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
Phylogenetic tree can be constructed from genetic sequences using distance-based methods or character-based methods. Distance-based methods, including unweighted pair group method with arithmetic means (UPGMA) and Neighbor-joining (NJ), are based on the matrix of pairwise genetic distances calculated between sequences. The character-based methods, including maximum parsimony (MP) (Fitch 1971), maximum likelihood (ML) (J. Felsenstein 1981), and Bayesian Markov Chain Monte Carlo (BMCMC) method (Rannala and Yang 1996), are based on mathematical model that describes the evolution of genetic characters and search for the best phylogenetic tree according to their own optimality criteria.. Maximum Parsimony (MP) method assumes that the evolutionary change is rare and minimizes the amount of character-state changes (e.g., number of DNA substitutions). The criterion is similar to Occams razor, that the simplest hypothesis that can explains the data is the best hypothesis. Unweighted parsimony assumes ...
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)
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 MLs 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. BIs long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve
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
Maximum likelihood (ML) assumes the best tree is the tree that is most likely with the given data, under a certain model. ML will take into account all the data we have generated so far in order to construct our final tree. It is a commonly used tree-building algorithm that will give us a single tree as our output.. Making it pretty. When we have created our tree, then its time to make it publication ready.. If we need to change the taxa names, font, or size, use Adobe Illustrator or a similar image manipulation program. Make sure our taxa names can be clearly read and the bootstrap values are visible above each node.. Not all data will require such robust analysis. But we will not know for certain how much better or different a tree produced from a more robust analysis will be until this analysis is performed.. In general, the output tree of a phylogenetic analysis is an estimate of the characters phylogeny (a gene tree) and not the phylogeny of the taxa (species tree) though ideally, both ...
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 ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under max-imum parsimony, maximum likelihood, and Bayesian techniques. The relative accuracy of species tree inference methods under simulation has received less study. The number of analytical techniques available for inferring species trees is in-creasing rapidly, and in this paper, we compare the performance of several species tree inference techniques at estimating recent species divergences using computer simulation. Simulating gene trees within species trees of different shapes and with varying tree lengths (T) and population sizes (θ), and evolving sequences on those gene trees, allows us to determine how phylogenetic accuracy changes in relation to different levels of deep coalescence and phylogenetic signal. When the probability of discordance between the gene trees and the species tree is high (i.e., T is small and/or
A multigene phylogeny of the fly superfamily Asiloidea (Insecta): Taxon sampling and additional genes reveal the sister-group to all higher flies (Cyclorrhapha ...
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 - Phylogeny and evolution of medical species of candida and related taxa. T2 - A multigenic analysis. AU - Diezmann, S.. AU - Cox, C. J.. AU - Schönian, G.. AU - Vilgalys, R. J.. AU - Mitchell, T. G.. PY - 2004/12/1. Y1 - 2004/12/1. N2 - Hemiascomycetes are species of yeasts within the order Saccharomycetales. The order encompasses disparate genera with a variety of life styles, including opportunistic human pathogens (e.g., Candida albicans), plant pathogens (e.g., Eremothecium gossypii), and cosmopolitan yeasts associated with water and decaying vegetation. To analyze the phylogeny of medically important species of yeasts, we selected 38 human pathogenic and related strains in the order Saccharomycetales. The DNA sequences of six nuclear genes were analyzed by maximum likelihood and Bayesian phylogenetic methods. The maximum likelihood analysis of the combined data for all six genes resolved three major lineages with significant support according to Bayesian posterior ...
UNLABELLED: Phylogenetic inference in bacterial genomics is fundamental to understanding problems such as population history, antimicrobial resistance, and transmission dynamics. The field has been plagued by an apparent state of contradiction since the distorting effects of recombination on phylogeny were discovered more than a decade ago. Researchers persist with detailed phylogenetic analyses while simultaneously acknowledging that recombination seriously misleads inference of population dynamics and selection. Here we resolve this paradox by showing that phylogenetic tree topologies based on whole genomes robustly reconstruct the clonal frame topology but that branch lengths are badly skewed. Surprisingly, removing recombining sites can exacerbate branch length distortion caused by recombination. IMPORTANCE: Phylogenetic tree reconstruction is a popular approach for understanding the relatedness of bacteria in a population from differences in their genome sequences. However, bacteria frequently
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 ...
