Biochemical phylogenies ofDrosophila: protein differences detected by two-dimensional electrophoresis

Proteomic similarity of the Littorinid snails in the evolutionary context

BACKGROUND

The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.

METHODS

Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation.

RESULTS

Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two Littoraria species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related Littorina fabalis and L. obtusata, possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the Littorina genus) and for genera (Littoraria and Echinolittorina species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five Littorina species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.

RACE FORMATION, SPECIATION, AND INTROGRESSION WITHIN DROSOPHILA SIMULANS, D. MAURITIANA, AND D. SECHELLIA INFERRED FROM MITOCHONDRIAL DNA ANALYSIS

Mitochondrial DNA cleavage maps from three chromosomally homosequential species Drosophila simulans, D. mauritiana, and D. sechellia, were established for 12 restriction enzymes. One isofemale strain was studied in D. sechellia (se), 13 in D. simulans, and 17 in D. mauritiana: in the last two species, respectively, three (siI, II, and III) and two (maI and II) cleavage morphs were found. The evolutionary relationships based on mtDNA cleavage map comparisons show that the maI and se mtDNAs are internal branches of the phylogenetic tree of the D. simulans mtDNA. D. mauritiana and D. sechellia species appear to be derived from a population of D. simulans which carried an ancestral form of the current siI mtDNA type. In addition, two cleavage morphs (siIII [only present in D. simulans from Madagascar] and maI) appeared to be identical, although found in different species. We present a speculative interpretation of data on biogeography and hybridization which is consistent with the hypothesis of a recent introgression of mitochondrial DNA of D. simulans from Madagascar into D. mauritiana.

Morphological comparison among Drosophila lini and its two new sibling species (Diptera: Drosophilidae)

Morphological differences are investigated using several culture strains of three sibling species collected from Taiwan and Guangdong in China and Pyinoolwin and Yangon in Myanmar. Careful examination of male terminalia reveals distinguishable differences in the paramere and the aedeagal basal process among the three species. In addition, a number of quantitative characters are compared. Kruskal-Wallis tests with Bonferroni correction, which are carried out separately for each sex, detect significant differences in 15 characters, of which two are male-specific, among the three species. Canonical discriminant analysis using these characters reveals that the three species can be distinguished from each other with high confidence for both sexes. The results clearly show the presence of three good species, Drosophila (Sophophora) lini Bock & Wheeler, 1972 and its two new siblings. The new species are described as Drosophila (Sophophora) ohnishii sp. nov. from Pyinoolwin and Drosophila (Sophophora) ogumai sp. nov. from Yangon. The morphological differentiation among the three sibling species does not coincide with the degree of reproductive isolation (based on a previous study). The premating isolation pattern suggests two possibilities that premating isolation has been evolved or reinforced in sympatric populations between D. ohnishii and D. lini and between D. ohnishii and D. ogumai or that it has evolved in a very restricted local population of D. ohnishii, possibly by a few mutations.

Protein variability in Meloidogyne spp. (Nematoda:Meloidogynidae) revealed by two-dimensional gel electrophoresis and mass spectrometry

Total protein variation as revealed by two-dimensional electrophoresis (2D-E) was studied in 18 isolates from populations of Meloidogyne arenaria (six isolates), Meloidogyne incognita (10 isolates), and Meloidogyne javanica (one isolate) plus an unclassified isolate. Gels (80 x 60 x 0.75 mm) were silverstained and digitized in order to compare their protein patterns. Optical density and position of protein patterns were measured using statistical cluster analysis and computer-assisted image analysis software. Only those protein stains or positions that were clearly defined (i.e., without background) were considered. The number of positions in gels ranged from 86 to 203. Each of these positions had 95 clearly expressed proteins that were present in at least two replicates for each isolate. Spot position was considered a taxonomical character with two different states: presence (1) and absence (0). Accordingly, genetic distance was estimated among isolates and species, and a phylogenetic tree was constructed following the cladistic approach based on maximum parsimony analysis. Isolates of M. arenaria--M. javanica--Meloidogyne sp. and of M. incognita formed two separate monophyletic groups. Both groups were clearly defined on the basis of two sets of protein positions that can be considered as diagnostic characters. An attempt to identify these proteins by mass spectrometry was made. Group diagnostic proteins for M. incognita and M. arenaria (and for other proteins common to all isolates) were distinguished by protonated mass signals in the MALDI fingerprinting spectrum.

