Academic literature on the topic 'Maximum Parsimony Analysis'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Maximum Parsimony Analysis.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "Maximum Parsimony Analysis"
1
Weng, J. F., I. Mareels, and D. A. Thomas. "Probability Steiner trees and maximum parsimony in phylogenetic analysis." Journal of Mathematical Biology 64, no. 7 (June 25, 2011): 1225–51. http://dx.doi.org/10.1007/s00285-011-0442-4.
Full text
2
Balogh, Gábor, Stephan H. Bernhart, Peter F. Stadler, and Jana Schor. "A probabilistic version of Sankoff’s maximum parsimony algorithm." Journal of Bioinformatics and Computational Biology 18, no. 01 (February 2020): 2050004. http://dx.doi.org/10.1142/s0219720020500043.
Full textAbstract:
The number of genes belonging to a multi-gene family usually varies substantially over their evolutionary history as a consequence of gene duplications and losses. A first step toward analyzing these histories in detail is the inference of the changes in copy number that take place along the individual edges of the underlying phylogenetic tree. The corresponding maximum parsimony minimizes the total number of changes along the edges of the species tree. Incorrectly determined numbers of family members however may influence the estimates drastically. We therefore augment the analysis by introducing a probabilistic model that also considers suboptimal assignments of changes. Technically, this amounts to a partition function variant of Sankoff’s parsimony algorithm. As a showcase application, we reanalyze the gain and loss patterns of metazoan microRNA families. As expected, the differences between the probabilistic and the parsimony method is moderate, in this limit of [Formula: see text], i.e. very little tolerance for deviations from parsimony, the total number of reconstructed changes is the same. However, we find that the partition function approach systematically predicts fewer gains and more loss events, showing that the data admit co-optimal solutions among which the parsimony approach selects biased representatives.
3
Kasap, Server, and Khaled Benkrid. "High Performance Phylogenetic Analysis With Maximum Parsimony on Reconfigurable Hardware." IEEE Transactions on Very Large Scale Integration (VLSI) Systems 19, no. 5 (May 2011): 796–808. http://dx.doi.org/10.1109/tvlsi.2009.2039588.
Full text
4
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar. "MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods." Molecular Biology and Evolution 28, no. 10 (May 4, 2011): 2731–39. http://dx.doi.org/10.1093/molbev/msr121.
Full text
5
Hill, Tobias, Andor Lundgren, Robert Fredriksson, and Helgi B. Schiöth. "Genetic algorithm for large-scale maximum parsimony phylogenetic analysis of proteins." Biochimica et Biophysica Acta (BBA) - General Subjects 1725, no. 1 (August 2005): 19–29. http://dx.doi.org/10.1016/j.bbagen.2005.04.027.
Full text
6
Riemann, O., A. Kieneke, and W. H. Ahlrichs. "Phylogeny of Dicranophoridae (Rotifera: Monogononta) - a maximum parsimony analysis based on morphological characters." Journal of Zoological Systematics and Evolutionary Research 47, no. 1 (February 2009): 61–76. http://dx.doi.org/10.1111/j.1439-0469.2008.00482.x.
Full text
7
Bhattacharya, Debashish. "Analysis of the Distribution of Bootstrap Tree Lengths Using the Maximum Parsimony Method." Molecular Phylogenetics and Evolution 6, no. 3 (December 1996): 339–50. http://dx.doi.org/10.1006/mpev.1996.0084.
Full text
8
Puttick, Mark N., Joseph E. O'Reilly, Alastair R. Tanner, James F. Fleming, James Clark, Lucy Holloway, Jesus Lozano-Fernandez, et al. "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data." Proceedings of the Royal Society B: Biological Sciences 284, no. 1846 (January 11, 2017): 20162290. http://dx.doi.org/10.1098/rspb.2016.2290.
