Biology subjects

Thomas, A. D.

Publications and source records attributed to Thomas, A. D..

4 recordsLinked to original sources

bioRxiv2025

Passive Acoustic Monitoring within the Northwest Forest Plan Area: 2024 Annual Report

Passive acoustic monitoring (PAM) has become the primary framework for assessing the status, distribution, and habitat associations of forest-dependent wildlife under the Northwest Forest Plan (NWFP). In 2024, the NWFP PAM program continued to operate as a fully integrated, range-wide monitoring network, building on deployments initiated in 2018 and now conducting surveys across approximately 24 million acres of federal land. Using a randomized 2+20% sampling design, more than 4,000 autonomous recording units generated over 2 million hours of acoustic data analyzed with convolutional neural networks, enabling statistically rigorous inference at regional and range-wide scales. This report summarizes 2024 field efforts and analytical advancements in the context of recent peer-reviewed and in-progress studies. Updated analyses confirm persistent, low occupancy of northern spotted owls (Strix occidentalis caurina), with detections concentrated in the Klamath Mountains and southern Cascades, consistent with long-term demographic declines. Range-wide models of barred owl (Strix varia) landscape use continue to show high occupancy across much of the NWFP area, reinforcing competitive displacement as the dominant driver of spotted owl range contraction. The PAM network also advanced monitoring of marbled murrelets (Brachyramphus marmoratus), with 2024 results supporting PAM as a cost-efficient alternative to traditional audio-visual surveys for assessing inland nesting habitat use in coastal forests. Beyond focal species, the program increasingly supports multi-taxa biodiversity monitoring through bioacoustic bycatch and soundscape analyses, linking species occurrence, habitat condition, and disturbance dynamics. Collectively, 2024 results demonstrate that PAM has reached operational maturity as the cornerstone of Phase II NWFP effectiveness monitoring. Sustaining adequate sampling effort and field capacity remains a challenge but essential, as reduced deployment intensity would increase uncertainty and weaken inference. Continued investment in PAM infrastructure and expertise is critical for informing adaptive management, supporting sustainable timber harvest, and evaluating ecosystem resilience under changing disturbance regimes.

ecology↗

bioRxiv2025

Passive Acoustic Monitoring within the Northwest Forest Plan Area: 2023 Annual Report

Here we document progress in implementing large-scale passive acoustic monitoring across the Northwest Forest Plan area to track population trends of northern spotted owls (Strix occidentalis caurina), barred owls (S. varia), marbled murrelets (Brachyramphus marmoratus), and a broad array of forest-adapted wildlife. In 2023, we deployed 4,012 autonomous recording units across 1,009 randomly selected 5-km{superscript 2} hexagons, generating nearly 2.2 million hours of recordings, representing approximately 1 petabyte of acoustic data. These data were processed with PNW-Cnet v5, the latest version of our convolutional neural network model, trained on 135 sound classes representing over 80 species and environmental sounds. Model performance demonstrated high precision for focal species and many additional taxa, substantially reducing manual review effort while enabling broad-scale biodiversity assessments. Results confirmed northern spotted owl detections in all 20% sample areas, with occupancy varying geographically and declining notably in the Tyee study area. Barred owls were widely detected, with the highest prevalence in Oregon and Washington and comparatively lower occupancy in California. Marbled murrelets were consistently detected in coastal areas, particularly the Olympic Peninsula and Oregon Coast Range. Beyond these focal species, PAM and PNW-Cnet generated robust datasets for a wide range of birds, mammals, and disturbance indicators, underscoring the value of random-site, multi-species monitoring. The 2023 field season marked the first full implementation of the 2% + 20% NWFP sampling design, expanding monitoring coverage while strengthening collaborations with federal and state partners. These efforts provide the foundation for long-term, cost-effective wildlife monitoring and inform conservation strategies in dynamic forest ecosystems.

ecology↗

bioRxiv2020

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

Biogeochemical exports of C, N, S and H2 from watersheds are modulated by the activity of microorganisms that function over micron scales. This disparity of scales presents a substantial challenge for development of predictive models describing watershed function. Here, we tested the hypothesis that meander-bound regions exhibit patterns of microbial metabolic potential that are broadly predictive of biogeochemical processes in floodplain soils along a river corridor. We intensively sampled floodplain soils located in the upper, middle, and lower reaches of the East River in Colorado and reconstructed 248 draft quality genomes representative at a sub-species level. Approximately one third of the representative genomes were detected across all three locations with similar levels of abundance, and despite the very high microbial diversity and complexity of the soils, ~15% of species were detected in two consecutive years. A core floodplain microbiome was enriched in bacterial capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. We did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, at the watershed scale meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations in floodplain soils. Given this, we conducted a transcriptomic analysis of the middle site. Overall, the most highly transcribed genes were amoCAB and nxrAB (for nitrification) followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Thus, widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.

microbiology↗

bioRxiv2018

HP1B is a euchromatic Drosophila HP1 homolog with links to metabolism

Heterochromatin Protein 1 (HP1) proteins are an important family of chromosomal proteins conserved among all major eukaryotic lineages. While HP1 proteins are best known for their role in heterochromatin, many HP1 proteins function in euchromatin as well. As a group, HP1 proteins carry out diverse functions, playing roles in the regulation of gene expression, genome stability, chromatin structure, and DNA repair. While the heterochromatic HP1 proteins are well studied, our knowledge of HP1 proteins with euchromatic distribution is lagging behind. We have created the first mutations in HP1B, a Drosophila HP1 protein with euchromatic function, and the Drosophila homolog most closely related to mammalian HP1, HP1{beta}, and HP1{gamma}. We find that HP1B is a non-essential protein in Drosophila, with mutations affecting fertility and animal activity levels. In addition, animals lacking HP1B show altered food intake and higher body fat levels. Gene expression analysis of animals lacking HP1B demonstrates that genes with functions in various metabolic processes are affected primarily by HP1B loss. Our findings suggest that there is a link between the chromatin protein HP1B and the regulation of metabolism.

genetics↗