MitochondrialReconstructionGenomesEvolutionGenusInferSequencesAnalysesEvolutionary historySpeciesTaxonomyChapterPrincipleAnalysisFoundMolecularTumorPerfect phylogenySpeciationPhylogenetic treesGenomeTaxonomySequenceOrganismsInferenceCladeTaxonomicGenePatternsAccuratelyDiversificationGenesMethodsStudyClassificationFamilyGroupsPresentDirectly
Mitochondrial5
- Reconstructing the phylogeny of African mitochondrial DNA lineages in Slavs. (blogspot.com)
- We reconstructed phylogenies for representatives of the two genera of lice and their hosts, using nuclear and mitochondrial DNA sequences. (unboundmedicine.com)
- Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
- Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. (biomedcentral.com)
- To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. (bl.uk)
Reconstruction5
- Gaffney, E. S. (1979) An introduction to the logic of phylogeny reconstruction, pp. 79-111 in Cracraft, J. and N. Eldredge (eds. (berkeley.edu)
- The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. (biomedcentral.com)
- Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. (usda.gov)
- One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. (usda.gov)
- To test this, they used ancestral sequence reconstruction to infer plausible sequences that would represent ancestral nodes on the RBD phylogeny and then evaluated ACE2 binding for the most probable reconstructed sequences. (news-medical.net)
Genomes2
- Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
- The pool of total DNA resulting from this process can be used to reconstruct the genomes of the host and associated symbionts, pathogens, or "food" DNA presumably present in cell vacuoles. (nature.com)
Evolution8
- MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. (treebase.org)
- Reconstructing the early evolution of Fungi using a six-gene phylogeny. (wikipedia.org)
- Anton R.F., Schrödl M. (2013) The gastropod-crustacean connection: towards the phylogeny and evolution of the parasitic copepod family Splanchnotrophidae. (mapress.com)
- These data are however often insufficient to reliably reconstruct ToL phylogenetic relationships and do not address genome evolution. (nature.com)
- To test competing hypotheses regarding the origins and evolution of social parasitism, we reconstructed the first global phylogeny of Formica ants and representative formicine outgroups. (biorxiv.org)
- New and published data were combined with a phylogeny, molecular clock dating, and C values (available for similar to 50% of the species) to reconstruct genome evolution. (uni-muenchen.de)
- Although the numbers of neurons can vary strikingly between different groups of avians studied so far, current sampling does not allow us to reconstruct the evolution of brain complexity and processing capacity in birds. (lu.se)
- Only a broader phylogeny sampling may deepen our understanding of brain evolution and related processes, and not only in birds. (lu.se)
Genus2
- Internal transcriber spacer (ITS) sequences and several chloroplast markers, rpoB , rpoC1 , and psbA-trnH were sequenced in order to infer a preliminary phylogeny of the genus. (bioone.org)
- Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. (bvsalud.org)
Infer1
- GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. (biomedcentral.com)
Sequences1
- We retrieved sequences with hmmer profiles for cytochrome C1 and D1 superfamilies (Pfam), and used them to reconstruct the corresponding phylogenies. (conicet.gov.ar)
Analyses3
- 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. (treebase.org)
- We compared the phylogenies of body lice and wing lice to the host phylogeny using reconciliation analyses. (unboundmedicine.com)
- Molecular phylogenies of many taxonomic groups are based on analyses of single loci. (biomedcentral.com)
Evolutionary history2
- Researchers have reconstructed historical changes in the African landscape using the evolutionary history of the African sharptooth catfish. (naturalsciences.be)
- Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. (bvsalud.org)
Species5
- We compared both methods, using the Vitis9kSNP array previously developed for grapes, to show the effects of ascertainment bias in reconstructing evolutionary relationships among grape species. (usda.gov)
- We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. (usda.gov)
- A Mexican clade of five species that includes papaya, however, has 2n = 18 (papaya), 2n = 16 (Horovitzia cnidoscoloides), and 2 n = 14 (Jarilla caudata and J. heterophylla;third Jarilla not counted), with the phylogeny indicating that the dysploidy events occurred similar to 16.6 and similar to 5.5 million years ago and that Jarilla underwent genome size doubling (similar to 450 to 830-920 Mbp/haploid genome). (uni-muenchen.de)
