• There we formed the impression that the field of phylogenetic networks had advanced to a point where there was enough material to warrant a book that gives an introduction to the field and attempts to present the different questions and approaches in a unified manner. (uni-tuebingen.de)
  • Phylogenetic approaches are an important tool to integrate ecological and evolutionary processes across a range of temporal and spatial scales. (els.net)
  • Despite advances in genetic mapping of quantitative traits and in phylogenetic comparative approaches, these two perspectives are rarely combined. (genetics.org)
  • First, QTL data would provide a mechanistic basis for the dynamics of phenotypic evolution uncovered by phylogenetic comparative approaches. (genetics.org)
  • We studied the mode of reproduction and its evolution in the fungal subgenus Penicillium Biverticillium using phylogenetic and experimental approaches. (scribd.com)
  • A rooted phylogenetic network N on X is a rooted DAG where the set of leaves is bijectively labeled by the taxa in X. (wikipedia.org)
  • Here we are interested in unrooted binary phylogenetic networks on a finite set X of taxa, or networks for short. (springer.com)
  • Targeting areas with high phylogenetic diversity may be an efficient means to maximize conservation of taxa with high diversity of ecological and economic features. (els.net)
  • Second, situating QTL data within a phylogenetic framework would directly account for the statistical dependencies that accompany any mapping comparison among three or more taxa. (genetics.org)
  • PhyloCode is a set of principles, rules, and recommendations governing phylogenetic nomenclature, a system for naming taxa by explicit reference to phylogeny. (routledge.com)
  • A branch in a phylogenetic tree and its associated internal node can be viewed as a split that separates the taxa into two nonempty subsets. (mun.ca)
  • Moreover, we show that split-specific measures are effective in determining which taxa or groups of taxa have low or high supports for an internal node, thus providing a valuable diagnostic tool to guide taxon sampling in experimental phylogenetic design. (mun.ca)
  • The evolutionary contribution of taxa is most commonly measured by phylogenetic diversity (PD) or the length of the shared pathway on a phylogeny represented by a set of taxa [ 5 ]. (royalsocietypublishing.org)
  • In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. (royalsocietypublishing.org)
  • Phylogenetic diversity - which can be measured as the sum of the branch lengths in a phylogeny - provides a valuable tool in conservation biology. (els.net)
  • Branch length is an important aspect of the phylogenetic information a tree can convey, but 2 traditionally-used metrics, the number of phylogenetic groups to which a taxon belongs ( I ) and the proportion that each taxon contributes to the total diversity of the group ( W ), are fully node-based and do not take branch length into account. (wiley.com)
  • Here, we integrate phylogenetic diversity (PD) with spatial reserve prioritization to evaluate how well the existing reserve system in Victoria, Australia captures the evolutionary lineages of eucalypts, which dominate forest canopies across the state. (royalsocietypublishing.org)
  • The possibility that the serotype S. paratyphi B contains clones of different phylogenetic origin and the consequent implications for nomenclature are discussed. (nih.gov)
  • A survey of combinatorial methods for phylogenetic networks Genome Biology and Evolution, 3:23-35. (wikipedia.org)
  • Phylogenetic profiling has led to numerous discoveries in biology, including previously unknown enzymes in metabolic pathways, transcription factors that bind to conserved regulatory sites, and explanations for roles of certain mutations in human disease. (wikipedia.org)
  • This textbook, by one of the leaders of the field (Daniel Huson) and his co-authors, provides a mathematically rigorous introduction to one of the most exciting and beautiful research areas in computational biology: phylogenetic networks. (uni-tuebingen.de)
  • Behold the superbly amazafying phylogenetic tree which was created in hopes of receiving a superbly amazafying grade for a superbly amazafying biology class. (prezi.com)
  • The rise of phylogenetic biology has revolutionized the study of molecular and developmental evolution, but has still had rather limited impact in ecology. (pnas.org)
  • Despite the successful application of QTL mapping and phylogenetic comparative methods to fundamental questions in evolutionary biology, the two frameworks are rarely integrated. (genetics.org)
  • Gambette P., Huber, K.T. On encodings of phylogenetic networks of bounded level, Journal of Mathematical Biology. (uea.ac.uk)
  • Phylogenetic evidence for multiple Alu source genes. (nih.gov)
  • A rooted phylogenetic tree (see two graphics at top) is a directed tree with a unique node - the root - corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. (wikipedia.org)
  • DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. (nih.gov)
  • Phylogenetic studies are revealing that major ecological niches are more conserved through evolutionary history than expected, implying that adaptations to major climate changes have not readily been accomplished in all lineages. (pnas.org)
  • Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. (plos.org)
  • Therefore, a more general phylogenetic network better depicts these situations. (wikipedia.org)
  • We hope this will open a largely unexplored world to the general phylogenetic audience. (r-project.org)
  • Not all transcription binding sites can be found using phylogenetic footprinting due to the statistical nature of this technique. (wikipedia.org)
  • Once we can produce meaningful measures of language difference and divergence, they can then feed into the growing trend for taking the latest techniques for phylogenetic, probabilistic and statistical analysis , drawn originally from the biological sciences, and applying them now to data on language divergence, to help analyse and represent how languages relate to each other. (mpg.de)
  • It may be less widely appreciated by molecular evolutionary biologists that the statistical phylogenetic revolution in molecular evolution has also been mirrored in the increasing application of statistical phylogenetic reasoning in macroevolutionary and systematic studies of the fossil record [ 14 - 17 ]. (royalsocietypublishing.org)
  • Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance-such as the burgeoning subfield of phylogenomics-and shows how ecologists might lean on these new perspectives to inform their research programs. (uchicago.edu)
  • Here we use crystallographic, genomic and phylogenetic perspectives to review the correlations between magnetosome mineral habits and the phylogenetic affiliations of MTB, and show that these correlations have important implications for the evolution of magnetosome synthesis, and thus magnetotaxis. (frontiersin.org)
  • Samples of contiguous sites are not representative of the entire genome, a condition that violates a basic assumption of the bootstrap method as it is applied in phylogenetic studies. (umd.edu)
  • JCVI: Impact of Donor-recipient Phylogenetic Distance on Bacterial Genome Transplantation. (jcvi.org)
  • While phylogenetic studies in the pre-genome era primarily focused on DNA or protein sequence differences among organisms, informative comparisons can in fact be made at various organizational levels. (biomedcentral.com)
  • Phylogenetic networks were one of the main topics of the four month research programme on Phylogenetics held at the Newton Institute of Cambridge University in 2007. (uni-tuebingen.de)
  • No one is claiming that phylogenetic taxon names will have stable group memberships or diagnoses. (cmnh.org)
  • Comments on the phylogenetic definition of taxon names and conventions regarding the naming of crown clades. (cmnh.org)
  • In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. (royalsocietypublishing.org)
  • The objective of their study, published recently in Virology Journal , was to analyse the phylogenetic distribution and perform molecular characterisation of PPVs isolated in China, as well as to identify two field strains, LZ and JY. (thepigsite.com)
  • Phylogenetic networks are used to represent reticulate evolution, that is, cases in which the tree-of-life metaphor for evolution breaks down, because some of its branches have merged at one or several points in the past. (plos.org)
  • The Evolution of Parasitism - A Phylogenetic Perspective aims to bring together a range of articles that exemplifies the phylogenetic approach as applied to various disciplines within parasitology and as applied by parasitologists. (elsevier.com)
  • By modeling the distribution of trait values across a tree, phylogenetic comparative methods also help to reconstruct the dynamics of phenotypic evolution. (genetics.org)
  • Comparative methods have been radically restructured over the past two decades, and now routinely incorporate both phylogenetic information and explicit models of character evolution. (biologists.org)
  • Viruses are known to undergo rapid evolution making it sometimes difficult to apply standard phylogenetic tools to help understand their past. (uea.ac.uk)
  • Step wise approach to Phylogenetic footprinting consists of : One should decide on the gene of interest. (wikipedia.org)
  • The phylogenetic affinities of the Red-bellied Grackle ( Hypopyrrhus pyrohypogaster ), a Colombian endemic and the only member of this genus, are enigmatic. (bioone.org)
  • In Phylogenetic Ecology , Nathan G. Swenson synthesizes this nascent field's major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. (uchicago.edu)
  • Swenson is emerging as the world-leading expert in phylogenetic ecology. (uchicago.edu)
  • An excellent introduction for all sorts of audiences, this book presents a modern synthesis of phylogenetic comparative ecology that takes some of the most fundamental questions raised by pioneer biologists (such as Darwin and Hutchinson) and puts them in a contemporary perspective. (uchicago.edu)
  • From this phylogenetic orientation, the polyvagal theory proposes a biological basis for social behavior and an intervention strategy to enhance positive social behavior. (rti.org)
  • Mühlsteinová, Johansen et Pietrasiak was used to obtain a phylogenetic reference point for Trichocoleus, a genus so far characterized by morphological description only. (fed.us)
  • It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania , including their respective primers for amplification and references, as well as details of PCR assays. (springer.com)