伊米果蝇种组（Drosophila immigrans species group）H2a-H2b和Cyt b分子系统发育关系（简报）

伊米果蝇种组(Drosophila immigrans speciesgroup)是果蝇科(Drosophilidae)、果蝇属(Drosophi-la)、果蝇亚属(Drosophila)中数量最多的一个类群,主要分布于东洋区。在分类学上该种组分为nasuta、immigrans、hypocausta、quadrilineata和curviceps五个种亚组(species subgroup)[1],东洋区果蝇区系中伊米果蝇种组中包括94个种,其中有45个种分布在中国[2]。而且curviceps种亚组是1992年新建立的中国特有果蝇类群[3]。迄今,对伊米果蝇种组分子系统关系的报道还很少,有些物种的归属仍存在争议。伊米果蝇种组还有些问题需要探讨[4]。组蛋白基因…     

Molecular phylogeny and divergence times of drosophilid species

The phylogenetic relationships and divergence times of 39 drosophilid species were studied by using the coding region of the Adh gene. Four genera--Scaptodrosophila, Zaprionus, Drosophila, and Scaptomyza (from Hawaii)--and three Drosophila subgenera--Drosophila, Engiscaptomyza, and Sophophora--were included. After conducting statistical analyses of the nucleotide sequences of the Adh, Adhr (Adh-related gene), and nuclear rRNA genes and a 905-bp segment of mitochondrial DNA, we used Scaptodrosophila as the outgroup. The phylogenetic tree obtained showed that the first major division of drosophilid species occurs between subgenus Sophophora (genus Drosophila) and the group including subgenera Drosophila and Engiscaptomyza plus the genera Zaprionus and Scaptomyza. Subgenus Sophophora is then divided into D. willistoni and the clade of D. obscura and D. melanogaster species groups. In the other major drosophilid group, Zaprionus first separates from the other species, and then D. immigrans leaves the remaining group of species. This remaining group then splits into the D. repleta group and the Hawaiian drosophilid cluster (Hawaiian Drosophila, Engiscaptomyza, and Scaptomyza). Engiscaptomyza and Scaptomyza are tightly clustered. Each of the D. repleta, D. obscura, and D. melanogaster groups is monophyletic. The splitting of subgenera Drosophila and Sophophora apparently occurred about 40 Mya, whereas the D. repleta group and the Hawaiian drosophilid cluster separated about 32 Mya. By contrast, the splitting of Engiscaptomyza and Scaptomyza occurred only about 11 Mya, suggesting that Scaptomyza experienced a rapid morphological evolution. The D. obscura and D. melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events.      

中国特有果蝇 Drosophila curviceps 种亚组在Drosophila immigrans种组中的种系发生地位

果蝇immigrans种组中的curviceps种亚组是1992年新建立的中国特有果蝇类群。该种亚组中的物种主要分布在中国大陆和台湾。目前除了形态学水平的研究外,还没有其他证据支持建立该种亚组的合理性及其起源和种系发生地位。为了在DNA分子水平上探讨果蝇curviceps种亚组在果蝇immigrans种组中的种系发生地位,从而为今后更深入地研究中国特有果蝇,甚至为果蝇亚属的进化遗传学提供理论依据,测定了immigrans种组5个种亚组（nasuta、immigrans、hypocausta、quadrilineata、curviceps)中12个代表物种的rDNA的ITS1和部分Adh基因的序列。其中ITS1序列的长度为513－587bp,共有191个信息位点;Adh基因片段的长度在714－747bp之间,共99个信息位点。考虑到单个分子提供的信息较少,将两个分子的序列综合起来,组成一个较长的复合序列。分别根据ITS1,Adh和两个分子的复合序列排比（Alignment)结果,和最大简约法和邻接法构建分子系统树,其中根据复合序列构建的系统树与形态学研究结果最为一致。分子树显示curviceps种亚组的特种确定单独形成一个分枝,为种亚组级的分类阶元,支持了形态学将其建立为一个新种亚组。根据Kimura距离,估算了复合分子的替换速率约为每百万年1．48％,进而计算出5个种亚组的分 歧年代。结合各物种的地理分布,推测了immigrans种组的进化历史：curviceps种亚组与quadrilineata种亚组的亲缘关系最近,主要分布在中国南部的温带地区。它们之间的分歧时间大约为3．4百万年,是最年轻的两个种亚组。主要分布在苏门答腊及附近的热带地区的hypocausta种亚组的物种是最早分化出来的,与其他种亚组的分歧时间约为9．2百万年。该结果与形态学和生物地理学研究相吻合。值得一提是的,目前归属仍存在争议的物种D.neohypocausta,在分子系统树中与hypocausta种亚组的物种相距较远,而与immiagrasn种亚组的关系较近,但分枝置信度较低（＜50％）。由于还缺乏其他方面的证据,因此D.neohypocausta的归属有待今后的研究来作定论。     

The phylogenetic relationships of flies in the family Drosophilidae deduced from mtDNA sequences.

