Molecular phylogeny in Indian Tinospora species by DNA based molecular markers

The phylogenetic relationships among the three species of Tinospora found in India are poorly understood. Morphology does not fully help to resolve the phylogeny and therefore a fast approach using molecular analysis was explored. Two molecular approaches viz Random Amplified Polymorphic DNA (RAPD) assay and restriction digestion of ITS1-5.8S-ITS2 rDNA (PCR-RFLP) were used to evaluate the genetic similarities between 40 different accessions belonging to three species. Of the 38 random primers used only six generated the polymorphism, while as three out of 11 restriction enzymes used gave polymorphic restriction patterns. The average proportion of polymorphic markers across primers was 95%, however restriction endonucleases showed 92% polymorphism. RAPD alone was found suitable for the species diversions. In contrast PCR- RFLP showed bias in detecting exact species variation. The correlation between the two markers was performed by Jaccard's coefficient of similarity. A significant (r= 0.574) but not very high correlation was obtained. Further to authenticate the results obtained by two markers, sequence analysis of ITS region of ribosomal DNA (ITS1 and ITS2, including 5.8S rDNA) was performed. Three independent clones of each species T. cordifolia, T. malabarica and T. crispa were sequenced. Phylogenetic relationship inferred from ITS sequences is in agreement with RAPD data.     

Genetic diversity of commercially grown Moringa oleifera Lam. cultivars from India by RAPD, ISSR and cytochrome P450-based markers

Moringa oleifera is a less used, drought-tolerant tropical plant, rich in nutritionally and nutraceutically important bioactive compounds. It is native to India and now under cultivation in many countries, but no data is available on genetic variability. Three DNA marker techniques, i.e., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and cytochrome P₄₅₀ gene-based markers were used for the detection of genetic variability in eight Indian cultivars of M. oleifera, collected from various states of India. A total of 17 RAPD, 6 ISSR and 7 pairs of cytochrome P₄₅₀-based markers generated 48.68, 48.57 and 40.00 % polymorphisms, respectively. The marker index (MI) for each of these marker systems (3.25 for RAPD, 4.73 ISSR and 2.95 for Cyt P₄₅₀-based markers) suggest that ISSR markers are the most effective for assessment of genetic diversity. Based on the three types of marker data, the eight cultivars of M. oleifera were grouped into four sub-clusters in a dendrogram, but without any distinct geographical pattern. This suggests spread of planting material and high rates of gene flow through cross pollination. High bootstrap values (94.4 and 82.3) were obtained at major nodes of the dendrogram using the winboot software. The dendrogram and PCA plots generated from the binary data matrices of the three marker systems were found highly concordant to each other. This study reveals a huge genetic diversity among the cultivars and this can be utilised for conservation and cultivar development in breeding programmes to produce high yielding, nutritionally superior cultivars.     

Efficiency of RAPD, SSR and Cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions

Finger millet (Eleusine coracana L.) is an important crop used for food, forage, and industrial products. Three DNA marker techniques, random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P₄₅₀ gene based markers were used for the detection of genetic polymorphism in 83 accessions of finger millet collected from various geographical regions of India and Africa. A total of 18 RAPD, 10 SSR and 10 pairs of cytochrome P₄₅₀ gene based markers were generated 56.17, 70.19 and 54.29% polymorphism, respectively. Mean polymorphism information content (PIC) for each of these marker systems (0.280 for RAPD, 0.89 for SSR and 0.327 for cytochrome P₄₅₀ gene based markers) suggested that SSR marker were highly effective in determining polymorphism. The phenograms based on the three markers data indicate that genotypes from different geographical regions are clearly distinguishable as separate clusters. Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.90 for all the three marker systems. The dendrograms and PCA plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Based on the results of present study, SSR and cytochrome P₄₅₀ gene based markers appear to be particularly useful for the estimation of genetic diversity. This study reveals the potential of RAPD, SSR and gene based markers for characterizing germplasm of Eleusine coracana and narrow down the vast germplasm into distinct core groups.     

