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Wang YL, Wang NN, Zhang Y, Tsaur SC, Chen HW. Cryptic diversity in the subgenus Oxyphortica (Diptera, Drosophilidae, Stegana). PeerJ 2021; 9:e12347. [PMID: 34760370 PMCID: PMC8559608 DOI: 10.7717/peerj.12347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Phylogenetic relationships of the subgenus Oxyphortica were reconstructed based on two mitochondrial genes (COI and ND2). The results revealed the paraphyly of Oxyphortica and supported high levels of cryptic diversity within this subgenus. By integrating morphological characteristics and molecular evidence, we identified 17 new species as members of Oxyphortica: S. (O.) amphigya sp. nov., S. (O.) armillata sp. nov., S. (O.) ashima sp. nov., S. (O.) bawo sp. nov., S. (O.) crypta sp. nov., S. (O.) gelea sp. nov., S. (O.) hengduanmontana sp. nov., S. (O.) jinmingi sp. nov., S. (O.) mengbalanaxi sp. nov., S. (O.) mouig sp. nov., S. (O.) setipes sp. nov., S. (O.) shangrila sp. nov., S. (O.) tsauri sp. nov., S. (O.) valleculata sp. nov., S. (O.) wanhei sp. nov., S. (O.) yangjin sp. nov. and S. (O.) hypophaia sp. nov. To test the early morphological identifications and confirm the species boundaries, different species delimitation methods, including Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics and Phylogeography (BP&P), were used, together with traditional distance. All species boundaries were clearly defined. As Oxyphortica species are mainly distributed across Southwest China (e.g., 20 spp. from the Hengduan Mountains), the complex climate and topographic landforms of the area may be responsible for the high levels of species diversity and endemism.
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Huang J, Gong LU, Tsaur SC, Zhu L, An K, Chen H. Revision of the subgenus Phortica (sensu stricto) (Diptera, Drosophilidae) from East Asia, with assessment of species delimitation using DNA barcodes. Zootaxa 2019; 4678:zootaxa.4678.1.1. [PMID: 31715979 DOI: 10.11646/zootaxa.4678.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Indexed: 11/04/2022]
Abstract
A total of 50 (43 known and seven new) species in the subgenus Phortica (sensu stricto) were surveyed and (re)described from China: P. bicornuta (Chen Toda, 1997); P. bipartita (Toda Peng, 1992); P. biprotrusa (Chen Toda, 1998); P. cardua (Okada, 1977); P. chi (Toda Sidorenko, 1996); P. conifera (Okada, 1977); P. eparmata (Okada, 1977); P. eugamma (Toda Peng, 1990); P. excrescentiosa (Toda Peng, 1990); P. fangae (Máca, 1993); P. flexuosa (Zhang Gan, 1986); P. foliata (Chen Toda, 1997); P. gamma (Toda Peng, 1990); P. gigas (Okada, 1977); P. glabtabula Chen Gao, 2005; P. hainanensis (Chen Toda, 1998); P. hongae (Máca, 1993); P. huazhii Cheng Chen, 2008; P. iota (Toda Sidorenko, 1996); P. jadete Zhu, Cao Chen, 2018; P. kappa (Máca, 1977); P. lambda (Toda Peng, 1990); P. latifoliacea Chen Watabe, 2008; P. magna (Okada, 1960); P. okadai (Máca, 1977); P. omega (Okada, 1977); P. orientalis (Hendel, 1914); P. pangi Chen Wen, 2005; P. paramagna (Okada, 1971); P. perforcipata (Máca Lin, 1993); P. pi (Toda Peng, 1990); P. protrusa (Zhang Shi, 1997); P. pseudopi (Toda Peng, 1990); P. pseudotau (Toda Peng, 1990); P. psi (Zhang Gan, 1986); P. rhagolobos Chen Gao, 2008; P. saeta (Zhang Gan, 1986); P. setitabula Chen Gao, 2005; P. subradiata (Okada, 1977); P. tau (Toda Peng, 1990); P. uncinata Chen Gao, 2005; P. unipetala Chen Wen, 2005; P. allomega Gong Chen, sp. nov.; P. archikappa Gong Chen, sp. nov.; P. dianzangensis Gong Chen, sp. nov.; P. imbacilia Gong Chen, sp. nov.; P. liukuni Gong Chen, sp. nov.; P. tibeta Gong Chen, sp. nov.; and P. xianfui Gong Chen, sp. nov. In addition, seven new synonyms were recognized: P. acongruens (Zhang Shi, 1997), syn. nov.; P. antillaria (Chen Toda, 1997), syn. nov.; P. kukuanensis Máca, 2003, syn. nov.; P. linae (Máca Chen, 1993), syn. nov.; P. shillongensis (Singh Gupta, 1979), syn. nov.; P. takadai (Okada, 1977), syn. nov.; and P. watanabei (Máca Lin, 1993), syn. nov. A key to all Asian species (except for the eparmata species complex) of this subgenus was provided. All currently available DNA barcode (partial mitochondrial cytochrome c oxidase subunit I (COI) gene) sequences of this subgenus (217 sequences of 54 species) are employed in a molecular analysis using different species delimitation methods. The results indicate that approximately 68.5% (37 of 54 spp.) of Phortica (s. str.) species could be clearly distinguished from closely related morphospecies or cryptic species.
