Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences

Skeleton phylogeny reconstructed with transcriptomes for the tribe Drosophilini (Diptera: Drosophilidae)

The family Drosophilidae is one of the most important model systems in evolutionary biology. Thanks to advances in high-throughput sequencing technology, a number of molecular phylogenetic analyses have been undertaken by using large data sets of many genes and many species sampled across this family. Especially, recent analyses using genome sequences have depicted the family-wide skeleton phylogeny with high confidence. However, the taxon sampling is still insufficient for minor lineages and non-Drosophila genera. In this study, we carried out phylogenetic analyses using a large number of transcriptome-based nucleotide sequences, focusing on the largest, core tribe Drosophilini in the Drosophilidae. In our analyses, some noise factors against phylogenetic reconstruction were taken into account by removing putative paralogy from the datasets and examining the effects of missing data, i.e. gene occupancy and site coverage, and incomplete lineage sorting. The inferred phylogeny has newly resolved the following phylogenetic positions/relationships at the genomic scale: (i) the monophyly of the subgenus Siphlodora including Zaprionus flavofasciatus to be transferred therein; (ii) the paraphyly of the robusta and melanica species groups within a clade comprised of the robusta, melanica and quadrisetata groups and Z. flavofasciatus; (iii) Drosophila curviceps (representing the curviceps group), D. annulipes (the quadrilineata subgroup of the immigrans group) and D. maculinotata clustered into a clade sister to the Idiomyia + Scaptomyza clade, forming together the expanded Hawaiian drosophilid lineage; (iv) Dichaetophora tenuicauda (representing the lineage comprised of the Zygothrica genus group and Dichaetophora) placed as the sister to the clade of the expanded Hawaiian drosophilid lineage and Siphlodora; and (v) relationships of the subgenus Drosophila and the genus Zaprionus as follows: (Zaprionus, (the quadrilineata subgroup, ((D. sternopleuralis, the immigrans group proper), (the quinaria radiation, the tripunctata radiation)))). These results are to be incorporated into the so-far published phylogenomic tree as a backbone (constraint) tree for grafting much more species based on sequences of a limited number of genes. Such a comprehensive, highly confident phylogenetic tree with extensive and dense taxon sampling will provide an essential framework for comparative studies of the Drosophilidae.

Divergence and introgression among the virilis group of Drosophila

Speciation with gene flow is now widely regarded as common. However, the frequency of introgression between recently diverged species and the evolutionary consequences of gene flow are still poorly understood. The virilis group of Drosophila contains 12 species that are geographically widespread and show varying levels of prezygotic and postzygotic isolation. Here, we use de novo genome assemblies and whole-genome sequencing data to resolve phylogenetic relationships and describe patterns of introgression and divergence across the group. We suggest that the virilis group consists of three, rather than the traditional two, subgroups. Some genes undergoing rapid sequence divergence across the group were involved in chemical communication and desiccation tolerance, and may be related to the evolution of sexual isolation and adaptation. We found evidence of pervasive phylogenetic discordance caused by ancient introgression events between distant lineages within the group, and more recent gene flow between closely related species. When assessing patterns of genome-wide divergence in species pairs across the group, we found no consistent genomic evidence of a disproportionate role for the X chromosome as has been found in other systems. Our results show how ancient and recent introgressions confuse phylogenetic reconstruction, but may play an important role during early radiation of a group.

Morphological and molecular evidence of eight new species of the genus Scaptodrosophila Duda (Diptera, Drosophilidae) from China

By integrating morphological and molecular evidences, seven new species of the Scaptodrosophila coracina species group and one new species of uncertain affinity to this genus from China are recognized and described: S. angustifolia sp. nov., S. apunctata sp. nov., S. latifoliacea sp. nov., S. longiciliata sp. nov., S. melanovittata sp. nov., S. polytricapillum sp. nov., S. undulata sp. nov. and S. curvata sp. nov. A key to the examined species is provided. Intra- and interspecific, pairwise p-distances with DNA barcodes (partial sequences of the mitochondrial COI, i.e., cytochrome c oxidase subunit I gene) are calculated and summarized. In addition, S. zebrina Liu & Chen, 2018 from Yunnan, China is recognized as junior homonym of S. zebrina (Bezzi, 1928) and renamed as S. zebromyia nom. nov.  

