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. ...
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 peak and a smaller ...
Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in almost all fields of applied molecular biology. This book starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including whole proteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a
Statistical methods for phylogeny estimation, especially maximum likelihood (ML), offer high accuracy with excellent theoretical properties. However, RAxML, the current leading method for large-scale ML estimation, can require weeks or longer when used on datasets with thousands of molecular sequences. Faster methods for ML estimation, among them FastTree, have also been developed, but their relative performance to RAxML is not yet fully understood. In this study, we explore the performance with respect to ML score, running time, and topological accuracy, of FastTree and RAxML on thousands of alignments (based on both simulated and biological nucleotide datasets) with up to 27,634 sequences. We find that when RAxML and FastTree are constrained to the same running time, FastTree produces topologically much more accurate trees in almost all cases. We also find that when RAxML is allowed to run to completion, it provides an advantage over FastTree in terms of the ML score, but does not produce
Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria. To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch
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 ...
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 ...
Mitochondrial and nuclear DNA phylogenies reveal a complex evolutionary history in the Australasian robins (Passeriformes: Petroicidae)
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 Carbacanthographis, Heiomasia, Topeliopsis, and
Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do
Phylogeny , Construct Phylogeny , Maximum Parsimony This command is used to construct phylogenetic trees under the maximum parsimony criterion. For a given topology, the sum of the minimum possible substitutions over all sites is known as the Tree Length. The topology with the minimum tree length is known as the Maximum Parsimony tree.. The phylogenetic tree(s) inferred using this criterion are unrooted trees, even though, for ease of inspection, they are often displayed in a manner similar to rooted trees. MEGA includes the Max-mini branch-and-bound search, which is guaranteed to find all the MP trees. However, it is often too time consuming for more than 15 sequences. In those cases, you should use the Close-Neighbor-Interchange (CNI) algorithm to find the MP tree. CNI is a branch swapping method that begins with a given initial tree. You can ask MEGA to automatically obtain a set of initial trees by using the Min-mini algorithm with a given search factor. Alternatively, you can produce the ...
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 ...
Life is extremely complex and amazingly diverse; it has taken billions of years of evolution to attain the level of complexity we observe in nature now and ranges from single-celled prokaryotes to multi-cellular human beings. With availability of molecular sequence data, algorithms inferring homology and gene families have emerged and similarity in gene content between two genes has been the major signal utilized for homology inference. Recently there has been a significant rise in number of species with fully sequenced genome, which provides an opportunity to investigate and infer homologs with greater accuracy and in a more informed way. Phylogeny analysis explains the relationship between member genes of a gene family in a simple, graphical and plausible way using a tree representation. Bayesian phylogenetic inference is a probabilistic method used to infer gene phylogenies and posteriors of other evolutionary parameters. Markov chain Monte Carlo (MCMC) algorithm, in particular using ...
A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision Stephen L. C
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.. ...
Citation. Basu, M. K., Selengut, J. D., Haft, D. H.. ProPhylo: Partial Phylogenetic Profiling to Guide Protein Family Construction and Assignment of Biological Process. BMC Bioinformatics. 2011 Dec 01; 12: 434.. PubMed Citation. Abstract. ABSTRACT: BACKGROUND: Phylogenetic profiling is a technique of scoring co-occurrence between a protein family and some other trait, usually another protein family, across a set of taxonomic groups. In spite of several refinements in recent years, the technique still invites significant improvement. To be its most effective, a phylogenetic profiling algorithm must be able to examine co-occurrences among protein families whose boundaries are uncertain within large homologous protein superfamilies. RESULTS: Partial Phylogenetic Profiling (PPP) is an iterative algorithm that scores a given taxonomic profile against the taxonomic distribution of families for all proteins in a genome. The method works through optimizing the boundary of each protein family, rather ...
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PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and ...
PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.. PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and ...
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 asiloid flies excluding ...
This MATLAB function computes PhyloTree, a phylogenetic tree object, from Distances, pairwise distances between the species or products, using the neighbor-joining method.
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 cant 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 dont 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 ...
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 ...
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
An 1871-nucleotide region including the phoA gene (the structural gene encoding alkaline phosphatase, EC 3.1.3.1) was cloned and sequenced from eight naturally occurring strains of Escherichia coli. Alignment with the sequence from E. coli K-12 made apparent that there were 87 polymorphic nucleotide sites, of which 42 were informative for phylogenetic analysis. Maximum parsimony analysis revealed six equally parsimonious trees with a consistency index of 0.80. Of the 42 informative sites, 22 were inconsistent with each of the maximum parsimony trees. The spatial distribution of the inconsistent sites was highly nonrandom in a manner implying that intragenic recombination has played a major role in determining the evolutionary history of the nine alleles. The implication is that different segments of the phoA gene have different phylogenetic histories.. ...
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], the R-package, phangorn,[5][6] 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.[7] Many kinds and subclasses of phylogenetic ...
Optional reference books: 1) Paul Lewiss unpublished text; 2) The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); 4) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 5) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference. Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will ...
Handy reference books: 1) Molecular Systematics, 2nd ed. (Hillis, Moritz & Mable, eds. 1996, Sinauer) especially Chapter 11 by Swofford et al. on Phylogenetic Inference; 2) Molecular Evolution: A phylogenetic Approach (Page & Holmes 1998, Blackwell); 3) Inferring Phylogenies (Felsenstein 2004, Sinauer); The Phylogenetic Handbook (eds. Philippe Lemey, Marco Salemi, and Anne-Mieke Vandamme, 2010). Lecture Goals: The course will focus on the basics of molecular systematics theory and practice from the point of view of the data. We will explore the ways in which an understanding of processes of evolution of molecular data can help in the construction of evolutionary trees. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Laboratory Goals: Labs will cover basic techniques in molecular ...
