Biology subjects

Li, Y.-W.

Publications and source records attributed to Li, Y.-W..

7 recordsLinked to original sources

bioRxiv2026

From pose to behavior: SABER integrates identity-resolved multi-animal pose tracking with language-model-based behavioral factor discovery

Quantifying social behavior requires accurate assignment of posture and actions to individual animals, which is often hindered by close contact, occlusion, and identity switches. Meanwhile, current behavioral recognition pipelines still lack stable predictive accuracy. Here we developed SABER, a locally deployable framework that couples multianimal pose estimation with identity preserving tracking, interpretable behavioral factor mining, and multiscale temporal behavior prediction from a single overhead video stream. Across spontaneous two mice social interaction, mating, aggression, and four mice recordings, SABER improved pose estimation accuracy and tracking continuity relative to comparator pipelines. Its behavioral factor-mining procedure identified interpretable kinematic, postural, and social descriptors, and temporal integration improved classification of behavioral categories. SABER offers an intuitive, open-source interface to facilitate use. Applied to social defeat stress mice, SABER detected reduced approach behavior and a multivariate behavioral profile that distinguished depression susceptible from control animals. SABER outputs could also be synchronized with miniscope calcium recordings, enabling joint analysis of behavioral states and neuronal population activity. SABER therefore provides an accessible, identity resolved route from single view social interaction video to behavioral phenotyping and brain behavior analysis.

animal behavior and cognition↗

bioRxiv2026

Single-cell RNA sequencing uncovers cell-type-specific reprogramming of water-channel and cell-wall genes in PFOA uptake by lettuce root tips

Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants that accumulate in edible crops, posing threats to food safety and human health. Breeding varieties with reduced PFAS accumulation offers a promising mitigation strategy, yet the underlying cellular mechanisms remain elusive. Here, we integrated short- and long-read single-cell RNA sequencing to generate a high-resolution transcriptomic atlas of lettuce (Lactuca sativa L.) root tips, comparing varieties with contrasting perfluorooctanoic acid (PFOA) accumulation capacities. Our analyses uncovered a synergistic mechanism underlying PFOA uptake: up-regulation of aquaporin genes in epidermal and xylem cells, coupled with down-regulation of cell-wall biosynthesis genes specifically in epidermal and xylem. Furthermore, we identified distinct RNA isoforms-including variants with altered coding potential-that may contribute to PFOA transport and deposition through structural modulation of the encoded proteins. This study represents the first application of single-cell sequencing to elucidate the cellular and molecular basis of crop responses to PFOA, providing new insights into pollutant-crop interactions and informing strategies for sustainable agriculture and food safety.

plant biology↗

bioRxiv2020

Recovery units under the Endangered Species Act could be used more widely

Recovering species is one of the main goals of the Endangered Species Act (ESA). In the face of limited budgets, diverse tools are needed to find efficient solutions. Recovery units may be one such tool - designated portions of a species range that must be recovered individually before an entire species can be considered recovered. Recovery units allow for spatial flexibility in recovery goals and may be used in regulatory decisions such as section 7 consultation. Despite their availability, there is very little information on how recovery units have been developed and used. We mined available public data to determine the number and types of species for which recovery units have been designated; evaluated species and geographic characteristics associated with recovery unit designation; and examined how recovery units have been used in the implementation of the ESA, such as during consultation. We found 49 listed species have designated recovery units through 2017, and that these species had similar characteristics. Namely, they had relatively large ranges and were well-studied. We found taxonomic biases in recovery unit designation as well, with fish species being disproportionately likely to have recovery units and plants disproportionately less. Improvements in recovery priority numbers among species with recovery units indicate that the theoretical benefits of this tool may have translated to improved status. These data indicate that recovery units could be applied to more wide-ranging species to improve recovery under the ESA.

ecology↗

bioRxiv2020

Recovery plans need better science to support decisions that allow species to decline in abundance but be recovered

The U.S. Endangered Species Act (ESA) is widely considered the strongest biodiversity conservation law in the world. Part of its strength comes from the mandate to use the best available science to make decisions under the law, including whether to list a species, setting the criteria for when a species can be considered recovered, and determining when those criteria have been met and a species can be delisted. Both biological status and threat factors are considered at each stage of the listing and delisting process. In most cases, conservation science would suggest that species at risk enough to be listed under the Act should be more abundant and secure at delisting than they were at listing. Surprisingly, we identified 130 ESA-listed species that the U.S. Fish and Wildlife Service could consider recovered with fewer populations or individuals than existed at the time of listing. We ask whether their ESA recovery plans present scientific data, rationale, or evidence to support a decline in abundance as part of recovery. We find that almost no plan clearly explains why a decline is allowed. Fewer than half of the plans provide scientific support for a decline in the form of literature references or modeling results. We recommend that the U.S. Fish and Wildlife Service and the National Marine Fisheries Service create a decision support system to inform when species can decline in abundance and still recover, including guidance on (a) the need to explicitly address the declines and (b) the science used to support the decisions.

ecology↗

bioRxiv2018

Data indicate the importance of expert agencies in conservation policy.

