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At least 973 records · Page 54Linked to original sources
PubMed2006

Extensive gene flow blurs phylogeographic but not phylogenetic signal in Olea europaea L.

Genetic structure and evolutionary patterns of the wild olive tree (Olea europaea L.) were investigated with AFLP fingerprinting data at three geographic levels: (a) phylogenetic relationships of the six currently recognized subspecies in Eurasia and Africa; (b) lineage identification in subsp. europaea of the Mediterranean basin; and (c) phylogeography in the western Mediterranean. Two statistical approaches (Bayesian inference and analysis of molecular variance) were used to analyse the AFLP fingerprints. To determine the congruency and transferability of results across studies previous RAPD and ISSR data were analysed in a similar manner. Comparisons proved that qualitative results were mostly congruent but quantitative values differed, depending on the method of analysis. Neighbour-Joining analysis of AFLP phenotypes supported current classification of subspecies. At a Mediterranean scale no clear cut phylogeographic pattern was recovered, likely due to extensive gene flow between populations of subsp. europaea. Gene flow estimates calculated with conventional F-statistics showed that reproductive barriers separated neither populations nor lineages of O. europaea. Genetic divergence between eastern and western parts of the Mediterranean basin was observed only when geographical and population information were incorporated into the analyses through hierarchical analysis of molecular variance (AMOVA). Within the western Mediterranean, the highest genetic diversity was found in two regions: on both sides of the Strait of Gibraltar and in the Balearic archipelago. Additionally, long-lasting isolation of the northern-most populations of the Iberian Peninsula appeared to be responsible for a significant divergence.

DNA Fingerprinting↗
PubMed2001

Sponge homologs of vertebrate protein tyrosine kinases and frequent domain shufflings in the early evolution of animals before the parazoan-eumetazoan split.

The protein tyrosine kinases (PTKs) diverged specifically in animal lineages by gene duplications and domain shufflings to form a large protein family comprising diverse subfamilies with distinct domain organizations and functions. On the basis of a phylogenetic tree inferred from a comparison of the shared kinase domains, we previously showed that gene duplications that gave rise to diverse subfamilies predate the divergence of parazoans and eumetazoans. There is, however, still a possibility that, although the kinase domain duplications are ancient events, the domain shufflings that gave rise to different subfamilies with distinct domain organization are more recent event than the kinase domain duplications. To clarify this problem, we have determined the complete sequences of 15 sponge PTKs and have compared the domain organizations of these sponge PTKs and those of eumetazoans. For each of ten sponge PTKs out of 15 analyzed here, a possible eumetazoan (human and Drosophila) ortholog has been identified. The sponge and eumetazoan orthologs are virtually identical in domain organization and belong to the same subfamily in the PTK family tree for each of ten orthologous pairs, except for one subfamily in which a considerable deletions and/or insertions of domains are observed. This result suggests that most, if not all, of the domain shufflings, together with gene duplications, are very old, going back to dates before the parazoan-eumetazoan split, the earliest divergence among extant animal phyla.

Animals↗
PubMed2002

Dealing with saturation at the amino acid level: a case study based on anciently duplicated zebrafish genes.

The ray-finned fishes (Actinopterygii) seem to have two copies of many tetrapod (Sarcopterygii) genes. The origin of these duplicate fish genes is the subject of some controversy. One explanation for the existence of these extra fish genes could be an increase in the rate of independent gene duplications in fishes. Alternatively, gene duplicates in fish may have been formed in the ancestor of all or most Actinopterygii during a complete genome duplication event. A third possibility is that tetrapods have lost more genes than fish after gene or genome duplication events in the common ancestor of both lineages. These three hypotheses can be tested by phylogenetic reconstruction. Previously, we found that a large number of anciently duplicated genes of zebrafish are sister sequences in evolutionary trees suggesting that they were produced in Actinopterygii after the divergence of Sarcopterygii [Phil. Trans. R. Soc. Lond. B 356 (2001) 119]. On the other hand, several well-supported trees showed one of the two fish genes as the sister sequence to a monophyletic clade that included the second fish gene and genes from frog, chicken, mouse and human. These so-called outgroup topologies suggest that the origin of many fish duplicates predates the divergence of the Sarcopterygii and Actinopterygii and support the hypothesis that tetrapods have lost duplicates that have been retained in fish. Here we show that many of these 'outgroup' tree topologies are erroneous and can be corrected when mutational saturation is taken into account. To this end, a Java-based application has been developed to visualize the amount of saturation in amino acid sequences. The program graphically displays the number of observed frequent and rare amino acid replacements between pairs of sequences against their overall evolutionary distance. Discrimination between frequent and rare amino acid replacements is based on substitution probability matrices (e.g. PAM and BLOSUM). Evolutionary distances between sequences can be computed from the fraction of unsaturated sites only and evolutionary trees inferred by pairwise distance methods. When trees are computed by omitting the saturated fraction of sites, most fish duplicates are sister sequences.

