Phylogenetic Noise Research Articles

Hepatitis C Virus Evolutionary Patterns Studied Through Analysis of Full-Genome Sequences

The evolutionary patterns of hepatitis C virus (HCV), including the best-fitting nucleotide substitution model and the molecular clock hypothesis, were investigated by analyzing full-genome sequences available in the HCV database. The likelihood ratio test allowed us to discriminate among different evolutionary hypotheses. The phylogeny of the six major HCV types was accurately inferred, and the final tree was rooted by reconstructing the hypothetical HCV common ancestor with the maximum likelihood method. The presence of phylogenetic noise and the relative nucleotide substitution rates in the different HCV genes were also examined. These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important insights on HCV origin and evolution.

Sources of error and confidence intervals in estimating the age of angiosperms from rbcL and 18S rDNA data

Molecular estimates of the age of angiosperms have varied widely, and many greatly predate the Early Cretaceous appearance of angiosperms in the fossil record, but there have been few attempts to assess confidence limits on ages. Experiments with rbcL and 18S data using maximum likelihood suggest that previous angiosperm age estimates were too old because they assumed equal rates across sites-use of a gamma distribution of rates to correct for site-to-site variation gives 10-30 my (million years) younger ages-and relied on herbaceous angiosperm taxa with high rates of molecular evolution. Ages based on first and second codon positions of rbcL are markedly older than those based on third positions, which conflict with the fossil record in being too young, but all examined data partitions of rbcL and 18S depart substantially from a molecular clock. Age estimates are surprisingly insensitive to different views on seed-plant relationships. Randomization schemes were used to quantify confidence intervals due to phylogenetic uncertainty, substitutional noise, and lineage effects (deviations from a molecular clock). Estimates of the age of crown-group angiosperms range from 68 to 281 mya (million years ago), depending on data, tree, and assumptions, with most ∼140-190 mya (Early Jurassic-earliest Cretaceous). Approximate 95% confidence intervals on ages are wider for rbcL than 18S, ranging up to 160 my for phylogenetic uncertainty, 90 my for substitutional noise, and 70 my for lineage effects. These intervals overlap the oldest occurrences of angiosperms in the fossil record, as well as some estimates from previous molecular studies.

Phylogeny of the Platyhelminthes and the evolution of parasitism

Robust phylogenies provide the basis for interpreting biological variation in the light of evolution. Homologous features provide phylogenetically informative characters whereas homoplasious characters provide phylogenetic noise. Both provide evolutionary signal. We have constructed molecular and morphologically based phylogenies of the phylum Platyhelminthes using a recently revised morphological character matrix and complete 18S and two partial 28S rRNA gene sequences in order to evaluate the emergence and subsequent divergence of parasitic forms. In total we examine 65 morphological characters, 97 18S rDNA, 41 Dl domain 28S rDNA, and 49 D3-D6 domain 28S rDNA sequences. For the molecular data there were 748, 132 and 249 phylogenetically informative sites for the 18S, Dl and D3-D6 28S rDNA data sets respectively. Morphological and molecular phylogenetic solutions are incongruent but not incompatible, and using the principles of conditional combination (18S rDNA + morphology passing Templeton's test) they demonstrate: a single and relatively early origin for the parasitic Neodermata (including the cestodes, trematodes and monogeneans); sister-group status between the cestodes and monogeneans, and between these taxa and the trematodes (digeneans and aspidogastreans). The sister-group to the Neodermata is likely to be a large clade of neoophoran turbellarians, based on combined evidence, or a clade consisting of the Fecampiid + Urastomid turbellarians, based on morphological evidence alone. The combined evidence solution for the phylogeny of fiatworms based on 18S rDNA and morphology is used to interpret morphological and life-history data and to support a model for the evolution and radiation of neodermatan parasites in the group.

Phylogeny of the Platyhelminthes and the evolution of parasitism

Robust phylogenies provide the basis for interpreting biological variation in the light of evolution. Homologous features provide phylogenetically informative characters whereas homoplasious characters provide phylogenetic noise. Both provide evolutionary signal. We have constructed molecular and morphologically based phylogenies of the phylum Platyhelminthes using a recently revised morphological character matrix and complete 18S and two partial 28S rRNA gene sequences in order to evaluate the emergence and subsequent divergence of parasitic forms. In total we examine 65 morphological characters, 97 18S rDNA, 41 D1 domain 28S rDNA, and 49 D3–D6 domain 28S rDNA sequences. For the molecular data there were 748, 132 and 249 phylogenetically informative sites for the 18S, D1 and D3–D6 28S rDNA data sets respectively. Morphological and molecular phylogenetic solutions are incongruent but not incompatible, and using the principles of conditional combination (18S rDNA + morphology passing Templeton's test) they demonstrate: a single and relatively early origin for the parasitic Neodermata (including the cestodes, trematodes and monogeneans); sister-group status between the cestodes and monogeneans, and between these taxa and the trematodes (digeneans and aspidogastreans). The sister-group to the Neodermata is likely to be a large clade of neoophoran turbellarians, based on combined evidence, or a clade consisting of the Fecampiid+Urastomid turbellarians, based on morphological evidence alone. The combined evidence solution for the phylogeny of flatworms based on 18S rDNA and morphology is used to interpret morphological and life-history data and to support a model for the evolution and radiation of neodermatan parasites in the group.

Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in cetaceans.

Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice of parameter settings and included taxa. This is particularly true in studies involving data sets where levels of homoplasy are high and likely to obscure the phylogenetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objectively which approach is best. Using a cytochrome b data set from cetaceans and artiodactyls, we examined the effects of a suite of parameter settings on the outcome of phylogenetic analyses. We tested 2968 combinations among the seven parameters that most often vary among phylogenetic studies. It is our contention that this sensitivity analysis identifies portions of the multidimensional parameter space where phylogenetic signal is most reliably recovered, and simple rules are given to guide the choice of settings. Portions of this data set have been used in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, the toothed whales. This analysis strongly supports the sister relationship between sperm whales and baleen whales.

Phylogenetic Noise Leads to Unbalanced Cladistic Tree Reconstructions

?Cladistic tree balance is the extent to which internal nodes on a cladistic tree define clades of equal size. More robust maximum-parsimony trees taken from the literature are more balanced. Simulation studies suggest that a methodological bias is responsible for this correlation because incorrect reconstructions are also likely to be less balanced than the true trees they esti? mate. Misinformative cladistic characters can be expected to make trees more unbalanced if there is marked variation in their rates of change. This bias may contribute to the excess of unbalanced phylogenies reported in the literature. [Cladistic tree balance; tree robustness; retention index; homoplasy; Markov models.] Guyer and Slowinski (1991) presented evidence that a subset of well-corroborated phylogenies having five tips was more bal? anced than a larger sample of published trees, where tree balance denotes the de? gree to which branch points define sub? groups of equal size (Heard, 1992). There are three types of explanation for the ob? served difference in the balance between well and poorly corroborated trees. First, poorer phylogenetic data may lead to more unbalanced reconstructions. Such an inter? action would affect the work of those sys? tematists and evolutionary biologists who assume that the shapes of trees are unbi? ased. A second possibility is that the to? pology of the true tree influences the qual? ity of the phylogenetic data measured at the tips. More unbalanced true trees may produce more phylogenetic noise; thus, true unbalanced trees might be more dif? ficult to reconstruct correctly. Finally, there may be some third factor that influences both tree balance and data quality inde? pendently (see Arnold, 1990, for an ex? ample). The empirical study of potential bias is difficult because true and false trees can almost never be distinguished in prac? tice (see Hillis et al., 1992, for a rare excep? tion). Without the true tree one cannot quantify how incorrect a given reconstruc? tion is or whether it is more or less bal1 Present address: Department of Zoology, Univer? sity of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada. E-mail: mooers@bcu.ubc.ca. anc than the true tree. However, if Guyer and Slowinski's well-corroborated trees are closer to the true tree, the prediction is that unbalanced reconstructed trees are more likely to be (more) incorrect than are bal? anced reconstructed trees. Here, we inves? tigate the relationship between data quali? ty and tree shape using published trees and simple computer simulation.

Phylogenetic Noise Leads to Unbalanced Cladistic Tree Reconstructions

Phylogenetic Noise Leads to Unbalanced Cladistic Tree Reconstructions

Limb Reduction in Squamates: Identification of the Lineages and Discussion of the Trends

Limb Reduction in Squamates: Identification of the Lineages and Discussion of the Trends

Effects of Prey Size and Type on Prey-Handling Behavior in Elaphe quadrivirgata

An attempt is made to identify all squamate lineages having undergone limb reduction in the sense of having lost one or more bones from either the front or rear limb. The limb osteology of the ancestors of these limb reduced lineages is also inferred. On this basis squamates have undergone limb reduction at least 62 times in 53 lineages. Most reductions begin with the loss of a single phalange; however, some may begin with loss of all elements more distal than the mesopodials. Three different patterns of incipient loss occur in the front limb and two in the rear limb. These trends are discussed in the light of the developmental constraint and adaptation hypotheses. l. , . , . 166-173, 1991 ibians and Reptiles : I i icatio of t e s Limb reduction in tetrapods is one of the few cases in which large scale evolutionary change is amenable to study. There are two reasons for this. First, in the absence of a detailed phylogeny for any particular taxon, the polarity of character state change can be inferred from a general knowledge of vertebrate relationships and limb structure. Second, many vertebrate taxa show many intermediate steps in limb reduction, allowing fairly detailed comparisons to be made. The vertebrate taxon with the largest number of lineages having experienced some limb reduction is squamates (lizards and snakes) and consequently this group has been much studied in this regard (e.g., Fiirbringer, 1870; Sewertzoff, 1904,1931; Essex, 1927; Bellairs, 1950; Gans, 1975; Presch, 1975; Renous and Gasc, 1979; Greer, 1987, 1990; Choquenot and Greer, 1989). The traditional approach in limb reduction studies is to bring together a variety of species showing various stages of reduction and then to arrange them in a morphocline based on a parsimonious sequence of primitive to derived. This method is dictated by the fact that actual phylogenies are generally unknown and is based on the assumption that reversals do not occur. Within this conceptual framework the history of limb reduction studies in squamates has been to focus on smaller and smaller taxonomic groups. For example, while early studies focused on species from several families (e.g., Fiirbringer, 1870; Sewertzoff, 1931; Steiner and Anders, 1946), more recent studies focus on species within several closely related genera (Renous and Gasc, 1979) or a single genus (e.g., Presch, 1975; Greer, 1987, 1990; Choquenot and Greer, 1989). This trend has been due largely to the increasing knowledge of the world lizard fauna. An important consequence of the trend is to eliminate much of the phylogenetic noise inherent in comparing species of distant relationship. ar ange them in a morph cline based on a arsimonious sequenc of primitive to derived. is method is dictated by the fact th t ac ual ylogenies are g nerally unknown and is based the assumption that reve sals do not occur. ithin this conceptual framework the his ory limb reduction studies in quamates has been 166 This content downloaded from 157.55.39.132 on Thu, 15 Sep 2016 05:58:03 UTC All use subject to http://about.jstor.org/terms