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Biology subjects

Roy, B. A.

Publications and source records attributed to Roy, B. A..

3 recordsLinked to original sources

New mining concessions will severely decrease biodiversity and ecosystem services in Ecuador

Ecuador has the worlds highest biodiversity, despite being a tiny fraction of the worlds land area. The threat of extinction for much of this biodiversity has dramatically increased since April 2016, during which time the Ecuadorian government has opened approximately 2.9 million hectares of land for mining exploration, with many of the concessions in previously protected forests. Herein, we describe the system of protected lands in Ecuador, their mining laws, and outline the scale of threat by comparing the mammals, amphibians, reptiles, birds, and orchids from several now threatened protected areas, classed as \"Bosques Protectores\" (BPs), in the NW montane cloud forests. We examine two large (>5,000 ha) BPs, Los Cedros and El Chontal, and two medium BPs, Mashpi (1,178 ha) and Maquipucuna (2,474 ha). Since BP El Chontal is so poorly explored, we used several other small reserves (<500 hectares) in the Intag Valley to gain an idea of its biodiversity. Together, these BPs and reserves form a buffer and a southern corridor for the still-protected Cotacachi-Cayapas Ecological Reserve, which is otherwise now surrounded by mining concessions. We gathered published literature, \"gray literature\", information from reserve records and websites, and our previously unpublished observations to make comparative species tables for each reserve. Our results from these still incompletely known reserves reveal the astonishing losses that mining will incur: eight critically endangered species, including two primates (brown-headed spider monkey and white-fronted capuchin), 37 endangered species, 149 vulnerable and 85 near threatened and a large number of less threatened species Our data show that each of the reserves protects a unique subset of taxa in this land of highly localized endemics. Each of the reserves also generates sustainable income for the local people. The short-term national profits from mining will not compensate for the permanent biodiversity losses, and the long-term ecosystem service and economic losses at the local and regional level.

ecology

Rolling a mycobiome down a hill: endophytes in the Taiwanese Cloud Forest

Fungal endophytes of plants are ubiquitous and important to host plant health. Despite their ecological importance, landscape-level patterns of microbial communities in plant hosts are not well-characterized. Fungal wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across a 25 ha subtropical research plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Of the variance that could be explained, host tree species was the most important driver of mycobiome community-composition. Within a single tree species, \"core\" mycobiomes were characterized using cooccurrence analysis. These core groups of endophytes in leaves and wood show divergent spatial patterns. For wood endophytes, a more consistent, \"minimal\" core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, \"gradient\" model of the core microbiome, changing across the topography and distance of the study.

microbiology

Understanding and mitigating some limitations of Illumina (C) MiSeq for environmental sequencing of fungi.

ITS-amplicon metabarcode studies using the illumina MiSeq sequencing platform are the current standard tool for fungal ecology studies. Here we report on some of the particular challenges experienced while creating and using a ribosomal RNA gene (rDNA) amplicon library for an ecological study. Two significant complications were encountered. First, artificial differences in read abundances among OTUs were observed, apparently resulting from bias at two stages: PCR amplification of genomic DNA with ITS-region Illumina-sequence-adapted-primers, and during Illumina sequencing. These differential read abundances were only partially corrected by a common variance-stabilization method. Second, tag-switching (or the shifting of amplicons to incorrect sample indices) occurred at high levels in positive mock-community controls. An example of a bioinformatic method to estimate the rate of tag switching is shown, some recommendations on the use of positive controls and primer choice are given, and one approach to reducing potential false positives resulting from these technological biases is presented.

bioinformatics