common origin. An estimate tightly constrained around 8 My was obtained for the age of the rearranged sex chromosomes in the melanica group; however, a more loosely constrained estimate of 10–15 My was obtained for the age of the rearrangement in the robusta group. Conclusion Independent acquisition of new chromosomal arms by the sex chromosomes in the melanica and robusta species groups represents a case of striking convergence at the karyotypic level. Our findings indicate that the parallel divergence experienced by newly sex-linked genomic regions in these groups represents an excellent system for studying the tempo of sex chromosome evolution.
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15
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Morán T, Fontdevila A. On the phylogeny of the Drosophila hydei subgroup: New insights from combined analyses of nuclear and mitochondrial data. Mol Phylogenet Evol 2007; 43:1198-205. [PMID: 17292635 DOI: 10.1016/j.ympev.2006.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 10/04/2006] [Accepted: 12/28/2006] [Indexed: 11/19/2022]
Affiliation(s)
- Tomás Morán
- Grup de Biologia Evolutiva, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.
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Da Lage JL, Kergoat GJ, Maczkowiak F, Silvain JF, Cariou ML, Lachaise D. A phylogeny of Drosophilidae using the Amyrel gene: questioning the Drosophila melanogaster species group boundaries. J ZOOL SYST EVOL RES 2007. [DOI: 10.1111/j.1439-0469.2006.00389.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang BC, Park J, Watabe HA, Gao JJ, Xiangyu JG, Aotsuka T, Chen HW, Zhang YP. Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences. Mol Phylogenet Evol 2006; 40:484-500. [PMID: 16678448 DOI: 10.1016/j.ympev.2006.03.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 03/17/2006] [Accepted: 03/18/2006] [Indexed: 11/23/2022]
Abstract
Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.
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Affiliation(s)
- Bao-cheng Wang
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Abstract
Species of the genus Drosophila exhibit enormous variation in all of their reproductive behaviors: resource use and specialization, courtship signaling, sperm utilization, and female remating. The genetic bases of this variability and its evolution are poorly understood. At the same time, Drosophila comparative genomics now has developed to a point at which approaches previously only possible with D. melanogaster can be exploited to address these questions. We have taken advantage of the known phylogenetic relationships of this group of flies not only to place these behaviors in an evolutionary framework, but to provide a roadmap for future genetic studies.
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Affiliation(s)
- Therese Ann Markow
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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Silva-Bernardi EC, Morales AC, Sene FM, Manfrin MH. Phylogenetic relationships in the Drosophila fasciola species subgroup (Diptera, Drosophilidae) inferred from partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000300029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Hodgetts RB, O'Keefe SL. Dopa decarboxylase: a model gene-enzyme system for studying development, behavior, and systematics. ANNUAL REVIEW OF ENTOMOLOGY 2006; 51:259-84. [PMID: 16332212 DOI: 10.1146/annurev.ento.51.110104.151143] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Throughout its long evolutionary history, the Dopa decarboxylase gene (Ddc) has acquired a variety of functions in insects. The enzyme (DDC) catalyzes the production of the neural transmitters dopamine and serotonin. Not surprisingly, evidence of the enzyme's involvement in the behavior of insects is beginning to accumulate. In addition, DDC plays a role in wound healing, parasite defense, pigmentation, and cuticle hardening. A high degree of sequence conservation has allowed comparisons of the Ddc-coding regions from various insects, facilitating a number of recent studies on insect systematics. This review outlines the diverse functions of Ddc and illustrates how studies of this model system address many questions on insect neurobiology, developmental biology, and systematics.
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Affiliation(s)
- Ross B Hodgetts
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.
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Morán T, Fontdevila A. Phylogeny and molecular evolution of the Drosophila hydei subgroup (Drosophila repleta group) inferred from the Xanthine dehydrogenase gene. Mol Phylogenet Evol 2005; 36:695-705. [PMID: 15935705 DOI: 10.1016/j.ympev.2005.04.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Revised: 03/18/2005] [Accepted: 04/05/2005] [Indexed: 11/30/2022]
Abstract
The hydei subgroup (Drosophila repleta group) consists of seven species divided into two complexes: bifurca and hydei, whose phylogenetic relationships are not well understood. To evaluate the molecular phylogeny of this subgroup, we analyzed 2085 bp of coding sequence of the Xanthine dehydrogenase gene in six available species of the hydei subgroup, with Drosophila buzzatii and Drosophila mulleri as an outgroup. For phylogenetic reconstruction we adopted a maximum-likelihood framework, based on the adjustment of descriptive models of nucleotide substitution to real data. We employed distance-based and weighted parsimony methods to construct candidate phylogenies. In all cases, we obtained only one completely resolved tree with strong statistical support for each node, that shows a phylogeny that is partially discordant with the proposed systematics of the subgroup. This tree suggests that the two species complexes are paraphyletic, as opposed to classic phylogenies using morphologic and cytologic traits. This discordance is discussed in relation to its implication for the evolutionary history of the hydei subgroup.