The genus Scaptodrosophila Duda (Diptera, Drosophilidae), part III: the riverata species group from China, with morphological and molecular evidence for five new species

A new species group, the riverata species group, is established within the genus Scaptodrosophila based on morphological and molecular evidence for five known and five new species from China: S.abdentatasp. nov., S.cederholmi (Okada, 1988), S.crocata (Bock, 1976), S.paraclubata (Sundaran & Gupta, 1991), S.platyrhinasp. nov., S.puncticeps (Okada, 1956), S.riverata (Singh & Gupta, 1977), S.serrateifoliaceasp. nov., S.sinuatasp. nov. and S.tanyrhinasp. nov. A key to this group is provided. Furthermore, 51 mtDNA COI sequences belonging to S.puncticeps, S.riverata and the five new species are used for verifying species boundaries defined by the morphological data.

Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

The repeatability or predictability of evolution is a central question in evolutionary biology and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage-compensation male-specific lethal (MSL) complex to study the mutational paths that have led to the acquisition of hundreds of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the D. melanica and D. robusta species groups by genome sequencing and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve hundreds of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element (TE) insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes and appears to be contingent on genomic properties of that species, such as simple repeat or TE density. This establishes the "genomic environment" as an important determinant in predicting the outcome of evolutionary adaptations.

Evolution of DNMT2 in drosophilids: Evidence for positive and purifying selection and insights into new protein (pathways) interactions

The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the DNA methyltransferase family. Nevertheless, its substrate specificity is still controversial and elusive. The genomic role and determinants of DNA methylation are poorly understood in invertebrates, and several mechanisms and associations are suggested. In Drosophila, the only known DNMT gene is Dnmt2. Here we present our findings from a wide search for Dnmt2 homologs in 68 species of Drosophilidae. We investigated its molecular evolution, and in our phylogenetic analyses the main clades of Drosophilidae species were recovered. We tested whether the Dnmt2 has evolved neutrally or under positive selection along the subgenera Drosophila and Sophophora and investigated positive selection in relation to several physicochemical properties. Despite of a major selective constraint on Dnmt2, we detected six sites under positive selection. Regarding the DNMT2 protein, 12 sites under positive-destabilizing selection were found, which suggests a selection that favors structural and functional shifts in the protein. The search for new potential protein partners with DNMT2 revealed 15 proteins with high evolutionary rate covariation (ERC), indicating a plurality of DNMT2 functions in different pathways. These events might represent signs of molecular adaptation, with molecular peculiarities arising from the diversity of evolutionary histories experienced by drosophilids.

The genus Scaptodrosophila Duda part I: the brunnea species group from the Oriental Region, with morphological and molecular evidence (Diptera, Drosophilidae)

Seven new species of the Scaptodrosophila brunnea species group are described from east Asia: S. maculatasp. n., S. melanogastersp. n., S. nigricostatasp. n., S. nigripectasp. n., S. obscuratasp. n., S. protenipenissp. n. and S. rhinasp. n. Three known species, S. parabrunnea (Tsacas & Chassagnard), S. pressobrunnea (Tsacas & Chassagnard) and S. scutellimargo (Duda) are redescribed. A key to all the examined species in the brunnea group is provided. Species delimitations have been improved by integrating the DNA sequences with morphological information. The intra- and interspecific pairwise p-distances (proportional distance) are summarized. Some nucleotide sites with fixed status in the alignment of the COI sequences (664 nucleotide sites in length) are used as "pure" molecular diagnostic characters to delineate species in the brunnea group.

