Mitochondrial DNA sequence divergence in the Melanogaster and oriental species subgroups of Drosophila

Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences

Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution.

Comparative genomics of Drosophila mtDNA: Novel features of conservation and change across functional domains and lineages

To gain insight on mitochondrial DNA (mtDNA) evolution, we assembled and analyzed the mitochondrial genomes of Drosophila erecta, D. ananassae, D. persimilis, D. willistoni, D. mojavensis, D. virilis and D. grimshawi together with the sequenced mtDNAs of the melanogaster subgroup. Genomic comparisons across the well-defined Drosophila phylogeny impart power for detecting conserved mtDNA regions that maintain metabolic function and regions that evolve uniquely on lineages. Evolutionary rate varies across intergenic regions of the mtDNA. Rapidly evolving intergenic regions harbor the majority of mitochondrial indel divergence. In contrast, patterns of nearly perfect conservation within intergenic regions reveal a refined set of nucleotides underlying the binding of transcription termination factors. Sequencing of 5' cDNA ends indicates that cytochrome C oxidase I (CoI) has a novel (T/C)CG start codon and that perfectly conserved regions upstream of two NADH dehydrogenase (ND) genes are transcribed and likely extend these protein sequences. Substitutions at synonymous sites in the Drosophila mitochondrial proteomes reflect a mutation process that is biased toward A and T nucleotides and differs between mtDNA strands. Differences in codon usage bias across genes reveal that weak selection at silent sites may offset the mutation bias. The mutation-selection balance at synonymous sites has also diverged between the Drosophila and Sophophora lineages. Rates of evolution are highly heterogeneous across the mitochondrial proteome, with ND accumulating many more amino acid substitutions than CO. These oxidative phosphorylation complex-specific rates of evolution vary across lineages and may reflect physiological and ecological change across the Drosophila phylogeny.

Phylogenetic incongruence in the Drosophila melanogaster species group

Drosophila melanogaster and its close relatives are used extensively in comparative biology. Despite the importance of phylogenetic information for such studies, relationships between some melanogaster species group members are unclear due to conflicting phylogenetic signals at different loci. In this study, we use twelve nuclear loci (eleven coding and one non-coding) to assess the degree of phylogenetic incongruence in this model system. We focus on two nodes: (1) the node joining the Drosophila erecta-Drosophila orena, Drosophila melanogaster-Drosophila simulans, and Drosophila yakuba-Drosophila teissieri lineages, and (2) the node joining the lineages leading to the melanogaster, takahashii, and eugracilis subgroups. We find limited evidence for incongruence at the first node; our data, as well as those of several previous studies, strongly support monophyly of a clade consisting of D. erecta-D. orena and D. yakuba-D. teissieri. By contrast, using likelihood based tests of congruence, we find robust evidence for topological incongruence at the second node. Different loci support different relationships among the melanogaster, takahashii, and eugracilis subgroups, and the observed incongruence is not easily attributable to homoplasy, non-equilibrium base composition, or positive selection on a subset of loci. We argue that lineage sorting in the common ancestor of these three subgroups is the most plausible explanation for our observations. Such lineage sorting may lead to biased estimation of tree topology and evolutionary rates, and may confound inferences of positive selection.

Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting

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.

To take full advantage of the growing number of genome sequences from different organisms, it is necessary to understand the evolutionary relationships (phylogeny) between organisms. Unfortunately, phylogenies inferred from individual genes often conflict, reflecting either poor inferences or real variation in the history of genes. In this study, the authors examine relationships within the Drosophila melanogaster species subgroup, a group of flies with three fully sequenced species in which phylogeny has been a source of controversy. Although the bulk of the data support a phylogeny with Drosophila melanogaster as an outgroup to sister species Drosophila erecta and Drosophila yakuba, large portions of their genes support alternative phylogenies. According to the authors, the most plausible explanation for these observations is that polymorphisms in the ancestral population were maintained during the two rapid speciation events that led to these species. Subsequent to speciation, polymorphisms were randomly fixed in each species, and in some cases non-sister species fixed the same ancestral polymorphisms, while sister species did not. In these cases the genes are correctly inferred to have conflicting phylogenies. The authors note that rapid speciation events will often lead to such conflict, which needs to be accounted for in evolutionary analyses.

The phylogeny of the subgroups within the melanogaster species group: likelihood tests on COI and COII sequences and a Bayesian estimate of phylogeny

The relationships among the majority of the subgroups in the Drosophila melanogaster species group remain unresolved. We present a 2223basepair dataset for mitochondrial cytochrome oxidase I and cytochrome oxidase II for 43 species (including new data from 11 species), sampled to include the major subgroups. After a brief review of competing hypotheses for the ananassae, montium, suzukii, and takahashii subgroups, we combine the two genes based on a new use of the SH test and present KH and SH likelihood comparisons (Kishino and Hasegawa, 1989. J. Mol. Evol. 29, 170-179; Shimodaira and Hasegawa, 1999) to test the monophyly and placement of these subgroups within the larger species group. Although we find insignificant differences between the two suggested placements for the ananassae subgroup, the ananassae is sister to the rest of the subgroups in the melanogaster species group in every investigation. For the takahashii subgroup, although we cannot reject monophyly, the species are so closely related to the suzukii subgroup for these data that the two subgroups often form one clade. Finally, we present a Bayesian estimate of the phylogeny for both genes combined, utilizing a recently published method that allows for different models of evolution for different sites.