Molecular phylogenetic is the branch of phylogeny that analyzes hereditary molecular diversity, mainly in DNA sequences, to increase data on an organisms evolutionary relationships. Due to the taxonomic levels of the study, various molecular markers are applied in molecular phylogeny. The selection of molecular instrument is of paramount matter to ensure that a proper level of variation is meliorated to respond the phylogenetic question. In this review, we have been trying to discuss about gene markers used in the plant phylogeny at various taxonomic levels. The current gene markers used in phylogeny include: the ribosomal nuclear genes, low copy nuclear genes and the extra-nuclear genome (mitochondrial and chloroplastic genomes). Conserved regions could be used at higher taxonomic levels in phylogenetics studies and regions with more changes could be applied between closely related taxa. One of the most common sequences for studying the phylogenetic relationships at the generic and infrageneric
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 ...
Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range from medical research, to drug discovery, to epidemiology, to population dynamics. The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives. Usually, such criteria can be expressed by means of objective functions, and the phylogenies that optimize them are referred to as optimal. One of the most important estimation criteria is the parsimony which states that the optimal phylogeny T∗for a set of n haplotype sequences over a common set of variable loci is the one that satisfies the following requirements: (i) it has the shortest length and (ii) it is such that, for each pair of
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. ...
Pyroleae (Ericaceae) consist of four genera, all of which are distributed widely in temperate coniferous or sometimes deciduous forests of the Northern Hemisphere. To investigate the phylogenetic relationships among these genera and to explore the evolution of the characteristics of the subfamily, we conducted maximum parsimony and Bayesian analyses with nrDNA ITS and three cpDNA intergenic spacers (atpB-rbcL, trnS-trnG and trnL-trnF). The results from cpDNA and combined cpDNA + ITS data sets strongly support the monophyly of Pyroleae as well as a sister relationship between Pyrola and Moneses-Chimaphila, with Orthilia as the basal lineage. The sister-group relationship between Moneses and Chimaphila is supported by a set of synapomorphies, e.g., single flower, colpate pollen, five bundles in the style, straight fruiting pedicel orientation, complete capsule dehiscence, and the basic chromosome number, x = 13. The Moneses-Chimaphila-Pyrola clade is supported by at least one homologous character ...
View Notes - Phylogeny from BIOL 301 at Waterloo. Introduction to Phylogeny Required Reading: chapter 4 (Ignore Box 4.1) Objectives The basics of phylogenetic trees How phylogenetic trees are
The results of the molecular phylogenetic analysis show both similarities and differences with respect to the previous morphology-based hypothesis [22]. Previously well-supported clades were recovered with broadly similar relationships, but (somewhat surprisingly) the small A. alala group was recovered as sister to Limenitis, rendering Adelpha paraphyletic. Four morphological synapomorphies support the alala group as sister to all other Adelpha [22], so the position of the alala group clearly merits further study, with obvious potential implications for taxonomic revision. Most importantly for the present study, North American and Palaearctic Limenitis are robustly supported as the most closely related group to Adelpha. Whether Adelpha (sensu stricto) is monophyletic or not, the data clearly reveal the significant variation in diversification rates across the broader phylogeny, and that the variation arose from a dramatic increase in diversification rate within the lowland Adelpha clade.. In ...
Molecular phylogenetic tree of MAIR gene family. Phylogenetic analysis of the MAIR family genes was performed by using the UPGMA method of GENETYX-MAC software
The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent ...
Recombination plays an important role in shaping the genetic diversity of a number of DNA and RNA viruses. Although some recent studies have reported bioinformatic evidence of mosaic sequences in a variety of influenza A viruses, it remains controversial as to whether these represent bona fide natural recombination events or laboratory artifacts. Importantly, mosaic genome structures can create significant topological incongruence during phylogenetic analyses, which can mislead additional phylogeny-based molecular evolutionary analyses such as molecular clock dating, the detection of selection pressures and phylogeographic inference. As a result, there is a strong need for systematic screenings for mosaic structures within the influenza virus genome database. We used a combination of sequence-based and phylogeny-based methods to identify 388 mosaic influenza genomic segments, of which 332 are previously unreported and are significantly supported by phylogenetic methods. It is impossible, however, to
In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other evolutionary events. Explicit modeling of substitution rates and divergence times makes formulation of informative prior distributions for branch lengths possible. Models with birth-death priors on tree branching and auto-correlated or iid substitution rates among lineages have been proposed, enabling simultaneous inference of substitution rates and divergence times. This problem has, however, mainly been analysed in the Markov chain Monte Carlo (MCMC) framework, an approach requiring computation times of hours or days when applied to large phylogenies. We demonstrate that a hill-climbing maximum a posteriori (MAP) adaptation of the MCMC scheme results in considerable gain in computational efficiency. We demonstrate also that a novel dynamic programming (DP) algorithm for branch length factorization, useful both in the hill-climbing and in the MCMC setting, further reduces
Phylogenomic approaches to the resolution of inter-species relationships have become well established in recent years. Often these involve concatenation of many orthologous genes found in the respective genomes followed by analysis using standard phylogenetic models. Genome-scale data promise increased resolution by minimising sampling error, yet are associated with well-known but often inappropriately addressed caveats arising through data heterogeneity and model violation. These can lead to the reconstruction of highly-supported but incorrect topologies. With the aim of obtaining a species tree for 18 species within the ascomycetous yeasts, we have investigated the use of appropriate evolutionary models to address inter-gene heterogeneities and the scalability and validity of supermatrix analysis as the phylogenetic problem becomes more difficult and the number of genes analysed approaches truly phylogenomic dimensions. We have extended a widely-known early phylogenomic study of yeasts by adding
The evolutionary history of scleractinian corals is based on knowledge of skeletal characters and their 250 million yr fossil record. However, homologies of skeletal characters are not well-understood and fossil documentation of these characters is incomplete. As a result, relationships among families and suborders are poorly understood. We have analyzed a 225 bp segment of the nuclear 28S ribosomal RNA gene from 45 species of corals and a 566 bp segment of the mitochondrial 16S ribosomal RNA gene from 68 species. Unlike previous analyses of smaller numbers of taxa, the dataset presented here includes both reef-building and non-reef-building taxa from 20 of 24 families and all seven suborders. Nuclear sequences analyzed under maximum parsimony and minimum evolution criteria did not resolve relationships among families and suborders. Similar analyses of mitochondrial sequences resulted in a robust phylogenetic hypothesis. The mitochondrial hypothesis, like previous analyses of a subset of these ...