Amino Acids↗
PubMed2000

Interpreting the universal phylogenetic tree.

The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

Cell Size↗
PubMed2005

Analysis of Acorus calamus chloroplast genome and its phylogenetic implications.

Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.

Acorus↗
PubMed2000

Phylogenetic analysis by rRNA comparison of the highly pathogenic sheep-infecting parasites Theileria lestoquardi and a Theileria species identified in China.

In the Northwestern part of China there have been reports of clinical cases in small ruminants of a haemoparasite with the characteristics of Theileria hirci (T. lestoquardi). However, some properties of this parasites argue against its classification as T. lestoquardi. In this paper, we present evidence that T. lestoquardi and the Chinese Theileria isolate are distinct parasite species. Phylogenetic analysis of determined nucleotide sequences of small subunit ribosomal RNA (srRNA) genes of T. lestoquardi and the Chinese Theileria parasite show that they belong to different clades within the phylogenetic tree of piroplasms. The srRNA sequence of the Chinese parasite was found to be most closely related to T. buffeli, which, with T. sergenti, belongs to an evolutionary lineage of non-lymphoproliferative Theileria species. On the other hand, it was clearly divergent to a lineage of lymphoproliferative Theileria species; T. annulata, T. parva, T. taurotragi, and T. lestoquardi, the latter being most closely related to T. annulata.

Animals↗
PubMed2006

Incorporating allelic variation for reconstructing the evolutionary history of organisms from multiple genes: An example from Rosa in North America.

Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one nonrecombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix among organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI), and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation, and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida-R. palustris, R. foliolosa, and R. blanda-R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.

Algorithms↗
PubMed2003

Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats.

The Asr2 gene encodes a putative transcription factor that is up-regulated in leaves and roots of tomato plants exposed to water-deficit stress. This gene was first cloned and characterized in a cultivar of commercial tomato (Lycopersicon esculentum cv. Ailsa Craig). In this work, we report the complete coding sequences of the orthologous Asr2 genes in six wild tomato lineages: L. hirsutum, L. cheesmanii, L. esculentum v. cerasiforme, L. chilense, L. peruvianum v. humifusum and L. peruvianum f. glandulosum. Estimates of the Ka/Ks ratio (omega) in pairwise comparisons within the genus Lycopersicon were equal or greater than 1 (a signature of adaptive evolution) when involving L. chilense and L. peruvianum v. humifusum. Interestingly, these two species are distinct from the others in their adaptation to dry habitats. We also mapped the detected substitutions onto a phylogenetic tree of the genus Lycopersicon. Remarkably, there are two and three amino acid substitutions, which contrast with the absence of synonymous substitutions along the terminal branches leading to L. chilense and L. peruvianum v. humifusum, respectively. Likelihood ratio tests confirmed that omega values in the branches leading to these species are significantly different from the remaining branches of the tree. Moreover, inferred changes in the branches leading to these species that inhabit dry areas are nonconservative and may be associated with dramatic alterations in ASR2 protein conformation. In this work, we demonstrate accelerated rates of amino acid substitutions in the Asr2 gene of tomato lineages living in dry habitats, thus giving support to the hypothesis of adaptive Darwinian evolution.

