scholarly journals Evolution of b-type cytochromes in prokaryotes

2015 ◽  
Author(s):  
Vassiliki Lila Koumandou ◽  
Sophia Kossida
Keyword(s):  
Cytochrome B ◽  
Bootstrap Support ◽  
Evolutionary Relationships ◽  
Photosynthetic Organisms ◽  
Full Diversity ◽  
Cytochrome B561 ◽  
Species Cluster ◽  
Form Part ◽  
Split Form ◽  
B6f Complex

Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b6f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fe-hydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b6f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b6; also, the split form of b6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.

scholarly journals Evolution of b-type cytochromes in prokaryotes

2015 ◽  
Author(s):  
Vassiliki Lila Koumandou ◽  
Sophia Kossida
Keyword(s):  
Cytochrome B ◽  
Bootstrap Support ◽  
Evolutionary Relationships ◽  
Photosynthetic Organisms ◽  
Full Diversity ◽  
Cytochrome B561 ◽  
Species Cluster ◽  
Form Part ◽  
Split Form ◽  
B6f Complex

Prokaryotes use a wide variety of bioenergetic pathways but the order of emergence of these pathways and their evolutionary relationships are still unresolved issues. In this study we focus on the evolutionary relationships of different families of b-type cytochromes, which form part of a variety of bioenergetic enzymes (the cytochrome b6f complex, ubiquinol and menaquinol reductases, formate dehydrogenase, Ni/Fe-hydrogenase, and succinate dehydrogenase). We use data from 272 species of fully sequenced bacteria and archaea, which represent the full diversity of prokaryotic lineages and multiple bioenergetic modes, to examine the distribution of these cytochromes across lineages, and ask the question of whether sequences from different species cluster by cytochrome-b family, by bioenergetic mode or by taxonomic group. Different cytochrome-b types are found in many lineages of the bacteria and archaea, and form distinct groups in phylogenetic analysis, which indicates an ancient origin for this complex, and diversification of different cytochrome-b types before the diversification of lineages. We find that species do not cluster based on bioenergetic mode. We also re-examine data from previous studies using this expanded sample of organisms spanning the full diversity of prokaryotic lineages. Concerning the b6f complex of photosynthetic organisms, our expanded phylogenies do not show significant bootstrap support for a "green clade" of cytochrome b6; also, the split form of b6 is not monophyletic, indicating that the split form arose independently multiple times. We also present data on the similarities between prokaryotic and eukaryotic cytochrome b561 sequences, in light of the recently reported structure of eukaryotic cytochrome b561.

Tree kangaroo molecular systematics based on partial cytochrome b sequences: are Matschie's tree kangaroo (Dendrolagus matschiei) and Goodfellow's tree kangaroo (D. goodfellowi buergersi) sister taxa?

2012 ◽  
Vol 34 (1) ◽  
pp. 18 ◽  
Author(s):  
Thomas J. McGreevy ◽  
Lisa Dabek ◽  
Thomas P. Husband
Keyword(s):  
Mitochondrial Dna ◽  
Papua New Guinea ◽  
Cytochrome B ◽  
Molecular Systematics ◽  
Phylogenetic Analyses ◽  
New Guinea ◽  
Critically Endangered ◽  
Evolutionary Relationships ◽  
Accurate Identification ◽  
Identification Of Species

New Guinea tree kangaroos (Dendrolagus spp.) are unique arboreal macropodid marsupials mainly listed as critically endangered or endangered. The molecular systematics of Dendrolagus has not been fully resolved and is critical for the accurate identification of species and their evolutionary relationships. Matschie’s tree kangaroo (D. matschiei) and Goodfellow’s tree kangaroo (D. goodfellowi buergersi) share numerous morphological, physiological, and behavioural traits. We analysed the partial mitochondrial DNA cytochrome b gene for D. matschiei (n = 67), D. g. buergersi (n = 8), D. goodfellowi unidentified ssp. (n = 8), golden-mantled tree kangaroo (D. g. pulcherrimus; n = 1), and two additional New Guinea Dendrolagus taxa to determine whether D. matschiei and D. g. buergersi are sister taxa. D. matschiei and D. g. buergersi were not placed as sister taxa in our phylogenetic analyses; however, we were unable to analyse a known sample from a D. g. goodfellowi. We found initial genetic evidence that D. matschiei and the Lowland tree kangaroo (D. spadix) are sister taxa – they may have diverged after the formation of the Huon Peninsula of Papua New Guinea. Our results also support the elevation of D. g. pulcherrimus to a full species. An improved understanding of Dendrolagus molecular systematics will contribute substantially to their conservation.

scholarly journals A Molecular Phylogeny of the Dove Genus Zenaida: Mitochondrial and Nuclear DNA Sequences

