The Methodology of Phylogenetic Inference Above the Species Level

1977 ◽  
pp. 3-51 ◽  
Author(s):  
Max K. Hecht ◽  
James L. Edwards
Keyword(s):  
Phylogenetic Inference ◽  
Species Level

scholarly journals A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Thomas H. A. Ederveen ◽  
Jos P. H. Smits ◽  
Karima Hajo ◽  
Saskia van Schalkwijk ◽  
Tessa A. Kouwenhoven ◽  
...  
Keyword(s):  
Phylogenetic Inference ◽  
Species Level ◽  
Single Locus ◽  
Bioinformatics Pipeline ◽  
Discriminative Ability ◽  
Staphylococcus Capitis ◽  
Complex Microbial Community ◽  
Reference Genomes

AbstractWe present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.

ERRORS ASSOCIATED WITH HERBAGE DISSECTION ANALYSES 2. Problems of species identification

1976 ◽  
pp. 213-225
Author(s):  
I.M. Ritchie ◽  
C.C. Boswell ◽  
A.M. Badland
Keyword(s):  
New Zealand ◽  
Dry Weight ◽  
Analytical Tool ◽  
Species Level ◽  
Weight Basis ◽  
Plant Identification ◽  
Leaf Fragment ◽  
Research Division ◽  
Or Groups ◽  
Botanical Analysis

HERBACE DISSECTION is the process in which samples of herbage cut from trials are separated by hand into component species. Heavy reliance is placed on herbage dissection as an analytical tool ,in New Zealand, and in the four botanical analysis laboratories in the Research Division of the Ministry of Agriculture and Fisheries about 20 000 samples are analysed each year. In the laboratory a representative subsample is taken by a rigorous quartering procedure until approximately 400 pieces of herbage remain. Each leaf fragment is then identified to species level or groups of these as appropriate. The fractions are then dried and the composition calculated on a percentage dry weight basis. The accuracy of the analyses of these laboratories has been monitored by a system of interchanging herbage dissection samples between them. From this, the need to separate subsampling errors from problems of plant identification was, appreciated and some of this work is described here.

FOSSIL PHYLOGENIES REVEAL SPECIES-LEVEL DIVERSIFICATION DYNAMICS DURING THE ORDOVICIAN RADIATION OF MARINE LIFE

2018 ◽  
Author(s):  
David F. Wright ◽  
◽  
Selina R. Cole ◽  
William I. Ausich
Keyword(s):  
Species Level ◽  
Marine Life

Near-memory Acceleration for Scalable Phylogenetic Inference

2020 ◽  
Author(s):  
Nikolaos Alachiotis ◽  
Panagiotis Skrimponis ◽  
Manolis Pissadakis ◽  
Sundeep Rangan ◽  
Dionisios Pnevmatikatos
Keyword(s):  
Phylogenetic Inference
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