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Asymmetric paralog evolution between the "cryptic" gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4. Sci Rep 2019; 9:3136. [PMID: 30816280 PMCID: PMC6395752 DOI: 10.1038/s41598-019-40055-1] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 02/07/2019] [Indexed: 12/05/2022] Open
Abstract
The vertebrate gene repertoire is characterized by “cryptic” genes whose identification has been hampered by their absence from the genomes of well-studied species. One example is the Bmp16 gene, a paralog of the developmental key genes Bmp2 and -4. We focus on the Bmp2/4/16 group of genes to study the evolutionary dynamics following gen(om)e duplications with special emphasis on the poorly studied Bmp16 gene. We reveal the presence of Bmp16 in chondrichthyans in addition to previously reported teleost fishes and reptiles. Using comprehensive, vertebrate-wide gene sampling, our phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution. We confirm that Bmp16 genes were lost independently in at least three lineages (mammals, archelosaurs and amphibians) and report that they have elevated rates of sequence evolution. This finding agrees with their more “flexible” deployment during development; while Bmp16 has limited embryonic expression domains in the cloudy catshark, it is broadly expressed in the green anole lizard. Our study illustrates the dynamics of gene family evolution by integrating insights from sequence diversification, gene repertoire changes, and shuffling of expression domains.
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Bennett KL, Kaddumukasa M, Shija F, Djouaka R, Misinzo G, Lutwama J, Linton YM, Walton C. Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa. Ecol Evol 2018; 8:3019-3036. [PMID: 29531714 PMCID: PMC5838080 DOI: 10.1002/ece3.3668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon-primed intron-crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate-driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.
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Affiliation(s)
- Kelly Louise Bennett
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
- WITS Institute for Malaria ResearchSchool of Pathology Faculty of Health SciencesUniversity of WitwatersrandParktownJohannesburg
| | - Fortunate Shija
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
- Department of Veterinary Microbiology and ParasitologySokoine University of AgricultureMorogoroTanzania
| | - Rousseau Djouaka
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Gerald Misinzo
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
| | - Yvonne Marie Linton
- Department of EntomologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Walter Reed Biosystematics UnitSmithsonian Institution Museum Support CenterSuitlandMDUSA
- Walter Reed Army Institute of ResearchSilver SpringMDUSA
- Uniformed Services University of Health SciencesBethesdaMDUSA
| | - Catherine Walton
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
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Bennett KL, Shija F, Linton YM, Misinzo G, Kaddumukasa M, Djouaka R, Anyaele O, Harris A, Irish S, Hlaing T, Prakash A, Lutwama J, Walton C. Historical environmental change in Africa drives divergence and admixture ofAedes aegyptimosquitoes: a precursor to successful worldwide colonization? Mol Ecol 2016; 25:4337-54. [DOI: 10.1111/mec.13762] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 06/10/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Kelly Louise Bennett
- Computational Evolutionary Biology Group; Faculty of Life Sciences; University of Manchester; Manchester UK
| | - Fortunate Shija
- Computational Evolutionary Biology Group; Faculty of Life Sciences; University of Manchester; Manchester UK
- Department of Veterinary Microbiology and Parasitology; Sokoine University of Agriculture; Morogoro Tanzania
| | - Yvonne-Marie Linton
- Walter Reed Biosystematics Unit; Smithsonian Institution Museum Support Center; Suitland MD USA
- Walter Reed Army Institute of Research; Silver Spring MD USA
- Uniformed Services University of Health Sciences; Bethesda MD USA
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; Washington DC USA
| | - Gerald Misinzo
- Department of Veterinary Microbiology and Parasitology; Sokoine University of Agriculture; Morogoro Tanzania
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re-emerging Infections; Uganda Virus Research Institute; Entebbe Uganda
| | - Rousseau Djouaka
- Agro-Eco-Health Platform for West and Central Africa; International Institute of Tropical Agriculture; Cotonou Republic of Benin
| | - Okorie Anyaele
- Entomology Unit; Department of Zoology; University of Ibadan; Ibadan Nigeria
| | - Angela Harris
- Mosquito Research & Control Unit; Cayman Islands Government; Grand Cayman Cayman Islands
| | - Seth Irish
- London School of Hygiene and Tropical Medicine; London UK
| | - Thaung Hlaing
- Medical Entomology Research Division; Department of Medical Research (Lower Myanmar); Ministry of Health; Yangon Myanmar
| | - Anil Prakash
- National Institute for Research in Environmental Health; Ministry of H & FW Government of India; Bhopal India
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infections; Uganda Virus Research Institute; Entebbe Uganda
| | - Catherine Walton
- Computational Evolutionary Biology Group; Faculty of Life Sciences; University of Manchester; Manchester UK
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Dixit J, Arunyawat U, Huong NT, Das A. Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus. Mol Ecol 2014; 23:5599-618. [PMID: 25266341 DOI: 10.1111/mec.12943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 01/11/2023]
Abstract
Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.
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Affiliation(s)
- Jyotsana Dixit
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
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Yoshizawa K, Johnson KP. Changes in base composition bias of nuclear and mitochondrial genes in lice (Insecta: Psocodea). Genetica 2014; 141:491-9. [PMID: 24233690 DOI: 10.1007/s10709-013-9748-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 11/05/2013] [Indexed: 11/30/2022]
Abstract
While it is well known that changes in the general processes of molecular evolution have occurred on a variety of timescales, the mechanisms underlying these changes are less well understood. Parasitic lice ("Phthiraptera") and their close relatives (infraorder Nanopsocetae of the insect order Psocodea) are a group of insects well known for their unusual features of molecular evolution. We examined changes in base composition across parasitic lice and bark lice. We identified substantial differences in percent GC content between the clade comprising parasitic lice plus closely related bark lice (=Nanopsocetae) versus all other bark lice. These changes occurred for both nuclear and mitochondrial protein coding and ribosomal RNA genes, often in the same direction. To evaluate whether correlations in base composition change also occurred within lineages, we used phylogenetically controlled comparisons, and in this case few significant correlations were identified. Examining more constrained sites (first/second codon positions and rRNA) revealed that, in comparison to the other bark lice, the GC content of parasitic lice and close relatives tended towards 50 % either up from less than 50 % GC or down from greater than 50 % GC. In contrast, less constrained sites (third codon positions) in both nuclear and mitochondrial genes showed less of a consistent change of base composition in parasitic lice and very close relatives. We conclude that relaxed selection on this group of insects is a potential explanation of the change in base composition for both mitochondrial and nuclear genes, which could lead to nucleotide frequencies closer to random expectation (i.e., 50 % GC) in the absence of any mutation bias. Evidence suggests this relaxed selection arose once in the non-parasitic common ancestor of Phthiraptera + Nanopsocetae and is not directly related to the evolution of the parasitism in lice.