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 ...
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 resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in ...
The increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, and tree rooting scenarios. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. ...
Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our
Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because the few genes available in past studies gave conflicting signals. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict. To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave
The Stomatopoda make up an order of crustaceans that have evolved for more than 400 million years since they emerged from their haplocarid ancestors. In previous phylogenetic studies based on morphological characters, seven superfamilies and 19 families were erected for more than 400 extant stomatopod species. Prior to this study, no effort was made to investigate the interrelationships among stomatopod superfamilies using molecular markers. In this study, 18s rDNA, 28s rDNA, and COI genes of 25 stomatopod species from 10 families and four superfamilies were sequenced to build a molecular phylogeny for these stomatopods. Whereas some interfamilial relationships are in congruence with previous studies, the deep structure of the fully resolved molecular phylogeny reconstructed in the present study is fundamentally different. Two previously proposed sister clades, the smashers and the spearers, were collapsed in the molecular tree. Hemisquilidae, other than closely related to other families from ...
INTRODUCTION. The genus Bacillus is a phenotypically large, diverse collection of Gram-positive or Gram-variable staining, endospore-forming, aerobic or facultatively anaerobic, rod-shaped bacteria that have undergone considerable reclassification as advances in molecular biology have revealed a high phylogenetic heterogeneity (5, 21). The genus Bacillus and related genera are distributed widely in nature and include thermophilic, psychrophilic, acidophilic, alkalophilic and halophilic bacteria that utilize a wide range of carbon sources for heterotrophic growth or grow autotrophically.. The investigations on phylogenetic divergence of the genus Bacillus and its mesophilic and thermophilic members indicated the need for further and extensive studies to place some of these bacilli in appropriate taxonomic levels (1, 23, 21). With the accumulation of further 16S rRNA gene sequence data, Bacillus has been divided into more manageable and better-defined groups (16). According to Ludwig et al. (2007) ...
The dictyostelids possess a complex life cycle including aggregative and multicellular stages. They also include one of the most widely studied protistan model organisms, Dictyostelium discoideum. The current molecular phylogeny of dictyostelids is based largely on SSU (18S) rDNA sequences and shows a deep taxon consisting of four major groups, none of which correspond to the three traditional morphologically-defined genera. However, due to the generally slowly evolving nature of SSU rDNA, these data fail to resolve the majority of branches within the four groups. Given the highly morphologically mixed nature of the dictyostelid groups, it is important to resolve relationships within them. We have determined sequences for the internal transcribed spacers (ITS) of rDNA for nearly all species in the original dictyostelid global phylogeny. Phylogenetic analyses of these data, in combination with the previously determined SSUr DNA sequences, confidently resolve nearly all branches in the tree. This ...
Based on morphological characters, peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the ...
Phylogeny reconstruction at the species level, especially using organellar markers, is often complicated by problems such as incomplete lineage sorting and interspecific hybridization. Single-copy nuclear genes may be useful for these cases because they have higher mutation rates and are biparentally inherited. One plant group in which hybridization and incomplete lineage sorting have been proposed based on analyses of internal transcribed spacer (ITS) and plastid data is a clade of mints from the southeastern United States: Conradina and the related genera Dicerandra, Piloblephis, Stachydeoma, and Clinopodium (Lamiaceae). To clarify the phylogeny in this clade and investigate the possibility of incomplete lineage sorting and interspecific hybridization, we isolated three members of the nuclear GapC gene family and used two to reconstruct phylogeny. Separate phylogenetic analyses of the two GapC loci did not resolve species relationships. We then used two approaches to concatenate the two ...
