Biology subjects

McCafferty, C.

Publications and source records attributed to McCafferty, C..

4 recordsLinked to original sources

bioRxiv2026

Passive Acoustic Monitoring within the Northwest Forest Plan Area: 2025 Annual Report

The Northwest Forest Plan (NWFP) Passive Acoustic Monitoring (PAM) program is a large-scale interagency biodiversity monitoring framework designed to assess the status and trends of northern spotted owls (Strix occidentalis caurina), barred owls (Strix varia), marbled murrelets (Brachyramphus marmoratus), and broader forest biodiversity across federally administered lands in the Pacific Northwest. In 2025, we deployed autonomous recording units at 2,095 sampling stations within 532 5-km2 hexagons randomly selected across approximately 24 million acres of federal forest lands in Washington, Oregon, and California. These deployments generated 1.37 million hours of acoustic recordings that we processed using the convolutional neural network PNW-Cnet v5 for automated species identification and subsequent human validation of focal species detections. Northern spotted owls were detected in 28% of sampled hexagons range-wide, including 16% in Washington, 25% in Oregon, and 60% in California. Occupancy patterns remained consistent compared to previous years, with higher occupancy concentrated in southern portions of the geographic range and continued low occupancy across much of the Washington Cascades and Oregon Coast Range. Barred owls were detected in 86% of sampled hexagons and remained broadly distributed throughout most of the NWFP area. Marbled murrelets were detected in 50% of reviewed hexagons within NWFP marbled murrelet management zones, with highest occupancy occurring in coastal forests of Oregon and Washington. The 2025 field season occurred under substantial operational constraints that reduced sampling effort by approximately half relative to 2023 and 2024 because of staffing limitations affecting participating federal agencies. Despite these reductions, the NWFP-PAM framework continued to provide broad-scale, spatially representative ecological information across the NWFP area. Results highlight the growing importance of passive acoustic monitoring and machine learning approaches for long-term biodiversity monitoring under changing environmental and operational conditions.

ecology↗

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↗

bioRxiv2025

The Luminal Ring Protein C2CD3 Acts as a Radial In-to-Out Organizer of the Distal Centriole and Appendages

Centrioles are polarized microtubule-based structures with appendages at their distal end that are essential for cilia formation and function. The protein C2CD3 is critical for distal appendage assembly, with mutations linked to orofaciodigital syndrome and other ciliopathies. However, its precise molecular role in appendage recruitment remains unclear. Using Ultrastructure Expansion Microscopy (U-ExM), iterative U-ExM, and in situ cryo-electron tomography (cryo-ET), we reveal that C2CD3 adopts a radially symmetric 9-fold organization within the centrioles distal lumen. We show that the C-terminal region of C2CD3 localizes close to a [~]100 nm luminal ring structure consisting of [~]27 nodes, while its N-terminal region localizes close to a hook-like structure that attaches to the A-microtubule as it extends from the centriole interior to exterior. This hook structure is adjacent to the DISCO complex (MNR/CEP90/OFD1), which marks future appendage sites. C2CD3 depletion disrupts not only the recruitment of the DISCO complex via direct interaction with MNR but also destabilizes the luminal ring network composed of C2CD3/SFI1/centrin-2/CEP135/NA14, as well as the distal microtubule tip protein CEP162. This reveals an intricate "in-to-out" molecular hub connecting the centriolar lumen, distal microtubule cap, and appendages. Although C2CD3 loss results in shorter centrioles and appendage defects, key structural elements remain intact, permitting continued centriole duplication. We propose that C2CD3 forms the luminal ring structure and extends radially to the space between triplet microtubules, functioning as an architectural hub that scaffolds the distal end of the centriole, orchestrating its assembly and directing appendage formation.

cell biology↗