Testing ascertainment BIAS and RNA secondary structure morphology for phylogenetic signals

Abstract

Phylogenetic reconstruction is essential to many decisions in the medical and agricultural sciences. However, a common drawback in many of these studies is the failure of different datasets to recover the same phylogeny, using the same individuals. Such incongruence result mainly from factors inherent in the evolutionary process itself such as homoplasy or evolutionary ‘noise’, not adequately treated in many analysis programs available. The current study evaluated the usefulness of ascertainment bias (increase in microsatellite allele size range with evolutionary distance from focal taxon) as well as RNA secondary structure morphology in reconstructing accurate phylogenetic relationships. Two domesticated animal systems, one with an unresolved and often controversial evolutionary history, (the camel) and another with a well resolved phylogeny at the species level (cattle), were used to test the reliability of the two methods, and as a spinoff, to revisit the camel’s unresolved history. Published camel and cattle microsatellite genotype data were used to test the utility of ascertainment bias, while cattle mitochondrial cytochrome b sequence data were obtained from a public repository at the National Centre for Biotechnology Information (NCBI). Allele frequency statistics, number of alleles and the allelic size ranges were estimated for each taxonomic group using Microsat toolkit. The means of the number of alleles and size ranges were determined, treating populations separately. The average of means, which is the mean of the means generated, was computed and compared with the mean of all, when the populations were combined. Secondary structures were predicted using MFOLD version 3.5, both at the default temperature (37oC) and at 25oC. The degree of congruence between predicted structures in different taxonomic groups were compared, based on shapes, sizes (in bases) and positioning of hairpins, and lengths of helices. The predicted secondary structure morphologies compared in a manner reflecting evolutionary distances of major Bovine lineages. Whereas individuals within species were the most congruent followed by those between species within the genus, the most distant ones also differed the most, reinforcing their usefulness in resolving enigmatic phylogenies. However, in both test systems used in this study (Camelini and Bovini), ascertainment bias did not exhibit the uniformity required of a good phylogenetic probe. In many cases and for many loci, the principle (reduced allele size range proportional to evolutionary distance from the focal taxon) was not obeyed especially in the Bovini. This confirms that ascertainment bias may reflect phylogenetic trends in some systems but not others. The results of this study contradicted two major evolutionary, migration and domestication theories. The data suggested that first, unlike the current tenet that cattle (Bos taurus and Bos indicus) descended from the Auroch in Eurasia and then B. indicus migrated into Africa, and that Bos javanicus (banteng) and the Auroch shared a common ancestor, it is evident that B. indicus may have evolved independently from the Auroch in North Africa, making the indicine-taurine clade paraphyletic with respect to banteng. Second, this study suggested that the one humped and two humped camels did not simultaneously radiate from their common ancestor (Paracamelus) in western Asia, rather, it showed the dromedary to recently emerge from the Bactrian. These are interesting paleontological questions needing further examination from whole genome scans, as the current study relied on single genes