| dc.description.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 | en |