Distance indices in a comparison between the A, D, I and R genomes of the Triticeae tribe

Two-dimensional gel electrophoresis of shoot proteins was used to study the relationships between Triticum, Secale, and Hordeum. A high level of polymorphism was found among the 1275 spots scored: only 198 spots were found common to all. But, under the hypothesis that only allelic variations were observed, the mean number of alleles per locus was only two. Phenograms were built from different distance indices. All of them showed Triticum genomes A and D close to each other, Hordeum far from the Triticum cluster, and Secale at an intermediate position. A discussion on the use of various distance indices is presented.

Two-dimensional protein electrophoretic analysis of postponed aging in Drosophila

Five populations of Drosophila melanogaster that had been selected for postponed aging were compared with five control populations using two-dimensional protein gel electrophoresis. The goals of the study were to identify specific proteins associated with postponed aging and to survey the population genetics of the response to selection. A total of 321 proteins were resolvable per population; these proteins were scored according to their intensity. The resulting data were analyzed using resampling, combinatoric, and maximum parsimony methods. The analysis indicated that the populations with postponed aging were different from their controls with respect to specific proteins and with respect to the variation between populations. The populations selected for postponed aging were more heterogeneous between populations than were the control populations. Maximum parsimony trees separate the selected populations, as a group, from their controls, thereby exhibiting a homoplastic pattern.

Molecular evolution and phylogeny of the Drosophila virilis species group as inferred by two-dimensional electrophoresis

Systematic relationship among the 12 species of the Drosophila virilis species group, and Drosophila robusta, were investigated by the use of two-dimensional electrophoresis (2-DE). A total of 389 protein characters (about 200 loci) were scored and analyzed both phylogenetically and phenetically. The resulting phylogeny was found to be largely concordant with the current views of evolution among these species based on other independent morphological, chromosomal, electrophoretic, and immunological data sets, although some notable differences were observed. The 2-DE data also appeared to be useful for constructing a molecular clock to date the absolute times of divergence among the species. It appears from this analysis that the evolution of the major clades within the species group occurred about 20 million years ago. Previous suggestions that the rate of molecular evolution was different between the virilis and montana phylads was not confirmed. The technique of 2-DE seems to be an excellent tool for reconstructing phylogenies and should be particularly valuable for examining relatively closely related species.

Genetic differentiation of Drosophila melanogaster populations as assessed by two-dimensional electrophoresis

Seven populations of Drosophila melanogaster, representing a worldwide distribution, were compared using two-dimensional protein gel electrophoresis. A total of 611 protein spots was scored, which probably represent a sample of over 500 loci that were surveyed. Of the protein spots scored, 521 spots were found to be invariant, but another 90 spots were found to be variable among the populations. Of these variable protein spots, 12 were found to be present in only one population. All the populations, except one, had at least one protein spot restricted to itself. However, the Japanese population had by far the most, with five protein spots restricted to this one population, which has been observed in previous studies of private alleles in oriental populations. The mean genetic similarity (F) found among the seven populations was 0.965, with a range of between 0.956 and 0.977. This is similar to previous reports of lower variation found in population genetic surveys using two-dimensional electrophoresis. It was found that the historical relationships among these populations was somewhat congruent with the geographic distribution of the populations, but as in previous studies, it was not exactly coincident.

