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PubMed1987

Accuracy of phylogenetic trees estimated from DNA sequence data.

The relative merits of four different tree-making methods in obtaining the correct topology were studied by using computer simulation. The methods studied were the unweighted pair-group method with arithmetic mean (UPGMA), Fitch and Margoliash's (FM) method, thd distance Wagner (DW) method, and Tateno et al.'s modified Farris (MF) method. An ancestral DNA sequence was assumed to evolve into eight sequences following a given model tree. Both constant and varying rates of nucleotide substitution were considered. Once the DNA sequences for the eight extant species were obtained, phylogenetic trees were constructed by using corrected (d) and uncorrected (p) nucleotide substitutions per site. The topologies of the trees obtained were then compared with that of the model tree. The results obtained can be summarized as follows: (1) The probability of obtaining the correct rooted or unrooted tree is low unless a large number of nucleotide differences exists between different sequences. (2) When the number of nucleotide substitutions per sequence is small or moderately large, the FM, DW, and MF methods show a better performance than UPGMA in recovering the correct topology. The former group of methods is particularly good for obtaining the correct unrooted tree. (3) When the number of substitutions per sequence is large, UPGMA is at least as good as the other methods, particularly for obtaining the correct rooted tree. (4) When the rate of nucleotide substitution varies with evolutionary lineage, the FM, DW, and MF methods show a better performance in obtaining the correct topology than UPGMA, except when a rooted tree is to be produced from data with a large number of nucleotide substitutions per sequence.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1991

Phylogeny of capsid proteins of small icosahedral RNA plant viruses.

Statistically significant alignment was generated between the amino acid sequences of the (putative) shell (S) domains of the capsid proteins of small RNA plant viruses with icosahedral capsids in the tombusvirus, carmovirus, dianthovirus, sobemovirus and luteovirus groups. Inspection of the alignment showed good correspondence between the experimentally defined beta-strands and alpha-helices of the capsid proteins of tomato bushy stunt, southern bean mosaic and turnip crinkle viruses, allowing prediction of the secondary structure elements in proteins with unresolved tertiary structure. It is concluded that this set of viral capsid proteins forms a tight evolutionary cluster. Comparison of the alignment of the proteins of this family with the sequences of other capsid proteins of icosahedral RNA viruses revealed more distant similarities to the satellites of tobacco necrosis, panicum mosaic, tobacco mosaic and maize white line mosaic viruses, as well as to nepo- and comoviruses. The tentative phylogenetic tree derived from the capsid protein alignment separated into three main lineages: (I) carmo-, tombus- and dianthoviruses, (II) southern bean mosaic, tobacco necrosis and maize chlorotic mottle viruses, and (III) luteoviruses. Comparison of this tree topology with the tentative evolutionary schemes for the respective virus RNA-dependent RNA polymerases suggested that gene shuffling is the universal trend in the evolution of small RNA plant virus genomes.

Amino Acid Sequence↗

PubMed2003

Comparative phylogenies of yellow fever isolates from Peru and Brazil.

We recently reported phylogenetic evidence to support the presence of enzootic transmission foci of yellow fever virus (YFV) in Peru [Bryant et al., Emerg. Infect. Dis. (2003)]. Because the prevailing paradigm of YFV transmission in Brazil is that of 'wandering epizootics' rather than discrete enzootic foci, we have now compared the molecular phylogenies of YFV isolates from Peru and Brazil, and re-examined the question of virus mobility by mapping the spatio-temporal distribution of genetic variants from these areas. Sequences were obtained for two genomic regions from 50 strains of YFV collected between 1954 and 2000 comprising 223 codons of the structural proteins (premembrane and envelope genes, 'prM/E'), and a distal region spanning the carboxy terminus of NS5 and part of the 3' non-coding region ('EMF'). Peruvian and Brazilian isolates formed two monophyletic clades with no evidence to support recombination between lineages. Variation within both coding and non-coding regions revealed similar substitution rates and overall levels of diversity within each clade. The branching structure of the prM/E and EMF trees of Brazilian sequences showed strong agreement of intra-lineage relationships; in contrast, the EMF sequences of Peruvian isolates failed to fully support the subclade structure of the prM/E phylogeny. These phylogenies suggest that transmission cycles of YFV in Peru and Brazil may sometimes be locally maintained within specific locales, but have also on occasion become very widely dispersed.

Amino Acid Sequence↗

PubMed2002

Cross-species infection of blood parasites between resident and migratory songbirds in Africa.

