Molecular phylogeny of the <Emphasis Type="Italic">Drosophila obscura</Emphasis> species group,with emphasis on the Old World species

Background  

Species of the Drosophila obscura species group (e.g., D. pseudoobscura, D. subobscura) 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.     

A method for numbering binary rooted and unrooted phylogenies and their hypothetical taxonomic units

A set of 2n−2 relations (edges) and a set ofn−1 hypothetical taxonomic units (HTUs) derive from the estimation of a binary phylogeny of a set ofn operational taxonomic units (OTUs). We propose an easy way for numbering thesen−1 hypothetical taxonomic units, as well as for then−2 interior points of an unrooted binary phylogeny. We also present an alternative method to the one proposed by Rohlf (Bull. math. Biol. 45, 33–40, 1983) for numbering the π _i=1 ⁿ (2i−3) possible rooted binary phylogenies and the π _i=1 ⁿ⁻¹ (2i−3) possible unrooted binary phylogenies conerning a set ofn operational taxonomic units. An illustrative example of the method is presented. It is hoped that some studies in phylogenetics will become more accessible, from the viewpoint of computational economy, by the use of this method.     

H2 as an energy source for mixotrophic acetogenesis from the reduction of CO2 and syringate by Acetobacterium woodii and Eubacterium limosum

Acetobacterium woodii and Eubacterium limosum were grown in a defined medium or suspended in buffer containing syringate as the sole organic carbon source to test whether H₂ would support acetogenesis from a phenylmethylether and CO₂. When growing and resting cell preparations were incubated under various headspace gas compositions, consistent O-demethylation activity and growth were observed on syringate-CO₂ when H₂ served as the sole energy source. However, the dependency for H₂ was relieved by addition of yeast extract. A hypothetical scheme representing hydrogenolytic (reductive) O-demethylation and mixotrophic acetogenesis is proposed in light of these results and other literature observations.     

CHROMOSOME NUMBERS IN THE LEGUMINOSAE II: AFRICAN SPECIES,INCLUDING PHYLETIC INTERPRETATIONS

Turner , B. L., and O. S. Fearing . (U. Texas, Austin.) Chromosome numbers in the Leguminosae. II. African species, including phyletic interpretations. Amer. Jour. Bot. 46(1) : 49-57. Illus. 1959.—Chromosome numbers for 30 African legume species have been reported. These include first reports for 28 taxa, including 12 genera (Bolusanthus, Calpurnia, Melolobium, Lessertia, Sulherlandia, Colophospermum, Guibourtia, Burkea, Julbernardia, Schotia, Piliostigma and Swartzia). The counts are discussed with respect to those previously reported for related groups, and this chromosomal information was used to construct hypothetical phyletic lines at the tribal level within the subfamilies Papilionoideae and Caesalpinioideae. A phyletic scheme for the Leguminosae (excluding the Mimosoideae) based on this evidence from chromosome studies is presented. Notable departures from previously suggested phyletic treatments include: (1) Suggestion for inclusion of genera of the Galegeae and Hedysareae with base numbers of x = 10 and 11 with the Phaseoleae and Dalbergieae. (2) Derivation of the Papilionoideae through caesalpinoid prototypes, possibly from Swartzia-like ancestors. (3) Recognition of several very old chromosomal lines stemming from the subfamily Caesalpinioideae, and the suggestion that parts of the tribes Sclerolobieae, Cynometreae, Swartzieae and Sophoreae are, perhaps, more closely related to each other and to the Papilionoideae than they are to the remaining caesalpinoid tribal lines.     

