Efficiency of nuclear and mitochondrial markers recovering and supporting known amniote groups

We have analysed the efficiency of all mitochondrial protein coding genes and six nuclear markers (Adora3, Adrb2, Bdnf, Irbp, Rag2 and Vwf) in reconstructing and statistically supporting known amniote groups (murines, rodents, primates, eutherians, metatherians, therians). The efficiencies of maximum likelihood, Bayesian inference, maximum parsimony, neighbor-joining and UPGMA were also evaluated, by assessing the number of correct and incorrect recovered groupings. In addition, we have compared support values using the conservative bootstrap test and the Bayesian posterior probabilities. First, no correlation was observed between gene size and marker efficiency in recovering or supporting correct nodes. As expected, tree-building methods performed similarly, even UPGMA that, in some cases, outperformed other most extensively used methods. Bayesian posterior probabilities tend to show much higher support values than the conservative bootstrap test, for correct and incorrect nodes. Our results also suggest that nuclear markers do not necessarily show a better performance than mitochondrial genes. The so-called dependency among mitochondrial markers was not observed comparing genome performances. Finally, the amniote groups with lowest recovery rates were therians and rodents, despite the morphological support for their monophyletic status. We suggest that, regardless of the tree-building method, a few carefully selected genes are able to unfold a detailed and robust scenario of phylogenetic hypotheses, particularly if taxon sampling is increased.

Population genetic analysis of cat populations from Mexico, Colombia, Bolivia, and the Dominican Republic: identification of different gene pools in Latin America

In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America, (2) the heterozygosity levels at these loci in the current Latin American cat populations, (3) the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and European cat populations, and (4) how many different cat gene pools are currently present in Latin America. We also include in our purview historical records of human migrations from Europe to and within the Americas. Our analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans.

Evolutionary analysis of the picornavirus family

An exhaustive evolutionary analysis of the picornavirus family has been carried out using the amino acid sequences of several proteins of the viruses including: the capsid proteins (1D, 1B, and 1C) situated at the 5' end of the genome and responsible for the serotype of the viruses, and the viral polymerase (3D), located at the 3' end of the genome. The evolutionary relationships found among the viruses studied support the new classification, recently suggested, in contrast to the classical one, and the existence of a new genus for the picornavirus family. In the new taxonomic organization, five genera form the picornavirus family: (1) aphthoviruses, (2) cardioviruses, (3) hepatoviruses (previously classified as enteroviruses), (4) renteroviruses (which mainly constitute a combination of the previous genera rhinovirus and enterovirus), and (5) a new genus, with a new and unique representative: the echovirus 22. Our analysis also allowed us, for the first time, to propose the most probable sequence of speciation events to have given rise to the current picornavirus family. The bootstrap procedure was used to check the reliability of the phylogenetic trees obtained. The application of the method of the statistical geometry in distance space to internal branches of the tree revealed a high degree of evolutionary "noise," which makes the resolution of some internal branching points difficult.

Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock

The statistical properties of sample estimation and bootstrap estimation of phylogenetic variability from a sample of nucleotide sequences were studied by considering model trees of three taxa with an outgroup. The cases of constant and varying rates of nucleotide substitution were compared. From sequences obtained by simulation, phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor-joining (NJ) methods. The effectiveness and consistency of the MP method were studied in terms of proportions of informative sites. The results of simulation showed that bootstrap estimation of the confidence level for an inferred phylogeny can be used even under unequal rates of evolution if the rate differences are not large so that the MP method is not misleading. The condition under which the MP method becomes misleading (inconsistent) is more stringent for slowly evolving sequences than for rapidly evolving ones, and it also depends on the length of the internal branch. If the rate differences are large so that the MP method becomes consistently misleading, then bootstrap estimation will reinforce an erroneous conclusion on topology. Similar conclusions apply to the NJ method with uncorrected distances. The NJ method with corrected distances performs poorly when the sequence length is short but can avoid the inconsistency problem if the sequence length is long and if the distances can be estimated accurately.