scholarly journals Subfamilies of cpmA, a gene involved in circadian output, have different evolutionary histories in cyanobacteria

Microbiology ◽  
2006 ◽  
Vol 152 (1) ◽  
pp. 75-84 ◽  
Author(s):  
Volodymyr Dvornyk
Keyword(s):  
Phylogenetic Trees ◽  
Photosynthetic Bacteria ◽  
Nonsynonymous Substitution ◽  
Circadian System ◽  
The Other ◽  
Sequence Evolution ◽  
Functional Constraints ◽  
Terminal Domain ◽  
Nonsynonymous Site ◽  
Nonsynonymous Substitution Rate

The cpmA gene mediates an output signal in the cyanobacterial circadian system. This gene and its homologues are evolutionarily old, and occur in some non-photosynthetic bacteria and archaea as well as in cyanobacteria. The gene has two functional domains that differ drastically in their level of polymorphism: the N-terminal domain is much more variable than the PurE homologous C-terminal domain. The phylogenetic tree of the cpmA homologues features four main clades (C1–C4), two of which (C1 and C3) belong to cyanobacteria. These cyanobacterial clades match respective ones in the previously reported phylogenetic trees of the other genes involved in the circadian system. The phylogenetic analysis suggested that the C3 subfamily, which comprises the genes from the cyanobacteria with the kaiBC-based circadian system, experienced a lateral transfer, probably from evolutionarily old proteobacteria about 1000 million years ago. The genes of this subfamily have a significantly higher nonsynonymous substitution rate than those of C1 (2·13×10−10 and 1·53×10−10 substitutions per nonsynonymous site per year, respectively). It appears that the functional and selective constraints of the kaiABC-based system have slowed down the rate of sequence evolution compared to the cpmA homologues of the kaiBC-based system. On the other hand, the differences in the mutation rates between the two cyanobacterial clades point to the different functional constraints of the systems with or without kaiA.

Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
Fossil Record ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Charles Darwin ◽  
The Other ◽  
Charles Lyell ◽  
Single Origin ◽  
Molecular Studies ◽  
Richard Owen ◽  
First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

scholarly journals Coevolution of theS-Locus GenesSRK,SLGandSP11/SCRinBrassica oleraceaandB. rapa

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 931-940 ◽  
Author(s):  
Keiichi Sato ◽  
Takeshi Nishio ◽  
Ryo Kimura ◽  
Makoto Kusaba ◽  
Tohru Suzuki ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Gene Conversion ◽  
Phylogenetic Trees ◽  
Hypervariable Region ◽  
Recognition System ◽  
Self Incompatibility ◽  
Male And Female ◽  
Diversifying Selection ◽  
Tight Linkage ◽  
Nonsynonymous Site

AbstractBrassica self-incompatibility (SI) is controlled by SLG and SRK expressed in the stigma and by SP11/SCR expressed in the anther. We determined the sequences of the S domains of 36 SRK alleles, 13 SLG alleles, and 14 SP11 alleles from Brassica oleracea and B. rapa. We found three S haplotypes lacking SLG genes in B. rapa, confirming that SLG is not essential for the SI recognition system. Together with reported sequences, the nucleotide diversities per synonymous and nonsynonymous site (πS and πN) at the SRK, SLG, and SP11 loci within B. oleracea were computed. The ratios of πN:πS for SP11 and the hypervariable region of SRK were significantly >1, suggesting operation of diversifying selection to maintain the diversity of these regions. In the phylogenetic trees of 12 SP11 sequences and their linked SRK alleles, the tree topology was not significantly different between SP11 and SRK, suggesting a tight linkage of male and female SI determinants during the evolutionary course of these haplotypes. Genetic exchanges between SLG and SRK seem to be frequent; three such recent exchanges were detected. The evolution of S haplotypes and the effect of gene conversion on self-incompatibility are discussed.

Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

2021 ◽  
pp. 1-8
Author(s):  
Zainab M. Almutairi
Keyword(s):  
Pearl Millet ◽  
Phylogenetic Trees ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Internal Transcribed Spacers ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region ◽  
Local Cultivars ◽  
Pearl Millet Cultivars

Abstract Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

Neutral Evolution of the Sex-Determining Gene transformer in Drosophila

Genetics ◽  
2000 ◽  
Vol 154 (4) ◽  
pp. 1711-1720 ◽  
Author(s):  
Bryant F McAllister ◽  
Gilean A T McVean
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Variation ◽  
Nonsynonymous Substitution ◽  
Neutral Evolution ◽  
Sequence Evolution ◽  
Statistical Support ◽  
Rapid Pace ◽  
Elevated Rate ◽  
Evolution Sequence

Abstract The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. These changes in amino acid sequence are the result of either natural selection or neutral evolution. To differentiate between selective and neutral causes of this evolutionary change, analyses of both intraspecific and interspecific patterns of molecular evolution of tra gene sequences are presented. Sequences of 31 tra alleles were obtained from Drosophila americana. Many replacement and silent nucleotide variants are present among the alleles; however, the distribution of this sequence variation is consistent with neutral evolution. Sequence evolution was also examined among six species representative of the genus Drosophila. For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. In exon 3 of D. virilis and D. americana we find evidence for an elevated rate of nonsynonymous substitution, but no statistical support for a greater rate of nonsynonymous relative to synonymous substitutions. Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function.

The Drosophila montium subgroup species. Phylogenetic relationships based on mitochondrial DNA analysis

Genome ◽  
1996 ◽  
Vol 39 (5) ◽  
pp. 874-883 ◽  
Author(s):  
Nikolas Nikolaidis ◽  
Zacharias G. Scouras
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Dna Analysis ◽  
Restriction Site ◽  
Species Group ◽  
The Other ◽  
Complex Species ◽  
Restriction Site Maps ◽  
Montium Subgroup

Mitochondrial DNA (mtDNA) restriction site maps for three Drosophila montium subgroup species of the melanogaster species group, inhabiting Indian and Afrotropical montium subgroup territories, were established. Taking into account previous mtDNA data concerning six oriental montium species, a phylogeny was established using distance-matrix and parsimony methods. Both genetic diversity and mtDNA size variations were found to be very narrow, suggesting close phylogenetic relationships among all montium species studied. The phylogenetic trees that were constructed revealed three main lineages for the montium subgroup species studied: one consisting of the Afrotropical species Drosophila seguyi, which is placed distantly from the other species, one comprising the north-oriental (Palearctic) species, and one comprising the southwestern (south-oriental, Australasian, Indian, and Afrotropical) species. The combination of the mtDNA data presented here with data from other species belonging to the melanogaster and obscura subgroups revealed two major clusters: melanogaster and obscura. The melanogaster cluster is further divided into two compact lineages, comprising the montium subgroup species and the melanogaster complex species; the species of the other complex of the melanogaster subgroup, yakuba, disperse among the obscura species. The above grouping is in agreement with the mtDNA size variations of the species. Overall, among all subgroups studied, the species of the montium subgroup seem to be the most closely related. Key words : mtDNA restriction site maps, mtDNA size variations, Drosophila, phylogeny.

scholarly journals Long-Term Persistence of Infection in Chimpanzees Inoculated with an Infectious Hepatitis C Virus Clone Is Associated with a Decrease in the Viral Amino Acid Substitution Rate and Low Levels of Heterogeneity

2004 ◽  
Vol 78 (18) ◽  
pp. 9782-9789 ◽  
Author(s):  
Javier Fernandez ◽  
Deborah Taylor ◽  
Duncan R. Morhardt ◽  
Kathleen Mihalik ◽  
Montserrat Puig ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Amino Acid ◽  
Substitution Rate ◽  
Selective Pressure ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Nonsynonymous Substitution Rate ◽  
Over Time

ABSTRACT Two chimpanzees, 1535 and 1536, became persistently infected following inoculation with RNA transcripts from cDNA clones of hepatitis C virus (HCV). Analysis of the HCV genomes from both animals showed an accumulation of amino acid substitutions over time. The appearance of substitutions in the envelope genes was associated with increased antienvelope antibody titers. However, extensive mutations were not incorporated into hypervariable region 1 (HVR1). A comparison of the nonsynonymous substitution rate/synonymous substitution rate was made at various time points to analyze selective pressure. The highest level of selective pressure occurred during the acute phase and decreased as the infection continued. The nonsynonymous substitution rate was initially higher than the synonymous substitution rate but decreased over time from 3.3 × 10−3 (chimpanzee 1535) and 3.2 × 10−3 (chimpanzee 1536) substitutions/site/year at week 26 to 1.4 × 10−3 (chimpanzee 1535) and 1.7 × 10−3 (chimpanzee 1536) at week 216, while the synonymous substitution rate remained steady at ∼1 × 10−3 substitutions/site/year. Analysis of PCR products using single-stranded conformational polymorphism indicated a low level of heterogeneity in the viral genome. The results of these studies confirm that the persistence of infection is not solely due to changes in HVR1 or heterogeneity and that the majority of variants observed in natural infections could not arise simply through mutation during the time period most humans and chimpanzees are observed. These data also indicate that immune pressure and selection continue throughout the chronic phase.

