A5013816936- Ecology and Vegetation Dynamics Studies
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Plant and animal studies
- Identification and Quantification in Food
- Yersinia bacterium, plague, ectoparasites research
- Species Distribution and Climate Change
- Bacillus and Francisella bacterial research
- Environmental DNA in Biodiversity Studies
- Vector-borne infectious diseases
- Plant Diversity and Evolution
- Antibiotic Resistance in Bacteria
- Wildlife Ecology and Conservation
- Vibrio bacteria research studies
- Bacteriophages and microbial interactions
- Bacterial biofilms and quorum sensing
- Forest ecology and management
- American Environmental and Regional History
- Milk Quality and Mastitis in Dairy Cows
- Probiotics and Fermented Foods
- Escherichia coli research studies
- Plant biochemistry and biosynthesis
- Insect and Pesticide Research
- Essential Oils and Antimicrobial Activity
- Mycorrhizal Fungi and Plant Interactions
Center for Devices and Radiological Health
2025
United States Food and Drug Administration
2017-2025
Brigham Young University
2013-2024
Center for Food Safety and Applied Nutrition
2017-2023
University of Maryland, College Park
2003-2023
National Museum of Natural History
2008-2017
Smithsonian Institution
2008-2017
Smithsonian Tropical Research Institute
2016
University of Minnesota
2009-2011
Hewlett-Packard (United States)
2009
DNA barcoding involves sequencing a standard region of as tool for species identification. However, there has been no agreement on which region(s) should be used land plants. To provide community recommendation plant barcode, we have compared the performance 7 leading candidate plastid regions (atpF-atpH spacer, matK gene, rbcL rpoB rpoC1 psbK-psbI and trnH-psbA spacer). Based assessments recoverability, sequence quality, levels discrimination, recommend 2-locus combination rbcL+matK...
A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range taxa. Discovery for land plants has been limited by intrinsically lower rates evolution in plant genomes than that observed animals. This low rate complicated the trade-off finding locus is universal readily sequenced sufficiently high divergence at species-level.
The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these sequences have the potential to improve investigations mechanisms underlying community and functional trait evolution. To date, no studies effectively applied barcodes sensu strictu in this manner. report, we demonstrate that a...
Significance Theory holds that sympatric large mammalian herbivores (LMH) must partition food resources to coexist, and traditional frameworks categorize LMH along a spectrum from grass-eating grazers non–grass-eating browsers. Yet it has never been clear how finely the enormous species diversity subsumed within these two broad plant types. By sequencing DNA fecal samples, we analyzed diets of an assemblage in Kenya. Diet composition was similar strongly divergent across species,...
The study of biodiversity has tended to focus primarily on relatively information‐poor measures species diversity. Recently, many studies local diversity (alpha diversity) have begun use functional and phylogenetic alpha Investigations into the dissimilarity (beta communities been far less numerous, but these potential infer mechanisms underlying community assembly dynamics. Here, we relate levels beta mechanism or responsible for tree in six forests located tropical temperate latitudes....
Abstract Theory predicts shifts in the magnitude and direction of biodiversity effects on ecosystem function ( BEF ) over succession, but this theory remains largely untested. We studied relationship between aboveground tree biomass dynamics (Δbiomass) multiple dimensions 8–16 years eight successional rainforests. tested whether changes diversity–Δbiomass correlations reflect predictions niche theories. Diversity–Δbiomass were positive early weak later suggesting saturation space with...
The use of phylogenetic information in community ecology and conservation has grown recent years. Two key issues for phylogenetics studies, however, are (i) low terminal resolution (ii) arbitrarily defined species pools.We used three DNA barcodes (plastid regions rbcL, matK, trnH-psbA) to infer a phylogeny 527 native naturalized trees Puerto Rico, representing the vast majority entire tree flora island (89%). We maximum likelihood (ML) approach with without constraint that enforced monophyly...