Molecular phylogeny of the subgenus Sophophora of Drosophila derived from large subunit of ribosomal RNA sequences

RNA sequencing has been used to assess the relationships among species of the subgenus Sophophora of the genus Drosophila. Two divergent domains, D1 and D2, of the large ribosomal RNA (28S), totalling 550 nucleotides have been sequenced using the rRNA direct sequencing method. A tree has been reconstructed from the neighbor-joining algorithm and the confidence intervals were evaluated by the bootstrap procedure. Results have shown that the branching of the willistoni and saltans groups of the subgenus Sophophora is very ancient and probably predates that of the subgenus Drosophila. The other groups and subgroups of Sophophora are clustered in three main lineages: 1) the melanogaster and oriental subgroups; 2) the montium subgroup; 3) the ananassae subgroup of the melanogaster group clustered with the fima and obscura groups. Thus, in comparison with our results, several taxa of various ranks appear paraphyletic (the genus Drosophila, the subgenus Sophophora and the melanogaster group). Our biochemical phylogeny is only in partial agreement with the pattern of Throckmorton's radiations as well as with classical taxonomy, both based on morphological data.

Discrepancy in divergence of the mitochondrial and nuclear genomes of Drosophila teissieri and Drosophila yakuba

Restriction sites were compared in the mitochondrial DNA (mtDNA) molecules from representatives of two closely related species of fruit flies: nine strains of Drosophila teissieri and eight strains of Drosophila yakuba. Nucleotide diversities among D. teissieri strains and among D. yakuba strains were 0.07% and 0.03%, respectively, and the nucleotide distance between the species was 0.22%. Also determined was the nucleotide sequence of a 2305-nucleotide pair (ntp) segment of the mtDNA molecule of D. teissieri that contains the noncoding adenine + thymine (A + T)-rich region (1091 ntp) as well as the genes for the mitochondrial small-subunit rRNA, tRNA(f-met), tRNA(gln), and tRNA(ile), and portions of the ND2 and tRNA(Val) genes. This sequence differs from the corresponding segment of the D. yakuba mtDNA by base substitutions at 0.1% and 0.8% of the positions in the coding and noncoding regions, respectively. The higher divergence due to base substitutions in the A + T-rich region is accompanied by a greater number of insertions/deletions than in the coding regions. From alignment of the D. teissieri A + T-rich sequence with those of D. yakuba and Drosophila virilis, it appears that the 40% of this sequence that lies adjacent to the tRNA(ile) gene has been highly conserved. Divergence between the entire D. teissieri and D. yakuba mtDNA molecules, estimated from the sequences, was 0.3%; this value is close to the value (0.22%) obtained from the restriction analysis, but 10 times lower than the value estimated from published DNA hybridization results.(ABSTRACT TRUNCATED AT 250 WORDS)

Biochemical phylogeny of seven Indian species of the montium subgroup of Drosophila

Seven species of the montium subgroup of Drosophila found in South India were analysed with polyacrylamide disc electrophoresis. Eleven loci coding for enzymes were surveyed. The genetic distances between species have been measured. The dendrogram revealed three clusters. The first cluster includes D. nagarholensis, D. agumbensis, D. jambulina and D. kikkawai; the second group consists of D. truncata and D. anomelani; while D. mysorensis was the only species of the third group.

The separation of whale myoglobins with two-dimensional electrophoresis

Five myoglobins (sperm whale, Sei whale, Hubbs' beaked whale, pilot whale, and Amazon River dolphin) were examined using two-dimensional electrophoresis. Previous reports indicated that none of these proteins could be separated by using denaturing (in the presence of 8-9 M urea) isoelectric focusing. This result is confirmed in the present study. However, all the proteins could be separated by using denaturing nonequilibrium pH-gradient electrophoresis in the first dimension. Additionally, all the myoglobins have characteristic mobilities in the second dimension (sodium dodecyl sulfate), but these mobilities do not correspond to the molecular weights of the proteins. We conclude that two-dimensional electrophoresis can be more sensitive to differences in primary protein structure than previous studies indicate and that the assessment seems to be incorrect that this technique can separate only proteins that have a unit charge difference.