The phylogenetic relationships of several taxa from representative genera, subgenera, groups, and subgroups in the Drosophilidae were examined using sequences from a 905-bp mtDNA fragment. Conventional cloning and sequencing techniques were used to obtain nucleotide sequences. In addition, polymerase chain reaction primers were designed for the rapid amplification and sequencing of this region for the species examined in the Drosophilidae. Phylogenetic analysis was done by cladistic techniques. Because of the coding nature of the 905-bp mtDNA fragment, several separate analyses of these sequences were performed. The genera Scaptomyza and Hirtodrosophila occupy ancestral branching positions in the molecular phylogeny. The genera Chymomyza and Zaprionus have intermediate branching positions, while the subgenera Drosophila and Sophophora are in the most derived position in the molecular phylogeny. Within the subgenus Sophophora, there is little resolution using these sequences, while within the subgenus Drosophila, D. melanica, D. funebris, and D. pinicola form a clade in a derived part of the phylogeny, with D. robusta and D. immigrans branching in an intermediate position in the phylogeny. D. mercatorum, a member of the repleta species group, occupies an ancestral position in the molecular phylogeny.     

Alcohol dehydrogenase from Drosophila funebris and Drosophila immigrans: Molecular and evolutionary aspects

Alcohol dehydrogenase from Drosophila funebris and D. immigrans is evident at all developmental stages. The highest activity level appears in third-instar larvae and declines to a lower level at all later stages of development. Both species are monomorphic. The enzyme is a dimer consisting of two identical subunits with molecular weight 27,600. The pI values are 8.6 for D. funebris and 9.02 for D. immigrans. The optimum pH is 8.6 and 8.7 for D. funebris and D. immigrans, respectively. The Km values for NAD+, propan-2-ol, and butan-2-ol are 0.15, 2.90, and 2.08 mM, respectively, for D. funebris and 0.16, 1.53, and 1.49 mM, respectively, for D. immigrans. The half-life for the purified enzyme is 45 days for D. funebris and 18 days for D. immigrans at 4 degrees C. Data on the amino acid composition of both enzymes and peptide maps of alcohol dehydrogenase of D. immigrans reveal that they have marked homologies between them and also with alcohol dehydrogenases of other species. D. funebris shows reduced levels of alcohol dehydrogenase synthesis but has the highest specific activity reported to date for a Drosophila species. D. immigrans synthesises six times more enzyme but the specific activity is comparable to that of other species of Drosophila. This evidence could explain their different alcohol tolerance. The molecular properties of these alcohol dehydrogenases together with other species of Drosophila suggest that the alcohol dehydrogenase of Drosophila has arisen by divergent evolution from a common ancestral gene.     

Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses

Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to include Scaptomyza and Zaprionus (considered distinct genera in the taxonomy of Wheeler, 1981) but excluding Scaptodrosophila. The genus Drosophila so defined is monophyletic. The subgenus Sophophora (including the melanogaster, obscura, and willistoni groups) is monophyletic and the sister clade to all other Drosophila subgenera. The Hawaiian Drosophila (including Scaptomyza) is a monophyletic group, but the subgenus Drosophila is not monophyletic, because the immigrans group is more closely related to the subgenus Hirtodrosophila than to other species of the subgenus Drosophila, such as the virilis and repleta groups.     

果蝇Drosophila nasuta亚群系统发育问题的探讨

果蝇Ｄｒｏｓｏｐｈｉｌａｎａｓｕｔａ亚群由在１４个处于不同物种分化阶段的种,亚种和分类元组成,这个亚群的物种有许多进化上的独特之处,使得它在物种分化研究方面倍受关注,然而,在形态学,生殖隔离,染色体和同工酶多态,线粒体ＤＮＡＲＦＬＰ,求偶歌特征惟及线粒体和核基因序列分析等方面的研究都未能清楚地阐明这一亚群的系统进化关系,本文综合分析了关于这一亚群的进化遗传学的研究结果,并提出了有待进一步的一些问题     

Phylogeny of the Drosophila mesophragmatica group (Diptera, Drosophilidae): an example of Andean evolution

