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At least 649 records · Page 36Linked to original sources
PubMed2006

Identification and molecular characterization of subsubtype A4 in central Africa.

Phylogenetic analysis on partial env sequences of HIV-1-positive samples obtained from sentinel population groups in HIV serosurveillance studies in 1997 and 2002 in the Democratic Republic of Congo (DRC) revealed a high genetic diversity in the number of cocirculating subtypes/CRFs as well as intrasubtype diversity. A cluster of three strains that formed a distinct and well-separated group within the subtype A radiation was observed. To determine a more precise structure of these viruses, the full-length genomes were sequenced. Phylogenetic tree and bootscan analysis showed that all three newly characterized viruses formed a new nonrecombinant lineage that was more closely related to subtype A. The SUDI (Subtype Distance) program showed that the distances of the newly derived HIV-1 sequences to subtype A references fell in the range of distances previously characterized for subsubtypes. According to current nomenclature rules, we have thus designated this new lineage as subsubtype A4. Analysis of viral sequences from other African countries suggests that the A4 strains seem restricted to DRC where they already circulated at the onset of the HIV/AIDS epidemic.

Africa, Central↗
PubMed2003

Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins.

The bacterial LacI/GalR family repressors such as lactose operon repressor (LacI), purine nucleotide synthesis repressor (PurR), and trehalose operon repressor (TreR) consist of not only the N-terminal helix-turn-helix DNA-binding domain but also the C-terminal ligand-binding domain that is structurally homologous to periplasmic sugar-binding proteins. These structural features imply that the repressor family evolved by acquiring the DNA-binding domain in the N-terminal of an ancestral periplasmic binding protein (PBP). Phylogenetic analysis of the LacI/GalR family repressors and their PBP homologues revealed that the acquisition of the DNA-binding domain occurred first in the family, and ligand specificity then evolved. The phylogenetic tree also indicates that the acquisition occurred only once before the divergence of the major lineages of eubacteria, and that the LacI/GalR and the PBP families have since undergone extensive gene duplication/loss independently along the evolutionary lineages. Multiple alignments of the repressors and PBPs furthermore revealed that repressors and PBPs with the same ligand specificity have the same or similar residues in their binding sites. This result, together with the phylogenetic relationship, demonstrates that the repressors and the PBPs individually acquired the same ligand specificity by homoplasious replacement, even though their genes are encoded in the same operon.

Amino Acid Sequence↗
PubMed2002

The structural organization of ascidian Halocynthia roretzi troponin I genes.

The organization of troponin I (TnI) genes from the ascidian Halocynthia roretzi have been determined. Halocynthia possesses roughly two types of TnI isoforms. One type is a single-copied adult TnI (adTnI) gene, which contains eight exons and seven introns. adTnI expresses two isoforms, the shorter body wall muscle TnI and the longer cardiac TnI, through alternative splicing. The mRNAs of these TnI isoforms may undergo trans-splicing of the 5'-leader sequences, like the TnI mRNA of another ascidian species, Ciona intestinalis. The other type comprises multi-copied larval TnI (laTnI) genes. Halocynthia has at least three laTnIs (alpha, beta, and gamma), which are composed of five exons and four introns, and two of them (alpha and gamma) are clustered in tandem. All laTnIs have B- and M-regions within their 5'-upstream regions, which have been discovered to be the regulatory elements of Halocynthia larval actin genes. The expression of Halocynthia laTnIs and larval actins may be regulated in the same manner. It is known that Ciona does not possess a larva-specific TnI isoform. The phylogenetic tree of ascidian TnIs suggests that laTnIs might have only been generated within the Pleurogona lineage after Enterogona/Pleurogona divergence, and this scenario well agrees with the absence of laTnIs in Ciona.

Amino Acid Sequence↗
PubMed2004

The genus Spiroplasma and its non-helical descendants: phylogenetic classification, correlation with phenotype and roots of the Mycoplasma mycoides clade.