Sequence analysis of a polymorphic Mhc class II gene in Pacific salmon

Polymorphism of the nucleotide sequences encoding 149 amino acids of linked major histocompatibility complex (Mhc) class II 131 and 132 peptides, and of the intervening intron (548–773 base pairs), was examined within and among seven Pacific salmon (Oncorhynchus) species. Levels of nucleotide diversity were higher for theB1 sequence than forB2 or the intron in comparisons both within and between species. For the codons of the peptide binding region of the BI sequence, the level of nonsynonymous nucleotide substitution (d_N) exceeded the level of synonymous substitution (d_S) by a factor of ten for within-species comparisons, and by a factor of four for between-species comparisons. The excess of d_N indicates that balancing selection maintains diversity at this salmonidMhc class II locus, as is common forMhc loci in other vertebrates. Levels of nucleotide diversity for both the exon and intron sequences were greater among than within species, and there were numerous species-specific nucleotides present in both the coding and noncoding regions. Thus, neighbor-joining analysis of both the intron and exon regions provided phylogenies in which the sequences clustered strongly by species. There was little evidence of shared ancestral (trans-species) polymorphism in the exon phylogeny, and the intron phylogeny depicted standard relationships among the Pacific salmon species. The lack of shared allelicB1 lineages in these closely related species may result from severe bottlenecks that occurred during speciation or during the ice ages that glaciated the rim of the north Pacific Ocean approximately every 100 000 years in the Pleistocene.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers U34692-U34720     

CHROMOSOME NUMBERS IN THE PHASEOLEAE (FABACEAE:FABOIDEAE) AND THEIR RELATION TO TAXONOMY

Chromosome numbers are reported for 33 species of the tribe Phaseoleae. Six reports are first counts for their species; one report (Ophrestia hedysaroides) is a first count for the genus. This increases the number of genera counted to 53 out of a total 84 for the tribe. A survey of base numbers shows a general pattern of numbers 10 or 11, the same base numbers as in the neighboring tribes Dalbergieae sensu lato, Galegeae sensu lato, and Abreae. The chromosomes are generally small and polyploidy is uncommon. Deviations from base numbers 10 or 11 are mostly found in those genera with morphological pecularities and puzzling taxonomic placements: Erythrina (21), Clitoria (8, 11, 12), Butea (9), Calopogonium (18), Teramnus (14), and Strongylodon (14). Two genera have base numbers which suggest derivation by polyploidy: Glycine (20) and Cologania (22).     

CHROMOSOME NUMBERS IN COMPOSITAE. II. HELENIEAE

Raven , Peter H. (Rancho Santa Ana Botanic Garden, Claremont, Calif.), and Donald W. Kyhos. Chromosome numbers in Compositae. II. Heleniae. Amer. Jour. Bot. 48(9): 842–850. Illus. 1961.—Chromosome counts are now available for 42 of the approximately 55 genera of Compositae, tribe Helenieae, which is predominantly a group of western North America. These chromosome numbers are summarized here at the generic level, and 100 original counts for the tribe are added, including what seem to be the first published reports for the genera Amblyopappus, Baeriopsis, Hulsea, Jaumea, Pericome, Rigiopappus, Trichoptilium, and Venegasia, as well as for many species. The phylogeny of Chaenactis is discussed in the light of published records and 46 original counts, and C. douglasii is shown to include plants in which n = 6, 12, and 18, which differ somewhat morphologically. Helenium has species which have a complete series of aneuploid numbers from n = 13 to n = 17. Chromosome numbers coincide with morphological variability in indicating that Helenieae are a diverse group. More detailed studies of various kinds will be necessary before the genera of Helenieae can be re-aligned effectively, but it is evident that different genera show affinities with various other tribes of the family. Nevertheless, it is thought to be convenient to continue to recognize Helenieae at the tribal level for the present.     

Can Microsatellites Be Used to Infer Phylogenies? Evidence from Population Affinities of the Western Canary Island Lizard (Gallotia galloti)

Population phylogeographic studies are generally based solely on mtDNA without corroboration, from an independent segregating unit (i.e., nuclear genes), that the mtDNA gene tree represents the organismal phylogeny. This paper attempts to evaluate the utility of microsatellites for this process by use of the Western Canary Island lacertid (Gallotia galloti) as a model. The geological times of island eruptions are known, and well-supported mtDNA phylogenies exist (corroborated as the organismal phylogeny rather than just a gene tree by nuclear random amplified polymorphic DNAs (RAPDs)). The allelic variation in 12 populations from four islands (representing five haplotype lineages) was investigated in five unlinked microsatellite loci. Analysis of molecular variance showed this data to be highly structured. A series of genetic distances among populations was computed based on both the variance in allele frequency (i.e., F_st related) and the variance in repeat numbers (i.e., R_st related). The genetic distances based on the former were more highly correlated with the mtDNA genetic distances than those based on the latter. All trees based on both models supported the primary division shown by mtDNA and RAPDs, which is dated at ca. 2.8 to 5.6 mybp (depending on calibration of the mtDNA clock) and which could, under the evolutionary species concept, be regarded separate species. This was achieved despite theoretical problems posed by the use of few loci, suspected bottlenecks, and large population sizes. The finer details were less consistently represented. Nevertheless, this study demonstrates that even a small number of microsatellites can be useful in corroborating the deeper divisions of a population phylogeny.     