The issue of whether coelomates form a single clade, the Coelomata, or whether all animals that moult an exoskeleton (such as the coelomate arthropods and the pseudocoelomate nematodes) form a distinct clade, the Ecdysozoa, is the most puzzling issue in animal systematics and a major open-ended subject in evolutionary biology. Previous single-gene and genome-scale analyses designed to resolve the issue have produced contradictory results. Here we present the first genome-scale phylogenetic evidence that strongly supports the Ecdysozoa hypothesis. Through the most extensive phylogenetic analysis carried out to date, the complete genomes of 11 eukaryotic species have been analyzed in order to find homologous sequences derived from 18 human chromosomes. Phylogenetic analysis of datasets showing an increased adjustment to equal evolutionary rates between nematode and arthropod sequences produced a gradual change from support for Coelomata to support for Ecdysozoa. Transition between topologies occurred when
BACKGROUND:Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for processes of gene evolution, such as gene duplication and loss, incomplete lineage sorting (deep coalescence), or horizontal gene transfer, that cause incongruence among gene trees. One such approach is gene tree parsimony, which, given a set of gene trees, seeks a species tree that requires the smallest number of evolutionary events to explain the incongruence of the gene trees. However, the only existing algorithms for gene tree parsimony under the duplication-loss or deep coalescence reconciliation cost are prohibitively slow for large datasets.RESULTS:We describe novel algorithms for SPR and TBR based local search heuristics under the duplication-loss cost, and we show how they can be adapted for the deep coalescence cost. These algorithms improve upon the best existing ...
The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago. To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and
Amino acid signature predictive of incident prediabetes: A case-control study nested within the longitudinal pathobiology of prediabetes in a biracial cohort.:
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. ...
A major goal of the SCATE project is to leverage the power of ontologies and the Phenoscape Knowledgebase to assist in evolutionary analyses of trait evolution. For example, researchers may wish to estimate phylogenies from phenotypic data, reconstruct ancestral states, or estimate correlations between phenotypes. Borrowing from molecular sequence data, the methods used for conducting such analyses typically make a series of assumptions that are very poorly suited for phenotypic data. For example, a common assumption is that every character in a character matrix is independent of each other. Phenotypic characters regularly violate this principle. By leveraging the information in phenotypic ontologies, we can correctly model character evolution by accounting for the dependencies of structures among each other. Furthermore, metrics such as semantic similarity can provide useful data that can be integrated into many steps in a phylogenetic comparative analysis. ...
Authors: SERAP MUTUN, HÜLYA KARAGÖZOĞLU Abstract: Abstract: Genetic diversity and diversification of the Anatolian populations of Andricus lignicola (Hartig, 1840) (Hymenoptera: Cynipidae) were investigated using 433 base pairs of the mitochondrial cytochrome b gene. Eighteen distinct haplotypes from 15 populations were determined. Analyses indicated average haplotype and nucleotide diversity as 0.325 and 0.008, respectively. Phylogenetic analyses conducted through the application of maximum likelihood and maximum parsimony produced similar topologies with two major clade structures supported by high bootstrap values. Bayesian analysis produced more polytomies without major basal groupings of the haplotypes. Parsimony network analysis revealed four haplogroups, and the largest group comprised half of the haplotypes. Our preliminary ABGD analysis implied the presence of four hidden lineages with the possibility of a cryptic species complex within A. lignicola. Hierarchical F-statistics (AMOVA) ...
A recent paper in MBE presents evidence that the Taphrinomycota (containing S. pombe and Pneumocystis) are in fact a monophyletic group. This is considered an early branch in the Ascomycota with the Pezizomycotina (filamentous ascomycete fungi like Neurospora and Aspergillus) and Saccharomycotina (fungi mainly with yeast forms including Candida and Saccharomyces). The monophyly of Taphrinomyoctina fungi is something that has been fairly accepted but there are a few publications reporting conflicting evidence in some sets gene trees. This conflict is most likely due to Long Branch Attraction (LBA) and the Philippe lab has long worked on this problem of LBA working to develop tools like PhyloBayes that attempt to correct for LBA with a parameter rich model and using lots of data (like whole genomes). These authors are employing phylogenomics in the sense that multiple genes are used to reconstruct the phylogeny. This use is different from the J.Eisen/Sjölander sense which is to infer gene ...
The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches. We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on
This chapter explores the evolution and phylogeny of the molluscan class Scaphopoda. It describes the main features of scaphopods including their shell, mantle and mantle cavity, feeding habits, digestive tract, and nervous system. It provides a brief account of the history of classification and phylogeny of scaphopods and characterizes its two main clades, Dentaliida and Gadilida. It stresses the need to increase taxonomic sampling and to develop better repositories of material suitable for molecular analysis in order to understand better the scaphopod phylogeny. ...
