Lineages In Phylogenetic Tree Research Articles

Establishment of rapid detection method and surveillance of budgerigar fledgling disease virus using a TaqMan Real-Time PCR

Budgerigar fledgling disease virus (BFDV) infection causes sudden death, abdominal distention, and feather abnormality in psittacine birds. In this study, we developed a TaqMan Real-time PCR assay to detect BFDV by targeting a conserved region in VP1 gene. The detection limit of the assay was 30 DNA gene copies, 1000 times more sensitive than conventional PCR. The coefficients of variation were less than 1.09% in either intra- or inter-assays, indicating high reproducibility. By using this method, the prevalence of BFDV in China was evaluated. 56 feces samples were collected from four psittacine birds breeding facilities in China. The results showed 28 out of 56 samples were positive for BFDV in Real-Time PCR assay, while only 19 samples were positive in PCR assay. Three facilities were positive for BFDV with positive rates from 60% to 87.5%. Further sequence analysis of VP1 genes from the positive samples indicated that VP1 genes fell into two different lineages in phylogenetic tree, suggesting that different genotypes BFDV are co-circulating in China.

When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model

Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feed at multiple trophic levels, high levels of turnover of species' identities and traits tend to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns.

Morphological hemiplasies in cladistic studies of phylogeny, with examples from birds

Cladograms usually include many evolutionary reversions, parallelisms, and convergences united under the term homoplasy. Recently, it has become evident that molecular traits that look like homoplasy may be in fact true homologies. The processes of independent sorting of genes, which provide the basis of these events, were recently termed hemiplasy. The present study demonstrates theoretical possibility of independent manifestation of true homology (synapomorphy) in remote lineages of phylogenetic tree, as morphological characters are analyzed; this phenomenon is similar in manifestation (but not in nature) to hemiplasy. In the case of “morphological hemiplasy,” characters that appeared only once in evolution may formally be treated by a cladist as parallelisms, since they occur in remote lineages of phylogenetic tree. It is proposed that “morphological hemiplasy” is responsible for a number of uncertain cases in avian phylogeny. Examples are provided by the ducklike bill in Paleogene Presbyornithidae and extant Anatidae and Anseranatidae (Anseriformes), the apomorphic structure of the flying apparatus in Paleogene Jungornithidae (Apodiformes) and extant Trochilidae, and “independent” development of a highly-modified zygodactyl foot in Zygodactylidae and Pici.

Evidence of gene conversion events between paralogous sequences produced by tetraploidization in Salmoninae fish.

We investigated the occurrence of gene conversions between paralogous sequences of Salmoninae derived from ancestral tetraploidization and their effect on the evolutionary history of DNA sequences. A microsatellite with long flanking regions (750 bp) including both coding and noncoding sequences was analyzed. Microsatellite size polymorphism was used to detect the alleles of both paralogous counterparts and infer linkage arrangement between loci. DNA sequencing of seven Salmoninae species revealed that paralogous sequences were highly differentiated within species, especially for noncoding regions. Ten gene conversion events between paralogous sequences were inferred. While these events appears to have homogenized regions of otherwise highly differential paralogous sequences, they amplified the differentiation among orthologous sequences. Their effects were larger on coding than on noncoding regions. As a consequence, noncoding sequences grouped by orthologous lineages in phylogenetic trees, whereas coding regions grouped by taxa. Based upon these results, we present a model showing how gene conversion events may also result in the PCR amplification of nonorthologous sequences in different taxa, with obvious complications for phylogenetic inferences, comparative mapping, and population genetic studies.