The genus Spiroplasma (helical mollicutes: Bacteria: Firmicutes: Mollicutes: Entomoplasmatales: Spiroplasmataceae) is associated primarily with insects. The Mycoplasma mycoides cluster (sensu Weisburg et al. 1989 and Johansson and Pettersson 2002) is a group of mollicutes that includes the type species - Mycoplasma mycoides - of Mycoplasmatales, Mycoplasmataceae and Mycoplasma. This cluster, associated solely with ruminants, contains five other species and subspecies. Earlier phylogenetic reconstructions based on partial 16S rDNA sequences and a limited sample of Spiroplasma and Mycoplasma sequences suggested that the genus Mycoplasma was polyphyletic, as the M. mycoides cluster and the grouping that consisted of the hominis and pneumoniae groups of Mycoplasma species were widely separated phylogenetically and the M. mycoides cluster was allied with Spiroplasma. It is shown here that the M. mycoides cluster arose from Spiroplasma through an intermediate group of non-helical spiroplasmal descendants - the Entomoplasmataceae. As this conclusion has profound implications in the taxonomy of Mollicutes, a detailed phylogenetic study of Spiroplasma and its non-helical descendants was undertaken. These analyses, done with maximum-parsimony, provide cladistic status; a new nomenclature is introduced here, based on 'bottom-up' rather than 'top-down' clade classification. The order Entomoplasmatales consists of four major clades: (i) the Mycoides-Entomoplasmataceae clade, which contains M. mycoides and its allies and Entomoplasma and Mesoplasma species and is a sister lineage to (ii) the Apis clade of Spiroplasma. Spiroplasma and the Entomoplasmataceae are paraphyletic, but this status does not diminish their phylogenetic usefulness. Five species that were previously unclassified phylogenetically are basal to the Apis clade sensu strictu and to the Mycoides clade. One of these species, Spiroplasma sp. TIUS-1, has very poor helicity and a very small genome (840 kbp); this putative species can be envisioned as a 'missing link' in the evolution of the Mycoides-Entomoplasmataceae clade. The other two Spiroplasma clades are: (iii) the Citri-Chrysopicola-Mirum clade (serogroups I, II, V and VIII) and (iv) the ixodetis clade (serogroup VI). As Mesoplasma lactucae represents a basal divergence within the Mycoides-Entomoplasmataceae clade, and as Entomoplasma freundtii is basal to the Mycoides clade, M. mycoides and its allies must have arisen from an ancestor in the Entomoplasmataceae. The paraphyletic grouping that consists of the Hominis and Pneumoniae groups (sensu Johansson & Pettersson 2002) of Mycoplasma species contains the ancestral roots of Ureaplasma spp. and haemoplasmas. This clade is a sister lineage to the Entomoplasmatales clade. Serological classifications of spiroplasma are very highly supported by the trees presented. Genome size and G+C content of micro-organismal DNA were moderately conserved, but there have been frequent and polyphyletically distributed genome reductions. Sterol requirements were polyphyletic, as was the ability to grow in the presence of polyoxyethylene sorbitan-supplemented, but not serum-supplemented, media. As this character is not phylogenetically distributed, Mesoplasma and Entomoplasma should be combined into a single genus. The phylogenetic trees presented here confirm previous reports of polyphyly of the genus Mycoplasma. As both clades of Mycoplasma contain several species of great practical importance, a change of the genus name for species in either clade would have immense practical implications. In addition, a change of the genus name for M. mycoides would have to be approved by the Judicial Commission. For these reasons, the Linnaean and phylogenetic classifications of Mycoplasma must for now be discrepant.

Base Composition↗
PubMed2004

Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.

Two Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30-37 degrees C and in the presence of 2-3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C(15 : 0) as the major fatty acid. The DNA G + C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the gamma-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the gamma-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98.5 % and a mean DNA-DNA relatedness level of 9.4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T = KCTC 12182T = DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T = KCTC 12183T = DSM 16071T).

Bacterial Typing Techniques↗
PubMed2006

Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure.

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species-rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome-specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.

Animals↗
PubMed2005

Multiple origins of U genome in two UM genome tetraploid Aegilops species, Ae. columnaris and Ae. triaristata, revealed based on the polymorphism of a genome-specific PCR fragment.

To elucidate the evolutionary mode of the formation of species via polyploidization, we conducted phylogenetic analysis of the U genome of the UM genome tetraploid Aegilops species, Ae. columnaris and Ae. triaristata. Using the genome-specific PCR primer set U31, we investigated the variation of the U genome of 48 accessions each of Ae. columnaris and Ae. triaristata and 72 accessions of their diploid ancestor Ae. umbellulata. As a result, three alleles were distinguishable by amplified length and CAPS polymorphisms, namely, allele I = normal size with an MspI site, allele II = normal size without an MspI site, and allele III = shorter size caused by a 123bp deletion. All three alleles were detected both in diploid and tetraploid accessions. Sequence comparison indicated the inheritance of alleles I and III from the diploid to the tetraploids, suggesting multiple origins of the U genome of the tetraploids. Regarding allele II, however, the sequence comparison indicated that parallel mutations at the MspI site produced allele II several times. The phylogenetic tree based on the sequences of the U31 region demonstrated the presence of a third lineage of the U genome from Ae. umbellulata to Ae. columnaris. Consequently, we concluded that the U genome had at least three origins in Ae. columnaris, and at least two, probably more, in Ae. triaristata.