Proteocephalidean tapeworms form a diverse group of parasites currently known from 315 valid species. Most of the diversity of adult proteocephalideans can be found in freshwater fishes (predominantly catfishes), a large proportion infects reptiles, but only a few infect amphibians, and a single species has been found to parasitize possums. Although they have a cosmopolitan distribution, a large proportion of taxa are exclusively found in South America. We analyzed the largest proteocephalidean cestode molecular dataset to date comprising more than 100 species (30 new), including representatives from 54 genera (80%) and all subfamilies, thus significantly improving upon previous works to develop a molecular phylogeny for the group. The Old World origin of proteocephalideans is confirmed, with their more recent expansion in South America. The earliest diverging lineages are composed of Acanthotaeniinae and Gangesiinae but most of the presently recognized subfamilies (and genera) appear not to be
Two forms of phylogenetic distortion are caused by recombination. The first affects the shape of the tree topology. Although this is a potentially serious difficulty, Jessica Hedge and I recently showed that phylogenies estimated from whole bacterial genomes are surprisingly robust to this problem. The second affects the lengths of the branches. When genetic material is replaced by a homologous but distantly related sequence, it gives the appearance of a cluster of substitutions in the genome, and this can exaggerate branch lengths. ClonalFrameML detects these clusters of substitutions, identifies them as recombination events, and corrects the branch lengths of the tree ...
The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA-DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all
Image phylogeny is the problem of reconstructing the structure that represents the history of generation of semantically similar images (e.g., near-duplicate images). Typical image phylogeny approaches break the problem into two steps: (1) estimating the dissimilarity between each pair of images and (2) reconstructing the phylogeny structure. In this article, the authors propose new approaches…
A proper understanding of the diversity, systematics, and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis - pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya) - has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools, and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analysis and computational methods. In this book, leading scientists from around the world explore current concepts in molecular phylogeny and their application with respect to microorganisms. The authors describe the
Harmon, L.J., Losos, J.B., Davies, T.J., Gillespie, R.G., Gittleman, J.L., Jennings, W.B. et al. (2010) Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64, 2385-2396 ...
Multiple alignments and phylogenetic tree constructions are established techniques for examining the evolutionary history of protease sequences in organisms such as humans, mice, fruitflies, nematode worms and yeast. They also facilitate the mapping of those conserved positions that are important for structure and catalytic function. However, the continued increase in completed or draft genomes offers new opportunities for examining protease evolution across a broader (e.g. more mammals) and deeper (e.g. more invertebrates) phylogenetic range. In addition, the improving annotation not only of proteases, but also of their substrates, interaction partners in proteolytic complexes and endogenous inhibitor proteins now means that aspects of co-evolution can be addressed. The increasing phylogenetic coverage is also important for resolving orthology issues that arise from protease gene duplication or loss in different lineages. Selected sequences will be used to exemplify the utility of Internet ...
Module: Constructing phylogenetic tree. The uniqueness of DNA (RNA) from one lineage to another allows to reconstuct the evolutionary history through a phylogenetic tree and get information on the past evolutionary processes. A phylogenetic tree constructed from sequences of human influenza virus (an epidemic simulated accross a small community) seeded in a community by an individual named -1 in the transmission network (see following image). The phylogenetic tree is composed of branches (edges) and nodes, where branches connect nodes (node: points at which two or more branches diverge). It has internal and external branches and nodes (terminal), and internal node corresponds to the hypothetical last common ancestor (LCA) of everything arising from it. Terminal nodes correspond to the sequences (DNA/RNA) from which the tree was constructed. The lengths of the branches correspond to sequence difference between the two nodes they connect. The phylogenetic tree is constructed by considering the ...
Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the
In mammals, the members of the tripartite motif (TRIM) protein family are involved in various cellular processes including innate immunity against viral infection. Viruses exert strong selective pressures on the defense system. Accordingly, antiviral TRIMs have diversified highly through gene expansion, positive selection and alternative splicing. Characterizing immune TRIMs in other vertebrates may enlighten their complex evolution. We describe here a large new subfamily of TRIMs in teleosts, called finTRIMs, identified in rainbow trout as virus-induced transcripts. FinTRIMs are formed of nearly identical RING/B-box regions and C-termini of variable length; the long variants include a B30.2 domain. The zebrafish genome harbors a striking diversity of finTRIMs, with 84 genes distributed in clusters on different chromosomes. A phylogenetic analysis revealed different subsets suggesting lineage-specific diversification events. Accordingly, the number of fintrim genes varies greatly among fish species.
Model violations constitute the major limitation in inferring accurate phylogenies. Characterizing properties of the data that are not being correctly handled by current models is therefore of prime importance. One of the properties of protein evolution is the variation of the relative rate of substitutions across sites and over time, the latter is the phenomenon called heterotachy. Its effect on phylogenetic inference has recently obtained considerable attention, which led to the development of new models of sequence evolution. However, thus far focus has been on the quantitative heterogeneity of the evolutionary process, thereby overlooking more qualitative variations. We studied the importance of variation of the site-specific amino-acid substitution process over time and its possible impact on phylogenetic inference. We used the CAT model to define an infinite mixture of substitution processes characterized by equilibrium frequencies over the twenty amino acids, a useful proxy for qualitatively
TY - JOUR. T1 - Phylogenetic investigation of Dogiels pericellular nests and Cajals initial glomeruli in the dorsal root ganglion. AU - Matsuda, Seiji. AU - Kobayashi, Naoto. AU - Terashita, Takehiro. AU - Shimokawa, Tetsuya. AU - Shigemoto, Kazuhiro. AU - Mominoki, Katsumi. AU - Wakisaka, Hiroyuki. AU - Saito, Shouichiro. AU - Miyawaki, Kyoujy. AU - Saito, Kyoko. AU - Kushihata, Fumiki. AU - Chen, Jie. AU - Gao, Shuang Yan. AU - Li, Chun Yu. AU - Wang, Min. AU - Fujiwara, Takashi. PY - 2005/10/24. Y1 - 2005/10/24. N2 - Cajals initial glomeruli (IG) and Dogiels pericellular nests (PCNs) were first described from methylene blue preparations of healthy animal tissues around the beginning of the last century. Since that time, although many reports have been published concerning these structures, few have focused on their development and phylogeny in healthy animals. The aim of this study was to examine the phylogenetic development of the sensory neurons in Cajals IG (also called axonal ...
