Investigating Populational Evolutionary Algorithms to Add Vertical Meaning in Phylogenetic Trees

2010 ◽  
pp. 240-247
Author(s):  
Francesco Cerutti ◽  
Luigi Bertolotti ◽  
Tony L. Goldberg ◽  
Mario Giacobini
Keyword(s):  
Evolutionary Algorithms ◽  
Phylogenetic Trees

scholarly journals Taxon ordering in phylogenetic trees by means of evolutionary algorithms

2011 ◽  
Vol 4 (1) ◽  
Author(s):  
Francesco Cerutti ◽  
Luigi Bertolotti ◽  
Tony L Goldberg ◽  
Mario Giacobini
Keyword(s):  
Evolutionary Algorithms ◽  
Phylogenetic Trees

Estimating Bifurcating Consensus Phylogenetic Trees Using Evolutionary Imperialist Competitive Algorithm

2019 ◽  
Vol 14 (8) ◽  
pp. 728-739
Author(s):  
Vageehe Nikkhah ◽  
Seyed M. Babamir ◽  
Seyed S. Arab
Keyword(s):  
Evolutionary Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Imperialist Competitive Algorithm ◽  
Species Level ◽  
Consensus Method ◽  
Gene Trees ◽  
Consensus Tree ◽  
Large Space ◽  
Competitive Algorithm

Background:One of the important goals of phylogenetic studies is the estimation of species-level phylogeny. A phylogenetic tree is an evolutionary classification of different species of creatures. There are several methods to generate such trees, where each method may produce a number of different trees for the species. By choosing the same proteins of all species, it is possible that the topology and arrangement of trees would be different.Objective:There are methods by which biologists summarize different phylogenetic trees to a tree, called consensus tree. A consensus method deals with the combination of gene trees to estimate a species tree. As the phylogenetic trees grow and their number is increased, estimating a consensus tree based on the species-level phylogenetic trees becomes a challenge.Methods:The current study aims at using the Imperialist Competitive Algorithm (ICA) to estimate bifurcating consensus trees. Evolutionary algorithms like ICA are suitable to resolve problems with the large space of candidate solutions.Results:The obtained consensus tree has more similarity to the native phylogenetic tree than related studies.Conclusion:The proposed method enjoys mechanisms and policies that enable us more than other evolutionary algorithms in tuning the proposed algorithm. Thanks to these policies and the mechanisms, the algorithm enjoyed efficiently in obtaining the optimum consensus tree. The algorithm increased the possibility of selecting an optimum solution by imposing some changes in its parameters.

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

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
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.

Analyzing the Phylogenetic Trees with Tree- building Methods

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

Opponent Center-Surround Contrast: Colour to Grey Conversion

2020 ◽  
Vol 2020 (1) ◽  
pp. 105-108
Author(s):  
Ali Alsam
Keyword(s):  
Evolutionary Algorithms ◽  
Three Dimensional ◽  
The State ◽  
Colour Space ◽  
Vision Science ◽  
State Of Art ◽  
Over Time

Vision is the science that informs us about the biological and evolutionary algorithms that our eyes, opticnerves and brains have chosen over time to see. This article is an attempt to solve the problem of colour to grey conversion, by borrowing ideas from vision science. We introduce an algorithm that measures contrast along the opponent colour directions and use the results to combine a three dimensional colour space into a grey. The results indicate that the proposed algorithm competes with the state of art algorithms.

PVT-Biomass-Battery systems optimized with evolutionary algorithms for small and highly shaded environments

2016 ◽  
pp. 568-573
Author(s):  
J.A. Fernández Fernández ◽  
P. González-Rodelas ◽  
E. Alameda-Hernández
Keyword(s):  
Evolutionary Algorithms ◽  
Battery Systems

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

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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