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At least 505 records · Page 28Linked to original sources
PubMed2001

Selective extinction and rapid loss of evolutionary history in the bird fauna.

The extinction of species results in a permanent loss of evolutionary history. Recent theoretical studies show that this loss may be proportionally much smaller than the loss of species, but under some conditions can exceed it. Such conditions occur when the phylogenetic tree that describes the evolutionary relationships among species is highly imbalanced due to differences between lineages in past speciation and/or extinction rates. I used the taxonomy by C. G. Sibley and B. L. Monroe Jr to estimate the global loss of bird evolutionary history from historical and predicted extinctions, and to quantify the ensuing changes in balance of the bird phylogenetic tree. In the global bird fauna, evolutionary history is being lost at a high rate, similar to the rate of species extinction. The bird phylogenetic tree is highly imbalanced, and the imbalance is increased significantly by anthropogenic extinction. Historically, the elevated loss of bird evolutionary history has been fuelled mostly by phylogenetic non-randomness in the extinction of species, but the direct effect of tree imbalance is substantial and could dominate in the future.

Animals↗
PubMed1999

Locus specificity of polymorphic alleles and evolution by a birth-and-death process in mammalian MHC genes.

We have conducted an extensive phylogenetic analysis of polymorphic alleles from human and mouse major histocompatibility complex (MHC) class I and class II genes. The phylogenetic tree obtained for 212 complete human class I allele sequences (HLA-A, -B, and -C) has shown that all alleles from the same locus form a single cluster, which is highly supported by bootstrap values, except for one HLA-B allele (HLA-B*7301). Mouse MHC class I loci did not show locus-specific clusters of polymorphic alleles. This was considered to be because of either interlocus genetic exchange or the confusing designation of loci in different haplotypes at the present time. The locus specificity of polymorphic alleles was also observed in human and mouse MHC class II loci. It was therefore concluded that interlocus recombination or gene conversion is not very important for generating MHC diversity, with a possible exception of mouse class I loci. According to the phylogenetic trees of complete coding sequences, we classified human MHC class I (HLA-A, -B, and -C) and class II (DRB1) alleles into three to five major allelic lineages (groups), which were monophyletic with high bootstrap values. Most of these allelic groups remained unchanged even in phylogenetic trees based on individual exons, though this does not exclude the possibility of intralocus recombination involving short DNA segments. These results, together with the previous observation that MHC loci are subject to frequent duplication and deletion, as well as to balancing selection, indicate that MHC evolution in mammals is in agreement with the birth-and-death model of evolution, rather than with the model of concerted evolution.

Alleles↗
PubMed2002

Whole-tree methods for detecting differential diversification rates.

Prolific cladogenesis, adaptive radiation, species selection, key innovations, and mass extinctions are a few examples of biological phenomena that lead to differential diversification among lineages. Central to the study of differential diversification rates is the ability to distinguish chance variation from that which requires deterministic explanation. To detect diversification rate variation among lineages, we propose a number of methods that incorporate information on the topological distribution of species diversity from all internal nodes of a phylogenetic tree. These whole-tree methods (M(Pi), M(Sigma), and M(R)) are explicitly connected to a null model of random diversification--the equal-rates Markov (ERM) random branching model--and an alternative model of differential diversification: M(Pi) is based on the product of individual nodal ERM probabilities; M(Sigma) is based on the sum of individual nodal ERM probabilities, and M(R) is based on a transformation of ERM probabilities that corresponds to a formalized system that orders trees by their relative symmetry. These methods have been implemented in a freely available computer program, SYMMETREE, to detect clades with variable diversification rates, thereby allowing the study of biological processes correlated with and possibly causal to shifts in diversification rate. Application of these methods to several published phylogenies demonstrates their ability to contend with relatively large, incompletely resolved trees. These topology-based methods do not require estimates of relative branch lengths, which should facilitate the analysis of phylogenies, such as supertrees, for which such data are unreliable or unavailable.

Animals↗
PubMed2002

Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian, European, and North American populations.