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What is amazing is the evolutionists high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is "no known mechanism or function that would account for this level of conservation at the observed evolutionary distances." Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are "astonishing ...
What is amazing is the evolutionists high confidence and self-assuredness in such a blatant misrepresentation of science. It would be difficult to imagine a bigger falsehood. Phylogenetic incongruence is rampant in evolutionary studies. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits. This paper reports on incongruent gene trees in bats. That is one example of many. These incongruences are caused by just about every kind of contradiction possible. Molecular sequences in one or a few species may be out of place amongst similar species. Or sequences in distant species may be strangely similar. As one paper admitted, there is "no known mechanism or function that would account for this level of conservation at the observed evolutionary distances." Or as another evolutionist admitted, the many examples of nearly identical molecular sequences of totally unrelated animals are "astonishing ...
We studied the evolution of colour pattern in Malagasy poison frogs, genus Mantella, a group of diurnal and toxic frogs endemic to Madagascar. Based on a phylogeny reconstructed using 1130 bp of the mitochondrial 16S rRNA gene, the genus can be divided into five species groups. Within some of these groups, inter-specific genetic divergences were very low (1.2 - 2.8% sequence divergence) while colour patterns were markedly different. In contrast, Mantella madagascariensis and M. baroni, two species which show extremely similar dorsal coloration patterns, were not included in the same clade. This conclusion was supported by high bootstrap values and by significant rejection of alternative topologies using KH-tests. Analysis of colour patterns and tentative reconstruction of ancestral states yielded five character states shared by these two species but not by their respective sister species, M. aurantiaca and M. nigricans. Considering these detailed similarities as symplesiomorphic therefore ...
(A) Anomeric region analysis of strain MMHC82 spectrum for MM. (B) Anomeric region analysis of strain MMHC82 spectrum for CD medium. (C) Anomeric region analysi
In 2001 I initiated a project at the University of Vienna, aiming at the first molecular phylogeny of pholcid spiders. When I left Vienna, the work was taken over by Branka Bruvo who did an excellent job in finishing the project. It was obvious that these were preliminary results, as both the numbers of taxa and genes were small, but the study provided a useful basis for further research on the molecular phylogeny of pholcid spiders. Due primarily to the constraint of getting access to fresh DNA-ready material, it took seven years for the next step, with significant increases in taxa and genes, but still far from complete (published in 2013 in Cladistics ...
The objective of this study was to investigate the relationship between nucleotide substitutions and time in evolving HIV-1 populations, i.e., if a molecular clock exists or not, and if so how the clock should be described. With this aim we investigated a unique set of samples for which the evolutionary history is exactly known (8, 9), which allowed direct correlation between the genetic distances and the time that separated the samples. Two important conclusions could be drawn from the study. First, we show that the concept of a molecular clock fits HIV-1 evolution well. Second, we demonstrate that a significant genetic distance at zero divergence time exists, a finding we show depends on a pretransmission interval.. Evolving HIV-1 populations display very high nucleotide substitution rates. During the evolution some sites will fluctuate rapidly in their nucleotide state whereas other sites will display substitutions that are stable over longer time intervals. Under these circumstances fixation ...
The near-simultaneous appearance of most modern animal body plans (phyla) ~530 million years ago during the Cambrian explosion is strong evidence for a brief interval of rapid phenotypic and genetic innovation, yet the exact speed and nature of this grand adaptive radiation remain debated [1-12]. Crucially, rates of morphological evolution in the past (i.e., in ancestral lineages) can be inferred from phenotypic differences among living organisms-just as molecular evolutionary rates in ancestral lineages can be inferred from genetic divergences [13]. We here employed Bayesian [14] and maximum likelihood [15] phylogenetic clock methods on an extensive anatomical[16]and genomic[17] data set for arthropods, the most diverse phylum in the Cambrian and today. Assuming an Ediacaran origin for arthropods, phenotypic evolution was ~4 times faster, and molecular evolution ~5.5 times faster, during the Cambrian explosion compared to all subsequent parts of the Phanerozoic. These rapid evolutionary rates ...
Temporal patterns in species occupancy and geographic range size are a major topic in evolutionary ecology research. Here we investigate these patterns in Pliocene to Recent large mammal species and genera in Western Eurasia. By using an extensively sampled fossil record including some 700 fossil localities, we found occupancy and range size trajectories over time to be predominantly peaked among both species and genera, meaning that occupancy and range size reached their maxima midway along taxon existence. These metrics are strongly correlated with each other and to body size, after phylogeny is accounted for by using two different phylogenetic topologies for both species and genera. Phylogenetic signal is strong in body size, and weaker but significant in both occupancy and range size mean values among genera, indicating that these variables are heritable. The intensity of phylogenetic signal is much weaker and often not significant at the species level. This suggests that within genera, ...
In this study, the collective microbial diversity in the rumen was examined by performing a meta-analysis of all the curated 16S rRNA gene (rrn) sequences deposited in the RDP database. As of November 2010, 13478 bacterial and 3516 archaeal rrn sequences were found. The bacterial sequences were assigned to 5271 operation taxonomic units (OTUs) at species level (0.03 phylogenetic distance) representing 19 existing phyla, of which the Firmicutes (2958 OTUs), Bacteroidetes (1610 OTUs) and Proteobacteria (226 OTUs) were the most predominant. These bacterial sequences were grouped into more than 3500 OTUs at genus level (0.05 distance), but only 180 existing genera were represented. Nearly all the archaeal sequences were assigned to 943 species-level OTUs in phylum Euryarchaeota. Although clustered into 670 genus-level OTUs, only 12 existing archaeal genera were represented. Based on rarefaction analysis, the current percent coverage at species level reached 71% for bacteria and 65% for archaea. At ...