Full textAbstract:
Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured but recent studies have shown that these approaches are less accurate than the Bayesian implementation of the Mk model. Here we expand on these findings in several ways: we assess the impact of tree shape and maximum-likelihood estimation using the Mk model, as well as analysing data composed of both binary and multistate characters. We find that all methods struggle to correctly resolve deep clades within asymmetric trees, and when analysing small character matrices. The Bayesian Mk model is the most accurate method for estimating topology, but with lower resolution than other methods. Equal weights parsimony is more accurate than implied weights parsimony, and maximum-likelihood estimation using the Mk model is the least accurate method. We conclude that the Bayesian implementation of the Mk model should be the default method for phylogenetic estimation from phenotype datasets, and we explore the implications of our simulations in reanalysing several empirical morphological character matrices. A consequence of our finding is that high levels of resolution or the ability to classify species or groups with much confidence should not be expected when using small datasets. It is now necessary to depart from the traditional parsimony paradigms of constructing character matrices, towards datasets constructed explicitly for Bayesian methods.
9
Krauss, Siegfried L. "A Phylogeographic Analysis of Allozyme Variation among Populations of Persoonia mollis (Proteaceae)." Australian Journal of Botany 46, no. 6 (1998): 571. http://dx.doi.org/10.1071/bt97051.
Full textAbstract:
The phylogeography of 18 populations representing all nine subspecies within Persoonia mollis R.Br. (Proteaceae) was estimated from allozyme frequency data. Trees were constructed using UPGMA, maximum likelihood (CONTML) and maximum parsimony (FREQPARS) procedures. Major differences in topology between the UPGMA tree and other trees indicated that evolutionary rates are probably heterogeneous in different lineages in P. mollis, and that the UPGMA tree is inaccurate as it assumes constant evolutionary rates in all lineages. The maximum likelihood and maximum parsimony trees produced near-identical topologies. The major patterns produced by these trees included the early differentiation of subspecies maxima, the well-supported clade of all other P. mollis populations and, within this clade, the split into two clades that, although distinct, was weakly differentiated at their base. Within these two clades, there is a strong correlation between geographical distance between populations and the position of populations on the tree. These trees are consistent with a scenario of range expansion along two distinct paths in a southerly direction from northern refugia since the last glacial maximum, which is supported by data on the vegetation history of the area. These southern paths currently terminate in populations that share a hybrid zone of apparently secondary origin west of the Budawang Range.
10
Fraix-Burnet, Didier, Mauro D’Onofrio, and Paola Marziani. "Maximum parsimony analysis of the effect of the environment on the evolution of galaxies." Astronomy & Astrophysics 630 (September 23, 2019): A63. http://dx.doi.org/10.1051/0004-6361/201935604.
Full textAbstract:
Context. Galaxy evolution and the effect of the environment are most often studied using scaling relations or regression analyses around a given property. However, these approaches do not take into account the complexity of the physics of the galaxies and their diversity. Aims. We here investigate the effect of the cluster environment on the evolution of galaxies through multivariate, unsupervised classification and phylogenetic analyses applied to two relatively large samples from the Wide-field Nearby Galaxy-cluster Survey (WINGS), one of cluster members and one of field galaxies (2624 and 1476 objects, respectively). Methods. These samples are the largest ones ever analysed with a phylogenetic approach in astrophysics. To be able to use the maximum parsimony (cladistics) method, we first performed a pre-clustering in 300 clusters with a hierarchical clustering technique, before applying it to these pre-clusters. All these computations used seven parameters: B − V, log(Re), nV, ⟨μ⟩e, Hβ, D4000, and log(M*). Results. We have obtained a tree for the combined samples and do not find different evolutionary paths for cluster and field galaxies. However, the cluster galaxies seem to have accelerated evolution in the sense that they are statistically more diversified from a primitive common ancestor. The separate analyses show a hint of a slightly more regular evolution of the variables for the cluster galaxies, which may indicate they are more homogeneous compared to field galaxies in the sense that the groups of the latter appear to have more specific properties. On the tree for the cluster galaxies, there is a separate branch that gathers rejuvenated or stripped-off groups of galaxies. This branch is clearly visible on the colour-magnitude diagram, going back from the red sequence towards the blue one. On this diagram, the distribution and the evolutionary paths of galaxies are strikingly different for the two samples. Globally, we do not find any dominant variable able to explain either the groups or the tree structures. Rather, co-evolution appears everywhere, and could depend itself on environment or mass. Conclusions. This study is another demonstration that unsupervised machine learning is able to go beyond simple scaling relations by taking into account several properties together. The phylogenetic approach is invaluable in tracing the evolutionary scenarios and projecting them onto any bivariate diagram without any a priori modelling. Our WINGS galaxies are all at low redshift, and we now need to go to higher redshfits to find more primitive galaxies and complete the map of the evolutionary paths of present day galaxies.