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Balakirev ES, Chechetkin VR, Lobzin VV, Ayala FJ. Computational methods of identification of pseudogenes based on functionality: entropy and GC content. Methods Mol Biol 2014; 1167:41-62. [PMID: 24823770 DOI: 10.1007/978-1-4939-0835-6_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and significance of entropy and GC content analyses for pseudogene identification and for the comparative study of gene-pseudogene evolution.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA,
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Barreto FS, Burton RS. Evidence for compensatory evolution of ribosomal proteins in response to rapid divergence of mitochondrial rRNA. Mol Biol Evol 2012; 30:310-4. [PMID: 22993236 DOI: 10.1093/molbev/mss228] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Rapid evolution of mitochondrial DNA (mtDNA) places intrinsic selective pressures on many nuclear genes involved in mitochondrial functions. Mitochondrial ribosomes, for example, are composed of mtDNA-encoded ribosomal RNAs (rRNAs) and a set of more than 60 nuclear-encoded ribosomal proteins (mRP) distinct from the cytosolic RPs (cRP). We hypothesized that the rapid divergence of mt-rRNA would result in rapid evolution of mRPs relative to cRPs, which respond to slowly evolving nuclear-encoded rRNA. In comparisons of rates of nonsynonymous and synonymous substitutions between a pair of divergent populations of the copepod Tigriopus californicus, we found that mRPs showed elevated levels of amino acid changes relative to cRPs. This pattern was equally strong at the interspecific level, between three pairs of sister species (Nasonia vitripennis vs. N. longicornis, Drosophila melanogaster vs. D. simulans, and Saccharomyces cerevisae vs. S. paradoxus). This high rate of mRP evolution may result in intergenomic incompatibilities between taxonomic lineages, and such incompatibilities could lead to dysfunction of mitochondrial ribosomes and the loss of fitness observed among interpopulation hybrids in T. californicus and interspecific hybrids in other species.
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Affiliation(s)
- Felipe S Barreto
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, USA.
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Lee YH, Lin CP. Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands. Mol Ecol 2012; 21:3739-56. [PMID: 22650764 DOI: 10.1111/j.1365-294x.2012.05654.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Climatic oscillations during the Pleistocene period could have had a profound impact on the origin of tropical species by the alternation of allopatric isolation and interpopulation gene flow cycles. However, whether tropical speciation involves strictly allopatric isolation, or proceeds in the face of homogenizing gene flow, is relatively unclear. Here, we investigated geographical modes of speciation in four closely related Euphaea damselfly species endemic to the subtropical and tropical East Asian islands using coalescent analyses of a multilocus data set. The reconstructed phylogenies demonstrated distinct species status for each of the four species and the existence of two sister species pairs, Euphaea formosa/E. yayeyamana and E. decorata/E. ornata. The species divergence time of the sibling Euphaea damselflies dates back to within the last one Mya of the Middle to Lower Pleistocene. The speciation between the populous E. formosa of Taiwan and the less numerous E. yayeyamana of the Yaeyama islands occurred despite significant bidirectional, asymmetric gene flow, which is strongly inconsistent with a strictly allopatric model. In contrast, speciation of the approximately equal-sized populations of E. decorata of the southeast Asian mainland and E. ornata of Hainan is inferred to have involved allopatric divergence without gene flow. Our findings suggest that differential selection of natural or sexual environments is a prominent driver of species divergence in subtropical E. formosa and E. yayeyamana; whereas for tropical E. decorata and E. ornata at lower latitudes, allopatric isolation may well be a pivotal promoter of species formation.
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Affiliation(s)
- Yat-Hung Lee
- Department of Life Science & Center for Tropical Ecology and Biodiversity, Tunghai University, Taichung 40704, Taiwan
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9
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Morgan K, Linton YM, Somboon P, Saikia P, Dev V, Socheat D, Walton C. Inter-specific gene flow dynamics during the Pleistocene-dated speciation of forest-dependent mosquitoes in Southeast Asia. Mol Ecol 2010; 19:2269-85. [PMID: 20444081 DOI: 10.1111/j.1365-294x.2010.04635.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Tropical forests have undergone repeated fragmentation and expansion during Pleistocene glacial and interglacial periods, respectively. The effects of this repeated forest fragmentation in driving vicariance in tropical taxa have been well studied. However, relatively little is known about how often this process results in allopatric speciation, since it may be inhibited by recurrent gene flow during repeated secondary contact, or to what extent Pleistocene-dated speciation results from ecological specialization in the face of gene flow. Here, divergence times and gene flow between three closely-related mosquito species of the Anopheles dirus species complex endemic to the forests of Southeast Asia, are inferred using coalescent based Bayesian analysis. An Isolation with Migration model is applied to sequences of two mitochondrial and three nuclear genes, and 11 microsatellites. The divergence of An. scanloni has occurred despite unidirectional nuclear gene flow from this species into An. dirus. The inferred asymmetric gene flow may result from the unique evolutionary adaptation of An. scanloni to limestone karst habitat, and therefore the fitness advantage of this species over An. dirus in regions of sympatry. Mitochondrial introgression has led to the complete replacement of An. dirus haplotypes with those of An. baimaii through a recent (approximately 62 kya) selective sweep. Speciation of An. baimaii and An. dirus is inferred to have involved allopatric divergence throughout much of the Pleistocene. Secondary contact and bidirectional gene flow has occurred only within the last 100 000 years, by which time the process of allopatric speciation seems to have been largely completed.
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Affiliation(s)
- Katy Morgan
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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Crow KD, Amemiya CT, Roth J, Wagner GP. HYPERMUTABILITY OFHOXA13AAND FUNCTIONAL DIVERGENCE FROM ITS PARALOG ARE ASSOCIATED WITH THE ORIGIN OF A NOVEL DEVELOPMENTAL FEATURE IN ZEBRAFISH AND RELATED TAXA (CYPRINIFORMES). Evolution 2009; 63:1574-92. [DOI: 10.1111/j.1558-5646.2009.00657.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hurt C, Anker A, Knowlton N. A MULTILOCUS TEST OF SIMULTANEOUS DIVERGENCE ACROSS THE ISTHMUS OF PANAMA USING SNAPPING SHRIMP IN THE GENUSALPHEUS. Evolution 2009; 63:514-30. [PMID: 19154357 DOI: 10.1111/j.1558-5646.2008.00566.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carla Hurt
- Department of Biology, University of Miami, Coral Gables, Florida 33124, USA.
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12
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Vicario S, Mason CE, White KP, Powell JR. Developmental stage and level of codon usage bias in Drosophila. Mol Biol Evol 2008; 25:2269-77. [PMID: 18755761 DOI: 10.1093/molbev/msn189] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Codon usage bias (CUB) is a ubiquitous observation in molecular evolution. As a model, Drosophila has been particularly well-studied and indications show that selection at least partially controls codon usage, probably through selection for translational efficiency. Although many aspects of Drosophila CUB have been studied, this is the first study relating codon usage to development in this holometabolous insect with very different life stages. Here we ask the question: What developmental stage of Drosophila melanogaster has the greatest CUB? Genes with maximum expression in the larval stage have the greatest overall CUB when compared with embryos, pupae, and adults. (The same pattern was observed in Drosophila pseudoobscura, see Supplementary Material online.) We hypothesize this is related to the very rapid growth of larvae, placing increased selective pressure to produce large amounts of protein: a 300-fold increase requiring an approximate doubling of protein content every 10 h. Genes with highest expression in adult males and early embryos, stages with the least de novo protein synthesis, display the least CUB. These results are consistent with the hypothesis that CUB is caused (at least in part) by selection for efficient protein production. This seems to hold on the individual gene level (highly expressed genes are more biased than lowly expressed genes) as well as on a more global scale where genes with maximum expression during times of very rapid growth and protein synthesis are more biased than genes with maximum expression during times of low growth.