In the case of the partly homoplasious data, the median-joining network reconstructs a synapomorphy of the clade BC, because A is not placed on the node. This is because one character in our matrix is a methodologically undetectable parallelism - the same trait evolved in the sister taxa B and C, but only after both evolved from A. Clade BC is non-inclusive (paraphyletic), since A is the direct ancestor of both B and C and the clade BC lacks a real synapomorphy (if we go back to Hennigs concept). The reconstructed A would, however, be a stem taxon and clade BC would be inclusive (monophyletic) with one (inferred) synapomorphy. But this is a purely semantic problem of cladistics. In the real world, we will hardly have the data to discern whether A represents: the last common ancestor of B and C, a stem taxon of the ABC-lineage (a), a very early precursor of B or C (b/c), or an ancient sister lineage of A, B, and/or C (a*). For practicality, one would eventually include all fossil forms with ...
CCD is a Java software package for the selection of core collections of diverse taxa (e.g. from germplasm collections) that are intended to capture the genetic diversity of the input dataset.. The software takes as input a binary matrix which transcribes the different alleles (genetic forms) for each taxon. It then tries to find a most diverse collection of alleles under various constraints (e.g. sample size, geographic location of samples).. The software implements many of the most popular methods for determining core collection. In addition it includes novel greedy methods for selection based on polymorphism information content, Shannon entropy and phylogenetic trees/networks. In particular, for the latter approach we construct either a Neighbor-joining tree or Neighbor-net network from a distance matrix computed in PHYLIP distance matrix format by CCD. The resulting structure (tree or network) in tabbed text or NEXUS format and can then be loaded into CCD to determine the core collection. The ...
Animal phylogeny is undergoing a major revolution due to the availability of an exponentially increasing amount of molecular data and the application of novel methods of phylogentic reconstruction, as well as the many spectacular advances in palaeontology and molecular developmental biology. Traditional views of the relationships among major phyla have been shaken and new, often unexpected, relationships are now being considered.
Recent developments are providing exciting new insights into the evolutionary dynamics of species diversification and the importance of evolutionary radiations, or rapid episodes of lineage diversification. The aim of this meeting is to explore questions about where, when and why plant evolutionary radiations happen, and how they proceed. The meeting will bring together contributions spanning: (i) new models of species diversification, including paleodiversity and trait evolution, and the increasingly sophisticated and powerful tools available for testing hypotheses about diversification trajectories and their causes; (ii) the proliferation of new molecular phylogenetic data, for more and larger plant clades spanning broader taxonomic, geographical and temporal levels, as well as opportunities for unprecedented phylogenetic resolution of rapidly evolving clades coming from genome-scale DNA sequence data; (iii) assembly of more comprehensive species geographic distribution, functional and life ...
This post belongs in the write it down before you forget category. Edit - this approach is necessary for handling the trees produced by RAxML, but not those produced by IQ-TREE. Edit #2 - Ancestral state reconstruction in RAxML does not seem to work very well. Im trying IQ-TREE (v1.6) instead. I have a tree…
The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory and concepts may be understood in systematics, which, in turn, provides data for a more general account ...
Dispersal and vicariance are often contrasted as competing processes primarily responsible for spatial and temporal patterns of biotic diversity. Recent methods of biogeographical reconstruction recognize the potential of both processes, and the emerging question is about discovering their relative frequencies. Relatively few empirical studies, especially those employing molecular phylogenies that allow a temporal perspective, have attempted to estimate the relative roles of dispersal and vicariance. In this study, the frequencies of vicariance and dispersal were estimated in six lineages of birds that occur mostly in the aridlands of North America. Phylogenetic trees derived from mitochondrial DNA sequence data were compared for towhees (genus Pipilo), gnatcatchers (genus Polioptila), quail (genus Callipepla), warblers (genus Vermivora) and two groups of thrashers (genus Toxostoma). Different area cladograms were obtained depending on how widespread and missing taxa were coded. Nonetheless, no ...
Registration open for this course, that will be held from September 11th-15th, 2017 in Barcelona (Spain).. Instructor: Dr. Chris Klingenberg (MAnchester University, UK).. This course provides an overview of the interface between geometric morphometrics and phylogenetics. It aims to give an overview of the different approaches and methods that link the two fields and to enable participants to apply them to their own research problems.. Lectures that introduce concepts and methods are integrated with demonstrations of software that put them into practice right away. The main emphasis is on mapping shape data on existing phylogenies to reconstruct the evolutionary history of shape diversification, as well as comparative methods that take phylogeny into account.. To enhance the practical approach of the course, participants are encouraged to bring their own data to conduct analyses and discuss results.. Software that will be used during the course: MorphoJ ...
First of all, Im a student in non-English-speaking country... Newbie in bioinformatics. My Question is about Phylogenetic tree and divergence time. (for training) For drawing Phylogenetic tree, I used MEGA 7 for windows 7 64bit, GUI.. I draw the tree with 16 species mtDNA .fasta data and new mtDNA data, and then I try to calculate the divergence time. But I dont know how to calculate this time. So... the first question is Is it possible to calculate divergence time with MEGA7? if possible, how? And if it is impossible or not recommendable, what tools can be used for it?. Anyway in this situation I did something with MEGA7. (maybe... pointless task?) I found "Compute Pairwise distance..." and get a matrix from it. But I dont know what these numbers mean. 0.05731, 1.012493, 1.42815, 1.197099 .... no unit. Surely this values looks like getting bigger if compared two species have distant evolutionary relationship. What is it? It is my second question. If you have an idea for at least one of ...
