Effects of sequence diversity and recombination on the accuracy of phylogenetic trees estimated by kSNP

Lassa Virus (LASV) is the etiological catalyst for Lassa fever, an acute hemorrhagic disease with a mortality rate of 15%. Many aspects of the Lassa virus are not understood, like the causation of deafness in ⅓ of surviving patients or why symptoms are benign for 80% of those infected with the virus. Ambiguities like these suggest that there might exist some genomic heterogeneity among infecting viruses and demonstrate a need to quantify and analyze polymorphisms within LASV. Patterns that emerge from phylogenetic trees can be used to assess the structure of a population while also providing insights to the genetic makeup. The purpose of this investigation was to develop a more streamlined means of calculating nucleotide diversity within a subpopulation of Lassa virus strains and to augment a phylogenetic tree of the Lassa Virus glycoprotein precursor (GPC) segment. A total of 25 partial and complete data sequences of LASV strains were obtained from the Genbank Archives. During phase one of this investigation, the sequence data was inputted into MEGA analytical software and the sequence diversity was derived on a nucleotide level. Data from the individual strand sequences was used to augment a phylogenetic tree using Treeview X software. In phase two of this investigation, an algorithm was created using RStudio, with BSGenome and BioStrings extensions. The sequence diversity derived from the statistical analyses on MEGA was compared to that of the algorithm created. A p-value of 0.08 was found, which deviates from the accepted range of non-medical p-value of 0.00 to 0.05. It is suggested that future research focuses on creating a refurbished version of the algorithm to calculate a nucleotide diversity within a percent error of 5%.

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Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

Archives of Natural History ◽

10.3366/anh.2012.0091 ◽

2012 ◽

Vol 39 (2) ◽

pp. 217-233 ◽

Cited By ~ 4

Author(s):

J. David Archibald

Keyword(s):

Fossil Record ◽

Evolutionary Biology ◽

Phylogenetic Trees ◽

Charles Darwin ◽

The Other ◽

Charles Lyell ◽

Single Origin ◽

Molecular Studies ◽

Richard Owen ◽

First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

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Analyzing the Phylogenetic Trees with Tree- building Methods

Indian Journal Of Applied Research ◽

10.15373/2249555x/apr2012/25 ◽

2011 ◽

Vol 1 (7) ◽

pp. 83-85

Author(s):

Jasmine Jasmine ◽

◽

Pankaj Bhambri ◽

Dr. O.P. Gupta Dr. O.P. Gupta

Keyword(s):

Phylogenetic Trees ◽

Tree Building ◽

Building Methods

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Application of DNA Barcoding in Taxonomy and Phylogeny: An Individual Case of COI Partial Gene Sequencing from Seven Animal Species

Vestnik Zoologii ◽

10.2478/vzoo-2019-0034 ◽

2019 ◽

Vol 53 (5) ◽

pp. 375-384

Author(s):

M. Drohvalenko ◽

A. Mykhailenko ◽

M. Rekrotchuk ◽

L. Shpak ◽

V. Shuba ◽

...

Keyword(s):

Phylogenetic Trees ◽

Far East ◽

Individual Case ◽

Ambystoma Mexicanum ◽

Leaf Miner ◽

Horse Chestnut ◽

Natural Reserve ◽

Rock Lizard ◽

Sand Lizard ◽

Lacerta Agilis

Abstract A part of the COI mitochondrial barcoding gene was sequenced from seven species of different taxonomical groups: Ambystoma mexicanum (Amphibia, Ambystomatidae), Darevskia lindholmi, Lacerta agilis exigua (Reptilia, Lacertidae), Erinaceus roumanicus (Mammalia, Erinaceidae), Macrobiotus sp. 1 and 2 (Eutardigrada, Macrobiotidae) and Cameraria ohridella (Insecta, Gracillariidae). The sequences were compared with available sequences from databases and positioned on phylogenetic trees when the taxa had not yet been sequenced. The presence of Mexican axolotls in herpetoculture in Ukraine was confirmed. The partial COI genes of the Crimean rock lizard and an eastern sub-species of the sand lizard were sequenced. We demonstrated the presence of two tardigrade mitochondrial lineages of the Macrobiotus hufelandi group in the same sample from the Zeya Natural Reserve in the Far East: one was nearly identical to the Italian M. macrocalix, and the other one is similar to M. persimilis and M. vladimiri. We also confirmed the presence of the invasive haplotype “A” of the horse chestnut leaf miner in Ukraine, in line with the hypothesized route of invasion from Central Europe.

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