Morphological and molecular phylogeny of Pistacia species in Turkey

This study addresses the taxonomic relationships and genetic variation of wild Pistacia germplasm in Turkey using morphological data and RAPD analysis. P. atlantica, P. terebinthus and P. eurycarpa are common wild species in the flora of Turkey, and their phenotypic appearance and productivity are highly variable. Understanding such variation would facilitate their use in rootstock breeding programs as rootstock for edible pistachio. We have sampled and characterized a total of 40 wild Pistacia genotypes from different parts of Turkey for this study. These included 10 P. eurycarpa (locally identified as P. khinjuk) genotypes from Siirt and Gaziantep provinces and 20 P. atlantica and 10 P. terebinthus genotypes from Adana, Aydin and Manisa provinces. In addition, two local P. vera varieties, cvs. Kirmizi and Siirt, were added for comparison. Cluster analysis based on morphological data revealed that the closest species to P. vera is P. eurycarpa, followed by P. atlantica and P. terebinthus. Ten polymorphic RAPD primers, yielding a total of 138 scorable bands, were selected and used for DNA fingerprinting of these genotypes. In the resulting molecular phylogeny, the four Pistacia species are clearly separated from each other. P. terebinthus appears to be the most diverged species, and the closest pair of species was found to be P. atlantica and P. eurycarpa. This supported the classification of trees that had been identified by local growers as P. khinjuk, as P. eurycarpa. Comparison of these samples with a reference P. khinjuk, obtained from a germplasm collection in the USA, also supported such identification. Several wild genotypes were found to be inter-specific hybrids, and the RAPD patterns revealed their probable origin. Species-specific markers were identified for each of the four species, and these may aid in future classification of new germplasm materials.     

Molecular and morphological phylogeny of Menispermaceae (Ranunculales)

The phylogeny of Menispermaceae (Ranunculales) is reconstructed here using both morphological and molecular data from a broad sample of species. Morphological data include characters of leaves, wood, flowers, fruits, seeds, pollen and phytochemistry from 73 species representing the different subgroups recognized within the family. This dataset allowed us to study the morphological evolutionary trends in Menispermaceae. The molecular data focused on cpDNA sequences: rbcL and atpB. Maximum parsimony (MP) and Bayesian methods were used to reconstruct the phylogeny of Menispermaceae. The results obtained from the three datasets are partly incongruent. The morphology indicates that Menispermaceae can be divided into two major groups, one including the tribes Fibraureae and Tinosporeae, the other one including the tribes Anomospermeae, Pachygoneae and Menispermeae. Only Burasaia Thouars was not included in any of these groups. The characters of fruits and seeds appeared to be most useful to differentiate these groups whereas convergences were found for the androecium.     

Comparative evaluation of genetic diversity using RAPD,SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (<Emphasis Type="Italic">Eleusine coracana</Emphasis> L. Gaertn.)

Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300–450 mg/100 g), medium calcium (200–300 mg/100 g) and low calcium (100–200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and amajor input into conservation biology of cereal crops.     

Genetic and morphometric markers are able to differentiate three morphotypes belonging to Section Algarobia of genus Prosopis (Leguminosae, Mimosoideae)

The section Algarobia of genus Prosopis includes promising species for reforestation and afforestation programmes in arid and semiarid regions, mainly of the Americas. Many interspecific natural hybrid combinations have been described in this group. In this paper we analysed a hybrid zone in Chaco biogeographical province in Argentina, where P. ruscifolia and P. alba overlap and hybridise producing intermediate fertile hybrid forms. Eleven morphological traits and 76 loci RAPD were analysed to determine the effect of hybridization between these species. The comparison of morphological traits among groups yielded significant or highly significant differences for all traits. Estimates of H _e in P. alba and P. ruscifolia did not differ from each other, but both showed significantly lower values than the hybrid group. The analysis of correlations between shared phenotypes and pair-wise relationships estimated from RAPD gave also strong support to the hypothesis that most of the phenotypic traits analysed have significant heritability. The analyses of population structure and clustering based on morphological and molecular data by DAPC and STRUCTURE were rather consistent and indicated that the three morphotypes studied here are differentiated with low overlapping. All results indicated that despite the occurrence of natural hybridization and introgression, interspecific gene flow would be limited by hybrid breakdown or natural selection favouring the maintenance of species integrity.     

Complete Mitochondrial Genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura,Arthropoda) and Implications for Chelicerate Phylogenetic Studies

Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.     