The Condor ◽  
2000 ◽  
Vol 102 (4) ◽  
pp. 864-870 ◽  
Author(s):  
Kevin P. Johnson ◽  
Dale H. Clayton
Keyword(s):  
Molecular Phylogeny ◽  
Cytochrome B ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Bootstrap Support ◽  
Zenaida Asiatica ◽  
Species Status ◽  
Combined Analysis ◽  
Significant Conflict

AbstractWe reconstructed a phylogeny for the seven species of doves in the genus Zenaida on the basis of a combined analysis of mitochondrial (ND2 and cytochrome b) and nuclear (fibrinogen intron 7) DNA sequences. This phylogeny, which is completely resolved, is well supported with all nodes showing greater than 50% bootstrap support. There was no significant conflict between trees based on each gene independently, although trees produced from fibrinogen intron 7 did not resolve relationships among five of the Zenaida species. The species status of Z. graysoni, as well as that of Z. meloda, is suggested based on their divergence from sister taxa (about 1% and 4%, respectively) and other differences. Zenaida can be divided into two major groups: Zenaida asiatica and Z. meloda versus Z. aurita, Z. galapagoensis, Z. auriculata, Z. graysoni, and Z. macroura.

scholarly journals New World Nine-Primaried Oscine Relationships: Constructing a Mitochondrial DNA Framework

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 321-336 ◽  
Author(s):  
John Klicka ◽  
Kevin P. Johnson ◽  
Scott M. Lanyon
Keyword(s):  
Cytochrome B ◽  
New World ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Bootstrap Support ◽  
Wood Warblers ◽  
Nadh Dehydrogenase Subunit 2 ◽  
Mitochondrial Cytochrome B ◽  
Strong Bootstrap Support ◽  
High Degree

AbstractHistorically, a paucity of comparative morphological characters has led to much debate regarding relationships within and among the major lineages of New World nine-primaried oscines. More recently, DNA-DNA hybridization studies have provided novel and testable hypotheses of relationships, although no consensus has been reached. For 40 songbird taxa, we obtained 1,929 base pairs (bp) of DNA sequence from the mitochondrial cytochrome-b (894 bp) and NADH dehydrogenase subunit 2 (1,035 bp) genes. Phylogenetic analyses confirm the monophyly of this assemblage as traditionally defined. The lineages delineated historically on morphological grounds are retained; finches (Fringillinae) are sister to a well-supported clade (Emberizinae) containing blackbirds (Icterini), sparrows (Emberizini), wood-warblers (Parulini), tanagers (Thraupini), and cardinal-grosbeaks (Cardinalini). However, each tribe individually is either paraphyletic or polyphyletic with respect to most recent songbird classifications. Our results suggest that Euphonia is not a tanager but perhaps represents a derived form of cardueline finch. Piranga, traditionally considered a typical tanager, is a cardinaline in all of our analyses. Calcarius falls outside the sparrow lineage in all of our analyses, but its true affinities remain unclear. Elements of four different AOU families are represented in our clade Thraupini. The inclusion of several “tanager-finches” (Haplospiza, Diglossa, Tiaris, Volatinia, Sporophila) and a nectarivore (Coereba) in this clade is consistent with findings from other molecular phylogenies in suggesting that convergence in feeding specializations among some lineages has confounded traditional morphological classifications. We obtained a novel arrangement of relationships among tribes in our “best” topology; Cardinalini is sister to the rest of the Emberizinae assemblage (as defined by Sibley and Ahlquist [1990]), and Thraupini is sister to a clade containing Icterini, Emberizini, and Parulini. Despite nearly 2,000 bp of sequence for each taxon, and a high degree of stability across most weighting schemes and analytical methods, most nodes lack strong bootstrap support. The ND2 gene provided higher resolution than did cytochrome b, but combining genes provided the most highly supported and resolved topology. We consider the phylogeny a working hypothesis to be used as a guide for further studies within the nine-primaried oscine assemblage.

scholarly journals Genetic Diversity and Relatedness Among Six Ranunculus Species Unraveled by SRAP Markers

2018 ◽  
Vol 75 (2) ◽  
Author(s):  
Cristina D. KELEMEN ◽  
Monica HÂRŢA ◽  
Orsolya BORSAI ◽  
Katalin SZABO ◽  
Doina CLAPA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Related Species ◽  
Gene Diversity ◽  
Similarity Coefficient ◽  
Evolutionary Relationships ◽  
Closely Related Species ◽  
Srap Markers ◽  
Subgroup Ii ◽  
Species Cluster ◽  
Cluster A