Molecular Evolution and Nucleotide Sequences of the Maize Plastid Genes for the α Subunit of CF1 (atpA) and the Proteolipid Subunit of CF0 (atpH)

Genetics ◽  
1987 ◽  
Vol 116 (1) ◽  
pp. 127-139
Author(s):  
Steven R Rodermel ◽  
Lawrence Bogorad
Keyword(s):  
Plastid Genome ◽  
Higher Plants ◽  
Rapid Evolution ◽  
Evolutionary Process ◽  
Nonsynonymous Substitution ◽  
Spatial Arrangement ◽  
Regulatory Elements ◽  
Nucleotide Sequences ◽  
Sequence Evolution ◽  
Α Subunit

ABSTRACT The nucleotide sequences of the maize plastid genes for the α subunit of CF1 (atpA) and the proteolipid subunit of CF 0 (atpH) are presented. The evolution of these genes among higher plants is characterized by a transition mutation bias of about 2:1 and by rates of synonymous and nonsynonymous substitution which are much lower than similar rates for genes from other sources. This is consistent with the notion that the plastid genome is evolving conservatively in primary sequence. Yet, the mode and tempo of sequence evolution of these and other plastid-encoded coupling factor genes are not the same. In particular, higher rates of nonsynonymous substitution in atpE (the gene for the ∊ subunit of CF1) and higher rates of synonymous substitution in atpH in the dicot vs. monocot lineages of higher plants indicate that these sequences are likely subject to different evolutionary constraints in these two lineages. The 5′- and 3′ transcribed flanking regions of atpA and atpH from maize, wheat and tobacco are conserved in size, but contain few putative regulatory elements which are conserved either in their spatial arrangement or sequence complexity. However, these regions likely contain variable numbers of "species-specific" regulatory elements. The present studies thus suggest that the plastid genome is not a passive participant in an evolutionary process governed by a more rapidly changing, readily adaptive, nuclear compartment, but that novel strategies for the coordinate expression of genes in the plastid genome may arise through rapid evolution of the flanking sequences of these genes.

European bumblebees (Hymenoptera: Bombini)- phylogenetic relationships inferred from DNA sequences

2002 ◽  
Vol 33 (4) ◽  
pp. 361-386 ◽  
Author(s):  
Vest Pedersen
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Elongation Factor ◽  
Nuclear Gene ◽  
The Other ◽  
Elongation Factor 1Α ◽  
Nucleotide Bias

AbstractThe phylogenetics of 40 taxa of European bumblebees were analysed based on PCR amplified and direct sequenced DNA from one region of the mitochondrial gene Cytochrome Oxidase I (1046 bp) and for 26 taxa from two regions in the nuclear gene Elongation Factor 1α (1056 bp). The sequences were aligned to the corresponding sequences in the honey bee. Phylogenetic analyses based on parsimony, as well as maximum likelihood, indicate that the bumblebees can be separated into several well-supported clades. Most of the terminal clades correspond very well with the clades known from former phylogenetic analyses based on morphology and recognized as the subgenera: Mendacibombus, Confusibombus, Psithyrus, Thoracobombus, Megabombus, Rhodobombus, Kallobombus, Alpinobombus, Subterraneobombus, Alpigenobombus, Pyrobombus, Bombus and Melanobombus. All the cuckoo bumblebees form a well-supported clade, the subgenus Psithyrus, within the true bumblebees. All the analyses place Kallobombus as the most basal taxon in contradiction to former analyses. The other deeper nodes of the phylogenetic trees, which are weakly supported, deviate significantly from former published trees - especially the trees based on mtCO-I. Presumably, the reasons are that multiple hits and the strong bias of the bases A and T blur the relationships in the deepest part of the trees. Analyses of the region in mtCO-I show a very strong A+T bias (A+T= 75%), which also indicate preferences in the use of codons with A or T in third positions. In closely related entities, there is only a weak transversion bias (A+T). In the studied regions in EF 1-α, no nucleotide bias is observed. The observed differences in bases between the investigated taxa are relatively small and the gene is too conserved to solve all the questions that the analyses of the deeper nodes using mtCO-I raise.

