Search results for "taxonomic"
showing 10 items of 148 documents
Comparative analysis of abundance–occupancy relationships for species at risk at both broad taxonomic and spatial scales
2015
The abundance–occupancy relationship is one of the most well-examined relationships in ecology. At the species level, a positive association has been widely documented. However, until recently, research on the nature of this relationship at broad taxonomic and spatial scales has been limited. Here, we perform a comparative analysis of 12 taxonomic groups across a large spatial scale (Canada), using data on Canadian species at risk: amphibians, arthropods, birds, freshwater fishes, lichens, marine fishes, marine mammals, molluscs, mosses, reptiles, terrestrial mammals, and vascular plants. We find a significantly positive relationship in all taxonomic groups with the exception of freshwater…
DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf
2019
We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-d…
Plant functional and taxonomic diversity in European grasslands along climatic gradients
2021
Aim European grassland communities are highly diverse, but patterns and drivers of their continental-scale diversity remain elusive. This study analyses taxonomic and functional richness in European grasslands along continental-scale temperature and precipitation gradients. Location Europe. Methods We quantified functional and taxonomic richness of 55,748 vegetation plots. Six plant traits, related to resource acquisition and conservation, were analysed to describe plant community functional composition. Using a null-model approach we derived functional richness effect sizes that indicate higher or lower diversity than expected given the taxonomic richness. We assessed the variation in abso…
The Global Naturalized Alien Flora (GloNAF) database.
2019
This dataset provides the Global Naturalized Alien Flora (GloNAF) database, ver-sion 1.2. Glo NAF represents a data compendium on th e occurrence and identit y of naturalizedalien vascular plant taxa across geographic regions (e.g. countries, states, provinces, districts,islands) around the globe. The dataset includes 13,939 taxa and covers 1,029 regions (including381 islands). The dataset is based on 210 data sources. For each ta x on-b y-region combination, wepr ovide information on whether the tax on is consider ed to be naturalized in the specific region(i.e. has established self-sustaining popula tions in the wild). Non-native taxa are marked as“alien”, when it is not clear whether the…
Aggregation patterns of helminth populations in the introduced fish, Liza haematocheilus (Teleostei: Mugilidae): disentangling host–parasite relation…
2018
International audience; A number of hypotheses exist to explain aggregated distributions, but they have seldom been used to investigate differences in parasite spatial distribution between native and introduced hosts. We applied two aggregation models, the negative binomial distribution and Taylor's power law, to study the aggregation patterns of helminth populations from Liza haematocheilus across its native (Sea of Japan) and introduced (Sea of Azov) distribution ranges. In accordance with the enemy release hypothesis, we predicted that parasite populations in the introduced host range would be less aggregated than in the native host area, because aggregation is tightly constrained by abu…
Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem
2017
Ecological and taxonomic knowledge is important for conservation and utilization of biodiversity. Biodiversity and ecology of fungi in Mediterranean ecosystems is poorly understood. Here, we examined the diversity and spatial dis- tribution of fungi along an elevational gradient in a Mediterranean ecosystem, using DNA metabarcoding. This study provides novel information about diversity of all eco- logical and taxonomic groups of fungi along an elevational gradient in a Mediterranean ecosystem. Our analyses revealed that among all biotic and abiotic variables tested, host species identity is the main driver of the fungal richness and fungal community composition. Fungal richness was strongly…
Environmental metabarcoding reveals contrasting microbial communities at two poplar phytomanagement sites
2016
The aim of the present study is to deepen the current understanding of the microbial communities at two poplar phytomanagement sites to reveal the environmental factors that drive the abundance, diversity and composition of microbial communities. A soil analysis revealed that the two soils displayed contrasting physico-chemical characteristics, with significant lower pH and higher Cd, Zn and Mn CaCl2-extractable fractions at Leforest site, compared with Pierrelaye site. The fungal and bacterial community profiles in the poplar roots and soils were assessed through Illumina MiSeq sequencing. Diversity indices and β-diversity measures illustrated that the root microbial communities were well …
Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions.
2020
Genetic diseases are driven by aberrations of the human genome. Identification of such aberrations including structural variations (SVs) is key to our understanding. Conventional short-reads whole genome sequencing (cWGS) can identify SVs to base-pair resolution, but utilizes only short-range information and suffers from high false discovery rate (FDR). Linked-reads sequencing (10XWGS) utilizes long-range information by linkage of short-reads originating from the same large DNA molecule. This can mitigate alignment-based artefacts especially in repetitive regions and should enable better prediction of SVs. However, an unbiased evaluation of this technology is not available. In this study, w…
Sample Preservation, DNA or RNA Extraction and Data Analysis for High-Throughput Phytoplankton Community Sequencing
2017
Phytoplankton is the basis for aquatic food webs and mirrors the water quality. Conventionally, phytoplankton analysis has been done using time consuming and partly subjective microscopic observations, but next generation sequencing (NGS) technologies provide promising potential for rapid automated examination of environmental samples. Because many phytoplankton species have tough cell walls, methods for cell lysis and DNA or RNA isolation need to be efficient to allow unbiased nucleic acid retrieval. Here, we analyzed how two phytoplankton preservation methods, three commercial DNA extraction kits and their improvements, three RNA extraction methods, and two data analysis procedures affect…
A practical method for barcoding and size-trimming PCR templates for amplicon sequencing
2016
Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5′ end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.