*  Difference between revisions of "CH391L/S13/Ancestral Sequence Reconstruction" - OpenWetWare
One visceral example of ancestral sequence reconstruction was done by the Matz group (currently residing at the University of Texas at Austin). Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have? Sequences for the common ancestor nodes were synthesized and tested for their activity. The ancestral sequences revealed an interesting evolutionary history. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. This evolution of this ancestor resolved into either a green or red peak, losing the emission bimodality and specializing. ...
  https://openwetware.org/wiki/?title=CH391L/S13/Ancestral_Sequence_Reconstruction&curid=130605&diff=677290&oldid=677281
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
One example of ancestral sequence reconstruction was done by the Matz group (currently residing at the University of Texas at Austin). Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red[3]. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have? Different models for reconstruction based on amino acids, codons and nucleotides resulted in reconstructed proteins differing in 4-8 amino acids out of 217. Gene synthesis utilized codons designed "to be degenerate in order to incorporate alternative predictions." [3] The reconstructed sequences included red, pre-red, Red/Green and ALL. The ancestral sequences revealed an interesting evolutionary history. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green ...
  https://openwetware.org/wiki/?title=CH391L/S13/Ancestral_Sequence_Reconstruction&oldid=678930
*  Difference between revisions of "CH391L/S13/Ancestral Sequence Reconstruction" - OpenWetWare
One example of ancestral sequence reconstruction was done by the Matz group (currently residing at the University of Texas at Austin). Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red[3]. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have? Different models for reconstruction based on amino acids, codons and nucleotides resulted in reconstructed proteins differing in 4-8 amino acids out of 217. Gene synthesis utilized codons designed "to be degenerate in order to incorporate alternative predictions." [3] The reconstructed sequences included red, pre-red, Red/Green and ALL. The ancestral sequences revealed an interesting evolutionary history. The ancestor to all the coral fluorescent proteins had a single green peak at 505nm. Gradually, a shift towards greater expression of lower wavelengths developed, ...
  https://openwetware.org/wiki/?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=679126&oldid=678991
*  Ancestral reconstruction - Wikipedia
Ancestral reconstruction (also known as Character Mapping or Character Optimization) is the extrapolation back in time from measured characteristics of individuals (or populations) to their common ancestors. It is an important application of phylogenetics, the reconstruction and study of the evolutionary relationships among individuals, populations or species to their ancestors. In the context of evolutionary biology, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the genetic sequence (ancestral sequence reconstruction), the amino acid sequence of a protein, the composition of a genome (e.g., gene order), a measurable characteristic of an organism (phenotype), and the geographic range of an ancestral population or species (ancestral range reconstruction). This is desirable because it allows us to examine parts of phylogenetic trees corresponding to the distant past, clarifying the ...
  https://en.wikipedia.org/wiki/Ancestral_reconstruction
*  PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and...
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416,093 trees and 165,840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic ...
  http://geuvadis.org/biblio/phylomedb_v30_an_expanding_repository_of_genome_wide_collections_of_trees_alignments_and_phyl
*  Experimental phylogenetics: generation of a known phylogeny - Bioinformatics2011
In order to test the accuracy of various phylogenetic inference methods, an experimental phylogeny was constructed for bacteriophage T7 driven by a mutagen.. All the methods produced the correct branching with the known phylogeny, however, none of them generated the correct distance between taxa. The methods are not able to faithfully predict the branch length because various assumptions do not hold in this experimental phylogeny. UPGMA had the worst performance in predicting phylogenetic distance in this experiment. This distance-based method makes the assumption that there is a constant rate of evolution among lineages. The tested bacteriophage T7 clearly does not have a molecular clock underlying its evolution. Similarly, the other distance-based method - neighbor-joining, is not able to take into account the multiple substitution at a site and therefore generates statistic errors in branch lengths. Maximum parsimony method produced the best result as there is no explicit assumption involved ...
  http://bioinformatics2011.wikidot.com/march-30th
*  The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution...
Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between ...
  http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162299
*  A molecular phylogeny of Graphidaceae (Ascomycota, Lecanoromycetes, Ostropales) including 428 species
We present a comprehensive molecular phylogeny of the lichen family Graphidaceae (subfamilies Graphidoideae and Fissurinoideae) based on partial sequences of the mtSSU, nuLSU rDNA, and RPB2 loci. The phylogeny includes all currently available sequences in Genbank plus 897 newly generated sequences, from a total of 908 ingroup OTUs representing 428 species. The phylogeny supports the synomymy of Graphidaceae and Thelotremataceae and confirms that rounded and lirellate ascomata evolved multiple times in unrelated clades within the family. The phylogenetic distinctiveness of Fissurinoideae versus Graphidoideae is also supported in our extended taxon sampling. The three-gene phylogeny suggest that in addition to the three tribes previously established for the major clades within subfamily Graphidoideae, several further clades exist that might represent additional tribes. Specifically, the Leptotrema clade is excluded from tribe Ocellularieae and the ...
  https://mycokeys.pensoft.net/article/1194
*  中国科学院昆明植物研究所机构知识库(KIB OpenIR): Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi)
A phylogeny of the fungal phylum Basidiomycota. is presented based on a survey of 160 taxa and five nuclear genes. Two genes, rpb2, and tef1, are presented in detail. The rpb2 gene is more variable than tef1 and recovers well-supported clades at shallow and deep taxonomic levels. The tef1 gene recovers some deep and ordinal-level relationships but with greater branch support from nucleotides compared to amino acids. Intron placement is dynamic in tef1, often lineage-specific, and diagnostic for many clades. Introns are fewer in rpb2 and tend to be highly conserved by position. When both protein-coding loci are combined with sequences of nuclear ribosomal RNA genes, 18 inclusive clades of Basidiomycota are strongly supported by Bayesian posterior probabilities and 16 by parsimony bootstrapping. These numbers are greater than produced by single genes and combined ribosomal RNA gene regions. Combination of nrDNA with amino acid sequences, or exons with third codon positions removed, produces strong ...
  http://ir.kib.ac.cn/handle/151853/2699
*  Evolution - A-Z - Phylogeny
A phylogenetic tree, also known as a tree of life or simply a phylogeny, describes branching relationships among species, showing which species shares its most recent common ancestor with which other species.. A phylogeny implicitly has a time axis, and time usually goes up the page. Phylogenetic relations have to be inferred using homologies because the splitting events and common ancestors existed in the past and cannot be directly observed. There are two methods of phylogenetic inference:. 1. Parsimony. Species are arranged in a phylogeny such that the smallest number of evolutionary changes is required.. 2. Distance (or similarity.) Species are arranged in a phylogeny such that each species is grouped with the other species that it shares the most characters with.. Figure: a phylogenetic tree of the main vertebrate groups. Lizards and snakes share a more common ancestor than other species and so are grouped together.. ...
  http://www.blackwellpublishing.com/ridley/a-z/Phylogeny.asp
*  BRANCH SUPPORT AND TREE STABILITY - Bremer - 1994 - Cladistics - Wiley Online Library
Abstract- Branch support is quantified as the extra length needed to lose a branch in the consensus of near-most-parsimonious trees. This approach is based solely on the original data, as opposed to the data perturbation used in the bootstrap procedure. If trees have been generated by Farris's successive approximations approach to character weighting, branch support should be examined in terms of weighted extra length needed to lose a branch. The sum of all branch support values over the tree divided by the length of the most parsimonious tree[s] provides a new index, the total support index. This index is a measure of tree stability in terms of supported resolutions, which is of prime importance in cladistic analysis. ...
  http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.1994.tb00179.x/abstract
*  A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group...
Asiloidea are a group of 9 lower brachyceran fly families, considered to be the closest relative to the large Metazoan radiation Eremoneura (Cyclorrhapha + Empidoidea). The evidence for asiloid monophyly is limited, and few characters define the relationships between the families of Asiloidea and Eremoneura. Additionally, enigmatic genera, Hilarimorpha and Apystomyia, retain morphological characters of both asiloids and higher flies. We use the nuclear protein-coding gene CAD and 28S rDNA to test the monophyly of Asiloidea and to resolve its relationship to Eremoneura. We explore the effects of taxon sampling on support values and topological stability, the resolving power of additional genes, and hypothesis testing using four-cluster likelihood mapping. We find that: (1) the 'asiloid' genus Apystomyia is sister to Cyclorrhapha, (2) the remaining asiloids are monophyletic at the exclusion of the family Bombyliidae, and (3) our best estimate of relationships places the ...
  https://asiloidflies.si.edu/bibliography/multigene-phylogeny-fly-superfamily-asiloidea-insecta-taxon-sampling-and-additional
*  The Bayesian kitchen: Site-specific selection and phylogenetic accuracy
In fact, the tree obtained under the LG model does not just show Microsporida sister to all other eukaryotes. It also gives a somewhat unusual phylogeny for those other eukaryotes, with Fungi branching first. However, if we ignore the rooting, this tree differs from the tree obtained by CAT-GTR by just moving Archaea from their branching point between unikonts and bikonts to a position where they are sister group to Microsporidia. Thus, here, it is not so much that Microsporidia 'move down' in the tree because they are attracted by the archaean outgroup. Instead, it is the outgroup itself which 'goes up' in the tree, being attracted by Microsporidia. In any case, whichever way you decide to see it, this is basically a long branch attracted by another long branch -- thus, a paradigmatic case of a long-branch attraction artifact ...