Genomic Diversity within the Genus Pediococcus as Revealed by Randomly Amplified Polymorphic DNA PCR and Pulsed-Field Gel Electrophoresis

The genomic diversity of 33 previously assigned strains from six species within the genus Pediococcus was assessed by randomly amplified polymorphic DNA (RAPD) PCR and pulsed-field-gel electrophoresis (PFGE). The RAPD PCR patterns produced by two separate random primers, termed P1 (ACGCGCCCT) and P2 (ATGTAACGCC), were compared by the Pearson correlation coefficient and the unweighted pair group method with arithmetic averages clustering algorithm. Pattern variations between repeat samples set a strain discrimination threshold of less than 70% similarity. P1 and P2 primers alone and in combination produced 14, 21, and 28 distinct patterns, respectively. When each strain was assigned with a type strain with which it shared the highest level of similarity, both primers grouped 17 of the 27 strains to their proposed species. PFGE following genomic digestion with the restriction enzymes ApaI, NotI, and AscI produced 30, 32, and 28 distinct macrorestriction patterns, respectively. Specific DNA fragments within the NotI and AscI macrorestriction patterns for each strain were observed that allowed 27 of the 33 strains to be assigned to their proposed species. For example, following digestion with AscI, all Pediococcus parvulus strains were characterized by two DNA fragments, one of approximately 220 kb and another between 700 and 800 kb. The exceptions correlated with those observed with both RAPD PCR primers and included three P. damnosus and two P. pentosaceus strains that grew at temperatures regarded as nonpermissive for their proposed species but not for those with which they grouped.     

Molecular docking analysis of glycogen phosphorylase with inhibitors from Cissampelos pareira Linn.

Cissampelos pareira Linn. is a climbing herb known in Indian traditional medicine as laghupatha. It belongs to the Menispermaceae family. The enzyme glycogen phosphorylase (GP) is a promising target for the treatment of type-2 diabetes (T2DM). A variety of natural product inhibitors with both pharmaceutical and nutraceutical potential have been reported in the search for powerful, selective and drug-like GP inhibitors that could lead to hypoglycemic medicines. Therefore, it is of interest to document the molecular docking analysis data of glycogen phosphorylase with compounds from Cissampelos pareira Linn. We report the optimal binding features of 4 compounds namely Trans-N-feruloyltyramine, Coclaurine, Magnoflorine, and Curine with the target protein for further consideration in the context of T2DM.     

Precise Detection and Tracing of Trichoderma hamatum 382 in Compost-Amended Potting Mixes by Using Molecular Markers

Randomly amplified polymorphic DNA (RAPD) analysis and the PCR assay were used in combination with dilution plating on a semiselective medium to detect and enumerate propagules of Trichoderma hamatum 382, a biocontrol agent utilized in compost-amended mixes. Distinct and reproducible fingerprints were obtained upon amplification of purified genomic DNA of T. hamatum 382 with the random primers OPE-16, OPH-19, and OPH-20. Three amplified DNA fragments of 0.35 (OPE-16_0.35), 0.6 (OPH-19_0.6), and 0.65 (OPH-20_0.65) kb were diagnostic for T. hamatum 382, clearly distinguishing it from 53 isolates of four other Trichoderma spp. tested. Some isolates of T. hamatum shared these low-molecular-weight fragments with T. hamatum 382. However, RAPD analysis of isolates of T. hamatum with all three random primers used in consecutive PCR tests distinguished T. hamatum 382 from other isolates of T. hamatum. These three RAPD amplicons were cloned and sequenced, and pairs of oligonucleotide primers for each cloned fragment were designed. Use of the primers in the PCR assay resulted in the amplification of DNA fragments of the same size as the cloned RAPD fragments from genomic DNA of T. hamatum 382. A combination of dilution plating on a semiselective medium for Trichoderma spp. and PCR, with the RAPD primers OPH-19, OPE-16, and OPH-20 or the three sequence-characterized primers, was used successfully to verify the presence of T. hamatum 382 propagules in nine different soil, compost, and potting mix samples. All 23 Trichoderma isolates recovered on semiselective medium from commercial potting mixes fortified with T. hamatum 382 were identified as T. hamatum 382, whereas 274 Trichoderma isolates recovered from the other nine samples were negative in the PCR assay. Thus, this highly specific combination of techniques allowed detection and enumeration of propagules of T. hamatum 382 in fortified compost-amended potting mixes. Sequence-characterized amplified region markers also facilitated the development of a very simple procedure to amplify DNA of T. hamatum 382 directly from fortified compost-amended potting mixes.     