Dissertations / Theses on the topic "Maximum Parsimony Analysis"
1
Park, Hyun Jung. "Large-scale analysis of phylogenetic search behavior." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1452.
Full text
2
Sawtell, Wayne MacLeod. "A Systematic Revision of the Carex Nardina Complex (Cyperaceae)." Thesis, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/23134.
Full textAbstract:
The Carex nardina complex is a group of one to three species (C. nardina, C. hepburnii, C. stantonensis) and six taxa of unispicate sedges (Cyperaceae), the taxonomy of which has been controversial since the 1800s. As initial DNA phylogenies suggested that the complex was nested within Carex section Filifoliae and sister to C. elynoides, a species often confused with C. nardina and sympatric with it in the western North American Cordillera, analyses were conducted to determine whether C. hepburnii, C. stantonensis and other infraspecific taxa could be the result of hybridization. Morphometric and molecular analyses found no substantial evidence for hybridization and supported the recognition of no taxon beyond C. nardina. Consequently, this study concludes that the complex comprises a single variable species, Carex nardina, distributed throughout arctic North America south through the western Cordillera to New Mexico with a minor portion of its range in northeastern Russia, northwestern Scandinavia and Iceland.
3
Yin, Zhaoming. "Enhance the understanding of whole-genome evolution by designing, accelerating and parallelizing phylogenetic algorithms." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/51875.
Full textAbstract:
The advent of new technology enhance the speed and reduce the cost for sequencing biological data. Making biological sense of this genomic data is a big challenge to the algorithm design as well as the high performance computing society. There are many problems in Bioinformatics, such as how new functional genes arise, why genes are organized into chromosomes, how species are connected through the evolutionary tree of life, or why arrangements are subject to change. Phylogenetic analyses have become essential to research on the evolutionary tree of life. It can help us to track the history of species and the relationship between different genes or genomes through millions of years. One of the fundamentals for phylogenetic construction is the computation of distances between genomes. Since there are much more complicated combinatoric patterns in rearrangement events, the distance computation is still a hot topic as much belongs to mathematics as to biology. For the distance computation with input of two genomes containing unequal gene contents (with insertions/deletions and duplications) the problem is especially hard. In this thesis, we will discuss about our contributions to the distance estimation for unequal gene order data. The problem of finding the median of three genomes is the key process in building the most parsimonious phylogenetic trees from genome rearrangement data. For genomes with unequal contents, to the best of our knowledge, there is no algorithm that can help to find the median. In this thesis, we make our contributions to the median computation in two aspects. 1) Algorithm engineering aspect, we harness the power of streaming graph analytics methods to implement an exact DCJ median algorithm which run as fast as the heuristic algorithm and can help construct a better phylogenetic tree. 2) Algorithmic aspect, we theoretically formulate the problem of finding median with input of genomes having unequal gene content, which leads to the design and implementation of an efficient Lin-Kernighan heuristic based median algorithm. Inferring phylogenies (evolutionary history) of a set of given species is the ultimate goal when the distance and median model are chosen. For more than a decade, biologists and computer scientists have studied how to infer phylogenies by the measurement of genome rearrangement events using gene order data. While evolution is not an inherently parsimonious process, maximum parsimony (MP) phylogenetic analysis has been supported by widely applied to the phylogeny inference to study the evolutionary patterns of genome rearrangements. There are generally two problems with the MP phylogenetic arose by genome rearrangement: One is, given a set of modern genomes, how to compute the topologies of the according phylogenetic tree; Another is, given the topology of a model tree, how to infer the gene orders of the ancestor species. To assemble a MP phylogenetic tree constructor, there are multiple NP hard problems involved, unfortunately, they organized as one problem on top of other problems. Which means, to solve a NP hard problem, we need to solve multiple NP hard sub-problems. For phylogenetic tree construction with the input of unequal content genomes, there are three layers of NP hard