We studied the phylogeny of avian haemosporidian parasites, Haemoproteus and Plasmodium, in a number of African resident and European migratory songbird species sampled during spring and autumn in northern Nigeria. The phylogeny of the parasites was constructed through sequencing part of their mitochondrial cytochrome b gene. We found eight parasite lineages, five Haemoproteus and three Plasmodium, infecting multiple host species. Thus, 44% of the 18 haemospiridian lineages found in this study were detected in more than one host species, indicating that host sharing is a more common feature than previously thought. Furthermore, one of the Plasmodium lineages infected species from different host families, Sylviidae and Ploceidae, expressing exceptionally large host range. We mapped transmission events, e.g. the occurrence of the parasite lineages in resident bird species in Europe or Africa, onto a phylogenetic tree. This yielded three clades, two Plasmodium and one Haemoproteus, in which transmission seems to occur solely in Africa. One Plasmodium clade showed European transmission, whereas the remaining two Haemoproteus clades contained mixes of lineages of African, European or unknown transmission. The mix of areas of transmission in several branches of the phylogenetic tree suggests that transmission of haemosporidian parasites to songbirds has arisen repeatedly in Africa and Europe. Blood parasites could be viewed as a cost of migration, as migratory species in several cases were infected with parasite lineages from African resident species. This cost of migration could have considerable impact on the evolution of migration and patterns of winter distribution in migrating birds.

Africa↗

PubMed2003

Standardized phylogenetic tree: a reference to discover functional evolution.

Functional evolution is often driven by positive natural selection. Although it is thought to be rare in evolution at the molecular level, its effects may be observed as the accelerated evolutionary rates. Therefore one of the effective ways to identify functional evolution is to identify accelerated evolution. Many methods have been developed to test the statistical significance of the accelerated evolutionary rate by comparison with the appropriate reference rate. The rates of synonymous substitution are one of the most useful and popular references, especially for large-scale analyses. On the other hand, these rates are applicable only to a limited evolutionary time period because they saturate quickly--i.e., multiple substitutions happen frequently because of the lower functional constraint. The relative rate test is an alternative method. This technique has an advantage in terms of the saturation effect but is not sufficiently powerful when the evolutionary rate differs considerably among phylogenetic lineages. For the aim to provide a universal reference tree, we propose a method to construct a standardized tree which serves as the reference for accelerated evolutionary rate. The method is based upon multiple molecular phylogenies of single genes with the aim of providing higher reliability. The tree has averaged and normalized branch lengths with standard deviations for statistical neutrality limits. The standard deviation also suggests the reliability level of the branch order. The resulting tree serves as a reference tree for the reliability level of the branch order and the test of evolutionary rate acceleration even when some of the species lineages show an accelerated evolutionary rate for most of their genes due to bottlenecking and other effects.

Animals↗

PubMed1995

Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum.

Thirty-two partial phytochrome sequences from algae, mosses, ferns, gymnosperms, and angiosperms (11 of them newly released ones from our laboratory) were analyzed by distance and character-state approaches (PHYLIP, TREECON, PAUP). In addition, 12 full-length sequences were analyzed. Despite low bootstrap values at individual internal nodes, the inferred trees (neighbor-joining, Fitch, maximum parsimony) generally showed similar branching orders consistent with other molecular data. Lower plants formed two distinct groups. One basal group consisted of Selaginella, Equisetum, and mosses; the other consisted of a monophyletic cluster of frond-bearing pteridophytes. Psilotum was a member of the latter group and hence perhaps was not, as sometimes suggested, a close relative of the first vascular plants. The results further suggest that phytochrome gene duplication giving rise to a- and b- and later to c-types may have taken place within seedfern genomes. Distance matrices dated the separation of mono- and dicotyledons back to about 260 million years before the present (Myr B.P.) and the separation of Metasequoia and Picea to a fossil record-compatible value of 230 Myr B.P. The Ephedra sequence clustered with the c- or a-type and Metasequoia and Picea sequences clustered with the b-type lineage. The "paleoherb" Nymphaea branched off from the c-type lineage prior to the divergence of mono- and dicotyledons on the a- and b-type branches. Sequences of Piper (another "paleoherb") created problems in that they branched off from different phytochrome lineages at nodes contradicting distance from the inferred trees' origin.

Base Sequence↗

PubMed2006

Listeria monocytogenes internalins are highly diverse and evolved by recombination and positive selection.