Evolutionary aspects of cephalic sensory papillae of the Indo‐Pacific species of Eleotris (Teleostei: Eleotridae)

Eleotris species (Teleostei: Eleotridae) are one of the most common fish in Indo‐Pacific estuaries and insular freshwater streams. In these rivers, they are a sit‐and‐wait predator. They have an amphidromous life cycle, that is adults grow, feed and reproduce in rivers, while larvae have a marine dispersal phase. Larvae recruit back to rivers and settle in stream habitats. Primary characters used to determine Eleotris species are the presence and the disposition of cephalic sensory papillae rows on the operculum and under the eyes as well as scale row numbers. The morphology of these cephalic sensory papillae is of particular importance in this predatory genus as it is generally correlated in fish to predation and feeding. In this paper, we have established a molecular phylogeny of the genus based on the 12 mitochondrial protein‐coding genes to discuss the relationship between Indo‐Pacific Eleotris species. There is a well‐supported dichotomy in the molecular phylogeny, and this separation into two main clades is also morphologically visible, as it reveals a difference in the arrangement of cephalic sensory papillae. Indeed, the phylogeny distinguishes the species with the “open” pattern of the operculum sensory papillae and the species with the “closed” one. This phylogeny thus reflects the morphology of the opercular papillae. The evolution of this character is discussed in terms of the adaptation of the Eleotris genus to life in tropical insular river systems.     

Characterization of heterochromatin in different species of the Scilla siberica group (Liliaceae) by in situ hybridization of satellite DNAs and fluorochrome banding

Satellite DNAs have been isolated from the monocotyledonous plants Scilla siberica, S. amoena, S. ingridae (all are highly GC-rich), and S. mischtschenkoana by using the Ag⁺ –Cs₂SO₄ density centrifugation technique. Hybridization in situ has been performed with ₃H-cRNA to these satellite DNAs in all four species. In each species, the endogenous satellite DNA is located mainly in intercalary and major heterochromatin bands associated with terminal regions and nucleolar organizer regions (NORs) but not in centromeric regions. Patterns observed after cross-species hybridization show a high degree of satellite DNA homology between S. siberica, S. amoena, and S. ingridae. By contrast, satellite DNA of S. mischtschenkoana consists largely of different, non homologous DNA sequences, with two exceptions: (i) the NORs of all four species contain similar satellite sequences, and (ii) a strong homology exists between the satellite DNA of S. mischtschenkoana and centromeric DNA of S. siberica but not with those of S. amoena and S. ingridae. — Heterochromatin has also been characterized by the AT-specific fluorochromes quinacrine (Q) and DAPI and the GC-specific agent chromomycin A₃ (CMA₃), in combination with two counterstaining techniques. While CMA₃-fluorescence is largely in agreement with data on base composition and location of the specific satellite DNAs, the results with Q and DAPI are conflicting. Prolonged fixation has been found to change the fluorescence character in certain instances, indicating that other factors than the base sequence of the DNA also play a role in fluorochrome staining of chromosomes. The results are discussed in relation to the taxonomy and phylogeny of the four species.     

Nonea pisidica (Boraginaceae-Boragineae), a new species from southwest Anatolia and its relationships inferred from karyology and cpDNA sequences