Amino Acid Sequence↗
PubMed1999

In situ detection of novel bacterial endosymbionts of Acanthamoeba spp. phylogenetically related to members of the order Rickettsiales.

Acanthamoebae are ubiquitous soil and water bactivores which may serve as amplification vehicles for a variety of pathogenic facultative bacteria and as hosts to other, presently uncultured bacterial endosymbionts. The spectrum of uncultured endosymbionts includes gram-negative rods and gram-variable cocci, the latter recently shown to be members of the Chlamydiales. We report here the isolation from corneal scrapings of two Acanthamoeba strains that harbor gram-negative rod endosymbionts that could not be cultured by standard techniques. These bacteria were phylogenetically characterized following amplification and sequencing of the near-full-length 16S rRNA gene. We used two fluorescently labelled oligonucleotide probes targeting signature regions within the retrieved sequences to detect these organisms in situ. Phylogenetic analyses demonstrated that they displayed 99.6% sequence similarity and formed an independent and well-separated lineage within the Rickettsiales branch of the alpha subdivision of the Proteobacteria. Nearest relatives included members of the genus Rickettsia, with sequence similarities of approximately 85 to 86%, suggesting that these symbionts are representatives of a new genus and, perhaps, family. Distance matrix, parsimony, and maximum-likelihood tree-generating methods all consistently supported deep branching of the 16S rDNA sequences within the Rickettsiales. The oligonucleotide probes displayed at least three mismatches to all other available 16S rDNA sequences, and they both readily permitted the unambiguous detection of rod-shaped bacteria within intact acanthamoebae by confocal laser-scanning microscopy. Considering the long-standing relationship of most Rickettsiales with arthropods, the finding of a related lineage of endosymbionts in protozoan hosts was unexpected and may have implications for the preadaptation and/or recruitment of rickettsia-like bacteria to metazoan hosts.

Acanthamoeba↗
PubMed1996

Rapid allelic diversification and intensified selection at antigen recognition sites of the Mhc class II DPB1 locus during hominoid evolution.

The evolution of polymorphism at the Mhc class II DPB1 locus was studied by comparison of chimpanzee (Pan troglodytes), pygmy chimpanzee (Pan paniscus), gorilla (Gorilla gorilla) and human DPB1 alleles. Extensive polymorphism was found in all hominoids. The clustering of sequences in the phylogenetic tree is consistent with rapid generation of the DPB1 polymorphism. Analysis of the substitution pattern for human alleles shows an excess of non-synonymous changes to synonymous changes at antigen recognition sites, indicating that the amino acid polymorphism at these sites is being maintained by selection. By contrast, no excess of nonsynonymous changes was found at the antigen recognition sites of nonhuman hominoid species. Thus, it appears that diversifying selection on the DPB1 polymorphism has intensified in the lineage leading to humans. No evidence was found for the existence of ancient allelic lineages predating the divergence of the hominoid species. The number of synonymous differences among DPB1 alleles is lower than among DQB1 and DRB1 alleles, indicative of a more recent origin for the DPB1 polymorphism and consistent with the more rapid evolution suggested by the phylogenetic tree.

Alleles↗
PubMed2005

Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree.

Current phylogenies of the intracellular bacteria belonging to the genus Wolbachia identify six major clades (A-F), termed 'supergroups', but the branching order of these supergroups remains unresolved. Supergroups A, B and E include most of the wolbachiae found thus far in arthropods, while supergroups C and D include most of those found in filarial nematodes. Members of supergroup F have been found in arthropods (i.e. termites), and have previously been detected in the nematode Mansonella ozzardi, a causative agent of human filariasis. To resolve the phylogenetic positions of Wolbachia from Mansonella spp., and other novel strains from the flea Ctenocephalides felis and the filarial nematode Dipetalonema gracile, the authors generated new DNA sequences of the Wolbachia genes encoding citrate synthase (gltA), heat-shock protein 60 (groEL), and the cell division protein ftsZ. Phylogenetic analysis confirmed the designation of Wolbachia from Mansonella spp. as a member of the F supergroup. In addition, it was found that divergent lineages from Dip. gracile and Cte. felis lack any clear affiliation with known supergroups, indicating further genetic diversity within the Wolbachia genus. Finally, although the data generated did not permit clear resolution of the root of the global Wolbachia tree, the results suggest that the transfer of Wolbachia spp. from arthropods to nematodes (or vice versa) probably occurred more than once.

