Biology subjects

Roy, B. A.

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

5 recordsLinked to original sources

bioRxiv2021

Evidence for alternate stable states in an Ecuadorian Andean Cloud Forest

We analyzed a set of historical data from rapid vegetation inventories in a tropical montane cloud forest in northern Andean Ecuador. Trees in plots from several types of forest were counted and measured, including: (1) primary forest, including mature and recently closed-canopy sites and naturally formed gaps, (2) abandoned pasture, and (3) intensively-farmed sites. The goal of the study was to understand in a specific period of time the similarities and differences among natural and anthropogenic disturbances and their potential long term effect on the forest plant community. We found that mature and intermediate close canopy sites are similar. Also old forest is quite resilient to gap-forming disturbance. Natural gaps are quickly colonized by old-forest-associated plant species, and return to an old-forest-type community of trees in a short time. In contrast, forests regenerating from anthropogenic disturbance appear to have multiple possible states: some regenerating forest sites where the anthropogenic disturbance were low are coming to closely resemble old-forest-type communities, but some where the anthropogenic disturbance was intense appear to be changing in a very different direction, which does not resemble any other vegetation community type currently in the forest. A major predictor of present ecological state is the type of land use before reforestation: pastures can occasionally transition back to the pre-disturbance state of forest. More intensively used sites, many of which are abandoned sugar cane plantations, do not return to a pre-disturbance ecological state, instead forming a new and different kind of forest, dominated by a different community of trees. We examined tree-seedling communities to understand the trajectory of the forest into the future, and find that new forest types may be forming that do not resemble any existing associationsintensive agricultural sites. We also found that Los Cedros is extremely diverse in tree species. We estimate approximately 500 species of tree in only the small southeastern area of the reserve that has been explored scientifically. Additionally, the forest tree community shows extremely rapid distance decay (beta-diversity), approaching near complete turn-over in the limited spatial extent of the study. This suggests that hundreds of other tree species remain to be observed in the reserve, in addition to the 350+ that are directly observed in the present study, including new observations of species with IUCN threatened-endangered status. We also highlight the conservation value of Reserva Los Cedros, which has managed to reverse deforestation within its boundaries despite a general trend of extensive deforestation in the surrounding region, and to protect large, contiguous areas of highly-endangered Andean primary cloud forest habitat.

ecology↗

bioRxiv2020

Drivers of grass endophyte communities in prairies of the Pacific Northwest, USA

Prairies of the Pacific Northwest are highly threatened, with only [~]2% of historic land area remaining. The combined risk of global climate change and land use change make these prairies a high conservation priority. However, little attention has been paid to the microbiota of these systems, including the hyper diverse fungi that live asymptomatically in their leaves, the endophytes. Using culture-free, full-community DNA sequencing, we investigated the diversity, composition, and structure of full fungal foliar endophyte and ecological guild communities in two native, cool-season bunchgrasses along a climate gradient. We quantified the relative importance of host, host fitness, environment, and spatial structuring in microbial community structure. We found markedly different communities between the southern and central-northern sites, suggesting a potential dispersal limitation in the Klamath Mountains. We also found that each host species was home to distinct fungal communities. Climate was the strongest predictor of endophyte community, while fitness (e.g., plant size, reproductive status, density) was less important for community structure. For both host species, seasonality contributed strongly to the variation we observed. At the ecological guild level, saprotrophs tended to decline with latitude, whereas symbiotrophs and pathotrophs both tended to increase with latitude. Our results suggest that climate change will have large consequences for these diverse fungal communities.

ecology↗

bioRxiv2018

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↗

bioRxiv2017

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↗

bioRxiv2017

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↗