problems. In this thesis, we will mainly discuss about our contributions to the design and implementation of the software package DCJUC (Phylogeny Inference using DCJ model to cope with Unequal Content Genomes), that can help to achieve both of these two goals. Aside from the biological problems, another issue we need to concern is about the use of the power of parallel computing to assist accelerating algorithms to handle huge data sets, such as the high resolution gene order data. For one thing, all of the method to tackle with phylogenetic problems are based on branch and bound algorithms, which are quite irregular and unfriendly to parallel computing. To parallelize these algorithms, we need to properly enhance the efficiency for localized memory access and load balance methods to make sure that each thread can put their potentials into full play. For the other, there is a revolution taking place in computing with the availability of commodity graphical processors such as Nvidia GPU and with many-core CPUs such as Cray-XMT, or Intel Xeon Phi Coprocessor with 60 cores. These architectures provide a new way for us to achieve high performance at much lower cost. However, code running on these machines are not so easily programmed, and scientific computing is hard to tune well on them. We try to explore the potentials of these architectures to help us accelerate branch and bound based phylogenetic algorithms.
4
Ghadie, Mohamed A. "Analysis and Reconstruction of the Hematopoietic Stem Cell Differentiation Tree: A Linear Programming Approach for Gene Selection." Thesis, Université d'Ottawa / University of Ottawa, 2015. http://hdl.handle.net/10393/32048.
Full textAbstract:
Stem cells differentiate through an organized hierarchy of intermediate cell types to terminally differentiated cell types. This process is largely guided by master transcriptional regulators, but it also depends on the expression of many other types of genes. The discrete cell types in the differentiation hierarchy are often identified based on the expression or non-expression of certain marker genes. Historically, these have often been various cell-surface proteins, which are fairly easy to assay biochemically but are not necessarily causative of the cell type, in the sense of being master transcriptional regulators. This raises important questions about how gene expression across the whole genome controls or reflects cell state, and in particular, differentiation hierarchies. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering and maximization of parsimony can organize the cell types into a tree, but in general this tree is different from the differentiation hierarchy. Using hematopoietic differentiation as an example, we demonstrate how many genes other than marker genes are able to discriminate between different branches of the differentiation tree by proposing two models for detecting genes that are up-regulated or down-regulated in distinct lineages. We then propose a novel approach to solving the following problem: Given the differentiation hierarchy and gene expression data at each node, construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming framework to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a sparse weighted Euclidean metric that uses just 175 genes. These 175 genes are different than the marker genes that were used to identify the 38 cell types, hence offering a novel alternative way of discriminating different branches of the tree. A DAVID functional annotation analysis shows that the 175 genes reflect major processes and pathways active in different parts of the tree. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. Our results show that the 175 genes frequently appear in the random metrics, implicating their significance from an empirical point of view as well. Finally, we show how our linear programming method is able to identify columns that were selected to build minimum spanning trees on the nodes of random variable-size matrices.
5
Juswara, Lina S. "Phylogenetic Analyses of subtribe Goodyerinae and Revision of Goodyera section Goodyera (Orchidaceae) from Indonesia, and Fungal Association of Goodyera section Goodyera." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1275490522.
Full text
6
Lehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses." Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-144067.
Full textAbstract:
Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences.
Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare.
To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach.
In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view.
As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles.
NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method).
In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated.
Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.