Animals↗
PubMed2002

Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism.

We used sequence polymorphism of the mitochondrial DNA D-loop (968 bp excluding the tandem repeat region) to determine genetic diversity of horses inhabiting Cheju (a southern island of Korea). Seventeen haplotypes with frequencies from 1.5 to 21.5% were found among 65 Cheju horse samples. Genetic diversity (h) of the 17 haplotypes was calculated to be 0.91, indicating that the extant Cheju horse population consists of diverse genetic groups in their maternal lineage. Phylogenetic analysis showed that 17 types of Cheju (D-loop sequences determined), 5 Mongolian, 6 Arabian, 3 Belgian, 2 Tsushima, 2 Yunnan, 1 Przewalskii, and 3 Thoroughbred horses (published sequences for the latter seven breeds) showed that Cheju horses were distributed into many different clusters in the tree. Four Mongolian horses clustered with separate Cheju horse groups, showing that some Cheju horses are clearly of Mongolian origin. The analysis of partial sequences (284 bp) of the D-loop of 109 horses showed that Thoroughbred, Mongolian, Lipizzan, and Arabian breeds are as diverse as Cheju horses. Our data together with others suggest that most horse breeds tested with reasonably sufficient numbers of samples are diverse in their maternal lineages and also are not uniquely different from each other.

Animals↗
PubMed2001

The hAT family: a versatile transposon group common to plants, fungi, animals, and man.

Transposons are ubiquitous mobile genetic elements found in all eu- and prokaryotic cells. The first transposon identified, the maize Activator element, belongs to the hAT family. hAT transposons have been identified in most eukaryotic lineages, including plants, fungi, animals and even man. The basic structural and functional features of this transposon family and its phylogenetic roots are discussed in detail, including a phylogenetic tree deduced from the amino acid sequence of the most conserved part of the transposon-encoded transposase. Emphasis is given to the use of hAT transposons as tools for gene tagging and insect transformation as well as to their biological function, i.e. are they selfish DNA, beneficial companions, or even both?

Amino Acid Sequence↗
PubMed1992

Allozyme evidence for crane systematics and polymorphisms within populations of Sandhill, Sarus, Siberian, and whooping cranes.

Electrophoretic analysis of proteins yielded evidence on the relationships of species of cranes and on genetic diversity within populations of some species. Diversity within the Greater Sandhill crane and a Florida population of the Florida Sandhill crane was similar to that of most other vertebrates, but diversity was low in the Mississippi Sandhill crane, in the Okefenokee population of the Florida Sandhill crane, and within the Siberian and Sarus cranes. Diversity was surprisingly high among whooping cranes, whose number dropped to less than 25 early in this century. Phylogenetic analysis, using both character state and distance algorithms, yielded highly concordant trees for the 15 species. The African crowned cranes (Balearica) were widely divergent from all other cranes. Species of Anthropoides, Bugeranus, and Grus clustered closely but sorted into two lineages: a Whooper Group consisted of the whooping, common, hooded, black-necked, white-naped, and red-crowned cranes of genus Grus; and a Sandhill Group included the Sandhill, Siberian, Sarus, and Brolga cranes of genus Grus, the wattled crane of genus Bugeranus, and the Demoiselle and blue cranes of genus Anthropoides.

Alleles↗
PubMed2005

Evidence from small-subunit ribosomal RNA sequences for a fungal origin of Microsporidia.