Members of phylum Acanthocephala are parasites of vertebrates and arthropods and are distributed worldwide. The phylum has traditionally been divided into three classes, Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala; a fourth class, Polyacanthocephala, has been recently proposed. However, erection of this new class, based on morphological characters, has been controversial. We sequenced the near complete 18S rRNA gene of Polyacanthorhynchus caballeroi (Polyacanthocephala) and Rhadinorhynchus sp. (Palaeacanthocephala); these sequences were aligned with another 21 sequences of acanthocephalans representing the three widely recognized classes of the phylum and with 16 sequences from outgroup taxa. Phylogenetic relationships inferred by maximum-likelihood and maximum-parsimony analyses showed Archiacanthocephala as the most basal group within the phylum, whereas classes Polyacanthocephala + Eoacanthocephala formed a monophyletic clade, with Palaeacanthocephala as its sister group. ...
Phylogenetic reconstructions of bacterial species from DNA sequences are hampered by the existence of horizontal gene transfer. One possible way to overcome the confounding influence of such movement of genes is to identify and remove sequences which are responsible for significant character incongruence when compared to a reference dataset free of horizontal transfer (e.g., multilocus enzyme electrophoresis, restriction fragment length polymorphism, or random amplified polymorphic DNA) using the incongruence length difference (ILD) test of Farris et al. {[}Cladistics 10 (1995) 315]. As obtaining this whole genome dataset prior to the reconstruction of a phylogeny is clearly troublesome, we have tested alternative approaches allowing the release from such reference dataset, designed for a species with modest level of horizontal gene transfer, i.e., Escherichia coli. Eleven different genes available or sequenced in this work were studied in a set of 30 E. coli reference (ECOR) strains. Either ...
Phylogenetic analyses of the family Trypanosomatidae have been conducted using both 18S rRNA gene sequences and a variety of protein sequences. Using a variety of phylogenetic methods, 18S rRNA phylogenies indicate that the genus Trypanosoma is not monophyletic. Rather, they suggest that the American and African trypanosomes constitute distinct clades. By contrast, phylogenetic analyses of available sequences in 42 protein families gene generally supported monophyly of the genus Trypanosoma. One possible explanation for these conflicting results is poor taxon sampling in the case of protein coding genes, most of which have been sequenced for only a few species of Trypanosomatidae.
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Molecular Phylogenetics and Evolution - in press. Abstract. The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the ...
Background In contrast to DNA-mediated transposable elements (TEs), retrotransposons, particularly non-long terminal repeat retrotransposons (non-LTRs), are generally considered to have a much lower propensity towards horizontal transfer. selection due to functional constraint. Vertical transmission of Juan and a few cases of phylogenetic incongruence Comparison of host phylogeny with TE phylogeny is one method used to address the question of vertical vs. horizontal transmission. A detailed mosquito phylogeny has been previously constructed using Vg-C [30]. We have only included Vg-C sequences from species for which Juan sequences were obtained in this study (Figure ?(Figure2A).2A). In addition, we have also obtained sequence for Vg-C from Ae. simpsoni, which was not available from the previous dataset [30]. We used nt sequences for phylogenetic inference as in the previous study, and our phylogeny is consistent with the phylogeny based on the larger Vg-C dataset [30]. Phylogenetic inference ...
TY - JOUR. T1 - Ontogeny discombobulates phylogeny. T2 - Paedomorphosis and higher-level salamander relationships. AU - Wiens, John J. AU - Bonett, Ronald M.. AU - Chippindale, Paul T.. PY - 2005/2. Y1 - 2005/2. N2 - Evolutionary developmental biology (evo-devo) has revolutionized evolutionary biology but has had relatively little impact on systematics. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of biology and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of ...