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Affiliation(s)
- Saverio Vicario
- Department of Ecology and Evolutionary Biology, Yale University, USA
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13
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de Setta N, Loreto ELS, Carareto CMA. Is the evolutionary history of the O-type P element in the saltans and willistoni groups of Drosophila similar to that of the canonical P element? J Mol Evol 2007; 65:715-24. [PMID: 18034216 DOI: 10.1007/s00239-007-9051-7] [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: 05/29/2006] [Revised: 07/26/2007] [Accepted: 10/15/2007] [Indexed: 11/26/2022]
Abstract
We studied the occurrence of O-type P elements in at least one species of each subgroup of the saltans group, in order to better understand the phylogenetic relationships among the elements within the saltans group and with those of species belonging to the willistoni group. We found that the O-type subfamily has a patchy distribution within the saltans group (it does not occur in D. neocordata and D. emarginata), low sequence divergence among species of the saltans group as well as in relation to species of the willistoni group, a lower rate of synonymous substitution for coding sequences compared to Adh, and phylogenetic incongruities. These findings suggest that the evolutionary history of the O-type subfamily within the saltans and willistoni groups follows the same model proposed for the canonical subfamily of P elements, i.e., events of horizontal transfer between species of the saltans and willistoni groups.
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Affiliation(s)
- Nathalia de Setta
- UNESP-Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
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14
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Pollard DA, Iyer VN, Moses AM, Eisen MB. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet 2006; 2:e173. [PMID: 17132051 PMCID: PMC1626107 DOI: 10.1371/journal.pgen.0020173] [Citation(s) in RCA: 261] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 08/28/2006] [Indexed: 11/19/2022] Open
Abstract
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics.
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Affiliation(s)
- Daniel A Pollard
- Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America
| | - Venky N Iyer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Alan M Moses
- Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America
| | - Michael B Eisen
- Graduate Group in Biophysics, University of California Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Genome Sciences, Genomics Division, Ernest Orlando Lawrence Berkeley National Lab, Berkeley, California, United States of America
- Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America
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15
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Kliman RM, Bernal CA. Unusual usage of AGG and TTG codons in humans and their viruses. Gene 2005; 352:92-9. [PMID: 15922516 DOI: 10.1016/j.gene.2005.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Revised: 12/28/2004] [Accepted: 04/01/2005] [Indexed: 11/22/2022]
Abstract
Prior analysis on human protein-coding DNA sequences has identified local base composition as the primary predictor of synonymous codon usage. However, in many organisms, codon usage is influenced by natural selection, particularly for efficient expression of functional gene products. Because viruses are expected to evolve codon usage in the context of their host's molecular machinery, their genomes provide another window into the forces that guide their host's molecular evolution. Factor analysis was performed on codon usage of 16,654 genes annotated in Build 34 of the human genome, and the primary factor was correlated strongly with local base composition. However, two codons, AGG and TTG, rose in frequency as all other C- and G-ending codons decreased in frequency. These two codons were the only C- or G-ending codons with usages that negatively correlated with gene expression. Variation among viruses in codon usage also strongly reflects variation in base composition and, again, AGG and TTG decrease in frequency as all other C- and G-ending codons increase in frequency. It appears that usages of these two codons can not be explained by local compositional biases, implying a more direct role of natural selection on codon usage in humans.
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Affiliation(s)
- Richard M Kliman
- Department of Biological Sciences, Cedar Crest College, 100 College Drive, Allentown, PA, USA.
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16
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Balakirev ES, Chechetkin VR, Lobzin VV, Ayala FJ. Entropy and GC Content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. Mol Biol Evol 2005; 22:2063-72. [PMID: 15972847 DOI: 10.1093/molbev/msi197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We perform spectral entropy and GC content analyses in the beta-esterase gene cluster, including the Est-6 gene and the psiEst-6 putative pseudogene, in seven species of the Drosophila melanogaster species subgroup. psiEst-6 combines features of functional and nonfunctional genes. The spectral entropies show distinctly lower structural ordering for psiEst-6 than for Est-6 in all species studied. Our observations agree with previous results for D. melanogaster and provide additional support to our hypothesis that after the duplication event Est-6 retained the esterase-coding function and its role during copulation, while psiEst-6 lost that function but now operates in conjunction with Est-6 as an intergene. Entropy accumulation is not a completely random process for either gene. Structural entropy is nucleotide dependent. The relative normalized deviations for structural entropy are higher for G than for C nucleotides. The entropy values are similar for Est-6 and psiEst-6 in the case of A and T but are lower for Est-6 in the case of G and C. The GC content in synonymous positions is uniformly higher in Est-6 than in psiEst-6, which agrees with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of psiEst-6 and Est-6 after the duplication event.
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Affiliation(s)
- Evgeniy S Balakirev
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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17
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de Almeida LM, Carareto CMA. Multiple events of horizontal transfer of the Minos transposable element between Drosophila species. Mol Phylogenet Evol 2005; 35:583-94. [PMID: 15878127 DOI: 10.1016/j.ympev.2004.11.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 11/17/2004] [Accepted: 11/19/2004] [Indexed: 11/15/2022]
Abstract
In this study the Minos element was analyzed in 26 species of the repleta group and seven species of the saltans group of the genus Drosophila. The PCR and Southern blot analysis showed a wide occurrence of the Minos transposable element among species of the repleta and the saltans groups and also a low number of insertions in both genomes. Three different analyses, nucleotide divergence, historical associations, and comparisons between substitution rates (d(N) and d(S)) of Minos and Adh host gene sequences, suggest the occurrence of horizontal transfer between repleta and saltans species. These data reinforce and extend the Arca and Savakis [Genetica 108 (2000) 263] results and suggest five events of horizontal transfer to explain the present Minos distribution: between D. saltans and the ancestor of the mulleri and the mojavensis clusters; between D. hydei and the ancestor of the mulleri and the mojavensis clusters; between D. mojavensis and D. aldrichi; between D. buzzatii and D. serido; and between D. spenceri and D. emarginata. An alternative explanation would be that repeated events of horizontal transfer involving D. hydei, which is a cosmopolitan species that diverged from the others repleta species as long as 14Mya, could have spread Minos within the repleta group and to D. saltans. The data presented in this article support a model in which distribution of Minos transposon among Drosophila species is determined by horizontal transmission balanced by vertical inactivation and extinction.
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Affiliation(s)
- Luciane M de Almeida
- Departamento de Biologia, UNESP - Universidade Estadual Paulista, 15054-000 São José do Rio Preto, SP, Brazil
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18
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Negre B, Casillas S, Suzanne M, Sánchez-Herrero E, Akam M, Nefedov M, Barbadilla A, de Jong P, Ruiz A. Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res 2005; 15:692-700. [PMID: 15867430 PMCID: PMC1088297 DOI: 10.1101/gr.3468605] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Accepted: 01/26/2005] [Indexed: 11/25/2022]
Abstract
Homeotic (Hox) genes are usually clustered and arranged in the same order as they are expressed along the anteroposterior body axis of metazoans. The mechanistic explanation for this colinearity has been elusive, and it may well be that a single and universal cause does not exist. The Hox-gene complex (HOM-C) has been rearranged differently in several Drosophila species, producing a striking diversity of Hox gene organizations. We investigated the genomic and functional consequences of the two HOM-C splits present in Drosophila buzzatii. Firstly, we sequenced two regions of the D. buzzatii genome, one containing the genes labial and abdominal A, and another one including proboscipedia, and compared their organization with that of D. melanogaster and D. pseudoobscura in order to map precisely the two splits. Then, a plethora of conserved noncoding sequences, which are putative enhancers, were identified around the three Hox genes closer to the splits. The position and order of these enhancers are conserved, with minor exceptions, between the three Drosophila species. Finally, we analyzed the expression patterns of the same three genes in embryos and imaginal discs of four Drosophila species with different Hox-gene organizations. The results show that their expression patterns are conserved despite the HOM-C splits. We conclude that, in Drosophila, Hox-gene clustering is not an absolute requirement for proper function. Rather, the organization of Hox genes is modular, and their clustering seems the result of phylogenetic inertia more than functional necessity.