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Liu FGR, Tsaur SC, Huang HT. Biogeography of Drosophila (Diptera: Drosophilidae) in East and Southeast Asia. JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:iev056. [PMID: 26078303 PMCID: PMC4535568 DOI: 10.1093/jisesa/iev056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
The causes of high biological diversity in biodiversity hotspots have long been a major subject of study in conservation biology. To investigate this matter, we conducted a phylogeographic study of five Drosophila (Diptera: Drosophilidae) species from East and Southeast Asia: Drosophila albomicans Duda, D. formosana Duda, D. immigrans Sturtevant, D. melanogaster Meigen, and D. simulans Sturtevant. We collected 185 samples from 28 localities in eight countries. From each collected individual, we sequenced the autosomal extra sex comb gene (esc) and seven mitochondrial genes, including nicotinamide adenine dinucleotide hydrate-reductase dehydrogenase subunit 4 (ND4), ND4L, tRNA-His, tRNA-Pro, tRNA-Thr, partial ND5, and partial ND6. Phylogenetic analyses using maximum- likelihood and Bayesian methods revealed interesting population structure and identified the existence of two distinct D. formosana lineages (Southeast Asian and Taiwanese populations). Genetic differentiation among groups of D. immigrans suggests the possibility of endemic speciation in Taiwan. In contrast, D. melanogaster remained one extensively large population throughout East and Southeast Asia, including nearby islets. A molecular clock was used to estimate divergence times, which were compared with past geographical events to infer evolutionary scenarios. Our findings suggest that interglacial periods may have caused population isolation, thus enhancing population differentiation more strongly for some of the Drosophila species. The population structure of each Drosophila species in East and Southeast Asia has been influenced by past geographic events.
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Yang H, He BZ, Ma H, Tsaur SC, Ma C, Wu Y, Ting CT, Zhang YE. Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population. Mol Biol Evol 2014; 32:216-28. [PMID: 25371429 PMCID: PMC4271532 DOI: 10.1093/molbev/msu299] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Widespread premature termination codon mutations (PTCs) were recently observed in human and fly populations. We took advantage of the population resequencing data in the Drosophila Genetic Reference Panel to investigate how the expression profile and the evolutionary age of genes shaped the allele frequency distribution of PTCs. After generating a high-quality data set of PTCs, we clustered genes harboring PTCs into three categories: genes encoding low-frequency PTCs (≤ 1.5%), moderate-frequency PTCs (1.5-10%), and high-frequency PTCs (>10%). All three groups show narrow transcription compared with PTC-free genes, with the moderate- and high-PTC frequency groups showing a pronounced pattern. Moreover, nearly half (42%) of the PTC-encoding genes are not expressed in any tissue. Interestingly, the moderate-frequency PTC group is strongly enriched for genes expressed in midgut, whereas genes harboring high-frequency PTCs tend to have sex-specific expression. We further find that although young genes born in the last 60 My compose a mere 9% of the genome, they represent 16%, 30%, and 50% of the genes containing low-, moderate-, and high-frequency PTCs, respectively. Among DNA-based and RNA-based duplicated genes, the child copy is approximately twice as likely to contain PTCs as the parent copy, whereas young de novo genes are as likely to encode PTCs as DNA-based duplicated new genes. Based on these results, we conclude that expression profile and gene age jointly shaped the landscape of PTC-mediated gene loss. Therefore, we propose that new genes may need a long time to become stably maintained after the origination.