Citation. Harasewych, M. G., Adamkewicz, S. L., Blake, J. A., Saudek, D., Spriggs, T., Bult, C. J.. Phylogeny and Relationships of Pleurotomariid Gastropods (Mollusca: Gastropoda): an Assessment Based on Partial 18S RDNA and Cytochrome C Oxidase I Sequences. Mol Mar Biol Biotechnol. 1997 Mar 01; 6(1): 1-20.. PubMed Citation. Abstract. The phylogenetic position of the ancient family Pleurotomariidae within the Molluscan class Gastropoda, as well as the relationships of its Recent genera and species, were assessed using an iterative, two-gene (18S rDNA and cytochrome c oxidase I) approach to phylogeny reconstruction. In order to orient the Pleurotomariidae within Gastropoda, partial 18S rDNA sequences were determined for 7 pleurotomariid and 22 other gastropods that span the major groups within the class as well as for one cephalopod and two polyplacophorans, which serve as outgroups. Cladistic analyses of a sequence of approximately 450 base pairs (bp) near the 5 end of the 18S rDNA support the ...
This research presents an analysis of two data sets, one consisting of mt16S rRNA sequences from 134 samples and the second a combination of four genes (12S rRNA, 16S rRNA, COI, GAPDH) from a subset of these samples to test species boundaries and establish phylogenetic hypotheses for New Guinean and selected northern Australian species. These data supports the recognition of 25 Cherax species, including three recently described species and five new species discovered in this study from Papua, Indonesia. Two main clades were identified based on phylogenetic analyses. The New Guinean crayfish does not form a monophyletic group but share relationships with northern Australian species at different evolutionary depths, which is consistent with the geological history of the region. The diverse highland Cherax fauna of the Wissel Lakes form a well support monophyletic lineage but show minimal molecular divergence, which is at odds with their high morphological diversity. The results of this study fill ...
The ant subfamily Formicinae is a large assemblage (2458 species (J. Nat. Hist. 29 (1995) 1037), including species that weave leaf nests together with larval silk and in which the metapleural gland-the ancestrally defining ant character-has been secondarily lost. We used sequences from two mitochondrial genes (cytochrome b and cytochrome oxidase 2) from 18 formicine and 4 outgroup taxa to derive a robust phylogeny, employing a search for tree islands using 10,000 randomly constructed trees as starting points and deriving a maximum likelihood consensus tree from the ML tree and those not significantly different from it. Non-parametric bootstrapping showed that the ML consensus tree fit the data significantly better than three scenarios based on morphology, with that of Bolton (Identification Guide to the Ant Genera of the World, Harvard University Press, Cambridge, MA) being the best among these alternative trees. Trait mapping showed that weaving had arisen at least four times and possibly been ...
The use of molecular clocks to estimate divergence times is controversially debated, due to conflicting results from different studies and disparities with paleontological or archaeological data [73-76]. Criticism focuses on the major problems such as faulty calibration, impact of rate heterogeneity among lineages, and time dependency of molecular rates [73, 75-77]. Some of the problems could be solved by the relaxed clock approach [78], and despite all pitfalls and criticism, molecular clock approaches have helped considerably to reveal the evolutionary history of life, especially when it comes to divergence times of groups with poor or no fossil record [75, 76, 79]. Thus, we consider it a valuable methodology to roughly estimate divergence times for tiny, sluggish gastropods for which there is no fossil record. Molecular clock dating stands and falls with the accuracy with which genetic distances can be estimated [80]; thus we consider the removal of ambiguous (i.e. potentially ...
Limosella is a small aquatic genus of Scrophulariaceae of twelve species, of which one is distributed in northern circumpolar regions, two in southern circumpolar regions, two in the Americas, one endemic to Australia, and six in tropical or southern Africa or both. The Australasian L. curdieana has always been considered distinct but its close phylogenetic relationships have never been inferred. Here, we investigated the following alternative phylogenetic hypotheses based on comparative leaf morphology and habitat preferences or floral morphology: (1) L. curdieana is sister to the African L. grandiflora; or (2) it is closely related to a group of other African species and the northern circumpolar L. aquatica. We tested these hypotheses in a phylogenetic framework using DNA sequence data from four plastid DNA regions and the nuclear ITS region. These were analyzed using maximum parsimony and Bayesian inference. We obtained moderately resolved, partially conflicting phylogenies, supporting that ...