- However, not all phylogenies are trees: hybridization can occur and create new species and this results into reticulate phylogenies. (biomedcentral.com)
- If we accept the validity of this new species, the age of the fossils (3.7 million years) and its reconstructed phylogeny (the connections between all groups of organisms as understood by ancestor relationships), the implications are far-reaching. (theconversation.com)
Taxonomy1
- The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. (biomedcentral.com)
Chapter1
- Sober, E. (1988) Reconstructing the past, Chapter 1. (berkeley.edu)
Principle1
- Ecological barriers responsible for specificity and genetic structure can, in principle, reinforce macroevolutionary processes that generate congruent host-parasite phylogenies. (unboundmedicine.com)
Analysis1
- constructed from an analysis of memetic similarity should reconstruct the known pattern of historical descent. (cfpm.org)
Found1
- They found that the reconstructed ancestor could also bind the R. affinis ACE2 allele (as well as broader ACE2 binding, including hACE2), but this binding was then lost along the branch to the clade 2 ancestor. (news-medical.net)
Molecular9
- The phylogeny and evolution of host choice in the Hippoboscoidea (Diptera) as reconstructed using four molecular markers. (ncsu.edu)
- We use comparative morphology and molecular methods to reconstruct the phylogeny of ants and aquatic arthropods. (uni-regensburg.de)
- Over the past three decades, several morphological and molecular phylogenetic studies have been used to access the relationships among the major clades, resulting in angiosperms being classified into 59 orders and 413 families ( The angiosperm phylogeny group III [APG III], 2009 ). (frontiersin.org)
- Molecular phylogenies of many taxonomic groups are based on analyses of single loci. (biomedcentral.com)
- Citation: Cruz M. Á, Arias S. & Terrazas T. 2016: Molecular phylogeny and taxonomy of the genus Disocactus (Cactaceae), based on the DNA sequences of six chloroplast markers. (researchgate.net)
- Molecular phylogeny reconstructed from nrLSU gene sequences, together with developmental data, support the hypothesis that the entrophosporoid mode of spore formation evolved many times and thus represents a convergent trait of little phylogenetic significance. (ku.edu)
- TY - JOUR T1 - Molecular phylogeny of Menthinae (Lamiaceae, Nepetoideae, Mentheae)--Taxonomy, biogeography and conflicts. (unboundmedicine.com)
- We used 461 ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2) sequences relating to 19 species to reconstruct the molecular phylogeny of the Hyrcanus Group across its range. (biomedcentral.com)
- In our previous study [ 22 ], cox 1 failed to distinguish between recently diverged taxa, suggesting that mtDNA may not be appropriate for investigating the molecular phylogeny of the Hyrcanus Group. (biomedcentral.com)
Tumor5
- However, such samples usually mix several distinct tumor subclones, which confounds the discovery of the tumor phylogeny. (helsinki.fi)
- We study a natural problem formulation requiring to decompose the tumor samples into several subclones with the objective of forming a minimum perfect phylogeny. (helsinki.fi)
- We tested the ability of MIPUP and of four popular tools LICHeE, AncesTree, CITUP, Treeomics to reconstruct the tumor phylogeny. (helsinki.fi)
- Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny. (nih.gov)
- Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. (nih.gov)
Perfect phylogeny1
Speciation3
- Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. (nature.com)
- In turn, understanding the origin of alleles requires reconstructing the history of populations undergoing speciation. (nature.com)
- My colleagues and I have now developed a well-resolved phylogeny for the orchids, based on large numbers of chloroplast genes, and I will show how we can use this phylogeny to identify the age and place of origin of the orchids, assess the role of different orchid traits in driving high rates of speciation, and reconstruct the geographic spread of orchids across the planet. (wisc.edu)
Phylogenetic trees1
- Here, we extend the recently described Genome BLAST Distance Phylogeny (GBDP) strategy to compute phylogenetic trees from all completely sequenced plastid genomes currently available and from a selection of mitochondrial genomes representing the major eukaryotic lineages. (biomedcentral.com)
Genome2
- Reconstructing core genome phylogeny. (nih.gov)
- To address these issues, we captured, sequenced, and reconstructed a draft genome of an ancient strain of VARV, sampled from a Lithuanian child mummy dating between 1643 and 1665 and close to the time of several documented European epidemics [1, 2, 10]. (scicombinator.com)
Taxonomy1
- The BIONJ algorithm results in phylogenies most in accordance with the current NCBI taxonomy, with NJ and FastME performing insignificantly worse, and STC performing as well if applied to high quality distance matrices. (biomedcentral.com)
Sequence3
- I use DNA sequence variation to reconstruct phylogenies, character evolution, and to understand phylogeographic patterns. (calacademy.org)
- The importance of this is that " Without a reliable root of the SARS ‐ CoV ‐ 2 phylogeny, the most recent ancestor sequence cannot be accurately reconstructed, and it is not possible to assess the genetic diversity of SARS ‐ CoV ‐ 2 that existed at the time of its first outbreak . (news-medical.net)
- O-ne important aspect of the HOMD, is that it presents a provisional naming scheme for the currently unnamed taxa, based o-n the 16S rRNA sequence phylogeny, so that strain, clone and probe data from any laboratory can be directly linked to a stably named reference scheme. (nih.gov)
Organisms3
- Reconstructing the phylogeny of organisms makes it possible to uncover relationships among extant taxa and to determine if particular life histories and adaptations have evolved only once or repeatedly. (uni-regensburg.de)
- This has allowed us to reconstruct evolutionary histories throughout history and understand how various organisms are related. (freescience.info)
- In this course we will provide the knowledge and tools needed to reconstruct the Tree of Life using the information avilable in the genomes of organisms, and to interpret it correctly to understand the processes that generate it. (ub.edu)
Inference1
- We generated a dated multilocus phylogeny of the Mellisugini based on a dense sampling using Bayesian inference, maximum-likelihood and maximum parsimony methods, and reconstructed the ancestral states of distributional areas in a Bayesian framework and migratory behavior using maximum parsimony, maximum-likelihood and re-rooting methods. (datadryad.org)
Clade1
- Both groups appear in the ITS phylogeny in a clade with Cyclotrichium and Mentha, relationships not suggested previously. (unboundmedicine.com)
Taxonomic2
- A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system. (datadryad.org)
- Our results indicate that, at this taxonomic level, plastid genomes are much more valuable for inferring phylogenies than are mitochondrial genomes, and that distances based on breakpoints are of little use. (biomedcentral.com)
Gene2
- Nowadays, an increasing number of completely sequenced genomes are available and a growing field of phylogenetic research deals with the question of how to infer reliable phylogenies from this large amount of data to overcome the limitations of single-gene phylogenies. (biomedcentral.com)
- If the substitution of nucleotides in the gene coding for cytochrome c occurred at a constant rate through time, one could determine the time elapsed along any branch of the phylogeny simply by examining the number of nucleotide substitutions along that branch. (britannica.com)
Patterns1
- The integration of fossils into phylogenies offers a deeper understanding of processes underlying biodiversity patterns in deep time. (researchgate.net)
Accurately1
- The limited genetic information of pre-pandemic seasonal IAVs in Chile has made it difficult to accurately reconstruct the phylogenetic relationships of these viruses within the country. (flu.org.cn)
Diversification1
Genes1
- We conducted a systematic survey for the presence of known host range genes and closely related family members in poxvirus genomes, classified them into subgroups based on their phylogenetic relationship and correlated their presence with the poxvirus phylogeny. (scicombinator.com)
Methods1
- GBDP-like methods can be used to reliably infer phylogenies from different kinds of genomic data. (biomedcentral.com)
Study2
- I study macroevolution with phylogenies and fossils. (researchgate.net)
- Get ready to dive into the captivating realm of science and scientific study, where every phylogeny and evolutionary discovery brings us closer to understanding how we fit into this remarkable web of life. (freescience.info)
Classification1
- Based on the family phylogeny, we proposed a unified six-group classification system for angiosperm ARFs. (usda.gov)
Family1
Groups2
- Unfortunately, some groups or regions lack a good fossil record, and dated phylogenies can be useful. (researchgate.net)
- 1 He reconstructed the phylogeny of all the major groups of beetles and noted their feeding characteristics. (berkeley.edu)
Present1
- We present a new Orchidaceae phylogeny based on high-throughput and Sanger sequencing datasets, coveri. (researchgate.net)
Directly1
- The suitability of these distance formulae for phylogeny reconstruction is directly estimated by computing a recently described measure of "treelikeness", the so-called δ value, from the respective distance matrices. (biomedcentral.com)