To probe the evolution of internalins with confirmed or suspected roles in Listeria monocytogenes virulence we sequenced the full inlB, inlC2, inlC, inlD, inlE, inlF, inlG, and inlH ORFs from 40 L. monocytogenes isolated from human (n=10) and animal (n=10) clinical cases, foods (n=10), and the natural environment (n=10). inlB and inlE were present in all isolates, representing 26 and 20 alleles, respectively. inlC was found in all lineage I and II isolates and represented 21 alleles. inlC2 and inlD represented 22 and 24 alleles, respectively, and were found in all L. monocytogenes isolates, with the exception of three lineage II isolates, which carried inlH, an apparent fusion of the 5' end of inlC2 with the 3' end of inlD. inlF and inlG were absent from lineage I isolates and represented 16 and 11 alleles, respectively. Average pairwise nucleotide differences per site (pi) ranged from 0.00849 (inlF) to 0.07020 (inlE). Phylogenetic trees generally showed clustering of internalin genes into two major evolutionary lineages consistent with lineages I and II previously assigned by ribotyping. In addition to detection of recombination events within each internalin gene, inlB, inlC, inlC2, and inlF showed significant evidence for positive selection (i.e., selection for an advantageous mutant allele). Overall, our data indicated that (i) internalin genes are highly diverse, (ii) internalin gene sequences cluster consistent with the phylogenetic lineages of L. monocytogenes, (iii) both intragenic recombination and positive selection have contributed to the evolution of L. monocytogenes internalins, and (iv) L. monocytogenes internalins show distinct evolutionary histories.

Alleles↗

PubMed1991

Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree.

Invariants are functions of the probabilities of state configurations among lineages, with expected values equal to zero under certain phylogenies. For two-state sequences, the existence of certain quadratic invariants requires a symmetric substitution model. For sequences with more than two states, the necessary condition for the existence of certain quadratic invariants in terms of independent events is much stronger than symmetry. For DNA sequences, only three parameters are allowed in the substitution model, which includes Kimura's two-parameter model as a special case.

Base Sequence↗

PubMed2000

Molecular phylogeny and biogeography of Linanthus (Polemoniaceae).

To better understand the evolutionary history of Linanthus (Polemoniaceae) and its relatives, molecular phylogenies based on DNA sequence data from the internal transcribed spacer (ITS) region of nrDNA and the chloroplast gene matK were estimated using several methods. Our data suggest two separate and well-supported lineages of Linanthus in close association with two other genera-Leptodactylon and Phlox. These results agree with previous molecular systematic work on the Polemoniaceae, but do not support the traditional classification of the genus as a natural group, nor do they support the sectional classification within the genus. With a distribution centered primarily in western North America and a high degree of endemism in the California Floristic Province, it has been suggested by Raven and Axelrod that the origin and diversification of Linanthus and its relatives were tied to the development of a summer-dry climate in western North America, which began around 13-15 million years ago (mya). Increased drying during the Pliocene (1.2-5 mya) has also been hypothesized by Axelrod to have led to an increase in plant speciation in California and adjacent areas. Divergence times within the Linanthus lineages were estimated from the ITS and matK gene trees. A log-likelihood ratio test could not reject clock-like evolution for the matK data; however, the clock was strongly rejected for the ITS data set. Although ITS molecular evolution was not clock-like, the estimated times of divergence were similar to those of the matK data set. Within both lineages of Linanthus there seems to have been considerable diversification that has occurred since the Pliocene.

Journal Article↗

PubMed1993

Phylogenetic analysis of the N8 neuraminidase gene of influenza A viruses.

Phylogenetic analysis of the N8 neuraminidase (NA) genes from 18 influenza A viruses, representing equine and avian hosts in different geographic locations, revealed three major lineages: (i) currently circulating equine 2 viruses; (ii) avian viruses isolated in the Eurasian region, including A/Equine/Jilin/1/89, a recent avian-like N8 isolate found in horses in China; and (iii) avian viruses isolated in North America. Comparison of mutation rates indicated that avian N8 genes have evolved more slowly than their equine counterparts. That is, in both avian lineages, 72% of the nucleotide changes were silent in the terminal branches of the phylogenetic tree, whereas in equine 2 viruses, 59% of the nucleotide changes were silent. This suggests greater selective pressure on the NA gene from the mammalian immune system, leading to progressive evolution. Alternatively, the slower mutation rate for avian N8 genes could reflect a selective advantage gained from a longer, continuous span of evolution. The shape of the phylogenetic tree, the evolutionary rate, and the calculated date of origin for the N8 equine 2 virus lineage were comparable to findings for the equine 2 virus hemagglutinin (HA) gene (Bean et al., J. Virol. 66, 1129-1138, 1992). This suggests that both viral membrane glycoproteins of equine 2 viruses have evolved together and have been subjected to similar levels of selective pressure. Several amino acid residues were found to differ among the three host-specific lineages, but they may not be involved in host restriction of the NA, as they are shared by EQ/Jilin/1/89 and viruses of avian origin. The present findings complement detailed structural information on the N2 and N9 subtypes and should prove valuable in understanding future X-ray diffraction studies of N8 crystals.