The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome revealed the existence of 10 GSK genes that fall into four major groups. Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences. We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms
Identifying the organisms behind novel environmental lineages has been one of several major targets in microbial biodiversity research (9, 23, 38, 41). This is especially important in the case of evolutionarily interesting lineages at higher taxonomic levels and in the case of lineages that occur frequently in different environmental systems and whose morphological diversity and ecological function are unknown. The uncultured MAST clades identified recently (23, 44) meet all of these criteria and therefore deserve further study. Due to the information obtained as a result of the research that we conducted, we were able to determine the morphotype for the 18S rRNA gene sequence that branches within the MAST-12 clade which we retrieved from a Norwegian estuarine microbial mat sample.. Our phylogenetic reconstruction of stramenopiles using 18S rRNA gene signatures is consistent with previous analyses. The previous analyses confirmed the monophyly of phototrophic stramenopiles, resulting in ...
Morphological and molecular data were analyzed using parsimony to trace character evolution within Anagallis s.l., including Anagallis, Asterolinon, Pelletiera, Lysimachia nemorum, and L. serpyllifolia, which are distributed among two sister clades. The first clade, comprising Anagallis arvensis, A. foemina, A monelli, Asterolinon, Pelletiera, Lysimachia nemorum, and L. serpyllifolia is supported by synapomorphies such as an annual, repeatedly branching habit, sessile leaves, flowers in almost all leaf axils, and membraneous slightly dentate calyx margins, of which all but the last are homoplasious within Anagallis s.l. The second clade, comprising Anagallis species only, is supported by a large number of synapomorphies, of which the majority are floral features. Placement of then taxa, for which no DNA was available, is porposed based on morphological characters evaluated in the ligth of the result of the phylogentis analysis of sequenced taxa.. ...
1. Hedges SB. The origin and evolution of model organism. Nature Reviews Genetics. 2003 ;3:838-849 2. Winchell CJ, Sullivan J, Cameron CB. et al. Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Mol Biol Evol. 2002 ;19:762-776 3. Brusca RC, Brusca GJ. Invertebrates. Sunderland, Massachusetts: Sinauer. 1990 4. Abouheif E, Zardoya R, Meyer A. Limitations of metazoans 18S rRNA sequence data: implications for reconstructiong a phylogeny the animal kingdom and inferring the reality of the Cambrian explosion. J Mol Evol. 1998 ;47:394-405 5. Takezaki N, Figueroa F, Zaleska-Rutczynska Z. et al. Molecular phylogeny of early vertebrates: Monophyly of the Agnathans as revealed by sequences of 35 genes. Mol Biol Evol. 2003 ;20:287-292 6. Jollie MJ. The origin of chordates. Acta Zool. 1973 ;54:81-100 7. Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa and ...
TY - JOUR. T1 - Synonymous substitution rates in Drosophila. T2 - Mitochondrial versus nuclear genes. AU - Moriyama, Etsuko N.. AU - Powell, Jeffrey R.. PY - 1997. Y1 - 1997. N2 - Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7-3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5-9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 ...
