Some time ago I published a blog post on Faux phylogenies in which I included a phylogeny of cartoon animals by Mike Keesey. In this phylog...
This is a site for various projects in evolutionary biology, molecular evolution and phylogenetic epidemiology being carried out by members of the research group of Andrew Rambaut at the Institute of Evolutionary Biology, University of Edinburgh.
Phylogenetics is the study of the evolutionary history and relationships among extant and extinct organisms. More than any other organizational scheme, this is the way biologists think about the living world. In vertebrate paleontology in particular, an understanding of the evolutionary relationships of animals as identified via minute anatomical details is absolutely fundamental to our science. One…
Elephant Head Papercraft - Free download as PDF File (.pdf), Text File (.txt) or read online for free. This document contains instructions for assembling a 3D papercraft elephant head model. It includes diagrams showing how to cut out and assemble the various parts of the elephant head, including the left and right ears, back, head, trunk, left and right tusks. The parts are labeled with numbers and the diagrams show how they fit together to form the completed elephant head papercraft.
Read "Bioinformatics and Phylogenetics Seminal Contributions of Bernard Moret" by available from Rakuten Kobo. This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the...
Abstract. With 72 species belonging to ten genera, Sarcolaenaceae are the largest and most diverse of Madagascar's endemic plant families. Comprising shrub
Fig. 1. Phylogeny of Malagasy scincine lizards, based on a 50% majority rule consensus tree inferred through Bayesian analysis of 12 co...
Deze Concept Map heeft informatie gerelateerd aan: theory of evolution, evidence includes Molecular biology, Darwin's Theory of natural selection (Darwinism) has been incorporated into genetics to create: neo-Darwinism synthetic theory of evolution modern synthesis (all mean the same thing), evidence includes Fossil evidence, evidence includes Biogeography, history including Lamarck's Theory (Use and Disuse), Homoplastic (Analagous) structures indicate convergent evolution, evidence includes Comparative Anatomy, The Theory of Evolution has evidence, Molecular biology includes DNA sequencing, Lamarck's Theory (Use and Disuse) was disproven, Fossil evidence incorporates radioisotopes, Comparative Anatomy such as Vestigial structures, Molecular biology includes phylogenetic tree, Comparative Anatomy such as Homologous structures, The Theory of Evolution has history, history including Darwin's Theory of natural selection (Darwinism), Comparative Anatomy such as Homoplastic (Analagous) structures, Fossil evidence incorporates index fossils, Molecular biology includes molecular clock, Biogeography such as continental drift
Portunoidea is a diverse lineage of ecologically and economically important marine crabs comprising 8 families and 14 subfamilies. Closely related portunid subfamilies Caphyrinae and Thalamitinae constitute some of this group’s greatest morphological and taxonomic diversity, and are the only known lineages to include symbiotic taxa. Emergence of symbiosis in decapods remains poorly studied and portunoid crabs provide an interesting, but often overlooked example. Yet the paucity of molecular phylogenetic data available for Portunoidea makes it challenging to investigate the evolution and systematics of the group. Phylogenetic analyses, though limited, suggest that many putative portunoid taxa are para- or polyphyletic. Here I augment existing molecular data—significantly increasing taxon sampling of Caphyrinae, Thalamitinae, and several disparate portunoid lineages—to investigate the phylogenetic origin of symbiosis within Portunoidea and reevaluate higher- and lower-level portunoid classifications. Phylogenetic analyses were carried out on sequences of H3, 28S rRNA, 16S rRNA, and CO1 for up to 168 portunoid taxa; this included, for the first time, molecular data from the genera Atoportunus, Brusinia, Caphyra, Coelocarcinus, Gonioinfradens, Raymanninus, and Thalamonyx. Results support the placement of all symbiotic taxa (Caphyra, Lissocarcinus, and two Thalamita) in a single clade derived within the thalamitine genus Thalamita. Caphyrina Paulson, 1875, nom. trans. is recognized here as a subtribe within the subfamily Thalamitinae. Results also support the following taxonomic actions: Cronius is reclassified as a thalamitine genus; Thalamonyx is reestablished as a valid genus; Goniosupradens is raised to the generic rank; and three new genera (Zygita gen. nov., Thranita gen. nov., and Trierarchus gen. nov.) are described to accommodate some Thalamita s.l. taxa rendered paraphyletic by Caphyrina. A new diagnosis of Thalamitinae is provided. Results also support a more conservative classification of Portunoidea comprising three instead of eight extant families: Geryonidae (Geryonidae + Ovalipidae; new diagnosis provided), Carcinidae (Carcinidae + Pirimelidae + Polybiidae + Thiidae + Coelocarcinus; new diagnosis provided) and Portunidae. Finally, 16s rRNA data suggests family Brusiniidae might not be a portunoid lineage.
Tree thinking, or phylogenetics, is an important way of understanding evolutionary relationships. Reading trees correctly can pose some challenges. This vi...
Phylogenetics refers to the evolutionary study of the organisms in a pedigree or tree-like format, known as the phylogenetic tree. #Bioinformatics #Courses #Python #R #computationalbiology #biology
Rather a while ago, back in 2003, we started working on a phylogeny of the complex thalloid liverworts at the Royal Botanic Garden Edinburgh (as a Molecular Phylogenetics Project). We were beautifully placed to conduct the work, with taxonomist Dr David Long on the staff, and all the necessary molec
Description The moral of the story is that trying to hand-draw a phylogeny of birds at the same time as doing a PhD is a poor decision. Insert disclaimer about how the phylogenetics of total-group birds is in a constant state of flux, and future studies will likely modify some of the relationships depicted here. Taxa that have been colored in are extant species. Nothing is to scale.
Together with an international team, Senckenberg scientist Uwe Fritz described a new species of mata mata turtle based on genetic analyses. Until now, it had been assumed that the genus Chelus only contained a single species. The new description also necessitates a reassessment of the conservation status of these species, which are frequently sold in the illegal animal trade. The study was recently published in the scientific journal Molecular Phylogenetics and Evolution.
Yes, birds are reptiles, but let me explain a bit. Biologists use two types of classification systems, the Linnaean and the phylogenetic. The Linnaean system was developed by Carolus Linnaeus in the 1730's. In the Linnaean system, organisms are grouped by characteristics regardless of their ancestry. So a reptile is an animal that is ectothermic and has scales, and birds would not be reptiles. In the 1940's, a biologist named Willi Hennig came up with another classification system that he called phylogenetics.
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.
