Parsimonious trees

Sequences of the mitochondrial cytochrome oxidase I (COI) gene of one Greek and 25 Turkish Myzus cerasi (Fabricus) (Hemiptera: Aphididae) populations collected from Prunus avium and Prunus cerasus were analyzed. The partial coding region of COI studied is 605 bp for all the populations, from which 565 nucleotides were conserved, 40 were variable, 37 were singleton, and 3 were parsimony-informative. Four haplotypes were identified based on nucleotide substitutions and the mean of intraspecific divergence was calculated to be 0.3%.

10p dolomite36 30-12-2021 19 0   Download

Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation.

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Many problems in comparative biology are, or are thought to be, best expressed as phylogenetic “networks” as opposed to trees. In trees, vertices may have only a single parent (ancestor), while networks allow for multiple parent vertices. There are two main interpretive types of networks, “softwired” and “hardwired.”

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Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach searches for a most parsimonious reconciliation between a gene tree and a (dated) species tree, considering four possible macro-evolutionary events (speciation, duplication, transfer, and loss) with specific costs.

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During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves.

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Stochastic mapping is frequently used in comparative biology to simulate character evolution, enabling the probabilistic computation of statistics such as number of state transitions along a tree and distribution of states in its internal nodes.

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Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs.

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Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes.

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An attempt has been made to determine the phylogenetic relationship to trace out the evolutionary pattern of the test sequence of Xiphinema pachydermum partial 28S rRNA gene and to find out relationship of the same with other selected sequences of NCBI by constructing phylogenetic trees. Nucleotide sequence of 28S ribosomal RNA gene of Xiphinema pachydermum from Solan, Himachal Pradesh (AM779749.1) showed maximum homology of 93% with Xiphinema inaequale isolate HP 28S large subunit ribosomal RNA gene, partial sequence (HM163210.1) from Baijnath, Himachal Pradesh.

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In this study, relationships among the 15 taxa of the genus Crocus L. distributed in Turkey were analysed using 29 morphological and 4 anatomical characters. Analysis of the data set utilising maximum parsimony criterion with Branchand-Bound search algorithm yielded 32 most parsimonious trees. Bootstrap analysis with the majority rule consensus algorithm generated a consensus tree supporting some branches.

8p vibasque27 27-03-2019 12 0   Download