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Zhang Y, Tsaur SC, Chen HW. Survey of the genus Stegana Meigen (Diptera, Drosophilidae) from Taiwan, with DNA barcodes and descriptions of three new species. Zool Stud 2014. [DOI: 10.1186/1810-522x-53-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Twelve Stegana species have been reported from Taiwan, yet only four were also recorded from Mainland China. This may not reflect the actual fauna between both sides of the strait. This report mainly deals with a fly collection of the genus Stegana during a short visit to Taiwan in 2012. It represents the most recent drosophilid faunal survey of Taiwan associating with bleeding trees.
Results
In this study, 17 species were recognized including three new ones and eight new records. They are Stegana (Oxyphortica) convergens (de Meijere, 1911); Stegana (Oxyphortica) nigripennis (Hendel, 1914); Stegana (Stegana) taiwana Okada, 1991; Stegana (Steganina) bacilla Chen and Aotsuka, 2004; Stegana (Steganina) chitouensis Sidorenko, 1998; Stegana (Steganina) ctenaria Nishiharu, 1979; Stegana (Steganina) euryphylla Chen and Chen, 2009; Stegana (Steganina) langufoliacea Wu, Gao and Chen, 2010; Stegana (Steganina) melanostoma Chen and Chen, 2009; Stegana (Steganina) nigrolimbata Duda, 1924; Stegana (Steganina) ornatipes Wheeler and Takada, 1964; Stegana (Steganina) reni Wang, Gao and Chen, 2010; Stegana (Steganina) tongi Wang, Gao and Chen, 2010; Stegana (Steganina) xui Wang, Gao and Chen, 2010; Stegana (Steganina) jianqinae sp. nov.; Stegana (Stegana) yangi sp. nov., and Stegana (Steganina) wulai sp. nov. Six recorded species are redescribed based on new materials. The key to all species of the genus Stegana in Taiwan is presented. The DNA barcoding fragments of the mitochondrial COI gene are sequenced and used to delineate species.
Conclusions
Among the 23 recorded species, two most widely distributed species range across two zoogeographic regions, and one occurs in both Taiwan and India. Five species are insular species recorded from Taiwan and Japan. The remaining 16 species are distributed in both Taiwan and southern Mainland China. One montane species was collected at an elevation of 1,500 m. As a whole, this implies that Taiwanese Stegana fauna should be largely of a Mainland China origin, probably as a consequence of the east- and/or southward dispersals of the ancestral species during the glacial epoch. The 20% (5/23) endemism at the genus level is comparable to that of the family level at 63/320. It is notable that the Fujian province, which is bordered by Guangdong to the south but isolated from Taiwan by the 180-km-wide strait, has no species in common with Guangdong and Taiwan. This may be due to insufficient drosophilid faunal survey in these areas, especially for Fujian.
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Cheng YJ, Fang S, Tsaur SC, Chen YL, Fu HW, Patel NH, Ting CT. Reduction of germ cells in the Odysseus null mutant causes male fertility defect in Drosophila melanogaster. Genes Genet Syst 2012; 87:273-6. [DOI: 10.1266/ggs.87.273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Fang S, Ting CT, Lee CR, Chu KH, Wang CC, Tsaur SC. Molecular evolution and functional diversification of fatty acid desaturases after recurrent gene duplication in Drosophila. Mol Biol Evol 2009; 26:1447-56. [PMID: 19307313 PMCID: PMC2693736 DOI: 10.1093/molbev/msp057] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2009] [Indexed: 01/04/2023] Open
Abstract
Frequent gene duplications in the genome incessantly supply new genetic materials for functional innovation presumably driven by positive Darwinian selection. This mechanism in the desaturase gene family has been proposed to be important in triggering the pheromonal diversification in insects. With the recent completion of a dozen Drosophila genomes, a genome-wide perspective is possible. In this study, we first identified homologs of desaturase genes in 12 Drosophila species and noted that while gene duplication events are relatively frequent, gene losses are not scarce, especially in the desat1-desat2-desatF clade. By reconciling the gene tree with species phylogeny and the chromosomal synteny of the sequenced Drosophila genomes, at least one gene loss in desat2 and a minimum of six gene gains (resulting in seven desatF homologs, alpha-eta), three gene losses and one relocation in desatF were inferred. Upon branching off the ancestral desat1 lineage, both desat2 and desatF gained novel functions through accelerating protein evolution. The amino acid residues under positive selection located near the catalytic sites and the C-terminal region might be responsible for altered substrate selectivity between closely related species. The association between the expression pattern of desatF-alpha and the chemical composition of cuticular hydrocarbons implies that the ancestral function of desatF-alpha is the second desaturation at the four carbons after the first double bond in diene synthesis, and the shift from bisexual to female-specific expression in desatF-alpha occurred in the ancestral lineage of Drosophila melanogaster subgroup. A relationship between the number of expressed desatF homologs and the diene diversification has also been observed. These results suggest that the molecular diversification of fatty acid desaturases after recurrent gene duplication plays an important role in pheromonal diversity in Drosophila.