Radiation of the Drosophila nannoptera species group in Mexico

The Drosophila nannoptera species group, a taxon of Mexican cactophilic flies, is an excellent model system to study the influence of abiotic and biotic factors on speciation, the genetic causes of ecological specialization and the evolution of unusual reproductive characters. However, the phylogenetic relationships in the nannoptera species group and its position within the virilis-repleta phylogeny have not been thoroughly investigated. Using a multilocus data set of gene coding regions of eight nuclear and three mitochondrial genes, we found that the four described nannoptera group species diverged rapidly, with very short internodes between divergence events. Phylogenetic analysis of repleta group lineages revealed that D. inca and D. canalinea are sister to all other repleta group species, whereas the annulimana species D. aracataca and D. pseudotalamancana are sister to the nannoptera and bromeliae species groups. Our divergence time estimates suggest that the nannoptera species group radiated following important geological events in Central America. Our results indicate that a single evolutionary transition to asymmetric genitalia and to unusual sperm storage may have occurred during evolution of the nannoptera group.

Survey of the genus Stegana Meigen (Diptera, Drosophilidae) from Taiwan, with DNA barcodes and descriptions of three new species

Background

Twelve Stegana species have been reported from Taiwan, yet only four were also recorded from Mainland China. This may not reflect the actual fauna between both sides of the strait. This report mainly deals with a fly collection of the genus Stegana during a short visit to Taiwan in 2012. It represents the most recent drosophilid faunal survey of Taiwan associating with bleeding trees.

Results

In this study, 17 species were recognized including three new ones and eight new records. They are Stegana (Oxyphortica) convergens (de Meijere, 1911); Stegana (Oxyphortica) nigripennis (Hendel, 1914); Stegana (Stegana) taiwana Okada, 1991; Stegana (Steganina) bacilla Chen and Aotsuka, 2004; Stegana (Steganina) chitouensis Sidorenko, 1998; Stegana (Steganina) ctenaria Nishiharu, 1979; Stegana (Steganina) euryphylla Chen and Chen, 2009; Stegana (Steganina) langufoliacea Wu, Gao and Chen, 2010; Stegana (Steganina) melanostoma Chen and Chen, 2009; Stegana (Steganina) nigrolimbata Duda, 1924; Stegana (Steganina) ornatipes Wheeler and Takada, 1964; Stegana (Steganina) reni Wang, Gao and Chen, 2010; Stegana (Steganina) tongi Wang, Gao and Chen, 2010; Stegana (Steganina) xui Wang, Gao and Chen, 2010; Stegana (Steganina) jianqinae sp. nov.; Stegana (Stegana) yangi sp. nov., and Stegana (Steganina) wulai sp. nov. Six recorded species are redescribed based on new materials. The key to all species of the genus Stegana in Taiwan is presented. The DNA barcoding fragments of the mitochondrial COI gene are sequenced and used to delineate species.

Conclusions

Among the 23 recorded species, two most widely distributed species range across two zoogeographic regions, and one occurs in both Taiwan and India. Five species are insular species recorded from Taiwan and Japan. The remaining 16 species are distributed in both Taiwan and southern Mainland China. One montane species was collected at an elevation of 1,500 m. As a whole, this implies that Taiwanese Stegana fauna should be largely of a Mainland China origin, probably as a consequence of the east- and/or southward dispersals of the ancestral species during the glacial epoch. The 20% (5/23) endemism at the genus level is comparable to that of the family level at 63/320. It is notable that the Fujian province, which is bordered by Guangdong to the south but isolated from Taiwan by the 180-km-wide strait, has no species in common with Guangdong and Taiwan. This may be due to insufficient drosophilid faunal survey in these areas, especially for Fujian.

