scholarly journals Using nuclear genes to reconstruct angiosperm phylogeny at the species level: A case study with Brassicaceae species

2016 ◽  
Vol 54 (4) ◽  
pp. 438-452 ◽  
Author(s):  
Liming Cai ◽  
Hong Ma
Keyword(s):  
Species Level ◽  
Nuclear Genes ◽  
Angiosperm Phylogeny ◽  
Brassicaceae Species

scholarly journals THE INFLUENCE OF TIDAL AND RAINFALL CYCLES ON INTERTIDAL NEMATODES: A CASE STUDY IN A TROPICAL SANDY BEACH

2014 ◽  
Vol 62 (4) ◽  
pp. 247-256 ◽  
Author(s):  
Virag Venekey ◽  
Paulo Jorge Parreira dos Santos ◽  
Verônica Gomes da Fonsêca-Genevois
Keyword(s):  
Tidal Cycle ◽  
Sandy Beach ◽  
Assemblage Structure ◽  
Species Level ◽  
Future Studies ◽  
Nematode Assemblage ◽  
Tidal Cycles ◽  
Clear Identification ◽  
Rainfall Flood

The present study describes the nematode assemblage of the bay of Tamandaré (Brazil), a tropical sandy beach, during the low, flood, high and ebb tides of two consecutive tidal cycles in four different months of the year (May, July, September and November). The nematode assemblage was dominated by Metachromadora and Perepsilonema and varied significantly between months and tides. Densities were lower in July, and changes in assemblage structure occurred during the transitional periods between rainy and dry months, which showed the influence of rainfall. Flood and ebb tides appeared to exercise the greatest influences over the tidal cycle, although the patterns were not very clear. Identification at genera/species level is recommended for future studies, to better understand the patterns of nematode assemblages during tidal cycles.

scholarly journals Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Liping Zeng ◽  
Qiang Zhang ◽  
Renran Sun ◽  
Hongzhi Kong ◽  
Ning Zhang ◽  
...  
Keyword(s):  
Nuclear Genes ◽  
Divergence Times ◽  
Angiosperm Phylogeny

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.

Using higher taxa as surrogates of species-level data in three Portuguese protected areas: a case study on Spheciformes (Hymenoptera)

2012 ◽  
Vol 21 (13) ◽  
pp. 3467-3486 ◽  
Author(s):  
L. C. Vieira ◽  
N. G. Oliveira ◽  
C. C. Brewster ◽  
S. F. Gayubo
Keyword(s):  
Protected Areas ◽  
Species Level ◽  
Higher Taxa ◽  
Level Data

Development of phylogenetic markers from single-copy nuclear genes for multi locus, species level analyses in the mint family (Lamiaceae)

2012 ◽  
Vol 63 (3) ◽  
pp. 758-767 ◽  
Author(s):  
Manuel António Curto ◽  
Pamela Puppo ◽  
Diana Ferreira ◽  
Marcos Nogueira ◽  
Harald Meimberg
Keyword(s):  
Single Copy ◽  
Species Level ◽  
Nuclear Genes

Impact of climate change at species level: a case study of teak in India

2010 ◽  
Vol 16 (2) ◽  
pp. 199-209 ◽  
Author(s):  
Ranjith Gopalakrishnan ◽  
Mathangi Jayaraman ◽  
Shilpa Swarnim ◽  
Rajiv K. Chaturvedi ◽  
Govindasamy Bala ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Level ◽  
Impact Of Climate Change
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