  http://bayesiancook.blogspot.com/2016/11/site-specific-selection-and.html
*  Diversification of Neoaves: integration of molecular sequence data and fossils | Biology Letters
Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves. ...
  http://rsbl.royalsocietypublishing.org/content/2/4/543
*  The Disillusioned Taxonomist: December 2010
But, as the debate over whale origins showed, I think an interdisciplinary approach can be useful to paleontologists. After all, any phylogeny is a hypothesis that is bound to shift as we learn more. (I can't even count all the phylogenies of theropod dinosaurs there have been...) Phylogenies are definitively provisional, and I think that molecular phylogenies can sometimes be useful in making predictions about relationships that can then be tested with data from the fossil record. If the origin of a particular group is unknown, for example, but a molecular phylogeny shows that two lineages are close together and shared a common ancestor, then paleontologists can examine the fossil evidence to see whether or not this relationship holds up. I don't really think about this debate in terms of which method is superior or inferior. Molecular phylogenies and anatomically-based phylogenies can be used as tools that test and complement each other, so I think a combined approach may continue to be ...
  http://subhumanfreak.blogspot.co.uk/2010/12/
*  The Disillusioned Taxonomist: December 2010
But, as the debate over whale origins showed, I think an interdisciplinary approach can be useful to paleontologists. After all, any phylogeny is a hypothesis that is bound to shift as we learn more. (I can't even count all the phylogenies of theropod dinosaurs there have been...) Phylogenies are definitively provisional, and I think that molecular phylogenies can sometimes be useful in making predictions about relationships that can then be tested with data from the fossil record. If the origin of a particular group is unknown, for example, but a molecular phylogeny shows that two lineages are close together and shared a common ancestor, then paleontologists can examine the fossil evidence to see whether or not this relationship holds up. I don't really think about this debate in terms of which method is superior or inferior. Molecular phylogenies and anatomically-based phylogenies can be used as tools that test and complement each other, so I think a combined approach may continue to be ...
  http://subhumanfreak.blogspot.com.au/2010/12/
*  Deep Green - Green Plant Phylogeny Research Coordination Group
... The green plants provide food, shelter, and medicines and represent one of evolution's great success stories. Their morphological and chemical diversity, and ecological dominance, are paramount among life's lineages. An improved understanding of their phylogeny will not only allow the intellectual satisfaction of discovering the 'roots' of this major component of the world's biotic diversity, but will have important practical benefits as well. A well-supported and detailed phylogenetic framework is critical to the solution of major open questions such as the evolutionary origin of multicellularity, diversification of life-history strategies, the conquest of land, the nature of the relationship between ontogeny and phylogeny, and modes of evolution at the molecular level. Addressing a phylogenetic study of this enormous scale has also necessitated improvements in data handling and analysis that have broad applicability to ...
  http://ucjeps.berkeley.edu/bryolab/GPphylo/
*  A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny<...
TY - JOUR. T1 - A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny. AU - Azani,Nasim. AU - Babineau,Marielle. AU - Bailey,C. Donovan. AU - Banks,Hannah. AU - Barbosa,Ariane R.. AU - Pinto,Rafael Barbosa. AU - Boatwright,James S.. AU - Borges,Leonardo M.. AU - Brown,Gillian K.. AU - Bruneau,Anne. AU - Candido,Elisa. AU - Cardoso,Domingos. AU - Chung,Kuo Fang. AU - Clark,Ruth P.. AU - Conceição,Adilva De S.. AU - Crisp,Michael. AU - Cubas,Paloma. AU - Delgado-Salinas,Alfonso. AU - Dexter,Kyle G.. AU - Doyle,Jeff J.. AU - Duminil,Jérôme. AU - Egan,Ashley N.. AU - De La Estrella,Manuel. AU - Falcão,Marcus J.. AU - Filatov,Dmitry A.. AU - Fortuna-Perez,Ana Paula. AU - Fortunato,Renée H.. AU - Gagnon,Edeline. AU - Gasson,Peter. AU - Rando,Juliana Gastaldello. AU - Tozzi,Ana Maria Goulart de Azevedo. AU - Gunn,Bee. AU - Harris,David. AU - Haston,Elspeth. AU - Hawkins,Julie A.. AU - Herendeen,Patrick S.. AU - Hughes,Colin E.. AU - Iganci,João ...
  https://arizona.pure.elsevier.com/en/publications/a-new-subfamily-classification-of-the-leguminosae-based-on-a-taxo
*  Minerals-1 - Ontogeny Recapitulates Phylogeny Ontogeny Recapitulates Phylogeny y Phylogeny the evolutionary development of...