The main aim of this study was to investigate the genetic diversity and phylogenetic relationships of six Ranunculus species using SRAP markers. The genotyping of 73 Ranunculus accessions showed that 12 primer pairs generated a total number of 212 polymorphic fragments with a 99.53 % level of polymorphism. Nei’s gene diversity ranged between 0.2237 and 0.3436 with an average of 0.3001. The UPGMA method with Nei72’s similarity coefficient ranging from 0.23 to 1.11 separated 73 accessions into two distinct groups (A and B). Cluster-A included R. acris members, while cluster-B included the rest of the tested species. Cluster-B was subsequently divided into two sub-groups (I and II). Subgroup-I consisted of R. carpaticus and R. serpens subsp. nemorosus accessions, while subgroup-II included the members of R. platanifolius, R. polyanthemos, and R. repens. R. polyanthemos and R. repens were founded the most closely related species. These findings provide a brand-new understanding of the evolutionary relationships of above mentioned Ranunculus species and may be useful tools for plant breeding and conservation purposes.

scholarly journals Presence of Novel, Potentially Homoacetogenic Bacteria in the Rumen as Determined by Analysis of Formyltetrahydrofolate Synthetase Sequences from Ruminants

2010 ◽  
Vol 76 (7) ◽  
pp. 2058-2066 ◽  
Author(s):  
Gemma Henderson ◽  
Graham E. Naylor ◽  
Sinead C. Leahy ◽  
Peter H. Janssen
Keyword(s):  
Amino Acid ◽  
Phylogenetic Trees ◽  
Amino Acid Sequences ◽  
Bootstrap Support ◽  
Bacterial Isolates ◽  
Conserved Residues ◽  
Formyltetrahydrofolate Synthetase ◽  
Full Diversity ◽  
Genes Encoding ◽  
Key Enzyme

ABSTRACT Homoacetogens produce acetate from H2 and CO2 via the Wood-Ljungdahl pathway. Some homoacetogens have been isolated from the rumen, but these organisms are expected to be only part of the full diversity present. To survey the presence of rumen homoacetogens, we analyzed sequences of formyltetrahydrofolate synthetase (FTHFS), a key enzyme of the Wood-Ljungdahl pathway. A total of 275 partial sequences of genes encoding FTHFS were PCR amplified from rumen contents of a cow, two sheep, and a deer. Phylogenetic trees were constructed using these FTHFS gene sequences and the translated amino acid sequences, together with other sequences from public databases and from novel nonhomoacetogenic bacteria isolated from the rumen. Over 90% of the FTHFS sequences fell into 34 clusters defined with good bootstrap support. Few rumen-derived FTHFS sequences clustered with sequences of known homoacetogens. Conserved residues were identified in the deduced FTHFS amino acid sequences from known homoacetogens, and their presence in the other sequences was used to determine a “homoacetogen similarity” (HS) score. A homoacetogen FTHFS profile hidden Markov model (HoF-HMM) was used to assess the homology of rumen and homoacetogen FTHFS sequences. Many clusters had low HS scores and HoF-HMM matches, raising doubts about whether the sequences originated from homoacetogens. In keeping with these findings, FTHFS sequences from nonhomoacetogenic bacterial isolates grouped in these clusters with low scores. However, sequences that formed 10 clusters containing no known isolates but representing 15% of our FTHFS sequences from rumen samples had high HS scores and HoF-HMM matches and so could represent novel homoacetogens.

scholarly journals Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees

2016 ◽  
Vol 33 (10) ◽  
pp. 2720-2734 ◽  
Author(s):  
Prabhav Kalaghatgi ◽  
Nico Pfeifer ◽  
Thomas Lengauer
Keyword(s):  
Simulated Data ◽  
Information Criterion ◽  
Bootstrap Support ◽  
Evolutionary Relationships ◽  
Distance Threshold ◽  
Labeled Trees ◽  
Wide Range ◽  
Branching Points ◽  
Cross Validation Error ◽  
Almost All

Abstract The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct ancestral relationship, or if there is not enough information to fully resolve all the branching points in the evolutionary tree. In this article, we present a fast distance-based agglomeration method called family-joining (FJ) for constructing so-called generally labeled trees in which taxa may be placed at internal vertices and the tree may contain polytomies. FJ constructs such trees on the basis of pairwise distances and a distance threshold. We tested three methods for threshold selection, FJ-AIC, FJ-BIC, and FJ-CV, which minimize Akaike information criterion, Bayesian information criterion, and cross-validation error, respectively. When compared with related methods on simulated data, FJ-BIC was among the best at reconstructing the correct tree across a wide range of simulation scenarios. FJ-BIC was applied to HIV sequences sampled from individuals involved in a known transmission chain. The FJ-BIC tree was found to be compatible with almost all transmission events. On average, internal branches in the FJ-BIC tree have higher bootstrap support than branches in the leaf-labeled bifurcating tree constructed using RAxML. 36% and 25% of the internal branches in the FJ-BIC tree and RAxML tree, respectively, have bootstrap support greater than 70%. To the best of our knowledge the method presented here is the first attempt at modeling evolutionary relationships using generally labeled trees.

Sign in / Sign up

Export Citation Format

Share Document