Molecular phylogeny of the Drosophila melanogaster species subgroup

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.

Macroevolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences

The phylogenetic relationships among the Drosophila melanogaster group species were analyzed using approximately 1700 nucleotide-long sequences of the mitochondrial DNA. Phylogenetic analysis was performed using this region consisting of a part of the cytochrome b (cytb) coding gene, the entire coding sequences of tRNA-Leu, tRNA-Ser and the first subunit of NADH dehydrogenase (NADH1), and a part of the 16S-rRNA gene. The study of these sequences showed that this region of mtDNA is very invariable, as regards with the type of the genes that it contains, as well as the order that they are located on it. The resulting phylogenetic trees reveal a topology that separates the species into three main ancestral lines, leading to the following subgroups: (a) ananassae subgroup, (b) montium subgroup, and (c) melanogaster and Oriental subgroups. The inferred topology complements and generally agrees with previously proposed classifications based on morphological and molecular data.

Molecular approaches to the study of myiasis-causing larvae

Among arthropod diseases affecting animals, larval infections - myiases - of domestic and wild animals have been considered important since ancient times. Besides the significant economic losses to livestock worldwide, myiasis-causing larvae have attracted the attention of scientists because some parasitise humans and are of interest in forensic entomology. In the past two decades, the biology, epidemiology, immunology, immunodiagnosis and control methods of myiasis-causing larvae have been focused on and more recently the number of molecular studies have also begun to increase. The 'new technologies' (i.e. molecular biology) are being used to study taxonomy, phylogenesis, molecular identification, diagnosis (recombinant antigens) and vaccination strategies. In particular, more in depth molecular studies have now been performed on Sarcophagidae, Calliphoridae and flies of the Oestridae sister group. This review discusses the most topical issues and recent studies on myiasis-causing larvae using molecular approaches. In the first part, PCR-based techniques and the genes that have already been analysed, or are potentially useful for the molecular phylogenesis and identification of myiasis-causing larvae, are described. The second section deals with the more recent advances concerning taxonomy, phylogenetics, population studies, molecular identification, diagnosis and vaccination.

Changes in the recombinational environment affect divergence in the yellow gene of Drosophila

The complete coding region of the yellow (y) gene was sequenced in different Drosophila species. In the species of the melanogaster subgroup (D. melanogaster, D. simulans, D. mauritiana, D. yakuba, and D. erecta), this gene is located at the tip of the X chromosome in a region with a strong reduction in recombination rate. In contrast, in D. ananassae (included in the ananassae subgroup of the melanogaster group) and in the obscura group species (D. subobscura, D. madeirensis, D. guanche, and D. pseudoobscura), the y gene is located in regions with normal recombination rates. As predicted by the hitchhiking and background selection models, this change in the recombinational environment affected synonymous divergence in the y-gene-coding region. Estimates of the number of synonymous substitutions per site were much lower between the obscura group species and D. ananassae than between the species of the obscura group and the melanogaster subgroup. In fact, a highly significant increase in the rate of synonymous substitution was detected in all lineages leading to the species of the melanogaster subgroup relative to the D. ananassae lineage. This increase can be explained by a higher fixation rate of mutations from preferred to unpreferred codons (slightly deleterious mutations). The lower codon bias detected in all species of the melanogaster subgroup relative to D. ananassae (or to the obscura group species) would be consistent with this proposal. Therefore, at least in Drosophila, changes in the recombination rate in different lineages might cause deviations of the molecular-clock hypothesis and contribute to the overdispersion of the rate of synonymous substitution. In contrast, the change in the recombinational environment of the y gene has no detectable effect on the rate of amino acid replacement in the Yellow protein.

Differentiation by polymerase chain reaction - restriction fragment length polymorphism of some Oestridae larvae causing myiasis

The cytochrome oxidase I (COI) gene of the most wide-spread Italian species of Oestridae larvae causing myiasis (Gasterophilus spp., Hypoderma bovis, Hypoderma lineatum, Oestrus ovis and Przhevalskiana silenus) was amplified by polymerase chain reaction (PCR) using conserved primers. Restriction fragment length polymorphism (RFLP) of amplicons was also carried out and their restriction profiles compared. A clear genetic difference between the Oestridae larvae examined was demonstrated by using Taq(alpha) I, Hinf I, Rsa I and Hpa II enzymes. No intra-specific variation in RFLPs was detected between the two species of Hypoderma. The results highlight the taxonomic and phylogenetic relationships among larvae belonging to the different subfamilies, and thus offer additional diagnostic and epidemiological instruments.