Uncovering Cryptic Parasitoid Diversity in Horismenus (Chalcidoidea,Eulophidae)

Horismenus parasitoids are an abundant and understudied group of eulophid wasps found mainly in the New World. Recent surveys based on morphological analyses in Costa Rica have quadrupled the number of named taxa, with more than 400 species described so far. This recent revision suggests that there is still a vast number of unknown species to be identified. As Horismenus wasps have been widely described as parasitoids of insect pests associated with crop plants, it is of high importance to properly establish the extant diversity of the genus, in order to provide biological control practitioners with an exhaustive catalog of putative control agents. In this study, we first collected Horismenus wasps from wild Phaseolus bean seeds in Central Mexico and Arizona to assess the genetic relatedness of three morphologically distinct species with overlapping host and geographical ranges. Sequence data from two nuclear and two mitochondrial gene regions uncovered three cryptic species within each of the three focal species (i.e., H. missouriensis, H. depressus and H. butcheri). The monophyly of each cryptic group is statistically supported (except in two of them represented by one single tip in which monophyly cannot be tested). The phylogenetic reconstruction is discussed with respect to differences between gene regions as well as likely reasons for the differences in variability between species.     

Genome-wide identification,annotation and characterization of novel thermostable cytochrome P450 monooxygenases from the thermophilic biomass-degrading fungi Thielavia terrestris and Myceliophthora thermophila

Cytochrome P450 monooxygenases (P450s) are ubiquitous heme-thiolate proteins that have potential biotechnological application. Thermostable-P450s that can withstand hostile industrial conditions, such as high temperatures, extremes of pH and organic solvents, are needed for biotechnological usage. Here, for the first time, we report a large number of thermostable-P450s from two thermophilic biomass-degrading fungi, Myceliophthora thermophila and Thielavia terrestris. Genome-wide P450 analysis revealed the presence of 79 and 70 P450s (P450ome) in T. terrestris and M. thermophila. Authentic P450s containing both the P450 signature domains (EXXR and CXG) were classified as follows: T. terrestris (50 families and 56 subfamilies) and M. thermophila (49 families and 53 subfamilies). Bioinformatics analysis of P450omes suggested the presence of a large number of thermostable-P450s. Based on aliphatic index cut-off (>90), 14 and 11 P450s were determined to be thermostable in T. terrestris and M. thermophila. Among the thermostable P450s, six P450s from T. terrestris and three from M. thermophila had a melting temperature (Tm) of >65 °C, suggesting their hyperthermal tolerance. Analysis of the instability index of two ascomycete P450omes revealed the presence of 12 and 19 in vitro stable P450s in T. terrestris and M. thermophila. Overall, six P450s from T. terrestris and four from M. thermophila showed both thermal tolerance and in vitro stability. Thermophilic ascomycetes P450s are of potential interest from a structural, mechanistic and biotechnological point of view, as five P450s showed higher thermal tolerance and five showed higher in vitro stability compared to the well-characterized thermostable-P450s CYP175A1 (bacteria) and CYP119 (archaea).     

Seed-specific identification of Larix gmelinii,Larix olgensis,and Larix principis-rupprechtii using sequence-characterised amplified region markers

Larix gmelinii, Larix olgensis, and Larix principis-rupprechtii are the three native and sympatric larch species in North China, and each of these species has a distinctive ecological niche. It is difficult to identify them based only on certain morphological characters, particularly the seed appearance. In this study, the seed endosperms of these three larch species were analysed using the random amplified polymorphic DNA (RAPD) technique to screen for interspecific differences. The following three RAPD markers linked to species-specific segments were observed in the different species: 1475-bp (Larix gmelinii and L. olgensis), 505-bp (Larix principis-rupprechtii), and 1121-bp (Larix gmelinii) markers. The three seed-specific fragments amplified by the RAPD markers were sequenced, and the sequences were used to design and synthesise species-specific SCAR markers. The size of the SCAR fragments was concordant with that of the RAPD species-specific fragments. Therefore, these SCAR markers can be used to identify the seeds of different larch species, thereby providing a new molecular tool for the identification of larch seeds that leads to considerable savings in terms of time and economic resources.     