To illustrate phylogeography of red deer (Cervus elaphus) populations of Xinjiang, we determined their mitochondrial DNA (mtDNA) control region sequences, and then investigated geographic variations and phylogenetic relationships between Xinjiang populations and other populations from Asia, Europe, and North America. The C. elaphus mtDNA control region shared different copy numbers of tandem repeats of 38 to 43-bp motifs which clearly distinguished the Western lineage from the Eastern lineage of this species in Eurasia. The western lineage comprised the Tarim populations from southern Xinjiang and the European populations, all of which had four copies of the motifs. By contrast, the Eastern lineage consisted of populations from northern Xinjiang (Tianshan and Altai Mountains), other Asian areas (Alashan, Gansu, Tibet, Mongolia, and northeastern China), and North America, all of which shared six copies of the motifs. MtDNA phylogenetic trees showed that there are two major clusters of haplotypes which referred to the Western and Eastern lineages, and that subgroupings of haplotypes in each cluster were congruent with their geographic distributions. The present study revealed that a boundary separating the Western lineage from the Eastern lineage occurs between Tarim Basin and Tianshan Mountains in Xinjiang. Meanwhile, North American populations were genetically closer to those of northern Xinjiang, northeastern China, and Mongolia, supporting that C. elaphus immigrated from northeastern Eurasia to North America through the glacier-induced land-bridge (Beringia) which had formed between the two continents after Late Pleistocene.

Animals↗
PubMed2003

Inter- and intra-strain variation and PCR detection of the internal transcribed spacer 1 (ITS-1) sequences of Australian isolates of Eimeria species from chickens.

The objective of this study was to confirm the presence of seven species of Eimeria involved in chicken coccidiosis in Australia by comparing internal transcribed spacer 1 (ITS-1) sequences, ITS-1 polymerase chain reaction (PCR) methods and to apply phylogenetic analysis to assess evolutionary relationships of Australian isolates. Twenty-two distinct ITS-1 regions of 15 Australian Eimeria isolates were sequenced, and analysed using maximum parsimony, distance and maximum likelihood methods. Poor bootstrap support, resulting from high ITS-1 sequence heterogeneity between all species groups, resulted in polychotomy of the Eimeria species in all three trees generated by these analyses. Percentage identity analyses revealed two distant ITS-1 lineages in both E. mitis and E. maxima at the same levels that separate the two species E. tenella and E. necatrix. One E. maxima lineage consisted of Australian isolates, the other American isolates, with one European sequence (originating from the same isolate) in each lineage. One Australian E. praecox sequence was only distantly related (33% variation) to three E. praecox sequences from Australian and European isolates. Short and long ITS-1 variants were isolated from both E. tenella (cloned line) and E. necatrix isolates with deletions (106 and 73 bp, respectively) in the short variants within the 3' region of the ITS-1 sequence. ITS-1 sequences of strains of both E. brunetti and E. acervulina species varied the least. Apart from E. maxima, all of the ITS-1 sequences of the six remaining individual species clustered to the exclusion of other species in all phylogenetic trees. Published ITS-1 tests for E. necatrix, E. acervulina, E. brunetti and E. tenella, combined with three new tests for E. mitis, E. praecox and Australian E. maxima amplified all respective Australian isolates specifically in a nested format using conserved ITS-1 PCR products as template to improve the sensitivity. All PCR tests were confirmed against a collection of 24 Australian chicken Eimeria isolates and contaminating species were detected in some instances. In conclusion, once the genetic variation between species and strains is determined, the ITS-1 is a good target for the development of species-specific assays, but the ITS-1 sequences alone do not seem suitable for the confirmation of phylogenetic inferences for these species. This study reports the first attempt at the analysis of the phylogeny and sequence comparison of the Eimeria species involved in chicken coccidiosis in Australia.

Animals↗
PubMed2006

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.

Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods used and their assumptions. Accurate dating of divergence times among the major eukaryote lineages will require a robust tree of eukaryotes, a much richer Proterozoic fossil record of microbial eukaryotes assignable to extant groups for calibration, more sophisticated relaxed molecular clock methods and many more genes sampled from the full diversity of microbial eukaryotes.

Eukaryotic Cells↗
PubMed1999

Substitution rate variation among sites in mitochondrial hypervariable region I of humans and chimpanzees.