scholarly journals In the Bacillus stearothermophilus DnaB-DnaG Complex, the Activities of the Two Proteins Are Modulated by Distinct but Overlapping Networks of Residues

2006 ◽  
Vol 188 (4) ◽  
pp. 1534-1539 ◽  
Author(s):  
Jenny Thirlway ◽  
Panos Soultanas
Keyword(s):  
Size Distribution ◽  
Bacillus Stearothermophilus ◽  
The Other ◽  
Linker Region ◽  
Terminal Domain ◽  
Structural Importance ◽  
Helicase Dnab ◽  
Terminal Domains

ABSTRACTWe demonstrate the primase activity ofBacillus stearothermophilusDnaG and show that it initiates at 3′-ATC-5′ and 3′-ATT-5′ sites synthesizing primers that are 22 or 23 nucleotides long. In the presence of the helicase DnaB the size distribution of primers is different, and a range of additional smaller primers are also synthesized. Nine residues from the N- and C-terminal domains of DnaB, as well as its linker region, have been reported previously to affect this interaction. InBacillus stearothermophilusonly three residues from the linker region (I119 and I125) and the N-terminal domain (Y88) of DnaB have been shown previously to have direct structural importance, and I119 and I125 mediate DnaG-induced effects on DnaB activity. The functions of the other residues (L138, T191, E192, R195, and M196) are still a mystery. Here we show that the E15A, Y88A, and E15A Y88A mutants bind DnaG but are not able to modulate primer size, whereas the R195A M196A mutant inhibited the primase activity. Therefore, four of these residues, E15 and Y88 (N-terminal domain) and R195 and M196 (C-terminal domain), mediate DnaB-induced effects on DnaG activity. Overall, the data suggest that the effects of DnaB on DnaG activity and vice versa are mediated by distinct but overlapping networks of residues.

Resolving the phylogenetic affinities of Kappaphycus inermis within the genus Kappaphycus (Gigartinales, Solieriaceae) using mitochondrial and plastid markers

Phytotaxa ◽  
2014 ◽  
Vol 162 (4) ◽  
pp. 223 ◽  
Author(s):  
Richard Verano Dumilag ◽  
Arturo Lluisma
Keyword(s):  
Phylogenetic Trees ◽  
The Philippines ◽  
The Other ◽  
Rubisco Spacer ◽  
Phylogenetic Placement ◽  
Sister Clade ◽  
Plastid Markers ◽  
The Subject ◽  
Phylogenetic Affinities ◽  
Local Farmers

Although the phylogeny of the genus Kappaphycus has been the subject of a number of published studies, the phylogenetic placement of Kappaphycus inermis within the genus has remained unresolved.  In this study, we sought to determine the phylogenetic affinities of K. inermis with the other congeneric species using mitochondrial (cox1 and cox2–3 spacer) and plastid (rbcL and RuBisCo spacer) markers, using specimens collected from northwestern Philippines. Morphological observations of the collected materials confirmed the presence of key morphological features that distinguish K. inermis from the other members of Kappaphycus. Molecular analyses based on the organellar genetic markers revealed that K. inermis is indeed phylogenetically distinct from K. alvarezii, K. striatus, K. cottonii and K. malesianus, a species which was recently erected based on specimens from Malaysia. The Philippine K. inermis specimens formed a sister clade to K. malesianus (also referred to as “Aring-aring” in Malaysia) in phylogenetic trees inferred from cox1, cox2–3 spacer and rbcL, but not the RuBisCo spacer whose sequence is identical in both K. inermis and K. malesianus.  The analysis also revealed  that specimens of unidentified Kappaphycus species collected from two other sites in the Philippines and referred to as “Aring-aring” by local farmers/traders were varieties of K. alvarezii and K. striatus.

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