Efficient catalytic turnover of cytochrome P450(cam) is supported by a T252N mutation

A Thr (or Ser) residue on the I-helix is a highly conserved structural feature of cytochrome P450 enzymes. It is believed to be indispensable as a proton delivery shuttle in the oxygen activation process. Previous work showed that P450_cin (CYP176A1), which contains an Asn instead of the conserved Thr, is fully functional in the catalytic oxidation of cineole [D.B. Hawkes, G.W. Adams, A.L. Burlingame, P.R. Ortiz de Montellano, J.J. De Voss, J. Biol. Chem. 277 (2002) 27725-27732]. To determine whether the substitution of Asn for Thr is specific or general, the conserved Thr252 in P450_cam (CYP101) was mutated to generate the T252N, T252N/V253T, and T252A mutants. Steady-state kinetic analysis of the oxidation of camphor by these mutants indicated that the T252N and T252N/V253T mutants have comparable turnover numbers but higher K_m values relative to the wild-type enzyme. Spectroscopic binding assays indicate that the higher K_m values reflect a decrease in the camphor binding affinity. Non-productive H₂O₂ generation was negligible with the T252N and T252N/V253T mutants, but, as previously observed, was dominant in the T252A mutant. Our results, and a structure model based on the crystal structures of the ferrous dioxygen complexes of P450_cam and its T252A mutant, suggest that Asn252 can stabilize the ferric hydroperoxy intermediate, preventing premature release of H₂O₂ and enabling addition of the second proton to the distal oxygen to generate the catalytic ferryl species.     

Molecular and morphological relationships between two closely related species, Turbinaria ornata and T. conoides (Sargassaceae,Phaeophyceae)

We employed four markers (two chloroplastic, one mitochondrial and one nuclear) to investigate whether Turbinaria ornata and Turbinaria conoides, two morphologically similar brown algae, are distinct species. The molecular data revealed reciprocal monophyly, thus confirming the two algae as discrete species. Nevertheless, taxonomical ambiguities remain. T. conoides is more morphologically variable than T. ornata. We identified an atypical T. conoides morphotype whose blade possesses intramarginal teeth, a morphological characteristic of the T. ornata group that is normally absent within T. conoides. The molecular data indicate, nonetheless, that this morphotype belongs genetically to the T. conoides group. Thus, the results cast doubt upon the validity of using intramarginal teeth for species diagnosis.     

Confirmation of relationships among Boesenbergia (Zingiberaceae) and related genera by RAPD

The relationships among 19 accessions of Zingiberaceae belonging to 11 species of Boesenbergia, six species of Kaempferia, and two species of Scaphochlamys from Southern Thailand were studied using random amplified polymorphic DNA (RAPD) profiles from leaf tissue samples. The RAPD was carried out using 10 random decamer arbitrary primers. Amplification occurred in five out of 10 tested primers (OPAM-01, OPAM-03, OPAM-12, OPB-14, OPZ-03). Total of 53 amplified bands were observed. Data obtained from the RAPD fingerprints from the samples clarified some doubts in morphological classification. The data were analyzed for the Nei and Li's Dice similarity coefficient for pair-wise comparison between individual samples and the distance matrix. The dendrogram resulting from cluster analysis, UPGMA and a principal component analysis of the RAPD result confirms a higher degree of relationship between Boesenbergia and Scaphochlamys than between Boesenbergia and Kaempferia.     

High Cryptic Diversity across the Global Range of the Migratory Planktonic Copepods Pleuromamma piseki and P. gracilis

Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide.     

Assessing the monophyly of polyploid Gossypium species

The origin and monophyly of the polyploid cotton (Gossypium) species has been largely accepted, despite the lack of explicit phylogenetic evidence. Recent studies in other polyploid systems have demonstrated that multiple origins for polyploid species are much more common than once thought, raising the possibility that Gossypium polyploids also had multiple origins, as postulated by some authors. To test the monophyly of polyploid cotton, we sequenced a 2.8-kb intergenic region from all diploid species belonging to the genome groups from which the polyploid originates. The resulting phylogenetic analyses strongly support a single origin of polyploid cotton involving a D-genome ancestor related to Gossypium raimondii and an A-genome ancestor that was sister to both extant A-genome species.