Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species

<p>Abstract</p> <p>Background</p> <p>Species of the <it>Drosophila obscura </it>species group (e.g., <it>D. pseudoobscura</it>, <it>D. subobscura</it>) have served as favorable models in evolutionary studies since the 1930's. Despite numbers of studies conducted with varied types of data, the basal phylogeny in this group is still controversial, presumably owing to not only the hypothetical 'rapid radiation' history of this group, but also limited taxon sampling from the Old World (esp. the Oriental and Afrotropical regions). Here we reconstruct the phylogeny of this group by using sequence data from 6 loci of 21 species (including 16 Old World ones) covering all the 6 subgroups of this group, estimate the divergence times among lineages, and statistically test the 'rapid radiation' hypothesis.</p> <p>Results</p> <p>Phylogenetic analyses indicate that each of the <it>subobscura</it>, <it>sinobscura</it>, <it>affinis</it>, and <it>pseudoobscura </it>subgroups is monophyletic. The <it>subobscura </it>and <it>microlabis </it>subgroups form the basal clade in the <it>obscura </it>group. Partial species of the <it>obscura </it>subgroup (the <it>D. ambigua</it>/<it>D. obscura</it>/<it>D. tristis </it>triad plus the <it>D. subsilvestris</it>/<it>D. dianensis </it>pair) forms a monophyletic group which appears to be most closely related to the <it>sinobscura </it>subgroup. The remaining basal relationships in the <it>obscura </it>group are not resolved by the present study. Divergence times on a ML tree based on mtDNA data are estimated with a calibration of 30–35 Mya for the divergence between the <it>obscura </it>and <it>melanogaster </it>groups. The result suggests that at least half of the current major lineages of the <it>obscura </it>group originated by the mid-Miocene time (~15 Mya), a time of the last developing and fragmentation of the temperate forest in North Hemisphere.</p> <p>Conclusion</p> <p>The <it>obscura </it>group began to diversify rapidly before invading into the New World. The <it>subobscura </it>and <it>microlabis </it>subgroups form the basal clade in this group. The <it>obscura </it>subgroup is paraphyletic. Partial members of this subgroup (<it>D. ambigua</it>, <it>D. obscura</it>, <it>D. tristis</it>, <it>D. subsilvestris</it>, and <it>D. dianensis</it>) form a monophyletic group which appears to be most closely related to the <it>sinobscura </it>subgroup.</p

The evolution of euhermaphroditism in caridean shrimps: a molecular perspective of sexual systems and systematics

<p>Abstract</p> <p>Background</p> <p>The hippolytid genus <it>Lysmata </it>is characterized by simultaneous hermaphroditism, a very rare sexual system among Decapoda. Specialized cleaning behavior is reported in a few pair-living species; these life history traits vary within the genus. Unfortunately, the systematics of <it>Lysmata </it>and the Hippolytidae itself are in contention, making it difficult to examine these taxa for trends in life history traits. A phylogeny of <it>Lysmata </it>and related taxa is needed, to clarify their evolutionary relationships and the origin of their unique sexual pattern. In this study, we present a molecular phylogenetic analysis among species of <it>Lysmata</it>, related genera, and several putative hippolytids. The analysis is based upon DNA sequences of two genes, 16S mtDNA and nuclear 28S rRNA. Phylogenetic trees were estimated using Bayesian Inference, Maximum Likelihood, and Maximum Parsimony.</p> <p>Results</p> <p>Phylogenetic analysis of 29 species of <it>Lysmata</it>, eight genera of Hippolytidae and two genera of Barbouriidae based on a single (16S, 28S) and combined gene approach (16S+28S) indicates that three groups of <it>Lysmata </it>differentiate according to antennular morphology: (1) <it>Lysmata</it>, having a multi-segmented accessory branch, (2) <it>Hippolysmata </it>(prior to Chace 1972), with a one-segmented accessory branch, and (3) a third group of <it>Lysmata </it>outliers, with one-segmented unguiform accessory branch, and close affinity to the genera <it>Exhippolysmata </it>and <it>Lysmatella</it>. The monophyly of the clade bearing a multi-segmented accessory branch is robust. Within the short accessory branch clade, species with specialized cleaning behaviors form a monophyletic clade, however, the integrity of the clade was sensitive to alignment criteria. Other hippolytid and barbouriid genera used in the analysis are basal to these three groups, including one displaying simultaneous hermaphroditism (<it>Parhippolyte</it>). The two barbouriid species occur in a separate clade, but among hippolytid taxa.</p> <p>Conclusions</p> <p>The data support the historical morphological division of <it>Lysmata </it>into clades based on accessory branch morphology. The position of the "cleaner" shrimps, indicates that specialized cleaning behavior is a derived trait. The topologies of the cladograms support the monophyly of the barbouriids, but do not support their elevation to familial status. Taxa ancestral to the genus <it>Lysmata </it>display simultaneous hermaphroditism, suggesting that this life history trait evolved outside the genus <it>Lysmata</it>.</p

Phylogeny of the Drosophila immigrans species group (Diptera : Drosophilidae) based on Adh and Gpdh sequences

The immigrans species group in the Drosophilinae is one of the representative species groups of Drosophila in East Asia. Although this group constitutes a significant part of the drosophilid fauna in the Old World, only a few species have been analyzed in previous molecular phylogenetic studies. To study the phylogeny of the immigrans group, we analyzed the nucleotide sequences of two nuclear genes, alcohol dehydrogenase (Adh) and glycerol-3-phosphate dehydrogenase (Gpdh), for 36 drosophilid species, including 12 species of the immigrans group. In the resultant phylogenetic trees, 10 species of the immigrans group (D. immigrans, D. formosana, D. ruberrima, D. albomicans, D. nasuta, D. neonasuta, D. pallidifrons, D. hypocausta, D. neohypocausta, D. siamana) consistently formed a clade (the immigrans group proper), although the phylogeny within this clade did not exactly correspond to the classification of species subgroups. However, D. annulipes and D. quadrilineata, both of which belong to the quadrilineata subgroup of the immigrans group, were not included in the immigrans group proper. Furthermore, we obtained the unexpected result that D. annulipes was included in a clade comprising Scaptomyza and Hawaiian Drosophila, together with D. maculinotata of the funebris group, although the phylogenetic relationships within this clade remain uncertain and need to be substantiated with further studies. Thus, according to the present study, the immigrans group is polyphyletic