Find the fascicles article Taxonomic rearrangement of |I|Anthostomella|/I| (Xylariaceae) based on a multigene phylogeny and morphology on the website of Scientific Publications of the Muséum national dHistoire naturelle, Paris
Refs - -. Agnarsson, I., Kuntner, M. & May-Collado, L. J. 2010. Dogs, cats, and kin: A molecular species-level phylogeny of Carnivora. Molecular Phylogenetics and Evolution 54, 726-745.. Baskin, J. A. 1998. Mustelidae. In Janis, C. M., Scott, K. M. & Jacobs, L. L. (eds) Evolution of Tertiary Mammals of North America. Volume 1: Terrestrial Carnivores, Ungulates, and Ungulatelike Mammals. Cambridge University Press, pp. 152-173.. Bininda, Emonds, O. R. P., Gittleman, J. L. & Purvis, A. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74, 143-175.. Bryant, H. N., Russell, A. P. & Fitch, W. D. 1993. Phylogenetic relationships within the extant Mustelidae (Carnivora): appraisal of the cladistic status of the Simpsonian subfamilies. Zoological Journal of the Linnean Society 108, 301-334.. Dragoo, J. W. & Honeycutt, R. L. 1997. Systematics of mustelid-like carnivores. Journal of Mammalogy 78, 426-443.. Eizirik, ...
Amphioxus, as the closest living animal of the last common ancestor of all vertebrates, occupies an extremely important phylogenetic position in the evolution of vertebrates and has attracted the interest of scientists from various research fields in recent years. However, despite their importance for the life sciences, taxonomic studies of amphioxus are relatively limited. In present review, we summarize current progress in both field investigations and taxonomic research of Chinese amphioxus. Based on the investigation data, we assume that amphioxus is distributed in all habitable sandy beaches along the Chinese coast from south to north. According to the rule of priority and recent taxonomic studies on amphioxus, we also propose that the original subspecies Brnachiostoma belcheri tsingtauense together with the population in most Japanese waters is an independent species and its name should be revised to B. japonicus. Consequently, there are at least two species of genus Brnachiostoma and 1-3 ...
Domain combinations containing the Bcl-2 inhibitors of programmed cell death superfamily in Amphimedon queenslandica. Domain architectures illustrate each occurrence of the Bcl-2 inhibitors of programmed cell death superfamily.
p,Hemichordates have occupied a central role in hypotheses of deuterostome and early chordate evolution. However, surprisingly little is understood about evolution within hemichordates, including hemichordate ancestral characters that may relate to other deuterostome taxa. Previous phylogenetic studies suggested that enteropneust worms are either monophyletic (based on 28S rDNA) or paraphyletic (based on 18S rDNA). Here, we expand the number of hemichordate taxa used in phylogenetic analyses for 18S rDNA data and employ more quickly evolving mitochondrial gene sequences. Novel data from an undescribed deep-sea enteropneust species similar to Torquarator bullocki and a Gulf Stream tornaria larva suggest that these taxa are closely allied to or possibly within Ptychoderidae. Saxipendium coronatum, another deep-sea species commonly called the spaghetti worm, is shown to be a member of Harrimaniidae. Recognition of these deep-sea lineages as distinct families calls into question features used in ...
Although tribe Stachydeae (Lamiaceae) is considered monophyletic, relationships within the tribe are still poorly understood. The complexity of Stachydeae includes paraphyletic genera, considerable morphological plasticity, a range of ploidy levels, and presumably frequent natural hybridization. We performed parsimony and Bayesian phylogenetic analyses of nuclear (ribosomal ITS) and plastid (trnL intron, trnL-trnF spacer, rps16 intron) DNA sequence data from a taxonomically and geographically broad sampling of the tribe to identify major evolutionary lineages and to test taxonomic hypotheses within this largest of all lamioid tribes. We included 143 accessions corresponding to 121 species, representing both Old and New World species, and all 12 recognized genera of tribe Stachydeae. Both nuclear and plastid data corroborate monophyly of the tribe, with Melittis as sister to all remaining Stachydeae. For the latter well-supported clade, we suggest the phylogenetic name Eurystachys. Within ...