View Notes - Minerals-1 from GEOL 1610 at North Texas. Ontogeny Recapitulates Phylogeny Ontogeny Recapitulates Phylogeny y Phylogeny ¡ the evolutionary development of any plant or animal. y Ontogeny
  https://www.coursehero.com/file/6180336/Minerals-1/
*  Phylogenetic network - Wikipedia
A phylogenetic network or reticulation is any graph used to visualize evolutionary relationships (either abstractly or explicitly)[1] between nucleotide sequences, genes, chromosomes, genomes, or species.[2] They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes (nodes with two parents) instead of only tree nodes (a hierarchy of nodes, each with only one parent).[3] Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree[4] and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.[5]. Many kinds and subclasses of phylogenetic networks have been defined based ...
  https://en.wikipedia.org/wiki/Phylogenetic_network
*  Phylogenesis - Wikipedia
Phylogenesis (from Greek φῦλον phylon "tribe" + γένεσις genesis "origin") is the biological process by which a taxon (of any rank) appears. The science that studies these processes is called phylogenetics. These terms may be confused with the term phylogenetics, the application of molecular - analytical methods (i.e. molecular biology and genomics), in the explanation of phylogeny and its research. Phylogenetic relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or overall morpho-anatomical, ethological, and other characteristics. The result of these analyses is a phylogeny (also known as a phylogenetic tree) - a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecological genetics and genomes. Cladistics (Greek κλάδος, klados, i.e. "branch") is an approach to ...
  https://en.wikipedia.org/wiki/Phylogenesis
*  Molecular phylogenetics - Wikipedia
Molecular phylogenetics (/məˈlɛkjʊlər ˌfaɪloʊdʒəˈnɛtɪks, mɒ-, moʊ-/) is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography. The theoretical frameworks for molecular systematics were laid in the 1960s in the works of Emile Zuckerkandl, Emanuel Margoliash, Linus Pauling, and Walter M. Fitch. Applications of molecular systematics were pioneered by Charles G. Sibley (birds), Herbert C. Dessauer (herpetology), and Morris Goodman (primates), followed by Allan C. Wilson, Robert K. Selander, and John C. Avise (who studied various groups). Work with protein electrophoresis began around 1956. Although the results were not quantitative and did not ...
  https://en.wikipedia.org/wiki/Molecular_phylogenetics
*  Leherensuge: December 2009
Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased inference of topology given an accurate model and increasingly reliable inferences as the amount of data increases. Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites ...
  http://leherensuge.blogspot.com/2009/12/
*  Morphological character evolution - Naturhistoriska riksmuseet
The main focus of my project is to learn more about morphological character evolution in a phylogenetic context.. One of the goals is to erect homology hypotheses of morphological characters. The morphological characters are then used as a data base for reconstructing of a hypothesis of phylogenetic relationships (=tree) in combination with existing DNA sequences or are mapped on existing trees to study the character evolution.. The emphasis of my research is to unravel annelid character evolution.. Several anatomical structures are studied: body wall muscles, epidermis and cuticle, and genital ducts, using different methods such as transmission electron microscopy (TEM) and routin histology.. Another goal of the project is to study the morphology of homologous characters; characters that come out as derived from a common ancestor in both DNA and morphological analyses and that have long been recognized by morphologists to unite a certain group of organisms, e.g. the clitellum of Clitellata and ...
  http://www.nrm.se/english/researchandcollections/zoology/ourresearch/morphologicalcharacterevolution.9004541.html
*  Краткий практический курс "Molecular phylogenies to answer ecological questions" - Биологический факультет МГУ
Defining units of diversity, disentangling the evolutionary history of a species, assessing the phylogenetic structure of communities are all pressing questions in ecology. Molecular phylogenies represent a pivotal help in unravelling them.. The two-day course will be devoted to: (1) providing a brief overview of the phylogenetic methods and software to obtain molecular phylogenies from DNA sequence data; (2) outlining the use the phylogenies as a base for DNA taxonomy.. During the course, students will be exposed to different ideas, rationale, methods, tools, and software that will widen their toolkit for their own research activities. Great emphasis will be placed on the use of the statistical software R to handle data and to perform specific statistical tests. All software used for the course is free and can be downloaded from the web.. Maximum number of participants: 10. Program. May 12th, overview of phylogenetic methods. morning, 2 hours lecture. ...
  http://www.bio.msu.ru/news/view.php?ID=1199