Abstract The ulvophytes are of particular evolutionary interest because they display a wide morphological and cytological diversity with unique features among green algae. In this review we describe this diversity in an evolutionary perspective, discuss recent progress made towards understanding the genetic underpinning of highly specialized cytomorphological types, such as siphonous cells, and describe the recent progresses made towards the understanding of the peculiar and highly diverse chloroplast genomes found among ulvophytes. We discuss the difficulties in resolving the ancient phylogenetic relationships among ulvophytes, and the core Chlorophyta lineages, even when applying chloroplast phylogenomic analyses. Furthermore, we highlight the advantages and opportunities in using phylotranscriptomics as an alternative tool to resolve difficult phylogenetic relationships and to unveil the evolution of major cyto-morphological innovations and molecular features associated to them. ...
There are three issues that you question in the above statements. First, the Nasonia gut microbiome recapitulates the hosts phylogeny. We demonstrated this pattern in our Evolution paper, this article, and a third set of experiments that we are currently working on. So we think your commentary here stems from a misinterpretation of what phylosymbiosis is, rather than its lack of evidence. Heres how we view it operationally. Phylosymbiosis is simply the reconstruction of the hosts phylogeny with a UniFrac inference method used to compare microbial community relationships. Like phylogenies, UniFrac trees are statistical inferences based on the weighted (Fig 2B) and unweighted abundances (Fig 2C) of OTUs. Remarkably, both the weighted and unweighted Unifrac trees are in complete agreement with a phylosymbiotic microbiome. We suspect you are laser focused on the pie charts, which create the illusion that G and V have very similar communities based on the single, dominant Providencia genus. The ...
U.S. Fish & Wildlife Service Candidate Conservation Agreements What Are Candidate Species? What the U.S. Fish and Wildlife Service (FWS) considers candidate species are those plants and animals that are candidates for listing under the Endangered Species Act (ESA). These are species for which the FWS has enough information regarding their biological status and threats to propose them as threatened or endangered, but listing is currently precluded by higher priority listing activities. Candidate species are not subject to the legal protections of the ESA. Proactive conservation efforts for these species can, in some cases, eliminate the need to list them under the ESA. What Are the Benefits of Conserving Candidate Species? Implementing conservation efforts before species are listed and their habitats become highly imperiled increases the likelihood that simpler, more cost-effective conservation options are available, and that conservation efforts will succeed. In addition, through early ...
This example of a molecular phylogenetic tree is an unrooted dendrogram. The length of the branches quantitatively represents the evolutionary distance separating gene sequences within these organisms.This particular tree is based on the analysis of small subunit ribosomal RNA sequences. In this tree, the tips of branches are modern organisms. Each node within the tree represents a common ancestor. The last common ancestor (the root) is here marked with the star. How this is determined will be described in a later lecture.. Notice that there is no explicit or implied ranking of above (superior) or below (inferior) in the tree. Evolutionary distance (divergence) is measured along the lengths of the branches connecting species. There are no axes in this graph.. One of the most exciting outcomes of this method early on was the discovery of a new type of organism - the Archaea (a.k.a. archaebacteria). Previously it was thought that all living things were either Bacteria (a.k.a. eubacteria) or ...
For example, our recent work includes the development of methods for reconstructing phylogenetic networks directly from molecular data such as the NeighborNet algorithm [1] (which is available as part of the software package Splitstree4 , and the QNet algorithm [2]. We have also developed methods [3] for computing consensus networks, phylogenetic networks used to summarise, for example, collections of gene trees. In case the collection of gene trees is built from patchy data, more sophisticated tools are needed to summarise them. One approach [4] developed by members of our group is implemented in the Q-imputation algorithm.. Another software package developed by our group, called PADRE, aims to provide tools for constructing an explicit representation of the evolutionary history of polyploid organisms such as plants . PADRE is based on our work on modelling reticulate evolution [5, 6], which includes recent theoretical results [7] concerning the complexity of computing multi-labelled trees. ...
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Three plant genera with South American-Australasian disjunctive distributions were studied: Eucryphia, Griselinia and Coriaria . The aims of the project were: a) to assess the utility of different chloroplast and nuclear DNA sequences for phylogenetic reconstruction and b) by means of molecular clocks to establish whether or not this distribution is due to vicariance (continental drift) or more recent dispersal events. DNA was extracted, and regions of interest were amplified and sequenced. These were rpoA, trnL-F and trnU-K from the chloroplast genome, and rDNA 5.8S and intergenic spacers 1 and 2, Adh and two loci of the G3pdh gene from the nuclear genome. In each of the three genera, a single trans-Antarctic disjunction was indicated. Molecular phylogenies were produced using parsimony. Individual base pair variation was analysed in detail, and graphs were drawn to highlight variable regions. Sequences providing the most resolution were trnL-F, ITS and the two loci of the G3pdh. Robust ...
Our work is largely done within the context of the software packages MrBayes and RevBayes. Among other things, we are interested in how evolutionary models can be formulated in a generic way, and we are trying to improve the numerical methods used in Bayesian phylogenetic inference. We also work with several different applications in evolutionary biology, for example, understanding how morphological characters change over time and how fossils can be used in dating past evolutionary events. ...
Ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantels test, computation of minimum spanning tree, the population parameter theta based on various approaches, nucleotide diversity, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using non-parametric rate smoothing, conversion of APE trees to and from hclust objects and for classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ and ML methods.
... Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time.. ...