Mitochondrial D-loop hypervariable region I (HVI) sequences are widely used in human molecular evolutionary studies, and therefore accurate assessment of rate heterogeneity among sites is essential. We used the maximum-likelihood method to estimate the gamma shape parameter alpha for variable substitution rates among sites for HVI from humans and chimpanzees to provide estimates for future studies. The complete data of 839 humans and 224 chimpanzees, as well as many subsets of these data, were analyzed to examine the effect of sequence sampling. The effects of the genealogical tree and the nucleotide substitution model were also examined. The transition/transversion rate ratio (kappa) is estimated to be about 25, although much larger and biased estimates were also obtained from small data sets at low divergences. Estimates of alpha were 0.28-0.39 for human data sets of different sizes and 0.20-0.39 for data sets including different chimpanzee subspecies. The combined data set of both species gave estimates of 0.42-0.45. While all those estimates suggest highly variable substitution rates among sites, smaller samples tend to give smaller estimates of alpha. Possible causes for this pattern were examined, such as biases in the estimation procedure and shifts in the rate distribution along certain lineages. Computer simulations suggest that the estimation procedure is quite reliable for large trees but can be biased for small samples at low divergences. Thus, an alpha of 0.4 appears suitable for both humans and chimpanzees. Estimates of alpha can be affected by the nucleotide sites included in the data, the overall tree length (the amount of sequence divergence), the number of rate classes used for the estimation, and to a lesser extent, the included sequences. The genealogical tree, the substitution model, and demographic processes such as population expansion do not have much effect.

Animals↗
PubMedDate not supplied

Evaluation of the monophyly of Fomitopsis using parsimony and MCMC methods.

To evaluate the monophyly of Fomitopsis and elucidate phylogenetic relationships of its members, partial nuclear large subunit (partial 28S) ribosomal RNA genes were sequenced from 10 species of Fomitopsis and 15 related species. Phylogenetic analyses indicated that Fomitopsis was phylogenetically heterogeneous and its members were divided into three subgroups. The constrained tree excluding F. palustris (the type species of Pilatoporus) from Fomitopsis core group was rejected, thus rejecting the taxonomic concept to segregate Pilatoporus from Fomitopsis. The monophyly of taxa belonging to F. rosea complex was rejected, thus rejecting the complex definition based on morphological similarities. The exclusion of Piptoporus betulinus (the type species of Piptoporus) from Fomitopsis core group was rejected and Piptoporus proved to be heterogeneous in both best MP and MAP trees. The monophyly of F. officinalis with Fomitopsis core group also was rejected. Fomitopsis officinalis was closely related to Antrodia xantha and formed an independent lineage from Fomitopsis core group at the basal position of brown rotting fungi comprising Antrodia, Daedalea, Fomitopsis, Piptoporus and Postia. The MAP tree topologyobtained from MCMC computation of Bayesian inference was similar to the one of the best MP tree based on the parsimony analysis but showed a higher likelihood score in the Kishino-Hasegawa test and reflected better evolutionary patterns for the phylogeny of Fomitopsis.

Bayes Theorem↗
PubMed2005

Sporobolomyces diospyroris sp. nov., Sporobolomyces lophatheri sp. nov. and Sporobolomyces pyrrosiae sp. nov., three new species of ballistoconidium-forming yeasts in the Agaricostilbum lineage isolated from plants in Taiwan.

Three strains of xylose-lacking and ubiquinone-10-having ballistoconidium-forming yeasts isolated from plant leaves collected in Taiwan were found to represent respective new species. In phylogenetic trees constructed based on the nucleotide sequences of 18S rDNA and D1/D2 domain of 26S rDNA, they were located in the Agaricostilbum lineage (Agaricostilbum/Bensingtonia cluster). Since the taxonomic properties of these species coincide with those of the genus Sporobolomyces, they are described as Sporobolomyces diospyroris sp. nov., Sporobolomyces lophatheri sp. nov. and Sporobolomyces pyrrosiae sp. nov., respectively.

Basidiomycota↗
PubMed2002

Evolution of viral structure.

Viruses vastly outnumber their host cells and must present a huge selective pressure. It is also becoming evident that only a small percent of the eukaryotic genome codes for molecules involved in cellular structures and functions, and that much of the remainder may have a viral origin. Viruses clearly play a central role in the biosphere, but how is this viral world organized? Classification was originally based on virus morphology and the particular host infected, but now there is an increasing trend to rely on sequence information. The type of genome (e.g., RNA or DNA, single- or double-stranded) provides fundamental classification criteria, while sequence comparisons can provide fine mapping for closely related viruses. However, it is currently very difficult to identify long-range evolutionary relationships. We present here a different approach, based on the idea that each virus has an innate "self." When the structures and functions characteristic of this "self" are identified, then they uncover relationships beyond those accessible from sequence information alone. The new approach is illustrated by sketching some possible viral lineages. We propose that urviruses were present before the division of cellular life into its current domains, and that the viral world has lineages that can be traced back to the root of the universal tree of life.

Biological Evolution↗
PubMed1995

Molecular evolution of the nicotinic acetylcholine receptor: an example of multigene family in excitable cells.

