Browsing by Subject "Phylogeny"

Now showing 1 - 10 of 10
  • Thumbnail Image
    Item
    Open Access
    Carbon and arsenic metabolism in Thiomonas strains: differences revealed diverse adaptation processes
    (BioMed Central Ltd, 2009) Bryan, Christopher; Marchal, Marie; Battaglia-Brunet, Fabienne; Kugler, Valerie; Lemaitre-Guillier, Christelle; Lievremont, Didier; Bertin, Philippe; Arsene-Ploetze, Florence
    BACKGROUND:Thiomonas strains are ubiquitous in arsenic-contaminated environments. Differences between Thiomonas strains in the way they have adapted and respond to arsenic have never been studied in detail. For this purpose, five Thiomonas strains, that are interesting in terms of arsenic metabolism were selected: T. arsenivorans, Thiomonas spp. WJ68 and 3As are able to oxidise As(III), while Thiomonas sp. Ynys1 and T. perometabolis are not. Moreover, T. arsenivorans and 3As present interesting physiological traits, in particular that these strains are able to use As(III) as an electron donor. RESULTS: The metabolism of carbon and arsenic was compared in the five Thiomonas strains belonging to two distinct phylogenetic groups. Greater physiological differences were found between these strains than might have been suggested by 16S rRNA/rpoA gene phylogeny, especially regarding arsenic metabolism. Physiologically, T. perometabolis and Ynys1 were unable to oxidise As(III) and were less arsenic-resistant than the other strains. Genetically, they appeared to lack the aox arsenic-oxidising genes and carried only a single ars arsenic resistance operon. Thiomonas arsenivorans belonged to a distinct phylogenetic group and increased its autotrophic metabolism when arsenic concentration increased. Differential proteomic analysis revealed that in T. arsenivorans, the rbc/cbb genes involved in the assimilation of inorganic carbon were induced in the presence of arsenic, whereas these genes were repressed in Thiomonas sp. 3As. CONCLUSION: Taken together, these results show that these closely related bacteria differ substantially in their response to arsenic, amongst other factors, and suggest different relationships between carbon assimilation and arsenic metabolism.
  • Thumbnail Image
    Item
    Open Access
    Discovery of parvovirus-related sequences in an unexpected broad range of animals
    (2016) François, S; Filloux, D; Roumagnac, P; Bigot, D; Gayral, P; Martin, D P; Froissart, R; Ogliastro, M
    Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.
  • Thumbnail Image
    Item
    Open Access
    Distribution and phylogenetic inference within the flightless spring katydids (Tettigoniidae: Brinckiella Chopard, 1955) in the Greater Cape Floristic Region
    (2022) Guta, Ricardo José; Janion-Scheepers, Charlene; Naskrecki, Piotr
    The genus Brinckiella is an endemic group from the Greater Cape Floristic region (GCFR) with several undescribed species. Some of them are of conservation concern, categorized by IUCN as Endangered (EN) and Vulnerable (VU) due to their restricted distribution caused by livestock overgrazing, agriculture, and urbanization. However, data are still missing to fully assess their distribution pattern and conservation status. Moreover, although the phylogeny of katydids was recently inferred, Brinckiella was not included in that analysis. Thus, its closest relatives and evolutionary history are still unknown. This study aimed to investigate the distribution and phylogenetic inference within the genus Brinckiella, map the distribution of its species, delimit the species through taxonomy and genetics, and elucidate the phylogenetic relationship and divergence time within the genus. Specimens were collected by hand and sweep netting. Phylogenetic inference was done using the COI gene and analysed under Maximum likelihood and Bayesian inference. This study identified 13 morphospecies of Brinckiella, of which five are new, undescribed species. The genus is currently distributed in 27 vegetation types in three biomes, and apart from the Fynbos and Succulent Karoo biomes, the genus also occurs in the Azonal vegetation biome. Fynbos had the highest number of species of Brinckiella, which is likely related to the vast diversity of plant that they are associated with and probably feed on. In the Succulent Karoo the distribution of Brinckiella might be associated with seasonal plants that occur in the spring and at the beginning of summer. The genus may be monophyletic, and it split from the common ancestor shared with Holochlora fruhstorferi Carl, 1914 about 14.2 Mya, and it split again from the common ancestor shared with Isophya major Brunner von Wattenwyl, 1878, Phaneroptera gracilis Burmeister, 1838 and Kuwayamaea chinensis (Brunner von Wattenwyl, 1878) at 10.16 Mya and diverged in the late Miocene around 8.79 Mya, producing two main clades (A and B). Clade A diverged 7.85 Mya and is composed by two closely related species: B. aptera and B. mauerbergerorum, while Clade B diverged 7.24 Mya and gave rise to two lineages (L1 and L2). Brinckiella wilsoni constitutes L1, and L2 split later in the early Pliocene around 4.74 Mya, and is represented by two sister species, B. arboricola and B. sp. n. 5.