154 Hurley Hall. Phylogenetic Species Trees as Optimization Problems and Connections to Statistics and Geometry.. The fundamental problem in phylogenetics is to infer the evolutionary history of a group of species. This history is usually represented as a rooted tree whose leaves are the extant species from which data can be gathered. Molecular phylogenetics has led to some grand scientific challenges, driven by advances in genome sequencing technology: (1) data is gathered from long genomes for which evolutionary transformations must be modeled by myriad processes, (2) different regions of these genomes may have different evolutionary histories, and (3) there are intractable computational issues presented by the amount of "big data" used in the inference process. Fortunately for the interested mathematician, some of the most promising methods in phylogenetic inference use information about probabiity distributions of genes within large genomes. We will show this leads to interesting connections ...
The aquatic plant genus Ruppia (Ruppiaceae) comprises eight species mainly in coastal brackish areas of the world. While the known taxa of Ruppia thus far generally had either four- or eight-carpelled flowers, our recent Ruppia collection from Western Cape, South Africa showed flowers with only two carpels. This characteristic morphological evidence, together with elongated coiled peduncles, implied either: i) extensive morphological variation of the cosmopolitan R. cirrhosa; or ii) the occurrence of a new species in the genus. We tested these alternative hypotheses of the bicarpellate Ruppia taxon in a phylogenetic framework. Sequence data from four plastid DNA regions and nuclear phyB were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We obtained moderately to highly resolved phytogenies with both data sets. The collection from Western Cape showed unique DNA sequences which were, in both plastid and nuclear phylogenetic trees, placed as sister to the rest of the ...
The history of life unfolds within a phylogenetic context. Comparative phylogenetic methods are statistical approaches for analyzing historical patterns along phylogenetic trees. This task view describes R packages that implement a variety of different comparative phylogenetic methods. This is an active research area and much of the information is subject to change. One thing to note is that many important packages are not on CRAN: either they were formerly on CRAN and were later archived (for example, if they failed to incorporate necessary changes as R is updated) or they are developed elsewhere and have not been put on CRAN yet. Such packages may be found on GitHub, R-Forge, or authors websites. Getting trees into R : Trees in R are usually stored in the S3 phylo class (implemented in ape), though the S4 phylo4 class (implemented in phylobase) is also available. ape can read trees from external files in newick format (sometimes popularly known as phylip format) or NEXUS format. It can also ...
The Geneco course "Making Phylogenetic Trees" run by Prof Niklas Wahlberg will be at Lund University from the 2nd to 4th of October . This 3 day course will provide an introduction to the fundamental principles of building phylogenies using molecular data, as well as the latest techniques and programmes in this field.. The aims of this course are to introduce the theory and practice of phylogenetic inference from molecular data and to provide an introduction to some of the most used methods and computer programs. The emphasis will be on model-based methods using maximum likelihood and Bayesian inference, with a focus on DNA sequences as data. We will introduce programs such as RAxML, MrBayes, as well as BEAST for timing of divergence analyses. The course will consist of lectures, demonstrations of computer programs, and independent projects on fully analysing an example dataset (either your own or given by the lecturer).. The course is available to everyone and there is no charge for attendance. ...
This is a common problem I have when trying to construct a phylogeny for a set of taxa when all taxa do not have sequence data associated. 1. read your tree into R as a phylo object 2a. label all the nodes tree|-makeNodeLabel(tree) 2b. your tree may not have branch lengths and thus no branching…
Darwin / Wallace Tree of Life = branching with a single common ancestor. vs. Lamarck Chain of Being = not branching, multiple common ancestors. Phylogenetics. Phylogeny = genealogy of a group of taxa; a kind of family tree. The goal of cladistics is to provide a phylogeny that reflects evolutionary history. Essentially we seek to make hierarchical groups.. Minimum Essential Terms (also see pg 437). 1) Monophyletic Group = a group that contains all descendants of a common ancestor. The motivation for creating these can be kind of confusing. Youre probably familiar with taxonomy (Kingdom, Phylum, Class, etc.) though. Imagine we have a bunch of squid-like things that Frank wants to put into the same genus and Curt does not. We can do a phylogenetic analysis to reveal the evolutionary relationships among these squid-like things. If they indeed form a monophyletic group, Frank has support for placing them in the same taxonomic group. If not, then these squid-like things are not closely related ...
3. Overview of Friday (Corey and Doug). 4. Back to the modules- break into 3 groups to discuss new module themes.. A) Chris, Tracy, Eileen, Tania: locomotion-related. B) Corey, Scott, Scott: limbs, trait evolution; cryptic diversity; evol @ molecular level and adaptation; evolution of sensory abilities; gene duplication and adaptation; evolution of domestication (Russian foxes, dogs, mustard plants); ring species; evolution of gliding ability. C) Kayce, Rob, Julie: molecules to ecosystems in space and time; glaciation effects, across landscapes; infectious disease. D) Doug, Pam, Ana: plant diversity, phylogeny, biogeography, climate change. E) Mark, Kurt, Joe: genomics-related concepts; pop gen to species level: phylogeography, processes that structure genetic variation within species, gene trees vs species trees, macroevolution, reconstruction of ancestral states; community assembly: history of populations in space and time; glaciation; parasites/emerging disease; stress gene trees vs species ...
HIV-1 CRF07_BC and CRF08_BC are closely related circulating recombinant forms (CRFs) with serious public health consequences in China. The temporal and spatial dynamics of these CRFs were determined by estimating their times of divergence, using phylogenetic and Bayesian coalescent methods. Studies of the timelines of CRF07_BC and CRF08_BC trace the expansion of these strains back their origins to Yunnan province. The present study highlights the relevance of incorporating evolutionary and molecular epidemiological analyses into an in-depth understanding of the genesis of HIV epidemic, providing information for determining regional and global public health policies, including future vaccine strategies.