An extensive phylogenetic analysis of the nicotinic-acetylcholine-receptor subunit gene family has been performed by cladistic and phenetic methods. The conserved parts of amino acid sequences have been analyzed by CLUSTAL V and PHYLIP software. The structure of the genes was also taken in consideration. The results show that a first gene duplication may have occurred before the appearance of Bilateria. Three subfamilies then appeared: I--the neuronal alpha-bungarotoxin binding-site subunits (alpha 7, alpha 8); III--the neuronal nicotinic subunits (alpha 2-alpha 6, beta 2-beta 4), which also contain the muscle acetylcholine-binding subunit (alpha 1); and IV--the muscle non-alpha subunits (beta 1, gamma, delta, epsilon). The Insecta subunits (subfamily II) could be orthologous to family III and IV. Several tissular switches of expression from neuron to muscle and the converse can be inferred from the extant expression of subunits and the reconstructed trees. The diversification of the neuronal nicotinic subfamily begins in the stem lineage of chordates, the last duplications occurring shortly before the onset of the mammalian lineage. Such evolution parallels the increase in complexity of the cholinergic systems.

Amino Acid Sequence↗
PubMed1985

Evolutionary implications of features of aromatic amino acid biosynthesis in the genus Acinetobacter.

Key enzymes of aromatic amino acid biosynthesis were examined in the genus Acinetobacter. Members of this genus belong to a suprafamilial assemblage of Gram-negative bacteria (denoted Superfamily B) for which a phylogenetic tree based upon oligonucleotide cataloging of 16S rRNA exists. Since the Acinetobacter lineage diverged at an early evolutionary time from other lineages within Superfamily B, an examination of aromatic biosynthesis in members of this genus has supplied important clues for the deduction of major evolutionary events leading to the contemporary aromatic pathways that now exist within Superfamily B. Together with Escherichia coli, Pseudomonas aeruginosa and Xanthomonas campestris, four well-spaced lineages have now been studied in comprehensive detail with respect to comparative enzymological features of aromatic amino acid biosynthesis. A. calcoaceticus and A. lwoffii both possess two chorismate mutase isozymes: one a monofunctional isozyme (chorismate mutase-F), and the other (chorismate mutase-P) a component of a bifunctional P-protein (chorismate mutase-prephenate dehydratase). While both P-protein activities were feedback inhibited by L-phenylalanine, the chorismate mutase-P activity was additionally inhibited by prephenate. Likewise, chorismate mutase-F was product inhibited by prephenate. Two isozymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase were detected. The major isozyme (greater than 95%) was sensitive to feedback inhibition by L-tyrosine, whereas the minor isozyme was apparently insensitive to allosteric control. Prephenate dehydrogenase and arogenate dehydrogenase activities were both detected, but could not be chromatographically resolved. Available evidence favors the existence of a single dehydrogenase enzyme, exhibiting substrate ambiguity for prephenate and L-arogenate.(ABSTRACT TRUNCATED AT 250 WORDS)

Acinetobacter↗
PubMed1996

Phylogenetic analysis using parsimony and likelihood methods.

The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981, J. Mol. Evol. 17: 368-376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were allowed to differ between nucleotides or across sites, the probability that MP recovers the true topology, and especially its performance relative to that of the likelihood method, generally deteriorates. As the complexity of the process of nucleotide substitution in real sequences is well recognized, the likelihood method appears preferable to parsimony. However, the development of a statistical methodology for the efficient estimation of the tree topology remains a difficult open problem.

Animals↗
PubMedDate not supplied

Sympatric convergence of the color pattern in the Chilean Ceroglossus ground beetles inferred from sequence comparisons of the mitochondrial ND5 gene.

The phylogenetic trees have been constructed using the mitochondrial ND5 gene sequences for 66 specimens of the Chilean Ceroglossus ground beetles collected from various localities of Chile. The trees show that the Ceroglossus specimens examined are composed of four phylogenetic lineages that have diverged 25-30 MYA. The results are consistent with the classification proposed by Jiroux (1996) based on morphology, in which Ceroglossus is divided into four species groups. Despite a remarkable color polymorphism revealed by these ground beetles, the color pattern is geographically linked and is not species-specific, suggesting that some ecological or environmental factors are involved in determining it.

Animals↗
PubMed2004

Pattern of phylogenetic diversification of the Cychrini ground beetles in the world as deduced mainly from sequence comparisons of the mitochondrial genes.