Molecular evolution among some Drosophila species groups as indicated by two-dimensional electrophoresis

The evolutionary and phylogenetic relationships of seven Drosophila species groups (represented by D. melanogaster, D. mulleri, D. mercatorum, D. robusta, D. virilis, D. immigrans, D. funebris, and D. melanica) were investigated by the use of two-dimensional electrophoresis. The resulting phylogeny is congruent with the current views of evolution among these groups based on morphological characters and immunological distances. Previous studies indicated that the ability of one-dimensional electrophoresis to resolve relationships between distantly related taxa extended to about the Miocene [25 million years (Myr) ago], but the present study demonstrates that two-dimensional electrophoresis is a useful indicator of phylogeny even back to the Paleocene (65 Myr ago). In addition, two-dimensional electrophoresis is shown to be a useful technique for detecting slowly evolving structural proteins such as actins and tropomyosins.

Biochemical phylogeny of the eight species in the Drosophila melanogaster subgroup, including D. sechellia and D. orena

The phylogenetic relationships of the eight species of the Drosophila melanogaster subgroup are examined on the basis of genetic variation at 33 putative enzyme loci. Values of Nei's genetic distance (ds) range from 0·28 to 1·74. D. sechellia appears closer to D. simulans than to D. mauritiana, the two former being the most closely related. D. orena is quite distantly related to D. erecta (ds = 1). Genetic differentiation supports the existence of three main lineages within the melanogaster subgroup and the yakuba-teissieri pair appears to be closer to the melanogaster lineage than to the erecta-orena one. Inferences of the times of species divergence from allozyme data are made and their agreement to other estimates is discussed.

Amylase gene duplication: an ancestral trait in the Drosophila melanogaster species subgroup

Electrophoretic polymorphism of amylases was studied in 45 geographic populations of the two cosmopolitan sibling species, D. melanogaster and D. simulans, and in one to three populations or strains of six other species in the D. melanogaster subgroup. Two species, D. erecta and D. orena, for which only a few strains were available were monomorphic. In the other species 2 or 3 amylase variants were identified while in D. melanogaster, 12 electrophoretic variants were characterized. Altogether 17 different amylase isozymes have been observed. The contrast in the level of polymorphism between D. melanogaster and the other species cannot be explained simply by the occurrence of a duplication in the former species. Genetic analysis demonstrated the existence of a duplication in at least 4 other species, namely D. simulans, D. mauritiana, D. yakuba, and D. teissieri. It is therefore suggested that the duplication occurred in a common ancestor and the phylogenetic implications of these observations are discussed.

Qualitative and quantitative variability in different classes of proteins: comparison of mouse and rat

Proteins of membranes and cytosols were extracted from the livers and brains of mice (inbred strain DBA/6J) and rats (inbred strain DA/Han) and separated by two-dimensional electrophoresis (2-DE). The 2-DE patterns were compared with regard to qualitative (spot position) and quantitative (spot intensity) characteristics of the proteins of these two species. The following results were obtained: Brain had more (higher percentage) conservative proteins (proteins found in both mice and rats) than liver; plasma membranes had more conservative proteins than the cytosols; organ-unspecific proteins contained more conservative proteins than relatively organ-specific proteins; the pattern of distribution of genetic variability among different classes of proteins represented by findings 1-3 was the same for the qualitative and quantitative characteristics of the proteins; and some observations indicated that quantitative variability occurred more frequently among proteins than did qualitative variability. Our conclusion is that regulatory sequences in the DNA (regulatory genes) are subjected to functional constraints that differ in strength among different classes of proteins by the same ratios as the constraints acting on the structural genes. The overall effect of the selective pressure is, however, less stringent for regulatory genes than for structural genes. The results obtained here by comparing two different species are very similar to previous results we obtained by studying different subspecies (inbred strains of the mouse). From this finding arises a new concept: the study of molecular evolution on the basis of different classes of proteins. Our results were compared with data from the literature that were obtained in part from studies on cultured cells. The comparison suggested that cultured cells have lost their tissue-specific proteins, and so generate predominantly extremely conservative proteins.