Alleles↗
PubMed1999

The population structure of Trypanosoma cruzi: expanded analysis of 54 strains using eight polymorphic CA-repeat microsatellites.

Recently we cloned and sequenced the first eight Trypanosoma cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite. We have now studied 23 further strains, increasing from 11 to 31 the number of strains obtained from patients with chronic Chagas disease. This expanded set of 54 strains and clones analyzed with the eight microsatellites markers confirmed the previously observed diploidy, clonal population organization and very high polymorphism of T. cruzi. Moreover, this new study disclosed two new features of the population genetic structure of T. cruzi. The first was the discovery that, similarly to what we had previously shown for strains isolated from insect vectors, mammals and humans with acute disease, isolates from patients in the chronic phase of Chagas disease could also be multiclonal, albeit at a reduced proportion. Second, when we used parsimony to display the genetic relationship among the clonal lineages in an unrooted Wagner network we observed, like before, a good correlation of the tree topography with the classification in three clusters on the basis of single locus analysis of the ribosomal RNA genes. However, a significant new finding was that now the strains belonging to cluster 2 split in two distant sub-clusters. This observation suggests that the evolutionary history of T. cruzi may be more complex than we previously thought.

Animals↗
PubMed2004

Trypanosomes are monophyletic: evidence from genes for glyceraldehyde phosphate dehydrogenase and small subunit ribosomal RNA.

The genomes of Trypanosoma brucei, Trypanosoma cruzi and Leishmania major have been sequenced, but the phylogenetic relationships of these three protozoa remain uncertain. We have constructed trypanosomatid phylogenies based on genes for glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) and small subunit ribosomal RNA (SSU rRNA). Trees based on gGAPDH nucleotide and amino acid sequences (51 taxa) robustly support monophyly of genus Trypanosoma, which is revealed to be a relatively late-evolving lineage of the family Trypanosomatidae. Other trypanosomatids, including genus Leishmania, branch paraphyletically at the base of the trypanosome clade. On the other hand, analysis of the SSU rRNA gene data produced equivocal results, as trees either robustly support or reject monophyly depending on the range of taxa included in the alignment. We conclude that the SSU rRNA gene is not a reliable marker for inferring deep level trypanosome phylogeny. The gGAPDH results support the hypothesis that trypanosomes evolved from an ancestral insect parasite, which adapted to a vertebrate/insect transmission cycle. This implies that the switch from terrestrial insect to aquatic leech vectors for fish and some amphibian trypanosomes was secondary. We conclude that the three sequenced pathogens, T. brucei, T. cruzi and L. major, are only distantly related and have distinct evolutionary histories.

Amino Acid Sequence↗
PubMed2006

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

BACKGROUND: Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. BLASTN, TBLASTX, or combinations of both are used to locate high-scoring segment pairs (HSPs) between two sequences from which pairwise similarities and distances are computed in different ways resulting in a total of 96 GBDP variants. The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called delta value, from the respective distance matrices. Additionally, we compare the trees inferred from these matrices using UPGMA, NJ, BIONJ, FastME, or STC, respectively, with the NCBI taxonomy tree of the taxa under study. RESULTS: Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. Distances based on the proportion of "matched" HSP length to average genome length were best for tree estimation. Additionally we found that using TBLASTX instead of BLASTN and, particularly, combining TBLASTX and BLASTN leads to a small but significant increase in accuracy. Other factors do not significantly affect the phylogenetic outcome. The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. delta values are found to be a reliable predictor of phylogenetic accuracy. CONCLUSION: Using the most treelike distance matrices, as judged by their delta values, distance methods are able to recover all major plant lineages, and are more in accordance with Apicomplexa organelles being derived from "green" plastids than from plastids of the "red" type. GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. A framework is established to further develop and improve such methods. delta values are a topology-independent tool of general use for the development and assessment of distance methods for phylogenetic inference.