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Ting CT, Tsaur SC, Sun S, Browne WE, Chen YC, Patel NH, Wu CI. Gene duplication and speciation in Drosophila: evidence from the Odysseus locus. Proc Natl Acad Sci U S A 2004; 101:12232-5. [PMID: 15304653 PMCID: PMC514461 DOI: 10.1073/pnas.0401975101] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Accepted: 06/30/2004] [Indexed: 11/18/2022] Open
Abstract
The importance of gene duplication in evolution has long been recognized. Because duplicated genes are prone to diverge in function, gene duplication could plausibly play a role in species differentiation. However, experimental evidence linking gene duplication with speciation is scarce. Here, we show that a hybrid-male sterility gene, Odysseus (OdsH), arose by gene duplication in the Drosophila genome. OdsH has evolved at a very high rate, whereas its most immediate paralog, unc-4, is nearly identical among species in the Drosophila melanogaster subgroup. The disparity in their sequence evolution is echoed by the divergence in their expression patterns in both soma and reproductive tissues. We suggest that duplicated genes that have yet to evolve a stable function at the time of speciation may be candidates for "speciation genes," which is broadly defined as genes that contribute to differential adaptation between species.
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Takahashi A, Tsaur SC, Coyne JA, Wu CI. The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster. Proc Natl Acad Sci U S A 2001; 98:3920-5. [PMID: 11259658 PMCID: PMC31154 DOI: 10.1073/pnas.061465098] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2000] [Indexed: 11/18/2022] Open
Abstract
The cuticular hydrocarbon (CH) pheromones in Drosophila melanogaster exhibit strong geographic variation. African and Caribbean populations have a high ratio of 5,9 heptacosadiene/7,11 heptacosadiene (the "High" CH type), whereas populations from all other areas have a low ratio ("Low" CH type). Based on previous genetic mapping, DNA markers were developed that localized the genetic basis of this CH polymorphism to within a 13-kb region. We then carried out a hierarchical search for diagnostic nucleotide sites starting with four lines, and increasing to 24 and 43 lines from a worldwide collection. Within the 13-kb region, only one variable site shows a complete concordance with the CH phenotype. This is a 16-bp deletion in the 5' region of a desaturase gene (desat2) that was recently suggested to be responsible for the CH polymorphism on the basis of its expression [Dallerac, R., Labeur, C., Jallon, J.-M., Knipple, D. C., Roelofs, W. L. & Wicker-Thomas, C. (2000) Proc. Natl. Acad. Sci. 97, 9449--9454]. The cosmopolitan Low type is derived from the ancestral High type, and DNA sequence variations suggest that the former spread worldwide with the aid of positive selection. Whether this CH variation could be a component of the sexual isolation between Zimbabwe and other cosmopolitan populations remains an interesting and unresolved question.
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Tsaur SC, Ting CT, Wu CI. Sex in Drosophila mauritiana: a very high level of amino acid polymorphism in a male reproductive protein gene, Acp26Aa. Mol Biol Evol 2001; 18:22-6. [PMID: 11141189 DOI: 10.1093/oxfordjournals.molbev.a003716] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many genes pertaining to male reproductive functions have been shown to evolve rapidly between species, and evidence increasingly suggest the influence of positive Darwinian selection. The accessory gland protein gene (Acp26Aa) of Drosophila is one such example. In order to understand the mechanism of selection, it is often helpful to examine the pattern of polymorphism. We report here that the level of amino acid polymorphism in the N-terminal quarter of Acp26Aa is high in Drosophila melanogaster and is unprecedented in its sibling species Drosophila mauritiana. We postulate that (1) this N-terminal segment may play a role in sperm competition, and (2) D. mauritiana may have been under much more intense sexual selection than other species. Both postulates have important ramifications and deserve to be tested rigorously.