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Affiliation(s)
- Bárbara Negre
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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19
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Ko WY, David RM, Akashi H. Molecular phylogeny of the Drosophila melanogaster species subgroup. J Mol Evol 2004; 57:562-73. [PMID: 14738315 DOI: 10.1007/s00239-003-2510-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2002] [Accepted: 06/02/2003] [Indexed: 11/30/2022]
Abstract
Although molecular and phenotypic evolution have been studied extensively in Drosophila melanogaster and its close relatives, phylogenetic relationships within the D. melanogaster species subgroup remain unresolved. In particular, recent molecular studies have not converged on the branching orders of the D. yakuba-D. teissieri and D. erecta-D. orena species pairs relative to the D. melanogaster-D. simulans-D. mauritiana-D. sechellia species complex. Here, we reconstruct the phylogeny of the melanogaster species subgroup using DNA sequence data from four nuclear genes. We have employed "vectorette PCR" to obtain sequence data for orthologous regions of the Alcohol dehydrogenase (Adh), Alcohol dehydrogenase related (Adhr), Glucose dehydrogenase (Gld), and rosy (ry) genes (totaling 7164 bp) from six melanogaster subgroup species (D. melanogaster, D. simulans, D. teissieri, D. yakuba, D. erecta, and D. orena) and three species from subgroups outside the melanogaster species subgroup [D. eugracilis (eugracilis subgroup), D. mimetica (suzukii subgroup), and D. lutescens (takahashii subgroup)]. Relationships within the D. simulans complex are not addressed. Phylogenetic analyses employing maximum parsimony, neighbor-joining, and maximum likelihood methods strongly support a D. yakuba-D. teissieri and D. erecta-D. orena clade within the melanogaster species subgroup. D. eugracilis is grouped closer to the melanogaster subgroup than a D. mimetica-D. lutescens clade. This tree topology is supported by reconstructions employing simple (single parameter) and more complex (nonreversible) substitution models.
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Affiliation(s)
- Wen-Ya Ko
- Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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20
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Abstract
Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.
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Affiliation(s)
- De-Xing Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 19 Zhongguancun Road, Beijing 100080, PR China.
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21
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Matzkin LM, Eanes WF. Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila. Genetics 2003; 163:181-94. [PMID: 12586706 PMCID: PMC1462434 DOI: 10.1093/genetics/163.1.181] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This study focuses on the population genetics of alcohol dehydrogenase (Adh) in cactophilic Drosophila. Drosophila mojavensis and D. arizonae utilize cactus hosts, and each host contains a characteristic mixture of alcohol compounds. In these Drosophila species there are two functional Adh loci, an adult form (Adh-2) and a larval and ovarian form (Adh-1). Overall, the greater level of variation segregating in D. arizonae than in D. mojavensis suggests a larger population size for D. arizonae. There are markedly different patterns of variation between the paralogs across both species. A 16-bp intron haplotype segregates in both species at Adh-2, apparently the product of an ancient gene conversion event between the paralogs, which suggests that there is selection for the maintenance of the intron structure possibly for the maintenance of pre-mRNA structure. We observe a pattern of variation consistent with adaptive protein evolution in the D. mojavensis lineage at Adh-1, suggesting that the cactus host shift that occurred in the divergence of D. mojavensis from D. arizonae had an effect on the evolution of the larval expressed paralog. Contrary to previous work we estimate a recent time for both the divergence of D. mojavensis and D. arizonae (2.4 +/- 0.7 MY) and the age of the gene duplication (3.95 +/- 0.45 MY).
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Affiliation(s)
- Luciano M Matzkin
- Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794-5245, USA.
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22
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Matsuo Y. Evolution of the GC content of the histone 3 gene in seven Drosophila species. Genes Genet Syst 2003; 78:309-18. [PMID: 14532710 DOI: 10.1266/ggs.78.309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The molecular evolution of the histone multigene family was studied by cloning and determining the nucleotide sequences of the histone 3 genes in seven Drosophila species, D. takahashii, D. lutescens, D. ficusphila, D. persimilis, D.pseudoobscura, D. americana and D. immigrans. CT repeats, a TATA box and an AGTG motif in the 5' region, and a hairpin loop and purine-rich motifs (CAA(T/G)GAGA) in the 3' region were conserved even in distantly related species. In D. hydei and D.americana, the GC content at the third codon position in the protein coding region was relatively low (49% and 45%), while in D. takahashii and D. lutescens it was relatively high (64% and 65%). The non- significant correlation between the GC contents in the 3' region and at the third codon position as well as the evidence of less constraint in the 3' region suggested that mutational bias may not be the major mechanism responsible for the biased nucleotide change at the third codon position or for codon usage bias.
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Affiliation(s)
- Yoshinori Matsuo
- Laboratory of Adaptive Evolution, Faculty of Integrated Arts and Sciences, The University of Tokushima, Tokushima, Japan.
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23
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Zhang L, Vision TJ, Gaut BS. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol 2002; 19:1464-73. [PMID: 12200474 DOI: 10.1093/oxfordjournals.molbev.a004209] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We characterized rates and patterns of synonymous and nonsynonymous substitution in 242 duplicated gene pairs on chromosomes 2 and 4 of Arabidopsis thaliana. Based on their collinear order along the two chromosomes, the gene pairs were likely duplicated contemporaneously, and therefore comparison of genetic distances among gene pairs provides insights into the distribution of nucleotide substitution rates among plant nuclear genes. Rates of synonymous substitution varied 13.8-fold among the duplicated gene pairs, but 90% of gene pairs differed by less than 2.6-fold. Average nonsynonymous rates were approximately fivefold lower than average synonymous rates; this rate difference is lower than that of previously studied nonplant lineages. The coefficient of variation of rates among genes was 0.65 for nonsynonymous rates and 0.44 for synonymous rates, indicating that synonymous and nonsynonymous rates vary among genes to roughly the same extent. The causes underlying rate variation were explored. Our analyses tentatively suggest an effect of physical location on synonymous substitution rates but no similar effect on nonsynonymous rates. Nonsynonymous substitution rates were negatively correlated with GC content at synonymous third codon positions, and synonymous substitution rates were negatively correlated with codon bias, as observed in other systems. Finally, the 242 gene pairs permitted investigation of the processes underlying divergence between paralogs. We found no evidence of positive selection, little evidence that paralogs evolve at different rates, and no evidence of differential codon usage or third position GC content.