The new species Nonea pisidica (Boraginaceae-Boragineae) is described based on two collections by the authors from the region of Lake Burdur in southwest Anatolia, Turkey. It shows a combination of morphological characteristics concerning habit, flower, and fruit that distinguishes it from N. caspica and N. pallens, the two more similar taxa in Nonea sect. Nonea. Karyological analyses corroborate the separation of the three species, which have different chromosome complements and even base numbers. N. pisidica is characterised by 2n = 30, a complement previously unknown for west Asiatic species of Nonea. The dibasic haploid number x = 15 may have originated through amphidiploid hybridisation between two annual, diploid taxa with x = 7 and x = 8, such as N. lutea and N. caspica. The relationships of the new species were further analysed using trnL_UAA sequences of the chloroplast genome, which were obtained for 16 selected species of Nonea. The resulting phylogeny confirms that it is related to N. caspica and N. lutea, but not to N. pallens, in spite of morphological resemblance. Lack of relationship with the south Mediterranean N. vesicaria, the only other species of Nonea known to have 2n = 30, suggests that amphidiploidy may have played an important role in speciation processes through recurrent and polytopical occurrence.     

Evolution of diploid chromosome number,sex‐determining systems,and heterochromatin in Western Mediterranean and Canarian species of the genus Pimelia (Coleoptera: Tenebrionidae)

A compilation of the diploid chromosome numbers and karyotype formulae of 30 species of the genus Pimelia from Morocco, Iberian Peninsula, Balearic and Canary Islands is presented. All species show a conservation of diploid numbers and karyotype formulae 2n = 18 (8 + Xy_p) except for Pimelia cribra, Pimelia elevata, and Pimelia interjecta 2n = 20 (9 + Xy_p) and Pimelia sparsa sparsa 2n = 18 (8 + neoXY). The ancestral state for the genus Pimelia is suggested to be 2n = 18 (8 + Xy_p) in accordance with a previously described phylogeny of these species based on mitochondrial and nuclear DNA. The derived state 2n = 20 (9 + Xy_p) is present in a monophyletic clade, which originated about 2.5–5 Mya. The male meiotic formula 8 + neoXY found in P. sparsa sparsa seems to have originated by the reorganization of the Xy_p pair resulting in two homomorphic sexual chromosomes and the lost of most of the heterochromatin from the former X chromosome. In all chromosomes C‐banding revealed conspicuous pericentromeric heterochromatic blocks, except in the Y chromosome in most of the species, and in situ hybridization of satellite DNA probes revealed the correspondence between heterochromatin and satellite DNA. Finally, the possible role of heterochromatin and satellite DNA is discussed in relation to the uniformity of the Tenebrionidae α‐karyology.     

MOLECULAR EVOLUTIONARY DIVERGENCE AMONG NORTH AMERICAN CAVE CRICKETS. II. DNA-DNA HYBRIDIZATION

Single-copy DNA divergence among 23 populations of cave crickets belonging to two genera (Euhadenoecus and Hadenoecus) has been determined by DNA-DNA hybridization employing the TEACL method. These same populations have been studied for allozyme variation (Caccone and Sbordoni, 1987). In addition, a European relative (Dolichopoda laetitiae) has been included as an outgroup for rooting the phylogeny. One of the most remarkable findings is the large degree of DNA divergence among these species and populations. A ΔT_m of up to 5°C has been found between populations of the same species; even further divergence is indicated by a lowered normalized percentage of reassociation. A phylogeny was constructed and tested for synchrony of rates, i.e., a molecular clock. Statistically, we could not reject the clock hypothesis. Attempts to calibrate the clock led to the conclusion that these insects are among the fastest evolving (with respect to single-copy DNA) groups yet studied—at least as fast as Drosophila and sea urchins—where a ΔT_m of 1°C indicates 0.5 to 1.5 MY since the last common ancestor. In general, the phylogeny derived from the DNA data agrees with that derived from isozymes. Nei's D and ΔT_m are correlated; in this group a D of 0.1 corresponds to a ΔT_m of about 1.5°C. This indicates that, relative to total single-copy DNA, the protein-coding regions of the genome are slowly evolving.     