ABSTRACT Individuals with cystic fibrosis (CF) are commonly colonized Pseudomonas aeruginosa . The chronic infections caused by P. punctuated acute exacerbations of the lung disease, which lead to significant morbidity and mortality. As regulators virulence determinants, quorum-sensing systems may be active in associated CF. We have examined levels autoinducer molecules transcript accumulation from bacterial populations found lungs patients detected biologically N -(3-oxododecanoyl)- l...
New genetic and archaeological approaches have substantially improved our understanding of the transition to agriculture, a major turning point in human history that began 10,000–5,000 years ago with independent domestication plants animals eight world regions. In Americas, however, initial World species has long been complicated by early presence an African enigma, bottle gourd ( Lagenaria siceraria ). Indigenous Africa, it reached East Asia 9,000–8,000 before present (B.P.) had broad...
The degree to which turnover in biological communities is structured by deterministic or stochastic factors and the identities of influential are fundamental, yet unresolved, questions ecology. Answers these particularly important for projecting fate forests with diverse disturbance histories worldwide. To uncover processes governing we use species-level molecular phylogenies functional trait data sets two long-term tropical forest plots contrasting histories: one older-growth, was recently...
Plants and their associated insect herbivores, represent more than 50% of all known species on earth. The first step in understanding the mechanisms generating maintaining this important component biodiversity is to identify plant-herbivore associations. In study we determined insect-host plant associations for an entire guild herbivores using DNA extracted from gut contents. Over two years, a tropical rain forest Costa Rica (La Selva Biological Station), recorded full diet breadth...
Ecologists have recently interpreted patterns of phylogenetic distance among coexisting species as indicative processes affecting community assembly during forest succession. We investigated plant structure along a successional gradient in New Guinean lowland rain forest. surveyed all trees with diameter at breast height ≥ 5 cm nineteen 0.25 ha plots representing younger secondary, older and primary estimated phylogeny from rbcL gene sequences to quantify change Mean co‐occurring increased...
Background Species number, functional traits, and phylogenetic history all contribute to characterizing the biological diversity in plant communities. The component of has been particularly difficult quantify species-rich tropical tree assemblages. compilation previously published (and often incomplete) data on evolutionary relationships species into a composite phylogeny taxa forest, through such programs as Phylomatic, proven useful building community phylogenies although limited...
Abstract Background We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina Oxford Nanopore sequencing by determining genome completeness accuracy, antimicrobial resistance (AMR), virulence potential, multilocus sequence typing (MLST), phylogeny, pan genome. Ten species (10 strains) were tested simulated reads both mediocre- low-quality, whereas 11 (12 real reads. Results performed best achieving contiguous genomes, closely...
Slow-growing juveniles of shade-tolerant plant species are predicted to have tough leaves because the high cost leaf replacement in shade relative potential carbon gain. We assessed degree correlated evolution among eight traits associated with toughness and relationships those growth mortality rates 197 tree shrub from understory 50-ha forest dynamics plot on Barro Colorado Island, Panama. Path analysis phylogenetically independent contrasts revealed that attained material (resistance...
Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into ecological evolutionary processes that determine how species are assembled communities. Understanding phylogenetic relationships among in a community has become an important component of assessing assembly processes. However, application information to questions ecology been limited large part by lack accurate estimates individual found within communities, is...
Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice study consequences selective foraging by herbivores. The quantification herbivore with respect native versus exotic plant species is particularly relevant given concerns invasive establishment their effects on ecosystems. While increased abundance white-tailed deer (
Niche differentiation has been proposed as an explanation for rarity in species assemblages. To test this hypothesis requires quantifying the ecological similarity of species. This can potentially be estimated by using phylogenetic relatedness. In study, we predicted that if niche does explain co-occurrence rare and common species, then should contribute greatly to overall community diversity (PD), abundance will have signal, phylogenetically dissimilar. We tested these predictions...
Background Plants interact with each other, nutrients, and microbial communities in soils through extensive root networks. Understanding these below ground interactions has been difficult natural systems, particularly those high plant species diversity where morphological identification of fine roots is difficult. We combine DNA-based a DNA barcode database above stem locations floristically diverse lowland tropical wet forest on Barro Colorado Island, Panama, all trees lianas >1 cm diameter...