Phylogenetic relationships and climatic adaptations in the Drosophila takahashii and montium species subgroups

We analyze phylogenetic relationships among temperate, subtropical highland, and subtropical lowland species of the Drosophila takahashii and montium species subgroups based on sequence data of COI and Gpdh genes and discuss the evolution of temperate species in these subgroups with reference to their climatic adaptations. In the takahashii subgroup, D. lutescens (the temperate species) branched off first in the tree based on the combined data set, but D. prostipennis (the subtropical highland species) branched off first in the trees based on single genes. Thus, phylogenetic relationships in this subgroup are still ambiguous. In the montium subgroup, the cool-temperate species are phylogenetically close to the warm-temperate species, and these cool- and warm-temperate species form a cluster with the subtropical highland species. This suggests that perhaps the cool-temperate species derived from the warm-temperate species and the warm-temperate species derived from the subtropical highland species. In comparison with the subtropical lowland species, the subtropical highland species may be better able to colonize temperate areas since, as in the temperate species, they have an ability to develop their ovaries at moderately low temperature. However, the subtropical highland species, as well as the subtropical lowland species, were much less cold tolerant than the temperate species. Therefore, considerable genetic reformation would be required for both the subtropical highland and the subtropical lowland species to adapt to temperate climates.

Rhodinocichla rosea is an emberizid (Aves; Passeriformes) based on mitochondrial DNA analyses

The systematic position of the avian species Rhodinocichla rosea is unclear. Recent opinions are that it is either a mockingbird (family Mimidae) or a tanager (Thraupinae; Emberizidae). In either case, it would be an atypical member of the family. We sequenced approximately 600 bases of the mitochondrial cytochrome oxidase I (COI) gene of Rhodinocichla, several mimids, tanagers, and other passerines. We used maximum likelihood (ML), distance and parsimony approaches to analyze the sequences and concluded that Rhodinocichla belongs to the family Emberizidae. Phenotypic characteristics that suggested its relationship with mimids are the product of convergent evolution. The precise relationships of Rhodinocichla within the Emberizidae could not be resolved. Short internal branches in ML and distance trees suggested, as did earlier genetic studies, that the radiation of that family was explosive. Apparently, the extent of the tanagers as a higher taxon needs to be clarified. Our analysis of the evolutionary dynamics of avian COI suggested that its usefulness for phylogenetic studies is limited because silent positions saturate rapidly and replacement substitutions are rare. Thus, our data indicate that COI nucleotide data will be most useful in intraspecific investigations, while other data suggested its usefulness at the interordinal level.

Assessment of the universality and utility of a set of conserved mitochondrial COI primers in insects

A set of mitochondrial COI primers has been studied by genomic PCR and many primer combinations shown to work universally well across Insecta. They are able to amplify various amplicons with different variability which enables the selection of a particular amplicon as a suitable DNA marker for a project. The potential usefulness of different amplicons is examined, with analysis on published study cases employing these regions. With respect to their variability, amplicons UEA5/UEA6, UEA7/UEA8 and UEA5/UEA8 could be useful for low- to mid-level phylogenetic analysis, i.e. from species, genus to perhaps family level depending on taxa involved. UEA5/UEA6 will be too conserved for intraspecific studies. Amplicons UEA3/UEA4 and UEA9/UEA10 would be better suited to low-level phylogenetic investigations, such a analysis of relationships among closely related species and population genetic studies. However, these guidelines should not be over-generalized for the reasons given. Amplification conditions of various primer combinations, and general problems in the use of conserved PCR primers are discussed.

Speciation in the Artemia genus: mitochondrial DNA analysis of bisexual and parthenogenetic brine shrimps

From the cloned mitochondrial DNAs (mtDNAs) isolated from two bisexual species, one Mediterranean, Artemia salina, and one American, Artemia franciscana, and two parthenogenetic (diploid and tetraploid) strains of Artemia parthenogenetica collected in Spain, physical maps have been constructed and compared. They are extremely different among themselves, much more than the differences between Drosophila melanogaster and D. yakuba and in the same range of different mammalian species such as mouse/rat or man/cow. The nucleotide sequences of two regions of mtDNA encoding parts of the cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) genes have been determined in the two bisexual species and the two parthenogenetic strains. Comparisons of these sequences have revealed a high degree of divergence at the nucleotide level, averaging more than 15%, in agreement with the differences found in the physical maps. The majority of the nucleotide changes are silent and there is a strong bias toward transitions, with the C<==>T substitutions being highly predominant. The evolutionary distance between the two Artemia parthenogenetica is high and there is no clear relationship with any of the bisexual species, including the one present nowadays in Spain. Using a combination of molecular (mtDNA) and morphological markers it is possible to conclude that all of these Artemia isolates should be actually considered as belonging to different species, even the two Artemia parthenogenetica diploidica and tetraploidica.