Genomic blot hybridization as a tool of phylogenetic analysis: evolutionary divergence in the genus Drosophila

Comparative, quantitative Southern analysis of genomic DNA, using single-copy sequence probes, potentially is valuable for phylogenetic analysis. We have examined 27 Drosophila species, belonging to two subgenera, seven species groups, and ten subgroups, using a variety of cloned and characterized probes: twelve cloned sequences from D. melanogaster, two from D. pseudoobscura, and two from D. grimshawi. The data are generally congruent with accepted phylogenetic relationships in Drosophila, and confirm or clarify some previously uncertain relationships. The potential and limitations of the method are discussed.

Location of an X-linked factor causing sterility in male hybrids of Drosophila simulans and D. mauritiana

We report the first mapping of a genetic factor responsible for reproductive isolation: a small segment of genome strongly affecting sperm motility in hybrids between the sibling species Drosophila simulans and D. mauritiana. Maximum-likelihood analysis of data from ten generations of backcrossing places this factor at 1.1 +/- 0.2 map units from the forked locus, at position 54.9 +/- 0.2 or 57.1 +/- 0.2 on the X chromosome.

Mitochondrial DNA evolution in the melanogaster species subgroup of Drosophila

Detailed restriction maps (40 cleavage sites on average) of mitochondrial DNAs (mtDNAs) from the eight species of the melanogaster species subgroup of Drosophila were established. Comparison of the cleavage sites allowed us to build a phylogenetic tree based on the matrix of nucleotide distances and to select the most parsimonious network. The two methods led to similar results, which were compared with those in the literature obtained from nuclear characters. The three chromosomally homosequential species D. simulans, D. mauritiana, and D. sechellia are mitochondrially very related, but exhibit complex phylogenetic relationships. D. melanogaster is their closest relative, and the four species form a monophyletic group (the D. melanogaster complex), which is confirmed by the shared unusual length of their mt genomes (18-19 kb). The other four species of the subgroup (D. yakuba, D. teissieri, D. erecta, and D. orena) are characterized by a much shorter mt genome (16-16.5 kb). The monophyletic character of the D. yakuba complex, however, is questionable. Two species of this complex, D. yakuba and D. teissieri, are mitochondrially indistinguishable (at the level of our investigation) in spite of their noticeable allozymic and chromosomal divergence. Finally, mtDNA distances were compared with the nuclear-DNA distances thus far established. These sequences seem to evolve at rather similar rates, the mtDNA rate being barely double that of nuclear DNA.

Genetic studies of three sibling species of Drosophila with relationship to theories of speciation

Drosophila melanogaster,D. simulansandD. mauritianaare closely related species, the first two cosmopolitan and the last restricted to the oceanic island of Mauritius.D. simulansandD. mauritianaare the most closely related pair, with the latter species probably resulting from a founder event. The relatedness of the three species and their ability to hybridize allow tests of recent theories of speciation. Genetic analysis of two characters differing betweenD. simulansandD. mauritiana(sex comb tooth number and testis colour) show that the differences are due to at least five and three loci respectively. Behavioural tests further demonstrate that sex combs are probably used by males at a crucial step in mating, and that the differences between the two species may be related to differences in their mating ability. These genetic studies and previous work indicate that differences among these species are polygenic and not (as proposed by recent theories) attributable to only one or two loci of large effect. Further studies of interspecific hybrids show that genetic divergence leading to developmental anomalies is more advanced in the older species pairD. simulans/D. melanogaeterthan in the younger pairD. simulans/D. mauritiana. This supports the neo-Darwinian contention that reproductive isolation is one step in a continuous process of genetic change among isolated populations, and does not support current theories that such change occurs only during the evolution of reproductive isolation. Finally, investigations of the degree of gonadal atrophy and its sensitivity to temperature inD. simulans/D. mauritianahybrids fail to support recent speculations that phenomena similar to hybrid dysgenesis (which causes such atrophy inD. melanogaster) play a role in speciation.

Conservation and change in the DNA sequences coding for alcohol dehydrogenase in sibling species of Drosophila

The DNA sequences of the alcohol dehydrogenase (Adh) genes of four very closely related species of Drosophila show that the rates of nucleotide change vary greatly in different functional domains of this gene. A phylogeny of these species based on the Adh sequence data is consistent with that based on polytene chromosome banding patterns.