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Affiliation(s)
- Liqing Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 92697-2525, USA
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24
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Oppentocht JE, van Delden W, van de Zande L. Isolation and characterization of the genomic region from Drosophila kuntzei containing the Adh and Adhr genes. Mol Biol Evol 2002; 19:1026-40. [PMID: 12082123 DOI: 10.1093/oxfordjournals.molbev.a004162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The nucleotide sequences of the Adh and Adhr genes of Drosophila kuntzei were derived from combined overlapping sequences of clones isolated from a genomic library and from cloned PCR and inverse-PCR fragments. Only a proximal promoter was detected upstream of the Adh gene, indicating that D. kuntzei Adh is regulated by a one-promoter system. Further upstream of the Adh structural gene, an adult enhancer region (AAE) was found that contains most of the regulatory sequences described for AAEs of other Drosophila species. Analysis of the ADH protein showed an amino acid change from valine to threonine in the active site at position 189 which is also found in D. funebris but is otherwise unique among Drosophila. This difference alone may be responsible for the very low ADH activity found in this species and may cause a difference in substrate usage pattern. Codon bias in Adh and Adhr was comparable and found to be very low compared with other species. Phylogenetic analysis showed that D. kuntzei is closest related to D. funebris and D. immigrans. The time of divergence between D. kuntzei and D. funebris was estimated to be 14.2-20.2 Myr and that between D. kuntzei-D. funebris and D. immigrans to be 30.8-44.0 Myr. An analysis of the genetic variation in the Adh gene and upstream sequences of four European strains showed that this gene was highly variable. Overall nucleotide diversity (pi) was 0.0139, which is two times higher than that in D. melanogaster.
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Affiliation(s)
- Jantien E Oppentocht
- Population Genetics, Center for Ecological and Evolutionary Studies, Biological Center, University of Groningen, The Netherlands
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25
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26
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Salomone N, Emerson BC, Hewitt GM, Bernini F. Phylogenetic relationships among the Canary Island Steganacaridae (Acari, Oribatida) inferred from mitochondrial DNA sequence data. Mol Ecol 2002; 11:79-89. [PMID: 11903906 DOI: 10.1046/j.0962-1083.2001.01421.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The mite genus Steganacarus is represented in the Canary Islands by three endemic species, one recently discovered species, and several morphotypes of uncertain taxonomic position. We used a fragment of the mitochondrial cytochrome oxidase I gene to reconstruct the phylogenetic relationships among representatives of the different taxa from the three central islands of the archipelago, Tenerife, La Gomera and Gran Canaria. Sequence data were analysed by both maximum parsimony and maximum likelihood methods. The inferred phylogenetic relationships do not correlate well with current morphological taxonomy but reveal four deeply divergent and geographically coherent lineages, one each on Gran Canaria and La Gomera and two on Tenerife. No pattern of molecular differentiation was observed among different morphotypes. Possible explanations for this incongruence are suggested in relation to the ecology and biogeography of the group. A recently discovered Steganacarus species from La Gomera, morphologically quite distinct from the other Canarian Steganacarus, is clearly identified as a taxon distantly related to all the other Canarian samples.
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Affiliation(s)
- N Salomone
- Department of Evolutionary Biology, University of Siena, 53100 Siena, Italy.
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27
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Musto H, Cruveiller S, D'Onofrio G, Romero H, Bernardi G. Translational selection on codon usage in Xenopus laevis. Mol Biol Evol 2001; 18:1703-7. [PMID: 11504850 DOI: 10.1093/oxfordjournals.molbev.a003958] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analysis of Expressed sequence tag frequencies. The comparison of codon usage of the sequences displaying the extreme values on the second axis indicates that several codons are statistically more frequent among the highly expressed (mainly housekeeping) genes. Translational selection appears, therefore, to influence synonymous codon usage in Xenopus.
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Affiliation(s)
- H Musto
- Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Naples, Italy
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28
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Albalat R, Arenas C, Mestres F. A statistical analysis of nucleotide substitutions in the Drosophila Adh region reflects irregularities in molecular clocks. Genes Genet Syst 2001; 76:209-12. [PMID: 11569504 DOI: 10.1266/ggs.76.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Substitutions rates are expected to be rather constant when a gene is compared between species. To analyze this feature, Ka/Ks ratios have been studied for Alcohol dehydrogenase (Adh) and Alcohol dehydrogenase duplication (Adh-dup) genes in Drosophila species. Adh Ka/Ks values are lower in intrasubgenus comparisons involving species of the Sophophora group than when these species are compared to the D. immigrans and S. lebanonensis, and this difference does not occur in the Adh-dup comparisons.
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Affiliation(s)
- R Albalat
- Department de Genètica, Facultat de Biologia. Universitat de Barcelona, Spain.
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29
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Sandrelli F, Campesan S, Rossetto M, Benna C, Zieger E, Megighian A, Couchman M, Kyriacou C, Costa R. Molecular Dissection of the 5' Region of no-on-transientA of Drosophila melanogaster Reveals cis-Regulation by Adjacent dGpi1 Sequences. Genetics 2001; 157:765-75. [PMID: 11156995 PMCID: PMC1461528 DOI: 10.1093/genetics/157.2.765] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The nonA gene of Drosophila melanogaster is important for normal vision, courtship song, and viability and lies approximately 350 bp downstream of the dGpi1 gene. Full rescue of nonA mutant phenotypes can be achieved by transformation with a genomic clone that carries approximately 2 kb of 5' regulatory material and that encodes most of the coding sequence of dGpi1. We have analyzed this 5' region by making a series of deleted fragments, fusing them to yeast GAL4 sequences, and driving UAS-nonA expression in a mutant nonA background. Regions that both silence and enhance developmental tissue-specific expression of nonA and that are necessary for generating optomotor visual responses are identified. Some of these overlap the dGpi1 sequences, revealing cis-regulation by neighboring gene sequences. The largest 5' fragment was unable to rescue the normal electroretinogram (ERG) consistently, and no rescue at all was observed for the courtship song phenotype. We suggest that sequences within the nonA introns that were missing in the UAS-nonA cDNA may carry enhancer elements for these two phenotypes. Finally, we speculate on the striking observation that some of the cis-regulatory regions of nonA appear to be embedded within the coding regions of dGpi1.
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Affiliation(s)
- F Sandrelli
- Dipartimento di Biologia, Università di Padova, 35131 Padova, Italy
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30
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Dunn KA, Bielawski JP, Yang Z. Substitution rates in Drosophila nuclear genes: implications for translational selection. Genetics 2001; 157:295-305. [PMID: 11139510 PMCID: PMC1461466 DOI: 10.1093/genetics/157.1.295] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this study we reexamine those relationships using maximum-likelihood methods to estimate substitution rates, which accommodate the transition/transversion rate bias and codon usage bias. We compiled a sample of homologous DNA sequences at 83 nuclear loci from Drosophila melanogaster and at least one other species of Drosophila. Our analysis was consistent with previous studies in finding that synonymous rates were positively correlated with nonsynonymous rates. Our analysis differed from previous studies, however, in that synonymous rates were unrelated to codon bias. We therefore conducted a simulation study to investigate the differences between approaches. The results suggested that failure to properly account for multiple substitutions at the same site and for biased codon usage by approximate methods can lead to an artifactual correlation between synonymous rate and codon bias. Implications of the results for translational selection are discussed.