The phylum Microsporidia comprises a species-rich group of minute, single-celled, and intra-cellular parasites. Lacking normal mitochondria and with unique cytology, microsporidians have sometimes been thought to be a lineage of ancient eukaryotes. Although phylogenetic analyses using small-subunit ribosomal RNA (SSU-rRNA) genes almost invariably place the Microsporidia among the earliest branches on the eukaryotic tree, many other molecules suggest instead a relationship with fungi. Using maximum likelihood methods and a diverse SSU-rRNA data set, we have re-evaluated the phylogenetic affiliations of Microsporidia. We demonstrate that tree topologies used to estimate likelihood model parameters can materially affect phylogenetic searches. We present a procedure for reducing this bias: "tree-based site partitioning," in which a comprehensive set of alternative topologies is used to estimate sequence data partitions based on inferred evolutionary rates. This hypothesis-driven approach appears to be capable of utilizing phylogenetic information that is not available to standard likelihood implementations (e.g., approximation to a gamma distribution); we have employed it in maximum likelihood and Bayesian analysis. Applying our method to a phylogenetically diverse SSU-rRNA data set revealed that the early diverging ("deep") placement of Microsporidia typically found in SSU-rRNA trees is no better than a fungal placement, and that the likeliest placement of Microsporidia among non-long-branch eukaryotic taxa is actually within fungi. These results illustrate the importance of hypothesis testing in parameter estimation, provide a way to address certain problems in difficult data sets, and support a fungal origin for the Microsporidia.

Animals↗
PubMed2004

Phylogeny and evolution of Digitulati ground beetles (Coleoptera, Carabidae) inferred from mitochondrial ND5 gene sequences.

Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 87 specimens consisting of 32 species which have been believed to belong to the division Digitulati (one of the lineages of the subtribe Carabina) of the world. There have been recognized six lineages, which are well separated from each other. Each lineage contains the following genus: (1) the lineage A: Ohomopterus from Japan; (2) the lineage B: Isiocarabus from eastern Eurasian Continent; (3) the lineage C: Carabus from China which are further subdivided into three sublineages; (4) the lineage D: Carabus from USA; (5) the lineage E: Carabus from the Eurasian Continent, Japan and North America; and (6) the lineage F: Eucarabus from the Eurasian Continent. Additionally, the genus Acrocarabus which had been treated as a constituent of the division Archicarabomorphi has been recognized to be the 7th lineage of the division Digitulati from the ND5 genealogical analysis as well as morphology. These lineages are assumed to have radiated within a short period and are largely linked to their geographic distribution.

Animals↗
PubMed1989

The evolution of lysozyme and alpha-lactalbumin.

From the analysis of phylogenetic trees constructed from the amino acid sequences and metal-binding properties of various lysozymes c and alpha-lactalbumins, it was found that before the divergence of the lineages of birds and mammals, calcium-binding lysozyme diverged from non-calcium-binding lysozyme. alpha-Lactalbumin evolved from the calcium-binding lysozyme along the mammalian lineage after the divergence of birds and mammals. Rapid evolution took place, not in the process of acquisition of the activity of alpha-lactalbumin, but after the loss of lysozyme activity, due to the change in the distribution of selective pressure on each amino acid site. A general process for the change in function of a protein during evolution is suggested to be as follows: after duplication of the gene, one of their protein products acquires a new function, besides that already present; the old function is eventually lost.

Amino Acid Sequence↗
PubMed1995

The sixth and seventh cholera pandemics are due to independent clones separately derived from environmental, nontoxigenic, non-O1 Vibrio cholerae.

The DNA sequences of the asd genes from 45 isolates of Vibrio cholerae (19 clinical O1 isolates, 2 environmental nontoxigenic O1 isolates, and 24 isolates with different non-O1 antigens) were determined. No differences were found within either sixth- or seventh-pandemic isolates; however, variation was found between the two forms and among the non-O1 isolates. O139 isolates had sequences identical to those of seventh-pandemic isolates. Phylogenetic trees with Vibrio mimicus as the outgroup suggest that the sixth-pandemic, seventh-pandemic, and U.S. Gulf isolates are three clones that have evolved independently from different lineages of environmental, nontoxigenic, non-O1 V. cholerae isolates. There is evidence for horizontal transfer of O antigen, since isolates with nearly identical asd sequences had different O antigens, and isolates with the O1 antigen did not cluster together but were found in different lineages. We also found evidence for recombination events within the asd gene of V. cholerae. V. cholerae may have a higher level of genetic exchange and a lower level of clonality than species such as Salmonella enterica and Escherichia coli.

Bacterial Vaccines↗