Algorithms↗
PubMed2000

A compound poisson process for relaxing the molecular clock.

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.

Bayes Theorem↗
PubMed2025

Whole genome sequencing-based detection of extensively drug-resistant tuberculosis from Ethiopia.

BACKGROUND: Rapid and accurate detection of extensively drug-resistant tuberculosis is crucial for effective intervention. Next-generation sequencing technologies have been recommended to rapidly and accurately detect resistance to second-line anti-TB drugs. We deployed whole-genome sequencing to detect mutations associated with drug resistance in pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis strains in Ethiopia. METHODS: This report is part of the routine laboratory-based drug-resistance surveillance in Ethiopia. Among 15 pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis isolates identified during the study period, eleven isolates were retrieved by Whole-genome sequencing. Illumina NextSeq 550 instruments were used to generate genomic data. Lineage and drug-resistance prediction were performed with Tuberculosis Profiler, while phylogeny was conducted by IQ-tree. RESULTS: Of the genotyped isolates, whole-genome sequencing identifies five extensively drug-resistant tuberculosis and four pre-extensively drug-resistant tuberculosis strains. It detects fluoroquinolone resistance mutations gyrA (Ala90Val, Asp94Tyr, Asp94Gly). Bedaquiline resistance mutations are found in atpE (Glu61Asp) and Rv0678 (139dupG, 141 and 142dupTC). Cross-resistance is identified between bedaquiline and clofazimine (n = 4) and delamanid and pretomanid (n = 1). Concordance result is observed between phenotypic drug-susceptibility testing and whole-genome sequencing for eight cases, while three cases are discordant (fluoroquinolones, delamanid, and pretomanid). Phylogenetic analysis reveals three major lineages: Lineage 4 (Euro-American, n = 6 isolates), Lineage 3 (East African-Indian, n = 3 isolates), and Lineage 1 (Indo-Oceanic, n = 2 isolates). CONCLUSIONS: Whole-genome sequencing identifies dominant mutations in genes such as gyrA, atpE, and Rv067 that are associated with resistance to second-line anti-tuberculosis drugs. Significant cross-resistance is observed between key second-line drugs, bedaquiline and clofazimine, as well as delamanid and pretomanid. This finding highlights the need for routine genomic surveillance to detect drug resistance early, improve treatment outcomes, and prevent transmission.

Journal Article↗
PubMed2003

Coalescence in a metapopulation with recurrent local extinction and recolonization.

Many species exist as metapopulations in balance between local population extinction and recolonization. The effect of these processes on average population differentiation, within-deme diversity, and species wide diversity has been considered previously. In this paper, coalescent simulations of Slatkin's propagule-pool and migrant-pool models are used to characterize the distribution of neutral genetic diversity within demes (pi(S)), diversity in the metapopulation a whole (pi(T)), the ratio F(ST) = (pi(T) - pi(S))/pi(T), Tajima's D statistic, and several ratios of gene-tree branch lengths. Using these distributions, power to detect differences in key metapopulation parameter values is determined under contrasting sampling regimes. The results indicate that it will be difficult to use sequence data from a single locus to detect a history of extinctions and recolonizations in a metapopulation because of high genealogical variance, the loss of diversity due to reductions in effective population size, and the fact that a genealogy of lineages from different demes under Slatkin's model differs from a neutral coalescent only in its time scale. Genetic indices of gene-tree shape that capture the effects of extinction/recolonization on both external branches and the length of the genealogy as a whole will provide the best indication of metapopulation dynamics if several lineages are sampled from several different demes.

Base Sequence↗
PubMed2002

Phylogenetic analysis reveals multiple lateral transfers of adenosine-5'-phosphosulfate reductase genes among sulfate-reducing microorganisms.

Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5'-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment ( approximately 900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the delta-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028-6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.

Cell Lineage↗
PubMed2004

Phylogeny, taxonomy and grouping of Trypanosoma rangeli isolates from man, triatomines and sylvatic mammals from widespread geographical origin based on SSU and ITS ribosomal sequences.