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Affiliation(s)
- K A Dunn
- Department of Biology, Galton Laboratory, University College, London NW1 2HE, United Kingdom.
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31
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McVean GA, Vieira J. Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 2001; 157:245-57. [PMID: 11139506 PMCID: PMC1461462 DOI: 10.1093/genetics/157.1.245] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Selection acting on codon usage can cause patterns of synonymous evolution to deviate considerably from those expected under neutrality. To investigate the quantitative relationship between parameters of mutation, selection, and demography, and patterns of synonymous site divergence, we have developed a novel combination of population genetic models and likelihood methods of phylogenetic sequence analysis. Comparing 50 orthologous gene pairs from Drosophila melanogaster and D. virilis and 27 from D. melanogaster and D. simulans, we show considerable variation between amino acids and genes in the strength of selection acting on codon usage and find evidence for both long-term and short-term changes in the strength of selection between species. Remarkably, D. melanogaster shows no evidence of current selection on codon usage, while its sister species D. simulans experiences only half the selection pressure for codon usage of their common ancestor. We also find evidence for considerable base asymmetries in the rate of mutation, such that the average synonymous mutation rate is 20-30% higher than in noncoding regions. A Bayesian approach is adopted to investigate how accounting for selection on codon usage influences estimates of the parameters of mutation.
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Affiliation(s)
- G A McVean
- Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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32
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Abstract
The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite the much older age (more than 40 Myr) of the P: family as a whole. The evolution of the canonical P: subfamily is characterized by weak selection at nonsynonymous sites. These sites have evolved at three quarters the rate of synonymous sites, in which no selective constraints were detected. Their recent horizontal transfer best explains the high degree of similarity among canonical P: elements from the saltans and willistoni species groups. These results are consistent with a model of P:-element evolution in which selective constraints are imposed at the time of horizontal transfer. Furthermore, it is estimated that the spread and diversification of the canonical subfamily involved a minimum of 11 horizontal transfer events among the 18 species surveyed within the past 3 Myr. The presence of multiple P: subfamilies in the saltans and willistoni species groups is likely to be the result of multiple invasions that have previously swept through these taxa in a succession of horizontal transfer events. These results suggest that horizontal transfer among eukaryotes might be more common than anticipated.
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Affiliation(s)
- J C Silva
- Interdisciplinary Program in Genetics, University of Arizona, Tucson, AR 85721, USA.
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33
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Alvarez-Valin F, Tort JF, Bernardi G. Nonrandom spatial distribution of synonymous substitutions in the GP63 gene from Leishmania. Genetics 2000; 155:1683-92. [PMID: 10924466 PMCID: PMC1461213 DOI: 10.1093/genetics/155.4.1683] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work we analyze the variability in substitution rates in the GP63 gene from Leishmania. By using a sliding window to estimate substitution rates along the gene, we found that the rate of synonymous substitutions along the GP63 gene is highly correlated with both the rate of amino acid substitution and codon bias. Furthermore, we show that comparisons involving genes that represent independent phylogenetic lines yield very similar divergence/conservation patterns, thus suggesting that deterministic forces (i.e., nonstochastic forces such as selection) generated these patterns. We present evidence indicating that the variability in substitution rates is unambiguously related to functionally relevant features. In particular, there is a clear relationship between rates and the tertiary structure of the encoded protein since all divergent segments are located on the surface of the molecule and facing one side (almost parallel to the cell membrane) on the exposed surface of the organism. Remarkably, the protein segments encoded by these variable regions encircle the active site in a funnel-like distribution. These results strongly suggest that the pattern of nucleotide divergence and, notably, of synonymous divergence is affected by functional constraints.
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Affiliation(s)
- F Alvarez-Valin
- Sección Biomatemática, Facultad de Ciencias, Montevideo 11400, Uruguay.
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34
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Matsuo Y. Evolutionary change of codon usage for the histone gene family in Drosophila melanogaster and Drosophila hydei. Mol Phylogenet Evol 2000; 15:283-91. [PMID: 10837157 DOI: 10.1006/mpev.1999.0749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleotide divergence in the protein-coding region for replication-dependent and replication-independent histone 3 and 4 genes of Drosophila melanogaster and Drosophila hydei occurred mostly at the synonymous site. Therefore, the pattern of codon usage was analyzed in the two species, considering the genomic codon bias, which is proposed for estimating the genomic composition pressure in the protein-coding regions. The results indicated that the codon usage in the histone gene family could be explained mostly by the genomic codon bias. However, biases for Ala and Arg were commonly observed for the histone 3 and histone 4 gene families, and biases for Ser, Leu, and Glu were observed in a gene-specific manner. This suggests that both genomic codon bias and gene- or codon-specific bias are responsible for the nucleotide differentiation in the protein-coding region of the histone genes.
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Affiliation(s)
- Y Matsuo
- Laboratory of Adaptive Evolution, Department of Mathematical and Natural Sciences, Faculty of Integrated Arts and Sciences, The University of Tokushima, Minamijosanjimacho 1-1, Tokushima, 770-8502, Japan
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Piccin A, Couchman M, Clayton JD, Chalmers D, Costa R, Kyriacou CP. The clock gene period of the housefly, Musca domestica, rescues behavioral rhythmicity in Drosophila melanogaster. Evidence for intermolecular coevolution? Genetics 2000; 154:747-58. [PMID: 10655226 PMCID: PMC1460960 DOI: 10.1093/genetics/154.2.747] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In Drosophila, the clock gene period (per), is an integral component of the circadian clock and acts via a negative autoregulatory feedback loop. Comparative analyses of per genes in insects and mammals have revealed that they may function in similar ways. However in the giant silkmoth, Antheraea pernyi, per expression and that of the partner gene, tim, is not consistent with the negative feedback role. As an initial step in developing an alternative dipteran model to Drosophila, we have identified the per orthologue in the housefly, Musca domestica. The Musca per sequence highlights a pattern of conservation and divergence similar to other insect per genes. The PAS dimerization domain shows an unexpected phylogenetic relationship in comparison with the corresponding region of other Drosophila species, and this appears to correlate with a functional assay of the Musca per transgene in Drosophila melanogaster per-mutant hosts. A simple hypothesis based on the coevolution of the PERIOD and TIMELESS proteins with respect to the PER PAS domain can explain the behavioral data gathered from transformants.
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Affiliation(s)
- A Piccin
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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Chen Y, Carlini DB, Baines JF, Parsch J, Braverman JM, Tanda S, Stephan W. RNA secondary structure and compensatory evolution. Genes Genet Syst 1999; 74:271-86. [PMID: 10791023 DOI: 10.1266/ggs.74.271] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The classic concept of epistatic fitness interactions between genes has been extended to study interactions within gene regions, especially between nucleotides that are important in maintaining pre-mRNA/mRNA secondary structures. It is shown that the majority of linkage disequilibria found within the Drosophila Adh gene are likely to be caused by epistatic selection operating on RNA secondary structures. A recently proposed method of RNA secondary structure prediction based on DNA sequence comparisons is reviewed and applied to several types of RNAs, including tRNA, rRNA, and mRNA. The patterns of covariation in these RNAs are analyzed based on Kimura's compensatory evolution model. The results suggest that this model describes the substitution process in the pairing regions (helices) of RNA secondary structures well when the helices are evolutionarily conserved and thermodynamically stable, but fails in some other cases. Epistatic selection maintaining pre-mRNA/mRNA secondary structures is compared to weak selective forces that determine features such as base composition and synonymous codon usage. The relationships among these forces and their relative strengths are addressed. Finally, our mutagenesis experiments using the Drosophila Adh locus are reviewed. These experiments analyze long-range compensatory interactions between the 5' and 3' ends of Adh mRNA, the different constraints on secondary structures in introns and exons, and the possible role of secondary structures in RNA splicing.
