PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (d(N) and d(S)) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use. The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html).

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

Summary: Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.

Availability: ProtTest is available under the GNU license from http://darwin.uvigo.es

Contact: fabascal@uvigo.es

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ProtTest: selection of best-fit models of protein evolution

Codon-substitution models for heterogeneous selection pressure at amino acid sites.

Comparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (omega = d(N)d(S)) is an important indicator of selective pressure at the protein level, with omega = 1 meaning neutral mutations, omega 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying omega ratios. We develop models that account for heterogeneous omega ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of omega among sites. In all data sets analyzed, the selective pressure indicated by the omega ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average omega ratio across sites is 1. Genes undergoing positive selection include the beta-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for omega and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of omega among sites from real data sets.

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Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup Trees estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated or summing up log-likelihood scores for each gene) Although the overall evidence strongly suggests ((primates, ferungulates), rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates) To clarify whether this contradiction is due to (1) a stochastic (sampling) error; (2) minor model-based errors (eg, ignoring site rate variability), or (3) convergent and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were sequenced The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both Neither more sophisticated evolutionary analyses nor the addition of species changed the previous conclusion That is, the statistical support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight range centered near 95% confidence These results and a site-by-site examination of the sequences clearly suggest that convergent or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup While the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders, marsupials, and montremes In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences

Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders.

In order to assess phylogenetic relationships of Taiwanese brown frogs (Rana longicrus and the R. sauteri complex), the partial sequences (587 base pairs) of the mitochondrial cytochrome b genes were compared with six brown frogs from Japan (R. pirica, R. ornativentris, R. japonica, R. tagoi tagoi, R. tsushimensis, and R. okinavana). Resultant phylogenetic trees indicated a considerable genetic differentiation between R. longicrus and R. japonica in spite of their close morphological and ecological similarities. The R. sauteri complex includes two genetically distinct groups that are not consistent with current classification. One group including populations of Alishan (central Taiwan) and Sanyi (western Taiwan) seemed to be closest to R. tagoi and the presumptive common ancestor of these frogs is thought to have diverged very early. Another group including a population from Wulai (northern Taiwan) showed a sister relationship with R. tsushimensis and R. okinavana, both isolated on small islands ...

/pdf/phylogenetic-relationships-of-brown-frogs-from-taiwan-and-3k0w62vhjy.pdf

Phylogenetic Relationships of Brown Frogs from Taiwan and Japan Assessed by Mitochondrial Cytochrome b Gene Sequences (Rana: Ranidae)

Comparisons of nucleotide sequences of mitochondrial cytochrome b gene revealed that the brown frog from Sakhalin has genetically little differentiated from Rana pirica from Hokkaido. Although they show some differences in adult morphology, they are considered to be conspecific. These frogs have sequences substantially different from R. dybowskii from the Maritime territory of Russia, and the current taxo-nomic idea to specifically separate them is genetically supported. On the other hand, R. dybowskii from the Maritime territory is genetically well differentiated from a conspecific population from Tsushima.

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Phylogenetic Relationships of Brown Frogs with 24 Chromosomes from Far East Russia and Hokkaido Assessed by Mitochondrial Cytochrome b Gene Sequences (Rana: Ranidae)

Local Population Differentiation and Phylogenetic Relationships of Russian Brown Frog, Rana amurensis Inferred by Mitochondrial Cytochrome b Gene Sequences (Amphibia, Ranidae)

Human D4 dopamine receptor (D4DR) is polymorphic in terms of the repeat, numbers of the 48-base pairs (bp) sequence located in the third cytoplasmic loop of the receptor. The repeated sequence and its polymorphism in D4DR genes have also been identified in higher non-human primates, suggesting that the structure of D4DR has been maintained during primate evolution. To clarify the origin and divergence of the polymorphism in the D4DR gene, we determined the nucleotide sequence of this region of the D4DR gene in several species of prosimians and the tree shrew, a species which is closely related to primates. Prosimians except the tarsier had one or two unit(s) of the 48-bp sequence, and conserved sequences were recognized in most of the units of the prosimians. The tree shrew had only one unit of the 48-bp sequence, and its sequence was 71–75% identical to those of the nuits of galago, loris, and lemur. These findings suggest that the ancestral primate presumably had one 48-bp unit, and duplication of the unit occurred at the stage of prosimians. Tarsiers appeared to be distinct from other prosimians and simians because of the high repeat numbers of units and their sequences.

Osamu Takenaka

Papers

Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders.

Phylogenetic Relationships of Brown Frogs from Taiwan and Japan Assessed by Mitochondrial Cytochrome b Gene Sequences (Rana: Ranidae)

Phylogenetic Relationships of Brown Frogs with 24 Chromosomes from Far East Russia and Hokkaido Assessed by Mitochondrial Cytochrome b Gene Sequences (Rana: Ranidae)

Local Population Differentiation and Phylogenetic Relationships of Russian Brown Frog, Rana amurensis Inferred by Mitochondrial Cytochrome b Gene Sequences (Amphibia, Ranidae)

Origin and divergence of tandem repeats of primate D4 dopamine receptor genes