Amino Acid Sequence↗

PubMed2004

AFLPs resolve phylogeny and reveal mitochondrial introgression within a species flock of African electric fish (Mormyroidea: Teleostei).

Estimating species phylogeny from a single gene tree can be especially problematic for studies of species flocks in which diversification has been rapid. Here we compare a phylogenetic hypothesis derived from cytochrome b (cyt b) sequences with another based on amplified fragment length polymorphisms (AFLP) for 60 specimens of a monophyletic riverine species flock of mormyrid electric fishes collected in Gabon, west-central Africa. We analyze the aligned cyt b sequences by Wagner parsimony and AFLP data generated from 10 primer combinations using neighbor-joining from a Nei-Li distance matrix, Wagner parsimony, and Dollo parsimony. The different analysis methods yield AFLP tree topologies with few conflicting nodes. Recovered basal relationships in the group are similar between cyt b and AFLP analyses, but differ substantially at many of the more derived nodes. More of the clades recovered with the AFLP characters are consistent with the morphological characters used to designate operational taxonomic units in this group. These results support our hypothesis that the mitochondrial gene tree differs from the overall species phylogeny due at least in part to mitochondrial introgession among lineages. Mapping the two forms of electric organ found in this group onto the AFLP tree suggests that posteriorly innervated electrocytes with nonpenetrating stalks have independently evolved from anteriorly innervated, penetrating-stalk electrocytes at least three times.

Animal Communication↗

PubMed1984

Stomach lysozymes of ruminants. II. Amino acid sequence of cow lysozyme 2 and immunological comparisons with other lysozymes.

The complete sequence of 129 amino acids has been determined for one of three closely related lysozymes c purified from cow stomach mucosa. The sequence differs from those known for 17 other lysozymes c at 39-60 positions, at one of which there has been a deletion of 1 amino acid. The glutamate replacement at position 101 and the deletion of proline at position 102 eliminate the aspartyl-prolyl bond that is present between these positions in all other mammalian lysozymes c tested. This bond appears to be the most acid-sensitive one in such lysozymes at physiological temperature. Of the 40 positions previously found to be invariant among lysozymes c, only one has undergone substitution in the cow lineage. This modest number of changes at novel positions is consistent with the inference, based on tree analysis and antigenic comparisons, that the tempo of evolutionary change in the cow lysozyme lineage has not been radically different from that in other lysozyme c lineages. The mutations responsible for the distinctive catalytic properties and stability of cow lysozyme c could be a minor fraction of the total that have been fixed in the cow lineage.

Amino Acid Sequence↗

PubMed2001

Using phylogeographic analyses of gene trees to test species status and processes.

A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.

Animals↗

PubMed2003

Mode of morphological differentiation in the Latitarsi-ground beetles (Coleoptera, Carabidae) of the world inferred from a phylogenetic tree of mitochondrial ND5 gene sequences.

The Latitarsi is one large division of the subtribe Carabina (subfamily Carabinae, family Carabidae), and has been considered as a discrete morphological group consisting of 17 genera. The phylogenetic relationships and evolutionary pattern of the Latitarsi ground beetles have been investigated by analyzing mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequences. The phylogenetic tree suggests that the Latitarsi members do not form a single cluster, i.e., not monophyletic and at least 16 lineages belonging to the so-called Latitarsi emerged at about the same time of the Carabina radiation together with the members of other divisions. This suggests that these lineages (A, B, C, H, L, N, O, P, Q, R, S, T, U, V, W and X in Fig. 2a) may be treated each as a phylogenetically distinct division equivalent to other divisions. The group with bootstrap value of more than 80 percent has been considered as a single lineage (division) with two exceptions, V and X. The independency of each lineage has been assumed by the traditional morphology as well as a single clustering on the trees constructed by independent methods, unchanged topology by replacement of outgroups, etc. Generally speaking, the members in a single lineage are geographically linked. Many phylogenetic lineages are composed of a single or only a few species without conspicuous morphological differentiation. In contrast to such a "silent morphological evolution", a remarkable morphological differentiation occasionally took place in several lineages.

Animals↗

PubMedDate not supplied

Phylogeny and taxonomy of the North American clade of the Ceratocystis fimbriata complex.