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Affiliation(s)
- Y Chen
- Department of Biology, University of Rochester, NY 14627, USA
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37
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Abstract
I studied the cause of the significant difference in the synonymous-substitution pattern found in the achaete-scute complex genes in two Drosophila lineages, higher codon bias in Drosophila yakuba, and lower bias in D. melanogaster. Besides these genes, the functionally unrelated yellow gene showed the same substitution pattern, suggesting a region-dependent phenomenon in the X-chromosome telomere. Because the numbers of A/T --> G/C substitutions were not significantly different from those of G/C --> A/T in the yellow noncoding regions of these species, a AT/GC mutational bias could not completely account for the synonymous-substitution biases. In contrast, we did find an approximately 14-fold difference in recombination rates in the X-chromosome telomere regions between the two species, suggesting that the reduction of recombination rates in this region resulted in the reduction of the efficacy of selection in D. melanogaster. In addition, the D. orena yellow showed a 5% increase in the G + C content at silent sites in the coding and noncoding regions since the divergence from D. erecta. This pattern was significantly different from those at the orena Adh and Amy loci. These results suggest that local changes in recombination rates and mutational pressures are contributing to the irregular synonymous-substitution patterns in Drosophila.
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Affiliation(s)
- T Takano-Shimizu
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan.
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Rodríguez-Trelles F, Tarrío R, Ayala FJ. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group. Genetics 1999; 153:339-50. [PMID: 10471717 PMCID: PMC1460741 DOI: 10.1093/genetics/153.1.339] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigated the nucleotide composition of five genes, Xdh, Adh, Sod, Per, and 28SrRNA, in nine species of Drosophila (subgenus Sophophora) and one of Scaptodrosophila. The six species of the Drosophila saltans group markedly differ from the others in GC content and codon use bias. The GC content in the third codon position, and to a lesser extent in the first position and the introns, is higher in the D. melanogaster and D. obscura groups than in the D. saltans group (in Scaptodrosophila it is intermediate but closer to the melanogaster and obscura species). Differences are greater for Xdh than for Adh, Sod, Per, and 28SrRNA, which are functionally more constrained. We infer that rapid evolution of GC content in the saltans lineage is largely due to a shift in mutation pressure, which may have been associated with diminished natural selection due to smaller effective population numbers rather than reduced recombination rates. The rate of GC content evolution impacts the rate of protein evolution and may distort phylogenetic inferences. Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated.
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Affiliation(s)
- F Rodríguez-Trelles
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697-2525, USA.
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Li YJ, Satta Y, Takahata N. Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method. Genes Genet Syst 1999; 74:117-27. [PMID: 10650839 DOI: 10.1266/ggs.74.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The species divergence times and demographic histories of Drosophila melanogaster and its three sibling species, D. mauritiana, D. simulans, and D. yakuba, were investigated using a maximum likelihood (ML) method. Thirty-nine orthologous loci for these four species were retrieved from DDBJ/EMBL/GenBank database. Both autosomal and X-linked loci were used in this study. A significant degree of rate heterogeneity across loci was observed for each pair of species. Most loci have the GC content greater than 50% at the third codon position. The codon usage bias in Drosophila loci is considered to result in the high GC content and the heterogenous rates across loci. The chi-square, G, and Fisher's exact tests indicated that data sets with 11, 23, and 9 pairs of DNA sequences for the comparison of D. melanogaster with D. mauritiana, D. simulans, and D. yakuba, respectively, retain homogeneous rates across loci. We applied the ML method to these data sets to estimate the DNA sequence divergences before and after speciation of each species pair along with their standard deviations. Using 1.6 x 10(-8) as the rate of nucleotide substitutions per silent site per year, our results indicate that the D. melanogaster lineage split from D. yakuba approximately 5.1 +/- 0.8 million years ago (mya), D. mauritiana 2.7 +/- 0.4 mya, and D. simulans 2.3 +/- 0.3 mya. It implies that D. melanogaster became distinct from D. mauritiana and D. simulans at approximately the same time and from D. yakuba no earlier than 10 mya. The effective ancestral population size of D. melanogaster appears to be stable over evolutionary time. Assuming 10 generations per year for Drosophila, the effective population size in the ancestral lineage immediately prior to the time of species divergence is approximately 3 x 10(6), which is close to that estimated for the extant D. melanogaster population. The D. melanogaster did not encounter any obvious bottleneck during the past 10 million years.
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Affiliation(s)
- Y J Li
- Department of Biosystems Science, Graduate University for Advanced Studies, Kanagawa, Japan
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Abstract
An interplay among experimental studies of protein synthesis, evolutionary theory, and comparisons of DNA sequence data has shed light on the roles of natural selection and genetic drift in 'silent' DNA evolution.
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Affiliation(s)
- H Akashi
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045-2106, USA.
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Comeron JM, Kreitman M. The correlation between synonymous and nonsynonymous substitutions in Drosophila: mutation, selection or relaxed constraints? Genetics 1998; 150:767-75. [PMID: 9755207 PMCID: PMC1460343 DOI: 10.1093/genetics/150.2.767] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Codon usage bias, the preferential use of particular codons within each codon family, is characteristic of synonymous base composition in many species, including Drosophila, yeast, and many bacteria. Preferential usage of particular codons in these species is maintained by natural selection acting largely at the level of translation. In Drosophila, as in bacteria, the rate of synonymous substitution per site is negatively correlated with the degree of codon usage bias, indicating stronger selection on codon usage in genes with high codon bias than in genes with low codon bias. Surprisingly, in these organisms, as well as in mammals, the rate of synonymous substitution is also positively correlated with the rate of nonsynonymous substitution. To investigate this correlation, we carried out a phylogenetic analysis of substitutions in 22 genes between two species of Drosophila, Drosophila pseudoobscura and D. subobscura, in codons that differ by one replacement and one synonymous change. We provide evidence for a relative excess of double substitutions in the same species lineage that cannot be explained by the simultaneous mutation of two adjacent bases. The synonymous changes in these codons also cannot be explained by a shift to a more preferred codon following a replacement substitution. We, therefore, interpret the excess of double codon substitutions within a lineage as being the result of relaxed constraints on both kinds of substitutions in particular codons.
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Affiliation(s)
- J M Comeron
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA.