Phylogenetic patterns of geographical and ecological diversification in the subgenus Drosophila

Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. Members of the subgenus Drosophila are distributed across the globe and show a large diversity of ecological niches. Furthermore, taxonomic classification of Drosophila includes the rank radiation, which refers to closely related species groups. Nevertheless, it has never been tested if these taxonomic radiations correspond to evolutionary radiations. Here we present a study of the patterns of diversification of Drosophila to test for increased diversification rates in relation to the geographic and ecological diversification processes. For this, we have estimated and dated a phylogeny of 218 species belonging to the major species groups of the subgenus. The obtained phylogenies are largely consistent with previous studies and indicate that the major groups appeared during the Oligocene/Miocene transition or early Miocene, characterized by a trend of climate warming with brief periods of glaciation. Ancestral reconstruction of geographic ranges and ecological resource use suggest at least two dispersals to the Neotropics from the ancestral Asiatic tropical disribution, and several transitions to specialized ecological resource use (mycophagous and cactophilic). Colonisation of new geographic regions and/or of new ecological resources can result in rapid species diversification into the new ecological niches available. However, diversification analyses show no significant support for adaptive radiations as a result of geographic dispersal or ecological resource shift. Also, cactophily has not resulted in an increase in the diversification rate of the repleta and related groups. It is thus concluded that the taxonomic radiations do not correspond to adaptive radiations.

Phylogeny of the African and Asian Phortica (Drosophilidae) deduced from nuclear and mitochondrial DNA sequences

Phylogenetic relationships of 26 Phortica species were investigated based on DNA sequence data of two mitochondrial (ND2, COI) and one nuclear (28S rRNA) genes. Five monophyletic groups were recovered in the genus Phortica, of which three were established as new subgenera, Alloparadisa, Ashima, and Shangrila. The subgenus Allophortica was suggested as the most basal lineage in Phortica, followed by the lineage of P. helva + P. sobodo + P. varipes. The remaining Phortica species, most of Oriental distribution, formed a monophyletic group, and were subdivided into three lineages (i.e., the subgenera Ashima, Phortica, and Shangrila). The subgenera Shangrila and Phortica were suggested as sister taxa, and four clades were recovered in the subgenus Ashima. The result of reconstruction of ancestral distribution and estimation of divergence times indicates that, the ancestor of the genus Phortica restricted to Africa, its initial diversification was dated back to ca. 23 Mya (coinciding with the Oligocene/Miocene boundary); sympatric speciation and an Africa-to-Asia dispersal was proposed to account for the current distribution of Allophortica and the rest Phortica; most of the rest diversification of Phortica occurred in southern China, and the divergence between the African clade and its Oriental counterpart was suggested as a result of vicariance following a dispersal of their ancestral species from southern China to Africa.

Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data

The Drosophila virilis group is one of the major lineages of Drosophila previously recognised and it has been used as a model for different types of studies. It comprises 13 species whose phylogenetic relationships are not well resolved. In the present study, six nuclear genes (Adh, fused, Gpdh, NonA, CG9631 and CG7219) and the mitochondrial ribosomal RNA genes (12S-16S) have been used to estimate the evolutionary tree of the group using different methods of phylogenetic reconstruction. Different competing evolutionary hypotheses have also been compared using the Approximately Unbiased test to further evaluate the robustness of the inferred trees. Results are, in general, consistent with previous studies in recovering the four major lineages of the group (D. virilis phylad, Drosophila montana subphylad, Drosophila kanekoi subphylad and Drosophila littoralis subphylad), although D. kanekoi, D. littoralis and Drosophila ezoana are here inferred to be more closely related to the D. virilis phylad than to the D. montana subphylad. The age of the crown group, estimated with a Bayesian method that assumes a relaxed molecular clock, is placed in the late Miocene (∼ 10 Mya). The oldest lineages also appeared during this period (∼ 7.5 to ∼ 8.9 Mya), while the ages of the basal nodes of the montana subphylad and the virilis phylad are located in the early Pliocene (∼ 4.9 and ∼ 4.1 Mya). Major cladogenesis events correlate to geological and palaeoclimatic occurrences that most likely affected the freshwater and deciduous forests where these species are found. The inferred biogeographical history of the group, based on the statistical dispersal-vicariance analysis, indicates that the last common ancestor of the group had a Holarctic distribution from which the North American and the Eurasian lineages evolved as a result of a vicariant event.