Diversity and host associations of parasitoids attacking mycophagous drosophilids (Diptera: Drosophilidae) in northern and central Japan

The diversity and host associations of parasitoids attacking mycophagous drosophilids were studied in Tokyo (a warm-temperate region) and Sapporo (a cool-temperate region) in Japan. Field collections were carried out using traps baited with mushrooms in May, June, September and October 2009 in Tokyo and in July and August 2010 in Sapporo. The major drosophilid species that emerged from mushroom baits was Drosophila bizonata in Tokyo and D.orientacea in Sapporo. In total, 13 parasitoid species emerged from drosophilids occurring in mushroom baits, and 11 of them were larval parasitoids belonging to Braconidae and Figitidae. Among the 11 larval parasitoids, 10 were collected in Tokyo, while only two were collected in Sapporo. It is not known why their diversity differed so much between these two regions. Four of the 11 larval parasitoids have also been recorded from drosophilid larvae occurring in fruit (banana). The use of these two habitats (mushrooms and fruit) by these four species seems to reflect the occurrence (i.e. resource use) of their suitable hosts. On the other hand, most larval parasitoids from Tokyo attacked D.bizonata, and two larval parasitoids from Sapporo attacked D.orientacea, suggesting that the abundance of potential hosts is one of the important factors affecting their host use

A Novel Chimeric Gene, siren, With Retroposed Promoter Sequence in the Drosophila bipectinata Complex

Retrotransposons often produce a copy of host genes by their reverse transcriptase activity operating on host gene transcripts. Since transcripts normally do not contain promoter, a retroposed gene copy usually becomes a retropseudogene. However, in Drosophila bipectinata and a closely related species we found a new chimeric gene, whose promoter was likely produced by retroposition. This chimeric gene, named siren, consists of a tandem duplicate of Adh and a retroposed fragment of CG11779 containing the promoter and a partial intron in addition to the first exon. We found that this unusual structure of a retroposed fragment was obtained by retroposition of nanos, which overlaps with CG11779 on the complementary strand. The potential of retroposition to produce a copy of promoter and intron sequences in the context of gene overlapping was demonstrated

Replication Origin of Mitochondrial DNA in Insects

The precise position of the replication origin (O(R)) of mtDNA was determined for insect species belonging to four different orders (four species of Drosophila, Bombyx mori, Triborium castaneum, and Locusta migratoria, which belong to Diptera, Lepidoptera, Coleoptera, and Orthoptera, respectively). Since the free 5′ ends of the DNA strands of mtDNA are interpreted as the O(R), their positions were mapped at 1-nucleotide resolution within the A + T-rich region by using the ligation-mediated PCR method. In all species examined, the free 5′ ends were found within a very narrow range of several nucleotides in the A + T-rich region. For four species of Drosophila, B. mori, and T. castaneum, which belong to holometabolous insects, although the O(R)'s were located at different positions, they were located immediately downstream of a series of thymine nucleotides, the so-called T-stretch. These results strongly indicate that the T-stretch is involved in the recognition of the O(R) of mtDNA at least among holometabolous insects. For L. migratoria (hemimetabolous insect), on the other hand, none of the long stretches of T's was found in the upstream portion of the O(R), suggesting that the regulatory sequences involved in the replication initiation process have changed through insect evolution

Evolutionary Genetics of the Drosophila montium Subgroup. II. Mitochondrial DNA Variation

Volume: 10Start Page: 991End Page: 99

Two Cryptic Species of the Phytophagous Ladybird Beetle Epilachna vigintioctopunctata (Coleoptera: Coccinellidae) Detected by Analyses of Mitochondrial DNA and Karyotypes, and Crossing Experiments

Analyses of a part of mitochondrial cytochrome c oxidase I gene sequences (645 bp) for seventeen individuals of Epilachna vigintioctopunctata (Fabricius) from eight localities in east and southeast Asia revealed that the populations are divided into two genetically distinct groups (Chiba, Tokyo, Naha, Iriomote, Bangkok vs. Kuala Lumpur, Padang, Bogor). The number of nucleotide substitutions between sequences of different groups was 57–60, while that between sequences within each group was 1–8. Karyotypes of the two groups were also distinctly different. Crossing experiments showed that there exist strong postmating barriers between the two groups: eggs obtained from between-group crossings usually did not hatch, whereas more than 90% of eggs from within-group crossings hatched. It is concluded that E. vigintioctopunctata, a notorious pest of solanaceous crops in Asia and Australia, is composed of at least two reproductively isolated biological species that probably occupy different geographic ranges

Molecular Phylogeny of Twelve Asian Species of Epilachnine Ladybird Beetles (Coleoptera, Coccinellidae) with Notes on the Direction of Host Shifts

We determined the nucleotide sequences of a part of the mitochondrial cytochrome c oxidase I gene (1,000 bp) for twelve species of Asian phytophagous ladybird beetles belonging to the genus Epilachna, and constructed molecular phylogenetic trees for ten "Henosepilachna" species, using two "Epilachna" species as outgroups. Based on the suggested phylogenetic trees, we discussed taxonomic issues and the direction of host shift in these epilachnines