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Da Lage JL, Renard E, Chartois F, Lemeunier F, Cariou ML. Amyrel, a paralogous gene of the amylase gene family in Drosophila melanogaster and the Sophophora subgenus. Proc Natl Acad Sci U S A 1998; 95:6848-53. [PMID: 9618501 PMCID: PMC22658 DOI: 10.1073/pnas.95.12.6848] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We describe a gene from Drosophila melanogaster related to the alpha-amylase gene Amy. This gene, which exists as a single copy, was named Amyrel. It is strikingly divergent from Amy because the amino acid divergence is 40%. The coding sequence is interrupted by a short intron at position 655, which is unusual in amylase genes. Amyrel has also been cloned in Drosophila ananassae, Drosophila pseudoobscura, and Drosophila subobscura and is likely to be present throughout the Sophophora subgenus, but, to our knowledge, it has not been detected outside. Unexpectedly, there is a strong conservation of 5' and 3' flanking regions between Amyrel genes from different species, which is not the case for Amy and which suggests that selection acts on these regions. In contrast to the Amy genes, Amyrel is transcribed in larvae of D. melanogaster but not in adults. However, the protein has not been detected yet. Amyrel evolves about twice as fast as Amy in the several species studied. We suggest that this gene could result from a duplication of Amy followed by accelerated and selected divergence toward a new adaptation.
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Affiliation(s)
- J L Da Lage
- Populations, Génétique et Evolution, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette cedex, France.
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Akhmanova A, Hennig W. Drosophila melanogaster histone H2B retropseudogene is inserted into a region rich in transposable elements. Genome 1998; 41:396-401. [PMID: 9729774 DOI: 10.1139/g98-035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have isolated and characterized the genomic sequence of a Drosophila melanogaster histone H2B pseudogene that is localized outside of the cluster of the replication-dependent histone genes and has all the properties of a retropseudogene. It is highly homologous to the transcribed region of the D. melanogaster histone H2B gene, but not to its flanking regions, and is surrounded by short direct repeats. The pseudogene contains several point mutations that preclude its translation. The sequence of the 3' region of this pseudogene is compatible with the hypothesis that the 3' terminal stem-loop structure of the histone H2B mRNA has served as a primer for the reverse transcription event from which this pseudogene originated. Analysis of the regions flanking the histone H2B pseudogene revealed the presence of three different types of transposable elements, suggesting that this chromosomal locus represents a hotspot for transposition.
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Affiliation(s)
- A Akhmanova
- Department of Physiological Chemistry and Pathobiochemistry, Johannes Gutenberg-Universität, Mainz, Germany
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44
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Abstract
Rate constancy of DNA sequence evolution was examined for three species of Drosophila, using two samples: the published sequences of eight genes from regions of the normal recombination rates and new data of the four AS-C (ac, sc, l'sc and ase) and ci genes. The AS-C and ci genes were chosen because these genes are located in the regions of very reduced recombination in Drosophila melanogaster and their locations remain unchanged throughout the entire lineages involved, yielding less effect of ancestral polymorphism in the study of rate constancy. The synonymous substitution pattern of the three lineages was found to be erratic in both samples. The dispersion index for replacement substitution was relatively high for the per, G6pd and ac genes. A significant heterogeneity was found in the number of synonymous substitutions in the three lineages between the two samples of genes with different recombination rates. This is partly due to a lack of the lineage effect in the D. melanogaster and Drosophila simulans lineages in the AS-C and ci genes in contrast to Akashi's observation of genes in regions of normal recombination. The higher codon bias in Drosophila yakuba as compared with D. melanogaster and D. simulans was observed in the four AS-C genes, which suggests change(s) in action of natural selection involved in codon usage on these genes. Fluctuating selection intensity may also be responsible for the observed locus-lineage interaction effects in synonymous substitution.
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Affiliation(s)
- T S Takano
- Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan.
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45
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Mutation pressure, natural selection, and the evolution of base composition in Drosophila. ACTA ACUST UNITED AC 1998. [DOI: 10.1007/978-94-011-5210-5_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
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Abstract
We have recently described a novel method of estimating neutral rates and patterns of spontaneous mutation (Petrov et al., 1996). This method takes advantage of the propensity of non-LTR retrotransposable elements to create non-functional, 'dead-on-arrival' copies as a product of transposition. Maximum parsimony analysis is used to separate the evolution of actively transposing lineages of a non-LTR element from the fate of individual inactive insertions, and thereby allows one to assess directly the relative rates of different types of mutation, including point substitutions, deletions and insertions. Because non-LTR elements enjoy wide phylogenetic distribution, this method can be used in taxa that do not harbor a significant number of bona fide pseudogenes, as is the case in Drosophila (Jeffs and Ashburner, 1991; Weiner et al., 1986). We used this method with Helena, a non-LTR retrotransposable element present in the Drosophila virilis species group. A striking finding was the virtual absence of insertions and remarkably high incidence of large deletions, which combine to produce a high overall rate of DNA loss. On average, the rate of DNA loss in D. virilis is approximately 75 times faster than that estimated for mammalian pseudogenes (Petrov et al., 1996). The high rate of DNA loss should lead to rapid elimination of non-essential DNA and thus may explain the seemingly paradoxical dearth of pseudogenes in Drosophila. Varying rates of DNA loss may also contribute to differences in genome size (Graur et al., 1989; Petrov et al., 1996), thus explaining the celebrated 'C-value' paradox (John and Miklos, 1988). In this paper we outline the theoretical basis of our method, examine the data from this perspective, and discuss potential problems that may bias our estimates.
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Affiliation(s)
- D A Petrov
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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47
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Moriyama EN, Powell JR. Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. J Mol Evol 1997; 45:378-91. [PMID: 9321417 DOI: 10.1007/pl00006243] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7-3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5-9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 (estimated from the melanogaster species subgroup) or 2.9 (estimated from the obscura group) times higher in mitochondrial genes than in nuclear genes. Synonymous transversions in mitochondrial genes occurred at an approximately equivalent rate to those in the fastest nuclear genes. This last result is not consistent with the hypothesis that the difference in turnover rates between mitochondrial and nuclear genomes is the major factor determining higher synonymous substitution rates in mtDNA. We conclude that the difference in synonymous substitution rates is due to a combination of two factors: a higher transitional mutation rate in mtDNA and constraints on nuclear genes due to selection for codon usage.
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Affiliation(s)
- E N Moriyama
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA
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48
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ThepsbE-F-L-J operon from chloroplast genome ofPopulus deltoides: Cloning, nucleotide sequence and transcript analysis. J Genet 1997. [DOI: 10.1007/bf02931770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. BIOCHEM SYST ECOL 1997. [DOI: 10.1016/s0305-1978(96)00042-7] [Citation(s) in RCA: 466] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Comeron JM, Aguadé M. Synonymous substitutions in the Xdh gene of Drosophila: heterogeneous distribution along the coding region. Genetics 1996; 144:1053-62. [PMID: 8913749 PMCID: PMC1207601 DOI: 10.1093/genetics/144.3.1053] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The Xdh (rosy) region of Drosophila subobscura has been sequenced and compared to the homologous region of D. pseudoobscura and D. melanogaster. Estimates of the numbers of synonymous substitutions per site (Ks) confirm that Xdh has a high synonymous substitution rate. The distributions of both nonsynonymous and synonymous substitutions along the coding region were found to be heterogeneous. Also, no relationship has been detected between Ks estimates and codon usage bias along the gene, in contrast with the generally observed relationship among genes. This heterogeneous distribution of synonymous substitutions along the Xdh gene, which is expression-level independent, could be explained by a differential selection pressure on synonymous sites along the coding region acting on mRNA secondary structure. The synonymous rate in the Xdh coding region is lower in the D. subobscura than in the D. pseudoobscura lineage, whereas the reverse is true for the Adh gene.
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Affiliation(s)
- J M Comeron
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Spain
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