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Affiliation(s)
- Tomás Morán
- Grup de Biología Evolutiva, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
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Robe LJ, Valente VLS, Budnik M, Loreto ELS. Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: A nuclear versus mitochondrial gene approach. Mol Phylogenet Evol 2005; 36:623-40. [PMID: 15970444 DOI: 10.1016/j.ympev.2005.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2004] [Revised: 04/26/2005] [Accepted: 05/10/2005] [Indexed: 11/23/2022]
Abstract
The genus Drosophila has played an essential role in many biological studies during the last 100 years but much controversy and many incompletely addressed issues still remain to be elucidated regarding the phylogeny of this genus. Because information on the Neotropical species contained in the subgenus Drosophila is particularly incomplete, with this taxonomic group being underrepresented in many studies, we designed a study to answer some evolutionary questions related to these species. We subjected at least 41 Drosophilidae taxa to a phylogenetic analysis using a 516-base pair (bp) fragment of the alpha-methyldopa (Amd) nuclear gene and a 672 bp fragment of the mitochondrial cytochrome oxidase subunit II (COII) gene both individually and in combination. We found that the subgenus Drosophila is paraphyletic and subdivided into two main clusters: the first containing species traditionally placed in the virilis-repleta radiation and the second assembling species of the immigrans-Hirtodrosophila radiation. Inside the first of these clusters we could detect the monophyly of both the flavopilosa (the sister-clade of the annulimana group) and the mesophragmatica (closely related to the repleta group) species groups. Concerning the immigrans-Hirtodrosophila lineage, Zaprionus, Liodrosophila, Samoaia, and Hirtodrosophila were the early offshoots, followed by the immigrans, quinaria, testacea, and funebris species groups. The tripunctata radiation appears to be a derived clade, composed of a paraphyletic tripunctata group, intimately interposed with members of the cardini, guarani, and guaramunu species groups. Overall, the COII gene yielded a poor phylogenetic performance when compared to the Amd gene, the evolutionary hypothesis of which agreed with the total evidence tree. This phenomenon can be explained by the fast saturation of transitional substitutions in COII, due to strong biases in both base composition and substitution patterns, as also by its great among-site rate variation heterogeneity.
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Affiliation(s)
- Lizandra J Robe
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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Houle D, Mezey J, Galpern P, Carter A. Automated measurement of Drosophila wings. BMC Evol Biol 2003; 3:25. [PMID: 14670094 PMCID: PMC317280 DOI: 10.1186/1471-2148-3-25] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2003] [Accepted: 12/11/2003] [Indexed: 11/17/2022] Open
Abstract
Background Many studies in evolutionary biology and genetics are limited by the rate at which phenotypic information can be acquired. The wings of Drosophila species are a favorable target for automated analysis because of the many interesting questions in evolution and development that can be addressed with them, and because of their simple structure. Results We have developed an automated image analysis system (WINGMACHINE) that measures the positions of all the veins and the edges of the wing blade of Drosophilid flies. A video image is obtained with the aid of a simple suction device that immobilizes the wing of a live fly. Low-level processing is used to find the major intersections of the veins. High-level processing then optimizes the fit of an a priori B-spline model of wing shape. WINGMACHINE allows the measurement of 1 wing per minute, including handling, imaging, analysis, and data editing. The repeatabilities of 12 vein intersections averaged 86% in a sample of flies of the same species and sex. Comparison of 2400 wings of 25 Drosophilid species shows that wing shape is quite conservative within the group, but that almost all taxa are diagnosably different from one another. Wing shape retains some phylogenetic structure, although some species have shapes very different from closely related species. The WINGMACHINE system facilitates artificial selection experiments on complex aspects of wing shape. We selected on an index which is a function of 14 separate measurements of each wing. After 14 generations, we achieved a 15 S.D. difference between up and down-selected treatments. Conclusion WINGMACHINE enables rapid, highly repeatable measurements of wings in the family Drosophilidae. Our approach to image analysis may be applicable to a variety of biological objects that can be represented as a framework of connected lines.
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Affiliation(s)
- David Houle
- Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5 Canada
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306 USA
| | - Jason Mezey
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306 USA
- Department of Evolution and Ecology, UC Davis, Davis, CA 95616, USA
| | - Paul Galpern
- Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5 Canada
| | - Ashley Carter
- Department of Biological Science, Florida State University, Tallahassee, Florida, 32306 USA
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