Divergent host plant specialization as the critical driving force in speciation between populations of a phytophagous ladybird beetle

Detecting the isolating barrier that arises earliest in speciation is critically important to understanding the mechanism of species formation. We tested isolating barriers between host races of a phytophagous ladybird beetle, Henosepilachna diekei (Coleoptera: Coccinellidae: Epilachnine), that occur sympatrically on distinct host plants. We conducted field surveys for the distribution of the beetles and host plants, rearing experiments to measure six potential isolating factors (adult host preference, adult and larval host performance, sexual isolation, egg hatchability, F(1) hybrid inviability, and sexual selection against F(1) hybrids), and molecular analyses of mitochondrial ND2 and the nuclear ITS2 sequences. We found significant genetic divergence between the host races, and extremely divergent host preference (i.e. habitat isolation) and host performance (i.e. immigrant inviability), but no other isolating barriers. The fidelity to particular host plants arises first and alone can prevent gene flow between differentiating populations of phytophagous specialists.

Phylogenetic relationships among bisexual and unisexual lineages of the weevil Scepticus insularis (Coleoptera: Curculionidae) on Hokkaido, Northern Japan

We examined the geographic distributions and phylogenetic relationships of bisexual and unisexual (parthenogenetic) forms of the weevil Scepticus insularis on Hokkaido Island, northern Japan. Unisexual beetles were widespread throughout Hokkaido, whereas bisexuals were found only in three remote areas. Bisexuals (females and males) and unisexual females occurred sympatrically in two areas. We determined nucleotide sequences for part of the mitochondrial NADH dehydrogenase subunit 2 (ND2; 633 bp) gene for 104 individuals, and for part of the nuclear internal transcribed spacer region 2 (ITS2; 360 bp) for 91 individuals. In an ND2 gene tree, haplotypes of S. insularis fell into two distinct clades (A and B), which were genetically differentiated from one another by 9.1% nucleotide sequence divergence. Haplotypes of females identified as unisexual were all in clade A, whereas those of females identified as bisexual belonged to clade B. Haplotypes of males were in clade B, except for two males having a clade-A haplotype. Circumstantial evidence suggests that these two males were produced by unisexual females. The ND2 tree suggests that the current unisexual form of S. insularis on Hokkaido was of a single origin. In contrast, a gene tree for ITS2 haplotypes show no clear divergence between the two modes of reproduction, with two major haplotypes shared by unisexual females, bisexual females, and males. This incongruence between the nuclear and mitochondrial phylogenies may be attributable to occasional gene flow between the unisexual and bisexual lineages through males occasionally produced by unisexual females, but our results do not exclude the possibility that the two lineages share polymorphic ancestral ITS2 haplotypes.