7
Amiri, Neda. "Molecular Phylogeny of Poa L. sensu lato (Poaceae) with a Focus on West Asian Species." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35018.
Full textAbstract:
Poa L., is known as a highly diverse cosmopolitan genus with taxonomic difficulties that includes unknown species and species with uncertain affinities mainly in West Asia and North Africa. Poa also exhibits a close relationship with two West Asian genera, Eremopoa Roshev. and Oreopoa H. Scholz & Parolly. This study was conducted to: 1) fill the gap of information on the affinities between Poa species with an emphasis on West Asian Poa; 2) revise and evaluate the accuracy of traditional infrageneric classification of West Asian Poa; and 3) clarify the relationship between Poa and two allied genera of Poaceae Barnhart, Eremopoa and Oreopoa. DNA molecular evidence from present phylogenetic analyses of West Asian species of Poa, Eremopoa and Oreopoa, resulted in some great findings as follow: I) Poa caucasica Trin., which is currently assigned to subsection Nivicolae of section Poa from subgenus Poa resolved as a unique new distinct lineage within Poa. II), New treatments are suggested for Poa densa Troitsky, Poa masenderana Freyn & Sint., Poa cenisia All., Poa psychrophila Boiss. & Heldr. and Poa lipskyi. III) Three unclassified species of Poa pseudobulbosa, Poa diversifolia and Poa aitchisonii are assigned here to subgenus Poa and supersection Poa. IV), The present molecular evidence supports inclusion of Eremopoa in Poa and confirms reduction of Eremopoa to a level of subgenus of Poa. V) Present phylogenetic analyses also indicate that monotypic genus Oreopoa H. Scholz & Parolly is part of Poa. These findings require an urgent modification in subgeneric and sectional classification of the genus Poa.
8
Lehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses." Doctoral thesis, 2013. https://ul.qucosa.de/id/qucosa%3A12477.
Full textAbstract:
Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences.
Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare.
To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach.
In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view.
As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles.
NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method).
In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated.
Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.
Book chapters on the topic "Maximum Parsimony Analysis"
1
Zhou, Jun, Yu Lin, Vaibhav Rajan, William Hoskins, and Jijun Tang. "Maximum Parsimony Analysis of Gene Copy Number Changes." In Lecture Notes in Computer Science, 108–20. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-48221-6_8.
Full text
2
Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0265.
Full textAbstract:
Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.
3
Subbotin, Sergei A. "Phylogenetic analysis of DNA sequence data." In Techniques for work with plant and soil nematodes, 265–82. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781786391759.0015.
Full textAbstract:
Abstract The goal of phylogenetics is to construct relationships that are true representations of the evolutionary history of a group of organisms or genes. The history inferred from phylogenetic analysis is usually depicted as branching in tree-like diagrams or networks. In nematology, phylogenetic studies have been applied to resolve a wide range of questions dealing with improving classifications and testing evolution processes, such as co-evolution, biogeography and many others. There are several main steps involved in a phylogenetic study: (i) selection of ingroup and outgroup taxa for a study; (ii) selection of one or several gene fragments for a study; (iii) sample collection, obtaining PCR products and sequencing of gene fragments; (iv) visualization, editing raw sequence data and sequence assembling; (v) search for sequence similarity in a public database; (vi) making and editing multiple alignment of sequences; (vii) selecting appropriate DNA model for a dataset; (viii) phylogenetic reconstruction using minimum evolution, maximum parsimony, maximum likelihood and Bayesian inference; (ix) visualization of tree files and preparation of tree for a publication; and (x) sequence submission to a public database. Molecular phylogenetic study requires particularly careful planning because it is usually relatively expensive in terms of the cost in reagents and time.
Conference papers on the topic "Maximum Parsimony Analysis"
1
Kasap, Server, and Khaled Benkrid. "A high performance FPGA-based core for phylogenetic analysis with Maximum Parsimony method." In 2009 International Conference on Field-Programmable Technology (FPT). IEEE, 2009. http://dx.doi.org/10.1109/fpt.2009.5377652.
Full text