AO_SCPCAPBSTRACTC_SCPCAPData on the implementation of laws and policies are essential to the evaluation and improvement of governance. For conservation laws like the U.S. Endangered Species Act (ESA), such data can inform actions that may determine the persistence or extinction of species. A central but controversial part of the ESA is section 7, which requires federal agencies to conserve threatened and endangered species. One way they do this is by consulting with expert agencies for the ESA, the U.S. Fish and Wildlife Service (FWS) and the National Marine Fisheries Service (NMFS), on actions they may undertake that impact listed species. Using data from all 24,893 consultations recorded by NMFS from 2000 through 2017, we show that federal agencies misestimated the effects of their actions on listed species in 21% of consultations, relative to the conclusions reached by NMFS. In 71% of these cases the federal agency underestimated the effects of their action. Those discrepancies were particularly important for the conservation of 14 species in 22 consultations, where the agency concluded that its action would not harm a species, while NMFS determined the action would jeopardize the species existence. Patterns of misestimation varied among federal agencies, and some of the agencies most frequently involved in consultation also frequently misestimated their effects. Jeopardy conclusions were very rare--about 0.3% of consultations--with a few project types more likely to lead to jeopardy. These data highlight the importance of consultation with the expert agencies and reveal opportunities to make the consultation process more effective.\n\nSO_SCPCAPIGNIFICANCE STATEMENTC_SCPCAPThe US Endangered Species Act is the strongest environmental law any nation has enacted to conserve imperiled species. However, policy debates over how the Act should be implemented continue to this day. This study provides the first comprehensive evaluation of how the National Marine Fisheries Service (NMFS) implements one of the Acts most important conservation programs - consultations under section 7. Our results reveal novel insights into the importance of NMFS role in ensuring federal actions do not jeopardize the existence of listed species. By using data to inform policy debate, we identify approaches to implementing section 7 that would undermine the conservation of imperiled species, and those that could improve the efficiency of the program without sacrificing these protections.

ecology↗

bioRxiv2017

Free Aerial Imagery as a Resource to Monitor Compliance with the Endangered Species Act

Compliance monitoring is an integral part of law and policy implementation. A lack of compliance monitoring for the Endangered Species Act (ESA), driven in part by resource limitations, may be undercutting efforts to recover threatened and endangered species. Here we evaluate the utility of freely available satellite and aerial imagery as a cost-efficient component of ESA compliance monitoring. Using data on actions authorized by the U.S. Fish and Wildlife Service (FWS) under section 7 of the ESA, we show that approximately 40% of actions can be found in remotely sensed imagery. Some types of actions, such as residential and commercial development, roadwork, and forestry, show substantially higher observability. Based on our results and the requirements of compliance monitoring, we recommend FWS standardize data collection requirements for consultations; record and publish terms and conditions of consultations; and encourage their staff to use technology such as remotely sensed data as a central part of their workflow for implementing the ESA.

ecology↗

bioRxiv2017

Same law, different results: comparative analysis of Endangered Species Act consultations by two federal agencies

Evaluating how wildlife conservation laws are implemented is critical for safeguarding biodiversity. Two agencies, the U.S. Fish and Wildlife Service and National Marine Fisheries Service (FWS and NMFS; Services collectively), are responsible for implementing the U.S. Endangered Species Act (ESA), which requires federal protection for threatened and endangered species. FWS and NMFS comparable role for terrestrial and marine taxa, respectively, provides the opportunity to examine how implementation of the same law varies between agencies. We analyzed how the Services implement a core component of the ESA, section 7 consultations, by objectively assessing the contents of >120 consultations on sea turtle species against the requirements in the Services consultation handbook, supplemented with in-person observations from Service biologists. Our results showed that NMFS consultations were 1.40 times as likely to have higher completeness scores than FWS consultations given the standard in the handbook. Consultations tiered from an FWS programmatic consultation inherited higher quality scores of generally more thorough programmatic consultations, indicating that programmatic consultations could increase the quality of consultations while improving efficiency. Both agencies commonly neglected to account for the effects of previous consultations and the potential for compounded effects on species. From these results, we recommend actions that can improve quality of consultation, including the use of a single database to track and integrate previously authorized harm in new analyses and the careful but more widespread use of programmatic consultations. Our study reveals several critical shortfalls in the current process of conducting ESA section 7 consultations that the Services could address to better safeguard North Americas most imperiled species.

ecology↗