In evolutionary biology, convergent evolution describes the process whereby organisms not closely related, independently evolve similar traits as they both adapt to similar environments or Ecological niche. On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see Long branch attraction. In cultural evolution, convergent evolution is the development of similar cultural adaptations to similar environmental conditions by different peoples with different ancestral cultures. An example of convergent evolution is the similar nature of the flight/wings of insects, birds, pterosaurs, and bats. All four serve the same function and are similar in structure, but each evolved independently. Some aspects of the lens of eyes also evolved independently in various animals. Convergent evolution is similar to, but distinguishable from, the phenomena of evolutionary relay and parallel evolution. Evolutionary relay refers to independent species acquiring similar ...
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular ...
Background: Annelida is one of the major protostome phyla, whose deep phylogeny is very poorly understood. Recent molecular phylogenies show that Annelida may include groups once considered separate phyla (Pogonophora, Echiurida, and Sipunculida) and that Clitellata are derived polychaetes. The total-evidence analyses combining morphological and molecular characters have been published for a few annelid taxa. No attempt has yet been made to analyse simultaneously morphological and molecular information concerning the Annelida as a whole. Results: Phylogenetic relationships within Annelida were analysed on the basis of 93 morphological characters and sequences of six genes (18S, 28S, and 16S rRNA, EF1 alpha, H3, COI), altogether, 87 terminals of all annelid families and 3,903 informative characters, by Bayesian and maximum-parsimony methods. The analysis of the combined dataset yields the following scheme of relationships: Phyllodocida and Eunicida are monophyletic groups, together probably ...
Understanding how quickly pathogens replicate and how quickly the immune system responds is important for predicting the epidemic spread of emerging pathogens. Host body size, through its correlation with metabolic rates, is theoretically predicted to impact pathogen replication rates and immune system response rates. Here, we use mathematical models of viral time courses from multiple species of birds infected by a generalist pathogen (West Nile Virus; WNV) to test more thoroughly how disease progression and immune response depend on mass and host phylogeny. We use hierarchical Bayesian models coupled with nonlinear dynamical models of disease dynamics to incorporate the hierarchical nature of host phylogeny. Our analysis suggests an important role for both host phylogeny and species mass in determining factors important for viral spread such as the basic reproductive number, WNV production rate, peak viraemia in blood and competency of a host to infect mosquitoes. Our model is based on a ...
Jonathan F. Wendel wrote: , = , A paper was recently published in which it was demonstrated that in , phylogenetic analysis, a potentially misleading resolution could be , obtained in cases where the sampled genes varied greatly in their GC , content. The conclusion was, as I recall, that high-GC genes were , spuriously linked by virtue of this compositional bias by itself. Im , going crazy trying to recall what this reference was..... can anyone , help? , = , Thanks, Jonathan Wendel There are a number of references for this kind of work as it is thought to be a major problem in phylogeny reconstruction. Methods that seek to circumvent the problem: Galtier, N. and Gouy, M. (1995). =93Inferring phylogenies from DNA sequences of unequal base compositions.=94 Proc. Natl. Acad. Sci. USA 92:= 11317-11321. Lake, J. A. (1994). =93Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances.=94 Proc. Natl. Acad. Sci. USA 91= : 1455-1459. Lockhart, P. J., Steel, M. A., Hendy, ...
The present study provides the first phylogenomic evidence to support the monophyletic origin of four major orders of copepods and the group of podopleans. The monophyletic status of Copepoda has been broadly accepted by both morphological [5, 14] and large-scale phylogenomic analyses [28-30]. Although this study does not include all copepod orders, there can be no doubt of the monophyly of copepods. The subclass Copepoda consists of two infraclasses, Progymnoplea and Neocopepoda, suggested by Huys and Boxshall [5]. The infraclass Neocopepoda can be further divided into two superorder groups, Gymnoplea and Podoplea (Fig. 1). The concept of this classification was proposed by Giesbrecht [67] and became generally accepted [5, 12, 68]. However, the naupliar musculature and the molecular phylogeny using partial nuclear 28S rRNA gene (a total aligned sequence length of 484 bp from the D9/D10 region) (Fig. 2A) showed conflicting results and suggested a possible paraphyletic origin of podopleans [15, ...