The mesophragmatica group of Drosophila belongs to the virilis-repleta radiation of the Drosophila subgenus. This group comprises 13 Neotropical species that are endemic to the South-American continent and seem to be fundamentally Andean in their distribution. The mesophragmatica-group phylogeny has been inferred previously by other authors based on morphological, cytological, and isozyme analyses. However, the relationships within the group have not yet been completely resolved, although its monophyletic origin has already been confirmed by molecular data. This work attempts to enhance the molecular approach to the relationships among the species of the mesophragmatica group, using both nuclear and mitochondrial markers. Phylogenetic analyses were performed using fragments of the nuclear alcohol dehydrogenase (Adh; 631 bp), alpha-methyldopa (Amd; 1211 bp), dopa-decarboxylase (Ddc; 1105 bp), and hunchback (Hb; 687 bp) genes and the mitochondrial cytochrome oxidase subunit II (COII; 672 bp) gene, and included a total of 4306 bp. The sequences obtained for eight representatives of the mesophragmatica group were analyzed both individually and in combination by distance methods, maximum parsimony, and maximum likelihood. Our results support subdivision of the mesophragmatica group into three main lineages: the first is composed of D. viracochi; the second comprises a clade grouping the sibling species D. pavani and D. gaucha; and the third encompasses D. gasici, D. brncici, and D. mesophragmatica. The best supported scenario suggests that D. viracochi is an early offshoot in the mesophragmatica group, with this and other early branchings occuring in the Pliocene/Pleistocene Epochs, possibly associated with Andean glacial refuges. Also based on the phylogenies obtained, we present a genealogical view of the evolution of previously described characters within the group.     

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

Basal relationships in the Drosophila melanogaster species group

The Drosophila melanogaster species group is a popular model for evolutionary studies due to its morphological and ecological diversity and its inclusion of the model species D. melanogaster. However, phylogenetic relationships among major lineages within this species group remain controversial. In this report, the phylogeny of 10 species representing each of the well-supported monophyletic clades in the melanogaster group was studied using the sequences of 14 loci that together comprise 9493 nucleotide positions. Combined Bayesian analysis using gene-specific substitution models produced a 100% credible set of two trees. In the strict consensus of these trees, the ananassae subgroup branches first in the melanogaster species group, followed by the montium subgroup. The remaining lineages form a monophyletic clade in which D. ficusphila and D. elegans branch first, followed by D. biarmipes, D. eugracilis, and the melanogaster subgroup. This strongly supported phylogeny resolves most basal relationships in the melanogaster species group, and provides a framework that can be extended in the future to encompass more species.     

A statistical analysis of nucleotide substitutions in the Drosophila Adh region reflects irregularities in molecular clocks

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.     

Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: a nuclear versus mitochondrial gene approach

The genus Drosophila has played an essential role in many biological studies during the last 100 years but much controversy and many incompletely addressed issues still remain to be elucidated regarding the phylogeny of this genus. Because information on the Neotropical species contained in the subgenus Drosophila is particularly incomplete, with this taxonomic group being underrepresented in many studies, we designed a study to answer some evolutionary questions related to these species. We subjected at least 41 Drosophilidae taxa to a phylogenetic analysis using a 516-base pair (bp) fragment of the alpha-methyldopa (Amd) nuclear gene and a 672 bp fragment of the mitochondrial cytochrome oxidase subunit II (COII) gene both individually and in combination. We found that the subgenus Drosophila is paraphyletic and subdivided into two main clusters: the first containing species traditionally placed in the virilis-repleta radiation and the second assembling species of the immigrans-Hirtodrosophila radiation. Inside the first of these clusters we could detect the monophyly of both the flavopilosa (the sister-clade of the annulimana group) and the mesophragmatica (closely related to the repleta group) species groups. Concerning the immigrans-Hirtodrosophila lineage, Zaprionus, Liodrosophila, Samoaia, and Hirtodrosophila were the early offshoots, followed by the immigrans, quinaria, testacea, and funebris species groups. The tripunctata radiation appears to be a derived clade, composed of a paraphyletic tripunctata group, intimately interposed with members of the cardini, guarani, and guaramunu species groups. Overall, the COII gene yielded a poor phylogenetic performance when compared to the Amd gene, the evolutionary hypothesis of which agreed with the total evidence tree. This phenomenon can be explained by the fast saturation of transitional substitutions in COII, due to strong biases in both base composition and substitution patterns, as also by its great among-site rate variation heterogeneity.     

A MOLECULAR PHYLOGENY OF THE DROSOPHILA WILLISTONI GROUP: CONFLICTS BETWEEN SPECIES CONCEPTS?

