Molecular Phylogenetic Inference Research Articles

Systemic Adenovirus Infection in Sulawesi Tortoises (Indotestudo Forsteni) Caused by a Novel Siadenovirus

A novel siadenovirus was identified in the Sulawesi tortoise (Indotestudo forsteni). A group of 105 Sulawesi tortoises was obtained by the Turtle Survival Alliance. Many of the tortoises were in poor health. Clinical signs included anorexia, lethargy, mucosal ulcerations and palatine erosions of the oral cavity, nasal and ocular discharge, and diarrhea. Initial diagnostic tests included fecal testing for parasites, complete blood count and plasma biochemical analysis, mycoplasma serology, and polymerase chain reaction (PCR) testing for intranuclear coccidia and chelonian herpesvirus. Treatment included administration of antibiotics, antiparasitic medications, parenteral fluids, and nutritional support. Tissue samples from animals that died were submitted for histopathologic evaluation. Histopathologic examination revealed systemic inflammation and necrosis associated with intranuclear inclusions consistent with a systemic viral infection in 35 tortoises out of 50 examined. Fecal testing results and histopathologic findings revealed intestinal and hepatic amoebiasis and nematodiasis in 31 animals. Two of 5 tortoises tested by PCR were positive for Chlamydophila sp. Aeromonas hydrophila and Escherichia coli were cultured from multiple organs of 2 animals. The mycoplasma serology and PCR results for intranuclear coccidia and chelonian herpesvirus were negative. Polymerase chain reaction testing of tissues, plasma, and choanal/cloacal samples from 41 out of 42 tortoises tested were positive for an adenovirus, which was characterized by sequence analysis and molecular phylogenetic inference as a novel adenovirus of the genus Siadenovirus. The present report details the clinical and anatomic pathologic findings associated with systemic infection of Sulawesi tortoises by this novel Siadenovirus, which extends the known reptilian adenoviruses to the chelonians and extends the known genera of reptilian Adenoviridae beyond Atadenovirus to include the genus Siadenovirus.

Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence

Although multiple gene sequences are becoming increasingly available for molecular phylogenetic inference, the analysis of such data has largely relied on inference methods designed for single genes. One of the common approaches to analyzing data from multiple genes is concatenation of the individual gene data to form a single supergene to which traditional phylogenetic inference procedures - e.g., maximum parsimony (MP) or maximum likelihood (ML) - are applied. Recent empirical studies have demonstrated that concatenation of sequences from multiple genes prior to phylogenetic analysis often results in inference of a single, well-supported phylogeny. Theoretical work, however, has shown that the coalescent can produce substantial variation in single-gene histories. Using simulation, we combine these ideas to examine the performance of the concatenation approach under conditions in which the coalescent produces a high level of discord among individual gene trees and show that it leads to statistically inconsistent estimation in this setting. Furthermore, use of the bootstrap to measure support for the inferred phylogeny can result in moderate to strong support for an incorrect tree under these conditions. These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics.

A Critical Study of Homoplasy in Molecular Data with the Use of a Morpholoogically Based Cladogram, and Its Consequences for Character Weighting

An improvement in molecular phylogenetic inference is usually expected with the elimination of highly variable positions from nucleotide sequences. In this paper, this point of view is addressed through the evaluation of 28s rRNA sequences of vertebrates by the use of the maximum-parsimony method. A tree based on morphological data, which is considered as true, has been used to determine these positions, which are homoplastic. The congruence of the tree constructed after the removal of such positions with the true tree was not better than that of the tree constructed with complete sequences; however, it displayed more multifurcations. The elimination of homoplastic sites appeared to decrease the signal rather than the noise. This is due to the fact that noise is created by multiple changes at a given site only if they occurred within a small time interval; when they occur over a broad time interval they, in fact, provide information. Thus, the global variability of a site is not a reliable indicator of noise. We have shown that, for a given position, changes were often concentrated in a limited area of the tree whatever the total number of substitutions was. This observation was generalized by comparing the number of steps in two sister groups for various molecules and taxonomic groups. The evolutionary rate of a given position was thus shown to vary throughout time. Two major conclusions emerged from this study: (1) substitution models should incorporate variation in evolutionary rate at a given site; and (2) the character weighting approach could be significantly improved if the weight given to a position depends on the area of the tree.

What's old and new in molecular phylogenetics

While it is fairly easy to devise a phylogenetic tree based on molecular data, it has proven difficult to tell how reliable any such tree is. Thus while the genetic inference that humans, chimpanzees, and gorillas cluster together is widely accepted, the genetic inference that the primary division among Old World human populations is between Asia and EurAfrica is not. A molecular phylogenetic inference linking humans and chimpanzees was proposed in the 1980s based on the technique of DNA hybridization. Despite several recent publications in primary and secondary source material, much confusion still exists surrounding the work. This paper tries to clarify issues that may still be confusing to physical anthropologists, and proposes criteria upon which to judge the robusticity of a phylogenetic inference based on DNA hybridization, in light of a recent published claim of replication. The claim of replication is considered critically. Interestingly, the original DNA hybridization data may actually show a chimp-gorilla link, in harmony with other phylogenetic results.