Ceratocystis fimbriata is a widely distributed, plant pathogenic fungus that causes wilts and cankers on many woody hosts. Earlier phylogenetic analyses of DNA sequences revealed three geographic clades within the C. fimbriata complex that are centered respectively in North America, Latin America and Asia. This study looked for cryptic species within the North American clade. The internal transcribed spacer regions (ITS) of the rDNA were sequenced, and phylogenetic analysis indicated that most isolates from the North American clade group into four host-associated lineages, referred to as the aspen, hickory, oak and cherry lineages, which were isolated primarily from wounds or diseased trees of Populus, Carya, Quercus and Prunus, respectively. A single isolate collected from P. serotina in Wisconsin had a unique ITS sequence. Allozyme electromorphs also were highly polymorphic within the North American clade, and the inferred phylogenies from these data were congruent with the ITS-rDNA analyses. In pairing experiments isolates from the aspen, hickory, oak and cherry lineages were interfertile only with other isolates from their respective lineages. Inoculation experiments with isolates of the four host-associated groupings showed strong host specialization by isolates from the aspen and hickory lineages on Populus tremuloides and Carya illinoensis, respectively, but isolates from the oak and cherry lineages did not consistently reveal host specialization. Morphological features distinguish isolates in the North American clade from those of the Latin American clade (including C. fimbriata sensu stricto). Based on the phylogenetic evidence, interfertility, host specialization and morphology, the oak and cherry lineages are recognized as the earlier described C. variospora, the poplar lineage as C. populicola sp. nov., and the hickory lineage as C. caryae sp. nov. A new species associated with the bark beetle Scolytus quadrispinosus on Carya is closely related to C. caryae and is described as C. smalleyi.

Ascomycota↗

PubMed1994

Levels of the genealogical hierarchy and the problem of hominoid phylogeny.

Molecular data are widely used to reconstruct phylogenetic relationships among species, and these phylogenies are often used as the basis for inferences about the history of evolutionary change in other nonmolecular characters. This approach is an appropriate and powerful one in many circumstances. But when several lineages diverge over a relatively short period of time, the assumption that a molecular (gene) tree will always be a valid basis for such inferences may not hold. Empirical evidence from humans, nonhuman primates, and other mammals indicates that the relationships among molecular divergence, morphological differentiation, and the origin of reproductive isolation between diverging lineages are complex. The simple dichotomously branching trees that result from molecular systematic studies of Homo, Gorilla, and Pan may be a misleading basis for reconstructions of evolutionary change in nonmolecular characters.

Animals↗

PubMed2005

Alternative designs and the evolution of functional diversity.

According to conventional wisdom, functional diversity is exclusively a consequence of species having evolved adaptations to fill different niches within a heterogeneous environment. This view anticipates only one optimal combination of trait values in a given environment, but it is also conceivable that alternative designs of equal fitness in the same environment might evolve. To investigate that possibility, we use a genetic algorithm to search for optimal combinations of 34 functional traits in a realistic model of tree seedling growth and survival. We show that separate lineages of seedlings evolving in identical environments result in many alternative functional designs of approximately equal fitness.

Algorithms↗

PubMed2003

Recent divergence of the HLA-DRB104 allelic lineage from the DRB10701 lineage after the separation of the human and chimpanzee species.

Conventional phylogenetic trees for the human leukocyte antigen (HLA)-DRB1 alleles constructed by the neighbor-joining (Saitou and Nei 1987) and UPGMA (Sneath and Sokal 1973) methods using nucleotide sequences of the DRB1 alleles suggest that DRB1*0701 may have diverged from other DRB1 alleles before the separation of the human and chimpanzee species, because of a large number of nucleotide changes in DRB1*0701 compared with any of the other DRB1 alleles. Here we show new evidence that the haplotypes centering on DRB1*0701 and DRB1*04 alleles are the most homologous. This suggests that these haplotypes have derived from the common ancestral haplotype, and that they have likely retained complete linkage disequilibrium even after the divergence of the DRB1*0701 and DRB1*04 allelic lineages. Together with the corresponding haplotype carrying chimpanzee DRB1*0701, which has a high sequence homology to HLA-DRB1*0701, these haplotypes reveal that: (1) the DRB1*04 allelic lineage may have been generated from the DRB1*0701 lineage after the separation of the human and chimpanzee species; (2) the DRB1*04 allelic lineage possibly has a higher substitution rate of DRB1 compared with pseudogene and neutral region; (3) there could be a significant difference in the substitution rate of DRB1 between the DRB1*0701 and DRB1*04 allelic lineages. Based on the difference between the present and previous results, we would like to propose that phylogenetic studies using not only nucleotide sequences of the DRB1 alleles but also haplotypes centering on the alleles should be conducted for understanding detailed phylogenetic relationships of the DRB1 alleles.

Alleles↗