Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic...
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alignment.py QIIME (settings: -g 0.5 -s).
Quality controlled alignments were then subject to various
Sudden oak death caused by the oomycete Phytophthora ramorum was first discovered in California toward the end of the 20th century and subsequently emerged on tanoak forests in Oregon before its first detection in 2001 by aerial surveys. The Oregon Department of Forestry has since monitored the epidemic and sampled...
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Nepusz 2006; Kahle and Wickham
2013; Kamvar et al. 2014b; Paradis et al. 2004; Wickham 2009).
Within
Root-knot nematodes (Meloidogyne spp.) are one of the most important global plant pathogens. Recent innovations in molecular techniques have allowed increased study of this important pest, including the ability to investigate associated microbiomes. This study used 16S rDNA metagenomic sequencing to characterize the microbiome of Meloidogyne hapla, the northern root-knot...
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(compare_categories.py) (Paradis, 2004; Team, R.C., 2014). Similar QIIME and R workflows
were followed for analyses of
Accessions of common wheat (Triticum aestivum
L. subsp. aestivum) from the USDA–ARS
National Small Grains Collection (NSGC) are a
resource for wheat scientists worldwide. The
genetic diversity of the wheat core subset, representing
approximately 10% of the collection’s
42,138 T. aestivum accessions, was examined
using 390 diversity arrays technology (DArT)...
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Grains Collection
Bonman, J. M., Babiker, E. M., Cuesta-Marcos, A., Esvelt-Klos, K.,
Brown-Guedira, G
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
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7 reads with a
G in that position and 3 with a C. In this case the consensus would have called a G
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that...
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Dumont76, Simon G. Dures4,77, Mats Dynesius78, Lars Edenius79,
Zolt�an Elek80, Martin H. Entling81, Nina
Pythium species are important soilborne pathogens occurring in the forest nursery industry of the Pacific Northwest. However, little is known about their genetic diversity or population structure and it is suspected that isolates are moved among forest nurseries on seedling stock and shared field equipment. In order to address these...
Human activity has been shown to considerably affect the spread of dangerous pests and pathogens worldwide. Therefore,
strict regulations of international trade exist for particularly harmful pathogenic organisms. Phytophthora plurivora, which is
not subject to regulations, is a plant pathogen frequently found on a broad range of host species, both...
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binomial distribution [45]. Moreover,
the inter-locus g-test [46] was used to compare observed versus
Fidelity to migratory destinations is an important driver of connectivity in marine and avian species. Here we assess the role of maternally directed learning of migratory habitats, or migratory culture, on the population structure of the endangered Australian and New Zealand southern right whale. Using DNA profiles, comprising mitochondrial DNA...
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v4.039 and the exact G test
was used in the same program to test for significant differences in allele
To address patterns of genetic connectivity in a mass-aggregating marine fish, we analyzed genetic variation in
mitochondrial DNA (mtDNA), microsatellites, and single nucleotide polymorphisms (SNPs) for Nassau grouper (Epinephelus
striatus). We expected Nassau grouper to exhibit genetic differentiation among its subpopulations due to its reproductive
behavior and retentive oceanographic conditions...
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, Richard S. Nemeth4,
Scott A. Heppell5, Phillippe G. Bush6, Alfonso Aguilar-Perera7, John A. B. Claydon8