The six sibling species of the Neotropical Drosophila willistoni group have a long history in studies of evolutionary biology, yet to date only one molecular study, which used allozymes, has been published on the phylogeny of the group. Here we present a phylogeny of the siblings based on the sequences of two nuclear genes, period (per) and Alcohol dehydrogenase (Adh), as well as the mitochondrial gene Cytochrome oxidase I (COI). Taken individually, only per has a strong phylogenetic signal supporting a well-resolved phylogeny of the group, and this phylogeny is different from that obtained using allozymes. The COI dataset by itself produces trees that disagree with per, and neither that data nor the Adh data have a strong phylogenetic signal, as indicated by low bootstrap values for all analyses. Combining the Adh and COI datasets results in the same tree as per alone. Combining all three genes results in the same topology, which is strongly supported. Two problematic taxa, D. pavlovskiana and a “Carmody strain,” which were identified as potentially separate species based on reproductive isolation, clearly cluster in the phylogenetic analyses within D. paulistorum and D. equinoxialis, respectively. Thus, there appears to be a conflict between the biological species concept and the phylogenetic species concept.     

Nematode parasitism in a northern European drosophilid community

Many factors may influence the structure of invertebrate communities. Among these is the presence of parasites which attack some or all members of a guild and potentially promote coexistence of competitor species. We assessed the prevalence of nematode (Allantonematidae) parasitism in Dutch woodland drosophilids (Diptera). Nematodes were found in 6 of the 18 drosophilid species sampled (percentage parasitism in parentheses): Drosophila phalerata (16%), D. kuntzei (5.1%), D. immigrans (0.5%), D. testacea (1.2%) and D. transversa (2.8%) were all parasitized by Howardula aoronymphium and D. subobscura (3%) was parasitized by Parazitylenchus diplogenus. This is the first report of nematode parasitism of D. immigrans and D. transversa. There were no important seasonal trends in percentage parasitism. We explored the consequences of nematode parasitism for individual drosophilids. Nematodes did not exert an important influence on the wing length (adult body size) of the drosophilids we sampled, but egg loads (fecundities) of female D. phalerata, D. subobscura and D. kuntzei were reduced by nematode parasitism. Parasitism rates were positively correlated with relative host abundance, in Dutch and other communities, suggesting that species diversity is promoted by a disproportionately high parasitism of more common host species.     

The Evolutionary History of the Transposable Element Penelope in the Drosophila virilis Group of Species

We have used phylogenetic techniques to study the evolutionary history of the Penelope transposable element in the Drosophila virilis species group. Two divergent types of Penelope have been detected, one previously described, clade I, and a new one which we have termed clade III. The phylogeny of some copies of the Penelope clade I element was partially consistent with the species phylogeny of the D. montana subphylad, suggesting cospeciation and allowing the estimation of the evolutionary rate of Penelope. Divergence times of elements found in different species are younger than the age of the species, suggesting horizontal transfer events. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Dmitri Petrov]     

Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium l., malvaceae)

The 13 "D-genome"cotton species are a monophyletic assemblage of morphologically diverse diploids that inhabit arid to semiarid regions in Mexico, with 1 disjunct species each in Peru and the Galapagos Islands and 1 species whose range extends northward into Arizona. While these species lack commercially significant fiber (i. e., cotton), they are important in that they represent one of the parental genomes of the cultivated tetraploid cottons. To assess phylogenetic relationships among these species, we sequenced and analyzed a region of a nuclear-encoded alcohol dehydrogenase gene (AdhA). Phylogenetic analysis resulted in a topology that is generally consistent with current taxonomic alignment of the species, although the phylogeny based on AdhA sequences conflicts with those inferred from cpDNA and ITS data sets, most notably in the position of the anomalous species Gossypium gossypioides. In one lineage, we detected both gene duplication and sequence polymorphisms that transcend species boundaries; sequences in this lineage formed a monophyletic clade, yet no taxon within the clade contained a monophyletic collection of sequences. Potential explanations for this latter phenomenon, including gene duplication, gene flow, and lineage sorting, are discussed.     

Reevaluation of phylogeny in the Drosophila obscura species group based on combined analysis of nucleotide sequences.

The Drosophila obscura species group has served as an important model system in many evolutionary and population genetic studies. Despite the amount of study this group has received, some phylogenetic relationships remain unclear. While individual analysis of different nuclear, mitochondrial, allozyme, restriction fragment, and morphological data partitions are able to discern relationships among closely related species, they are unable to resolve relationships among the five obscura species subgroups. A combined analysis of several nucleotide data sets is able to provide resolution and support for some nodes not seen or well supported in analyses of individual loci. A phylogeny of the obscura species group based on combined analysis of nucleotide sequences from six mitochondrial and five nuclear loci is presented here. The results of several different combined analyses indicate that the Old World obscura and subobscura subgroups form a monophyletic clade, although they are unable to resolve the relationships among the major lineages within the obscura species group.