  • Thumbnail Image
    Item
    Open Access
    Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant’s foot tubers
    (2016) Maurin, Olivier; Muasya, A Muthama; Catalan, Pilar; Shongwe, Eugene Z; Viruel, Juan; Wilkin, Paul; van der Bank, Michelle
    Abstract Background Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or “elephant’s foot” structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal. Results The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet. Conclusions Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin to just at the base or at the apex of it, or has been even replaced by an elaiosome.
  • Thumbnail Image
    Item
    Open Access
    A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family
    (BioMed Central Ltd, 2009) Varsani, Arvind; Shepherd, Dionne; Dent, Kyle; Monjane, Aderito; Rybicki, Edward; Martin, Darren
    BACKGROUND:We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has a mixture of features normally associated with other specific geminivirus genera. RESULTS: Whereas the ECSV genome is predicted to express a replication associated protein (Rep) from an unspliced complementary strand transcript that is most similar to those of begomoviruses, curtoviruses and topocuviruses, its Rep also contains what is apparently a canonical retinoblastoma related protein interaction motif such as that found in mastreviruses. Similarly, while ECSV has the same unusual TAAGATTCC virion strand replication origin nonanucleotide found in another recently described divergent geminivirus, Beet curly top Iran virus (BCTIV), the rest of the transcription and replication origin is structurally more similar to those found in begomoviruses and curtoviruses than it is to those found in BCTIV and mastreviruses. ECSV also has what might be a homologue of the begomovirus transcription activator protein gene found in begomoviruses, a mastrevirus-like coat protein gene and two intergenic regions. CONCLUSION: Although it superficially resembles a chimaera of geminiviruses from different genera, the ECSV genome is not obviously recombinant, implying that the features it shares with other geminiviruses are those that were probably present within the last common ancestor of these viruses. In addition to inferring how the ancestral geminivirus genome may have looked, we use the discovery of ECSV to refine various hypotheses regarding the recombinant origins of the major geminivirus lineages.
  • Thumbnail Image
    Item
    Open Access
    Microbial solvent formation revisited by comparative genome analysis
    (BioMed Central, 2017-03-09) Poehlein, Anja; Solano, José D M; Flitsch, Stefanie K; Krabben, Preben; Winzer, Klaus; Reid, Sharon J; Jones, David T; Green, Edward; Minton, Nigel P; Daniel, Rolf; Dürre, Peter
    Background: Microbial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for the chemical and biofuel industry. However, biological synthesis suffers from high substrate costs and competition from chemical synthesis supported by the low price of crude oil. To render the biotechnological production economically viable again, improvements in microbial and fermentation performance are necessary. However, no comprehensive comparisons of respective species and strains used and their specific abilities exist today. Results: The genomes of a total 30 saccharolytic Clostridium strains, representative of the species Clostridium acetobutylicum, C. aurantibutyricum, C. beijerinckii, C. diolis, C. felsineum, C. pasteurianum, C. puniceum, C. roseum, C. saccharobutylicum, and C. saccharoperbutylacetonicum, have been determined; 10 of them completely, and compared to 14 published genomes of other solvent-forming clostridia. Two major groups could be differentiated and several misclassified species were detected. Conclusions: Our findings represent a comprehensive study of phylogeny and taxonomy of clostridial solvent producers that highlights differences in energy conservation mechanisms and substrate utilization between strains, and allow for the first time a direct comparison of sequentially selected industrial strains at the genetic level. Detailed data mining is now possible, supporting the identification of new engineering targets for improved solvent production.
  • Thumbnail Image
    Item
    Open Access
    Molecular phylogenetics and conservation aspects of antelopes
    (1996) Rebholz, Wilhelmus Ewald Reinaard; Harley, Eric H
    This thesis concerns the molecular phylogenetics of three tribes of the family Bovidae, the Antilopini, Neotragini, and Tragelaphini. None of these tribes have been studied extensively with molecular techniques. The tribe Antilopini is one of the most speciose tribes (it includes 6 genera with 20 species) and the classification of several species of the genus Gazella is not clear. The tribe Neotragini is thought to be paraphyletic. Mitochondrial sequences of the cytochrome c oxidase ill and cytochrome b genes totalling 1083 base pairs have been determined for 52 taxa and used to determine phylogenetic relationships using cladistic and distance methods. Karyological analysis identified polymorphisms in several species (especially in Gazella saudiya and G. subgutturosa). Karyotypes of G. dorcas pelzelni and an XXY karyotype of a G. dorcas individual are shown for the first time. The main conclusions are that the Antilopini and the Tragelaphini are monophyletic and that the tribe Neotragini is paraphyletic. There is a lack of phylogenetic resolution between tribes which is probably due to the rapid radiation of the different tribes about 20 million years ago. The genus Taurotragus in the tribe Tragelaphini is shown to be paraphyletic and it would be appropriate to incorporate these taxa in the genus Tragelaphus. The genus Gazella could be paraphyletic, due to the position of Antilope cervicapra, in which case the genus needs to be split into two genera or renamed as Antilope. It is also argued that the use of the subgenus Trachelocele should be discontinued and that its only species, G. subgutturosa should be included in the subgenus Gazella. G. rufifrons and G. thomsonii may be more appropriately considered as conspecific. Cytogenetic and sequence data reveal that the herd of G. saudiya in Al Areen Wildlife Park is hybridised with G. bennettii and it is argued that it is important to identify unhybridised G. saudiya in other collections, since this species is on the brink of extinction. This case study demonstrates the need to genetically screen individuals which are part of a captive breeding program, especially if they are intended for reintroduction into the wild.