A supermatrix-based molecular phylogeny of the family Drosophilidae

The genus Drosophila is diverse and heterogeneous and contains a large number of easy-to-rear species, so it is an attractive subject for comparative studies. The ability to perform such studies is currently compromised by the lack of a comprehensive phylogeny for Drosophila and related genera. The genus Drosophila as currently defined is known to be paraphyletic with respect to several other genera, but considerable uncertainty remains about other aspects of the phylogeny. Here, we estimate a phylogeny for 176 drosophilid (12 genera) and four non-drosophilid species, using gene sequences for up to 13 different genes per species (average: 4333 bp, five genes per species). This is the most extensive set of molecular data on drosophilids yet analysed. Phylogenetic analyses were conducted with maximum-likelihood (ML) and Bayesian approaches. Our analysis confirms that the genus Drosophila is paraphyletic with 100% support in the Bayesian analysis and 90% bootstrap support in the ML analysis. The subgenus Sophophora, which includes Drosophila melanogaster, is the sister clade of all the other subgenera as well as of most species of six other genera. This sister clade contains two large, well-supported subclades. The first subclade contains the Hawaiian Drosophila, the genus Scaptomyza, and the virilis-repleta radiation. The second contains the immigrans-tripunctata radiation as well as the genera Hirtodrosophila (except Hirtodrosophila duncani), Mycodrosophila, Zaprionus and Liodrosophila. We argue that these results support a taxonomic revision of the genus Drosophila.

Assigning sequences to species in the absence of large interspecific differences

Barcoding is an initiative to define a standard fragment of DNA to be used to assign unknown sequences to existing known species groups that have been pre-identified externally (by a taxonomist). Several methods have been described that attempt to place this assignment into a Bayesian statistical framework. Here we describe an algorithm that makes use of segregating sites and we examine how well these methods perform in the absence of an interspecific 'barcoding gap'. When a barcoding gap exists, that is when the data are clearly delimited, most methods perform well. Here we have used data from the Drosophila genus because this genus includes sibling species and the species relationships within this species while complex are, arguably, better understood than in any other group. The results show that the Bayesian methods perform well even in the absence of a barcoding gap. The sequences from Drosophila are correctly identified and only when the degree of incomplete lineage sorting is extreme in simulations or within the Drosophila species, do they fail in their identifications and even then, the "correct" species has a high posterior probability.

An old bilbo-like non-LTR retroelement insertion provides insight into the relationship of species of the virilis group

In Drosophila, at the population and species level, fixation of a TE insertion is an unlikely fate. Of the few reported fixations at the species level most involve non-LTR retroelements. In this work we report the fixation of a non-LTR retroelement in five species (Drosophila littoralis, Drosophila virilis, Drosophila lummei, Drosophila americana and Drosophila novamexicana) of the virilis group of Drosophila. In most species, this TE insertion is being lost through the accumulation of small deletions, but there is also evidence for the accumulation of large deletions. In the americana lineage an insertion of about 900 bp of the non-LTR retroelement is a marker for the Xc inversion. This insertion is, at most, 80 kb away from the basal Xc inversion breakpoint. The presence of a bilbo-like element in D. littoralis but not in D. kanekoi, suggests that D. littoralis is more closely related to species of the virilis phylad than to species of the montana phylad, which is in contrast with the traditional view. Nevertheless, the phylogenetic analyses here performed using a 7 gene dataset suggest that D. littoralis is indeed more closely related to species of the virilis phylad than to species of the montana phylad. The re-evaluation of the phylogenetic relationship of the species of the virilis group, under the assumption of a relaxed molecular clock, results in an estimated age of the bilbo-like element insertion of at least 7.5 Mya.

Signals of demographic expansion in Drosophila virilis

BACKGROUND

The pattern of genetic variation within and among populations of a species is strongly affected by its phylogeographic history. Analyses based on putatively neutral markers provide data from which past events, such as population expansions and colonizations, can be inferred. Drosophila virilis is a cosmopolitan species belonging to the virilis group, where divergence times between different phylads go back to the early Miocene. We analysed mitochondrial DNA sequence variation among 35 Drosophila virilis strains covering the species' range in order to detect demographic events that could be used to understand the present characteristics of the species, as well as its differences from other members of the group.

RESULTS

Drosophila virilis showed very low nucleotide diversity with haplotypes distributed in a star-like network, consistent with a recent world-wide exponential expansion possibly associated either with domestication or post-glacial colonization. All analyses point towards a rapid population expansion. Coalescence models support this interpretation. The central haplotype in the network, which could be interpreted as ancestral, is widely distributed and gives no information about the geographical origin of the population expansion. The species showed no geographic structure in the distribution of mitochondrial haplotypes, in contrast to results of a recent microsatellite-based analysis.