The phylogenetic position of the tribe Cychrini within the subfamily Carabinae (the family Carabidae) was estimated by comparing the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene and the nuclear 28S ribosomal DNA (rDNA). The phylogenetic trees suggest that the Cychrini would most probably be the oldest line within the Carabinae. Phylogenetic trees were constructed by comparing the mitochondrial cytochrome C oxidase subunit I (COI) gene sequences from 33 species of the Cychrini from various localities that include the whole distribution ranges of the representative species within all the known genera in the world. The trees suggest that the Cychrini members radiated into a number of phylogenetic lineages within a short period, starting about 44 million years ago (MYA). Most of the phylogenetic lineages or sublineages are geographically linked, each consisting of a single or only a few species without scarce morphological differentiation in spite of their long evolutionary histories (silent or near-silent evolution [see Adv. Biophys. 36 (1999) 65; J. Mol. Evol. 53 (2001) 517]). The fact suggests that the geographic isolation per se did not bring about conspicuous morphological differentiation. The phylogenetic lineages of the Cychrini well correspond to the taxonomically defined genera and the subgenera.

Animals↗
PubMed2005

Comparison of the evolutionary distances among syngens and sibling species of Paramecium.

The morphospecies of the genus Paramecium have several mating type groups, so-called syngens, composed of cells of complementary mating types. The Paramecium aurelia complex is composed of 15 sibling species assigned to the species from the syngen. To increase our understanding of the evolutionary relationships among syngen and sibling species of the genus Paramecium, we investigated the gene sequences of cytosol-type hsp70 from 7 syngens of Paramecium caudatum and 15 sibling species of P. aurelia. Molecular phylogenetic trees indicated that the P. aurelia complex could be divided into four lineages and separated into each sibling species. However, we did not find any obvious genetic distance among syngens of P. caudatum, and they could only be separated into two closely related groups. These results indicated that the concept of syngens in P. caudatum differs quite markedly from that of the P. aurelia complex. In addition, we also discuss the relationships among these species and other species, Paramecium jenningsi and Paramecium multimicronucleatum, which were once classified as varieties of P. aurelia.

Animals↗
PubMed2006

The genetic diversity of mtDNA D-loop and the origin of Chinese goats.

The complete sequences of mitochondrial DNA D-loop of 128 individuals in nine Chinese goat (Capra hircu) breeds were analyzed by DNA sequencing technology. The results show that the length of mtDNA D-loop in Chinese goats is 1,212-1,213 bp. There are 102 polymorphic sites, accounting for 8.42% of 1,212 bp sequence. Ninety-two mtDNA haplotypes were determined. The haplotype diversity and nucleotide diversity are 0.9333-1.0000 and 0.7062%-1.8265%, respectively. The results indicate that the genetic diversity of Chinese goats is very abundant. The NJ tree indicates that Chinese goats have two types of maternal origins from lineage A and lineage B. The possibility of lineage B originating from China is also discussed.

Animals↗
PubMed2003

Origin, world-wide dispersion, bio-geographical diversification, radiation and recombination: an evolutionary history of Yam mild mosaic virus (YMMV).

We developed an evolutionary epidemiological approach to understand the regional and world-wide dispersion of Yam mild mosaic virus (YMMV) by retracing its evolutionary history. Analyses of the distribution and the prevalence of YMMV in the Caribbean islands of Guadeloupe and Martinique, and in French Guyana revealed that YMMV has a wide repartition and different prevalence on Dioscorea alata L. (Asian and Oceanic origin), on D. cayenensis Lam.-D. rotundata Poir. (African origin) and on D. trifida L. (Amazon and the Caribbean origin) in this region. Considering the data on the current dispersion of the virus and the evolution and the history of the yams, the phylogenetic analysis of the 3' terminal part of the YMMV genome gave a consistent support of the Asian-Pacific origin of YMMV from D. alata species. The YMMV phylogenetic tree is star-like, suggesting an early split of the genetic lineages. An important part of the clades is constituted by a single lineage arisen by recombination. The largest emerging monophyletic group illustrates well YMMV geographical dispersion. This evolutionary pattern contrasts with the one revealed by the African distinct lineages and by the second significant monophyletic group, for which a host adaptation to D. trifida is suggested. The analysis of the pattern of nucleotide substitutions in the CP gene revealed that purifying selection dominates the evolution of the CP of potyviruses and strongly operates on the YMMV. Switching events, radiation, host and geographical adaptation and recombination events are proposed as major traits of YMMV evolutionary history.

3' Flanking Region↗