VASCULAR PATTERNS IN STEMS OF ARACEAE: SUBFAMILIES COLOCASIOIDEAE,AROIDEAE AND PISTIOIDEAE

The stem vasculature of ten genera of Colocasioideae and three genera of Aroideae was analyzed by films of series of cross sections. The technique was unsuited for the numerous tuberous genera of Aroideae (and Pistia), which have shortened internodes. The Colocasioideae has long been recognized as one of the most natural large assemblages in the Araceae, a concept further supported by information from stem anatomy and vasculature. All species examined have amphivasal axial bundles that undergo frequent anastomosis and bifurcation of a seemingly irregular kind. Syngonium is the only viny genus and is exceptional in a number of anatomical features which are associated with its unusual morphology. One of the principle points of diversity in the Colocasioideae is the presence or absence of a permanent cortical vascular system. All four genera with a permanent cortical system (Caladiopsis, Caladium, Xanthosoma, and Syngonium) are neotropical. In the Aroideae (and Pistioideae) all of the tuberous genera have a highly condensed vascular system. Genera with elongated internodes (Stylochiton, Lagenandra, Cryptocoryne) also have a similar pattern, which makes taxonomic comparisons based on stem vasculature in the Aroideae of little value. Branch trace insertion is much less well developed in Colocasioideae and Aroideae than in most other subfamilies.     

CHROMOSOME NUMBERS AND PHYLOGENY IN MELAMPODIUM (COMPOSITAE)

The haplord chromosome numbers of n = 9, 10, 11, 12, 18, 20, 23, 25 ± 1, 27, 30, and 33 have been reported by various authors from 26 of the 37 recognized species of Melampodium. A chromosomal survey of 375 plants from 275 different populations suggests that the recorded numbers are stable within the genus and that infraspecific euploidy and aneuploidy are uncommon. These chromosome numbers can be arranged numerically, with morphological and limited cytogenetic substantiation, into four euploid series of x2 = 9, 10, 11, and 12. Of these four groups of species, the x = 10 series is the largest and morphologically most diverse. This consideration, along with additional evidence from the morphology of sterile disc ovaries, suggests that x = 10 is the ancestral chromosomal base in Melampodium. A comparison of morphological and cytological data from the closely related genera, Acanthospermum and Lecocarpus, indicates that the latter are probably on a common base of x = 11. Present day distributional patterns of all three genera support the hypothesis that x = 10 is the ancestral base for the entire complex.     

PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA,ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES1

The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast‐encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family‐level classification. The genus Cymopolia Lamouroux was inferred to be the basal‐most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier‐Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition‐to‐transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g₁ values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies.     

Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data

The evolutionary history of living African amphibians remains poorly understood. This study estimates the phylogeny within the frog genera Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA sequence data (12S, tRNA-Valine, and 16S genes) from half of the described species. Analyses are conducted using parsimony, maximum likelihood, and Bayesian methods. The effect of alignment on phylogeny estimation is explored by separately analyzing alignments generated with different gap costs and a consensus alignment. The consensus alignment results in species paraphyly, low nodal support, and incongruence with the results based on other alignments, which produced largely similar results. Most nodes in the phylogeny are highly supported, yet several topologies are inconsistent with previous hypotheses. The monophyly of Cardioglossa and of miniature species previously assigned to Schoutedenella was further examined using Templeton and Shimodaira–Hasegawa tests. Cardioglossa monophyly is rejected and C. aureoli is transferred to Arthroleptis. These tests do not reject Schoutedenella monophyly, but this hypothesis receives no support from non-parametric bootstrapping or Bayesian posterior probabilities. This phylogeny provides a framework for reconstructing historical biogeography and analyzing the evolution of body size and life history. Direct development and miniaturization appear at the base of Arthroleptis phylogeny concomitant with a range expansion from Central Africa to throughout most of sub-Saharan Africa.     

PHYLETIC TRENDS IN SECTIONS EUBLEPHARIS AND CALLIOPSIS OF THE GENUS COREOPSIS (COMPOSITAE)

Artificial hybridization, fertility of interspecific and intersectional hybrids, chromosome numbers, and trends in habit and morphology in taxa of sections Eublepharis and Calliopsis of the genus Coreopsis are used to consider the sectional relationships and to derive a presumed phylogeny for the two sections. The two sections are closely related and show a low level of interfertility, but this level is as high as in some interspecific crosses within sections. The sections differ in base chromosome number and achene winging. The problematic C. rosea evidently should remain in section Eublepharis. Both sections probably arose from x = 13 stock resembling C. integrifolia or C. pubescens. Descending aneuploidy was involved in the derivation of section Calliopsis, while chromosome evolution in section Eublepharis has involved polyploidy.     

aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

Background  

Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B₂ variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B₁ variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene.