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Chapter 3: Hierarchy Theory as the Formal Basis of Evolutionary
Chapter 3: Hierarchy Theory as the Formal Basis of Evolutionary

... self-assertive and integrative tendencies is inherent in the concept of hierarchic order; and a universal characteristic of life. The self-assertive tendencies are the dynamic expression of holon wholeness, the integrative tendencies of its partness’ (Koestler, 1967: 343). The distinctiveness of an ...
Gene tree reconstruction and orthology analysis based on
Gene tree reconstruction and orthology analysis based on

... the present paper, we advance the frontier of these areas in several respects and provide important computational tools. First, exact algorithms are given for several probabilistic reconciliation problems with respect to the probabilistic gene evolution model, previously developed by the authors. Un ...
Conservation genetics of the endangered grassland earless dragon
Conservation genetics of the endangered grassland earless dragon

... ACT and Cooma is still realised (Figure 1b). As can be seen in Figure 1, bootstrap support is exceptionally high, and in particular we point out the 100% bootstrap value between the ACT and Cooma populations. The trees not only indicate the magnitude of divergence between the ACT and Cooma groups bu ...
Parasitism and Mutualism in Wolbachia: What the
Parasitism and Mutualism in Wolbachia: What the

... codependencies with reproductive parasites to the point where the Wolbachia are essential to host fertility (Starr and Cline 2002; Pannebakker et al. 2007). In contrast to the arthropods, antibiotic curing experiments suggest that in nematodes, Wolbachia infections are primarily beneficial to nemato ...
Making a Phylogenetic Tree
Making a Phylogenetic Tree

... Giovane ...
Full-Text PDF
Full-Text PDF

... T. pigmentosa, T. pyriformis, and T. thermophile. The CATA sequence (boldfaced in Table 1) corresponds to the YRTA consensus of promoters in plant mitochondria [21]. HCE 234 has been found in all Tetrahymena species between the ymf76 and ymf66 genes (both on the complementary strand). In four specie ...
Evolutionary History of Free-Swimming and
Evolutionary History of Free-Swimming and

... as for locomotion. The points at issue are which of these lifestyles represents the primitive condition for urochordates, and which lifestyle was possessed by the ancestor of all chordates. Haeckel (1868) extended his recapitulation theory to this case and proposed that the first chordates were free ...
How Should Species Phylogenies Be Inferred from
How Should Species Phylogenies Be Inferred from

... at multiple loci. In this situation, it is not obvious how the sequences from the different loci can be incorporated into a combined matrix, unless the loci are physically linked on each sampled sequence. Any logical approach to the inference of species phylogenies from sequence data must be able to ...
Document
Document

... biology • Comparative biology is based upon evolutionary relationships between compared entities • Evolutionary relationships are normally depicted in a phylogenetic tree ...
Algorithms in Computational Biology Building Phylogenetic Trees
Algorithms in Computational Biology Building Phylogenetic Trees

... • The distances dij are said to be ultrametric, if for any triplet of sequences, xi, xj, xk, the distances dij, djk, dik are either all equal, or two are equal and the remaining one is smaller • True for a tree with a molecular clock ...
Comparison of Target-Capture and Restriction
Comparison of Target-Capture and Restriction

... a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylog ...
GENOTYPE-PHENOTYPE CORRELATION USING
GENOTYPE-PHENOTYPE CORRELATION USING

... As our programs can be used to correlate any two binary variables which can be optimized on a phylogenetic tree, it was used to find correlations between avian influenza strains and various traits of the species or organisms affected. In particular, we find correlations between spread of influenza a ...
Comparison of Microarray Pre-Processing Methods
Comparison of Microarray Pre-Processing Methods

... analyze the false discovery rate. From the dispersion analysis, we found that variability is reduced more effectively by LWPM and RMA methods. From the false positive analysis, and for both parametric and non-parametric approaches, LWMM is found to perform best. Based on a complementary q-value anal ...
Essential Knowledge 1.B.1
Essential Knowledge 1.B.1

... • It is constructed by using evidence from systematics, a discipline that focuses on classifying organisms and their evolutionary relationships. Its tools include fossils, morphology, genes, and molecular evidence. • Taxonomy is an ordered division of organisms into categories based on a set of char ...
Package `MBCluster.Seq`
Package `MBCluster.Seq`

... The probability model for the count data. The distances between the cluster centroids will be calculated based on the likelihood functions. The model can be ’poisson’ for Poisson or ’nbinom’ for negative binomial distribution. print out the proceeding steps or not ...
Phylogeny of elasmobranchs based on LSU and SSU ribosomal
Phylogeny of elasmobranchs based on LSU and SSU ribosomal

... test makes so many simplifying assumptions that it is highly prone to Type 2 errors (Antezana, 2003; Goldman et al., 2000). Thus, we included both tests as guides in assessing the actual level of support for the alternate (i.e., anatomy-based) hypotheses. In parametric bootstrapping, the null hypoth ...
Use of classification trees for association studies
Use of classification trees for association studies

... can be validated by sample reuse methods [Breiman et al., 1984] or assessed with the use of χ2 test for 2 × 2 tables as described in Zhang and Singer [1999]. We adopt the χ2 test to follow the tradition in linkage and association analyses. A split is regarded as unnecessary if the χ2 tests from this ...
arthropod-success-and-phylogeny 224 kb arthropod-success
arthropod-success-and-phylogeny 224 kb arthropod-success

... arthropods? How has our understanding of the relationships of the four major groups of arthropods been changed by analysis of molecular data? Do arthropods form a monophyletic group?” Arthropods are widely cited as being the most successful group of animals on Earth – and for good reason: they’re es ...
Organismal lineages
Organismal lineages

... -Unexpected taxonomic juxtaposition. ex) rickettsias & mycobacteria= ostensible sister relationship (2-I,M aaRS) -But, same basic branching pattern -Same major taxonomic grouping within each domain as does the rRNA tree Consequently, aaRS trees cannot itself be the result of HGT An organismal gene t ...
Sequence Alignment
Sequence Alignment

... • There are a, quite complicated, set of rules for the naming Bacteria and Archaea. They must have two names: the first refers to the genus (= slekt) and the second refers to the species (= art). • The names can be derived from any language but they must be Latinized. Take for example Staphylococcus ...
Phylogenetic Tree Construction using Pathway Analysis
Phylogenetic Tree Construction using Pathway Analysis

... Hierarchical Clustering New Distances are determined between the new group and each of the remaining organisms ...
Text S1.
Text S1.

... Each node has two possible conditions, presence or absence. There are four possible combinations between parent and child, as illustrated in Figure S3. The most straightforward method to find the most parsimony dataset would be to traverse the whole tree and test every possible combination. However ...
Bioinformatics Dr. Víctor Treviño  Pabellón Tec
Bioinformatics Dr. Víctor Treviño Pabellón Tec

... a tree is referred to as the tree length. The tree is also a bifurcating or binary tree, in that only two branches emanate from each node. Trees can have more than one branch emanating from a node if the events separating taxa are so close that they cannot be resolved, or to simplify the tree. The u ...
Single-copy nuclear genes resolve the phylogeny of the
Single-copy nuclear genes resolve the phylogeny of the

... often placed as sister to Mecopterida and the latter traditionally included either within, or as sister to, Coleoptera [9,10]. The consensus view is that most morphological features of Hymenoptera and Strepsiptera are too highly modified to unequivocally resolve their phylogenetic positions [11,12]. ...
We need an optimality criterion to choose a best estimate (tree
We need an optimality criterion to choose a best estimate (tree

... Maximum Likelihood (for DNA sequence data): Start with a model of nucleotide evolution, then begin examining possible trees. Ask: what is the likelihood that a given tree would have produced the actual observed sequence data under the model of evolution? The most optimal tree is the one with the hig ...
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Maximum parsimony (phylogenetics)

In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy (i.e., convergent evolution, parallel evolution, and evolutionary reversals). In other words, under this criterion, the shortest possible tree that explains the data is considered best. The principle is akin to Occam's razor, which states that—all else being equal—the simplest hypothesis that explains the data should be selected. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.Maximum parsimony is an intuitive and simple criterion, and it is popular for this reason. However, although it is easy to score a phylogenetic tree (by counting the number of character-state changes), there is no algorithm to quickly generate the most-parsimonious tree. Instead, the most-parsimonious tree must be found in ""tree space"" (i.e., amongst all possible trees). For a small number of taxa (i.e., less than nine) it is possible to do an exhaustive search, in which every possible tree is scored, and the best one is selected. For nine to twenty taxa, it will generally be preferable to use branch-and-bound, which is also guaranteed to return the best tree. For greater numbers of taxa, a heuristic search must be performed.Because the most-parsimonious tree is always the shortest possible tree, this means that—in comparison to the ""true"" tree that actually describes the evolutionary history of the organisms under study—the ""best"" tree according to the maximum-parsimony criterion will often underestimate the actual evolutionary change that has occurred. In addition, maximum parsimony is not statistically consistent. That is, it is not guaranteed to produce the true tree with high probability, given sufficient data. As demonstrated in 1978 by Joe Felsenstein, maximum parsimony can be inconsistent under certain conditions, such as long-branch attraction.
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