  • Thumbnail Image
    Item
    Restricted
    Nuclear and chloroplast DNA-based phylogenies of Chrysanthemoides Tourn. ex Medik. (Calenduleae; Asteraceae) reveal extensive incongruence and generic paraphyly, but support the recognition of infrasp
    (2009) Barker, N. P.; Howis, S.; Nordenstam, B.; Källersjö, M.; Eldenäs, P.; Griffioen, C.; Linder, H. P.
    The small genus Chrysanthemoides comprises two species within which a number of infraspecific taxa have been recognized, some of which are invasive aliens in Australia and New Zealand. Here we investigate the relationships of the species and infraspecific taxa using both chloroplast and nuclear non-coding DNA sequence data. Results of the analyses of the plastid and nuclear data sets are incongruent, and neither Chrysanthemoides nor Osteospermum is resolved as monophyletic, although there is some support for the recognition of infraspecific taxa. Analyses of the separate and combined data sets resolve two clades within Chrysanthemoides (which include some species of Osteospermum), and these appear to have a geographic basis, one being restricted to the mainly winter rainfall region, the other the eastern bi-seasonal rainfall area. Our results suggest that there is evidence of past or ongoing hybridization within and possibly between these two lineages.
  • Thumbnail Image
    Item
    Open Access
    Phylogenetic analysis of three genes of Penguinpox virus corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L reveals that it is most closely related to Turkeypox virus, Ostrichpox virus and Pigeonpox virus
    (BioMed Central Ltd, 2009) Carulei, Olivia; Douglass, Nicola; Williamson, Anna-Lise
    Phylogenetic analysis of three genes of Penguinpox virus, a novel Avipoxvirus isolated from African penguins, reveals its relationship to other poxviruses. The genes corresponding to Vaccinia virus G8R (VLTF-1), A3L (P4b) and H3L were sequenced and phylogenetic trees (Neighbour-Joining and UPGMA) constructed from MUSCLE nucleotide and amino acid alignments of the equivalent sequences from several different poxviruses. Based on this analysis, PEPV was confirmed to belong to the genus Avipoxvirus, specifically, clade A, subclade A2 and to be most closely related to Turkeypox virus (TKPV), Ostrichpox virus (OSPV)and Pigeonpox virus (PGPV).
  • Thumbnail Image
    Item
    Open Access
    Systematics of cetaceans using restriction site mapping of mitochondrial DNA
    (1992) Ohland, Derek Paul; Harley, Eric H
    A phylogenetic study of eleven cetaceans was undertaken using Restriction Endonuclease Maps (RSM) of mitochondrial DNA (mtDNA). One species from the suborder mysticeti (baleen whales) was sampled, and of the ten odontocetes (toothed whales) sampled two were from the family Ziphiidae (beaked whales) and eight were from the family Delphinidae (dolphins) (each representing a different genus). The primarily opportunistically obtained (i.e. from strandings or accidental death in commercial trawl nets) heart tissue generally yielded high quantities of mtDNA which is needed for double digest fragment analysis. The mtDNA extracted from the sampled taxa was cleaved with fifteen different six-base Restriction Enzymes (RE's). Using the three-way method of analysis and aided by the computer program Resolve (Ver. 2.7) (Harley, unpublished), RSM's were constructed. Distance (Neighbor-Joining and Fitsch-Margoliash) and cladistic (Maximum Parsimony and Bootstrap) methods were used to infer phylogenies. The baleen whale was used as an outgroup for the cladistic analysis. Both the distance and both the cladistic methods produced the same single topology, which is concordant with morphologically based classifications. The two differences (within the Delphinidae), viz. Grampus' most basally rooted position and Cephalorhynchus' grouping with the Delphininae are of taxa whose groupings are unresolved in the morphologically based classifications. Using Brown et al's (1979) molecular clock, very recent divergence times at the generic, family and suborder levels were obtained, when compared to fossil based estimates. Using the odontoceti/mysticeti split the base substitution rate of cetacean mtDNA was estimated to be much slower than that of terrestrial mammals (0,3% compared to 1,0% Myr⁻¹). A similarly slow rate was calculated for cetacean nuclear DNA (nDNA) (0,09% Myr⁻¹) (Schlotterer et al, 1991). It remains an unresolved issue as to whether the base substitution rate of cetacean DNA is slower than terrestrial mammals or whether the fossil evidence needs to be reinterpreted. The time of the mysticeti/odontoceti split is palaeontologically uncertain and the suggested monophyletic status of the extant suborders has been questioned, thus making the calculation of cetacean base substitution rate risky. Equally, the incomplete fossil record can lend itself to misinterpretation.