CONCLUSION

The lack of geographic structure and the star-like topology depicted by the D. virilis haplotypes indicate a pattern of global demographic expansion, probably related to human movements, although this interpretation cannot be distinguished from a selective sweep in the mitochondrial DNA until nuclear sequence data become available. The particular behavioural traits of this species, including weak species-discrimination and intraspecific mate choice exercised by the females, can be understood from this perspective.

Independent origins of new sex-linked chromosomes in the melanica and robusta species groups of Drosophila

Background

Recent translocations of autosomal regions to the sex chromosomes represent important systems for identifying the evolutionary forces affecting convergent patterns of sex-chromosome heteromorphism. Additions to the sex chromosomes have been reported in the melanica and robusta species groups, two sister clades of Drosophila. The close relationship between these two species groups and the similarity of their rearranged karyotypes motivates this test of alternative hypotheses; the rearranged sex chromosomes in both groups are derived through a common origin, or the rearrangements are derived through at least two independent origins. Here we examine chromosomal arrangement in representatives of the melanica and the robusta species groups and test these alternative hypotheses using a phylogenetic approach.

Results

Two mitochondrial and two nuclear gene sequences were used to reconstruct phylogenetic relationships of a set of nine ingroup species having fused and unfused sex chromosomes and representing a broad sample of both species groups. Different methods of phylogenetic inference, coupled with concurrent cytogenetic analysis, indicate that the hypothesis of independent origins of rearranged sex chromosomes within each species group is significantly more likely than the alternative hypothesis of a single common origin. An estimate tightly constrained around 8 My was obtained for the age of the rearranged sex chromosomes in the melanica group; however, a more loosely constrained estimate of 10–15 My was obtained for the age of the rearrangement in the robusta group.

Conclusion

Independent acquisition of new chromosomal arms by the sex chromosomes in the melanica and robusta species groups represents a case of striking convergence at the karyotypic level. Our findings indicate that the parallel divergence experienced by newly sex-linked genomic regions in these groups represents an excellent system for studying the tempo of sex chromosome evolution.

Taxonomic problems in the Drosophila melanica species group (Diptera: Drosophilidae) from Southern China, with special reference to karyotypes and reproductive isolation

Karyotypes and reproductive isolation were studied in two allopatric populations of Drosophila tsigana, one from Guizhou Province in southern China and the other from Hokkaido in northern Japan, and in one population of a closely related species, D. longiserrata, from Guizhou. In metaphase plates of larval brain cells, both geographic strains of Drosophila tsigana showed 2n=10 chromosomes, with 2 pairs of metacentric (V-shape), 2 pairs of acrocentric (R-shape), and 1 pair of dot-liked (D-shape) chromosomes. Drosophila longiserrata showed the same number, 10 chromosomes, comprising 2V, 1J (sub-metacentric chromosome), 1R, and 1D. X chromosomes of both species were acrocentric, the presumed ancestral form. Premating isolation was complete between D. tsigana and D. longiserrata, and successful mating was also limited in crosses between the two geographic populations of D. tsigana, especially in crosses between Japanese (JP) females and Guizhou (GZ) males. F1 hybrids were obtained only from crosses between GZ females and JP males, and fertilities of both F1 females and males were quite incomplete. The results of morphological observations, karyotypic analyses, and crossing experiments clearly showed that the GZ and JP populations of "D. tsigana" were highly divergent from each other and that each population should be recognized as a biologically valid species. The present morphological observations and chromosomal analyses, together with the original descriptions, strongly suggest that "Guizhou D. tsigana" might be conspecific with D. bisetata Toda, 1988 from Myanmar, and that D. longiserrata might be conspecific with D. afer Tan, Hsu, and Sheng, 1949 from Meitan, Guizhou.