A molecular phylogeny of the salamandrid genus Neurergus was reconstructed based on two sections of the 12S and 16S mitochondrial ribosomal genes (810 bp), 19 allozyme and three plasma protein loci. When representative species of all closely related salamandrid groups were included, mitochondrial data provided evidence for monophyly of Neurergus within the Salamandridae. Mitochondrial and allozyme data showed homogenous intrageneric tree topologies, but different estimates of times of separation. We calibrated the evolutionary rate to 0.46% pairwise sequence divergence per million years. Accordingly Neurergus diverged 18 million years ago (mya) from a lineage that comprised Euproctus asper and large bodied newts of the genus Triturus. A split around 11 mya produced two major clades within Neurergus. Further separation within the southern 'N. crocatus-clade' (comprising N. crocatus, N. microspilotus and N. kaiseri) occurred ca. 5 mya. The northern 'N. strauchii-clade' separated into N
Historically, morphological characters have been used to support the monophyly, composition, and phylogenetic relationships of scorpion families. Although recent phylogenomic analyses have recovered most of these traditional higher level relationships as non-monophyletic, certain key taxa have yet to be sampled using a phylogenomic approach. Salient among these is the monotypic genus Caraboctonus Pocock, 1893, the type species of the family Caraboctonidae Kraepelin, 1905. Here, we examined the putative monophyly and phylogenetic placement of this family, sampling the library of C. keyserlingi Pocock, 1893 using high throughput transcriptomic sequencing. Our phylogenomic analyses recovered Caraboctonidae as polyphyletic due to the distant placement of the genera Caraboctonus and Hadrurus Thorell, 1876. Caraboctonus was stably recovered as the sister-group of the monotypic family Superstitioniidae Stahnke, 1940, whereas Hadrurus formed an unstable relationship with Uroctonus Thorell, 1876 and ...
abstract) Ericson, P.G.P., I. Envall, M. Irestedt, and J.A. Norman (2003), Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data, BMC Evol. Biol. 3, 16. DOI: 10.1186/1471-2148-3-16. (pdf) Fain, M.G., and P. Houde (2007), Multilocus perspectives on the monophyly and phylogeny of the order Charadriiformes, BMC Evol. Biol. 7, 35. DOI: 10.1186/1471-2148-7-35. (pdf) Gibson, R. and A. Baker (2012), Multiple gene sequences resolve phylogenetic relationships in the shorebird suborder Scolopaci (Aves: Charadriiformes), Mol. Phylogenet. Evol. 64, 66-72. DOI: 10.1016/j.ympev.2012.03.008. (abstract) Hu, C. C. Zhang, l. Sun, Y. Zhang, W. Xie, B. Zhang, and Q. Chang (2017), The mitochondrial genome of the pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes, PloS ONE 12(4), e0175244. DOI: 10.1371/journal.pone.0175244. (pdf) Jackson, D.G, S.D. Emslie, and M. van Tuinen (2012), Genome skimming identifies polymorphism in ...
After aligning the sequences from all loci, (i) models of sequence evolution were determined for each locus. Gene trees were calculated for each locus with (ii) the sequences derived from the diploid taxa by Bayesian phylogenetic inference (BI), and (iii) sequences from all diploid plus, consecutively, single polyploid individuals were clustered by neighbor-joining analysis to determine phylogenetic affiliation (phasing) of the homoeologous gene copies found in polyploid taxa. Concatenated sequences from all loci (supermatrices) were used for BI of (iv) diploid and (v) diploid plus phased homoeologs of polyploid taxa. (vi) A MSC-based [multispecies coalescent] analysis was conducted to infer species trees from gene trees for the diploid individuals. (vii) To date nodes within the Hordeum phylogeny a molecular clock approach was conducted together with the MSC. (viii) A BCA [Bayesian concordance analysis] was conducted on the diploid taxa to estimate gene tree incongruences. Finally, (ix) ...