Phylogenetic relationships among Trypanosoma rangeli isolates from man, wild mammals and triatomine bugs from widespread geographical origin were inferred by comparison of the small subunit of ribosomal gene sequences. The phylogenetic trees indicated that the subgenus Herpetosoma is polyphyletic and strongly supported division of this group into two monophyletic lineages, one made up of T. rangeli, T. rangeli-like and allied species and other consisting of T. lewisi and related taxa. Based on phylogenetic analysis, morphology, behaviour in vertebrate and invertebrate hosts and epidemiology we propose: a) the validation of Herpetosoma as a taxon comprised only for species of group lewisi and the maintenance of T. lewisi as the type-species of this subgenus; b) the classification of T. rangeli, T. rangeli-like and allied species into a 'T. rangeli-clade' more closely related to Schizotrypanum than to T. lewisi or T. brucei. The phylogenetic tree disclosed at least 4 groups within the clade T. rangeli, all confirmed by polymorphism of the internal transcribed spacer, thus conferring for the first time phylogenetic support to groups of T. rangeli and corroborating the high complexity of this taxon. Grouping was independent of their mammalian host-species and geographical origin, indicating that other factors are determining this segregation.

Animals↗
PubMed2000

What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree.

The cnemophiline 'birds of paradise' (Cnemophilinae) and Macgregor's 'bird of paradise' (Macgregoria) have traditionally been included in the Paradisaeidae although their relationships within the group have been enigmatic and subject to repeated discussion in the literature. Here we use sequences from two mitochondrial genes, cytochrome b and cytochrome oxidase I, along with a suite of morphological characters, to investigate their relationships to paradisaeids and other members of the passerine Parvorder Corvida. The combined data strongly support the removal of both groups from the birds of paradise: the cnemophilines are basal members of the Corvoidea and Macgregoria is a member of the Meliphagoidea and embedded in the honeyeaters (Meliphagidae) close to the genus Melipotes. The amount of sequence divergence among basal passeriforms and members of the Corvida, as well as available fossil evidence for Australian corvidans, suggest that cnemophilines represent an ancient lineage within the corvoid radiation. Because cnemophilines and Macgregoria have been placed at the base of the paradisaeid tree, hypotheses of morphological, behavioural and ecological character-state transformations within the family will require reanalysis.

Animals↗
PubMed2003

Two highly divergent ancient allelic lineages of the transporter associated with antigen processing (TAP) gene in Xenopus: further evidence for co-evolution among MHC class I region genes.

In the frog Xenopus, MHC class I antigen presentation and processing genes (the immunoproteasome LMP2 and LMP7 and the transporter TAP1 and TAP2) seem to be closely linked in a primordial organization. Two distinct lineages of class Ia and LMP7 loci were previously identified, thus strongly suggesting co-evolution among 'class I region' genes. We now show that the Xenopus MHC 'class I region' lies between class II and class III genes and we have isolated two distinct alleles at both the TAP1 and TAP2 loci. The alleles at each locus are remarkably divergent from each other and phylogenetic tree analysis revealed in both cases that they diverged from each other 60-100 million years ago (MYA). For lineage-frequency and linkage analysis, 25 wild-caught X. laevis and 16 X. tropicalis were examined. The two lineages were present in different frequencies for X. laevis and X. tropicalis. Nevertheless, in all cases, the LMP7, TAP1, and TAP2 lineages were found in a set comprising one of the two lineages. Furthermore, like the LMP7 lineages, the TAP lineages were detected in most Xenopus species that diverged from a common ancestor 80-100 MYA, suggesting that the 'class I region' biallelic lineages are under balancing selection.

Alleles↗
PubMed1999

The mitochondrial DNA molecule of the aardvark, Orycteropus afer, and the position of the Tubulidentata in the eutherian tree.

An outstanding problem in mammal phylogeny is the relationship of the aardvark (Orycteropus afer), the only living species of the order Tubulidentata, to the extant eutherian lineages. In order to examine this problem the complete mitochondrial DNA (mtDNA) molecule of the aardvark was sequenced and analysed. The aardvark tRNA-Ser (UCN) differs from that of other mammalian mtDNAs reported and appears to have reversed to the ancestral secondary structure of non-mammalian vertebrates and mitochondrial tRNAs in general. Phylogenetic analysis of 12 concatenated protein-coding genes (3325 amino acids) included the aardvark and 15 additional eutherians, two marsupials and a monotreme. The most strongly supported tree identified the aardvark as a sister group of a clade including the armadillo (Xenarthra) and the Cetferungulata (carnivores, perissodactyls, artiodactyls and cetaceans). By applying three molecular calibration points the divergence between the aardvark and armadillo-cetferungulates was estimated at ca. 90 million years before present.

Animals↗