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Ting CT, Tsaur SC, Wu CI. The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc Natl Acad Sci U S A 2000; 97:5313-6. [PMID: 10779562 PMCID: PMC25825 DOI: 10.1073/pnas.090541597] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/1999] [Indexed: 11/18/2022] Open
Abstract
Molecular differentiation between races or closely related species is often incongruent with the reproductive divergence of the taxa of interest. Shared ancient polymorphism and/or introgression during secondary contact may be responsible for the incongruence. At loci contributing to speciation, these two complications should be minimized (1, 2); hence, their variation may more faithfully reflect the history of the species' reproductive differentiation. In this study, we analyzed DNA polymorphism at the Odysseus (OdsH) locus of hybrid sterility between Drosophila mauritiana and Drosophila simulans and were able to verify such a prediction. Interestingly, DNA variation only a short distance away (1.8 kb) appears not to be influenced by the forces that shape the recent evolution of the OdsH coding region. This locus thus may represent a test case of inferring phylogeny of very closely related species.
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Abstract
The homeodomain is a DNA binding motif that is usually conserved among diverse taxa. Rapidly evolving homeodomains are thus of interest because their divergence may be associated with speciation. The exact site of the Odysseus (Ods) locus of hybrid male sterility in Drosophila contains such a homeobox gene. In the past half million years, this homeodomain has experienced more amino acid substitutions than it did in the preceding 700 million years; during this period, it has also evolved faster than other parts of the protein or even the introns. Such rapid sequence divergence is driven by positive selection and may contribute to reproductive isolation.
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Tsaur SC, Ting CT, Wu CI. Positive selection driving the evolution of a gene of male reproduction, Acp26Aa, of Drosophila: II. Divergence versus polymorphism. Mol Biol Evol 1998; 15:1040-6. [PMID: 9718731 DOI: 10.1093/oxfordjournals.molbev.a026002] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The evolution of the gene for a male ejaculatory protein, Acp26Aa, has been shown to be driven by positive selection when nonsibling species in the Drosophila melanogaster subgroup are compared. To know if selection has been operating in the recent past and to understand the details of its dynamics, we obtained DNA sequences of Acp26Aa and the nearby Acp26Ab gene from 39 D. melanogaster chromosomes. Together with the 10 published sequences, we analyzed 49 sequences from five populations in four continents. The southern African population is somewhat differentiated from all other populations, but its nucleotide diversity is lower at these two loci. We find the following results for Acp26Aa: (1) The R: S (replacement : silent changes) ratio is significantly higher in the between-species comparisons than in the within-species data by the McDonald and Kreitman test. Positive selection is probably responsible for the excess of amino acid replacements between species. (2) However, within-species nucleotide diversity is high. Neither the Tajima test nor the Fu and Li test indicates a reduction in nucleotide diversity due to positive selection in the recent past. (3) The newly derived nucleotides in D. melanogaster are at high frequency significantly more often than predicted by the neutral equilibrium. Since the nearby Acp26Ab gene does not show these patterns, these observations cannot be attributed to the characteristics of this chromosomal region. We suggest that positive selection is active, but may be weak, for each amino acid change in the Acp26Aa gene.
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Tsaur SC, Wu CI. Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa of Drosophila. Mol Biol Evol 1997; 14:544-9. [PMID: 9159932 DOI: 10.1093/oxfordjournals.molbev.a025791] [Citation(s) in RCA: 183] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The gene for a male ejaculatory protein, Acp26Aa, in four sibling species of the Drosophila melanogaster subgroup has previously been shown to have a nonsynonymous rate (Ka) of nucleotide substitution that is indistinguishable from the synonymous rate (Ks). By examining this gene in two other species of this subgroup, we found that Ka is generally large and can sometimes be more than twice as large as Ks. This suggests that positive selection may be operating at this locus of male reproduction.
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