Biology subjects

Shen, S.-F.

Publications and source records attributed to Shen, S.-F..

9 recordsLinked to original sources

bioRxiv2026

MorphQ: label-free quantification and visualisation of complex morphology from standardised specimen images

O_LIQuantifying complex morphology from images remains difficult because predefined descriptors capture only selected traits. Yet, supervised machine learning models for images require labels and often produce task-specific features that are hard to interpret as biological traits. C_LIO_LIWe present MorphQ, a label-free, self-supervised method that learns a quantitative morphospace from standardised specimen images. Its encoder produces feature vectors for statistical analysis, and its decoder converts analysed positions in morphospace into human-interpretable images, including hypothetical forms not represented by sampled specimens or sampled taxa. C_LIO_LIUsing 1,868 Lepidoptera species, we tested whether MorphQs label-free features were more useful for downstream analysis than features from principal component analysis (PCA) or a supervised species-classification machine learning model. As a diagnostic probe of downstream biological utility, MorphQ features supported higher low-label family-classification accuracy than comparator features, and retained stronger family-level similarity for species absent from model training, indicating better generalisation to species not seen during model training. C_LIO_LITwo case studies link MorphQ morphospaces to species-level elevation and assemblage-level functional diversity while keeping statistical patterns visually inspectable. MorphQ provides a reproducible framework for constructing interpretable morphological trait spaces when predefined descriptors are incomplete and labelled data are limited. C_LI Data/code for peer review: An anonymised repository containing the source code, trained model weights, example data, configuration files and scripts required to reproduce the analyses is available at https://anonymous.4open.science/r/MorphQ-ECD4/.

ecology↗

bioRxiv2025

Eco-genomic analysis uncovers precision-conservation targets for the western Pacific's southernmost salmonid

Understanding how isolated small populations persist and adapt in adverse environments is instrumental to evolutionary and conservation biology. We combine a chromosome-level genome assembly, population resequencing and forward-time simulations to reconstruct the history and viability of the Formosan landlocked salmon (Oncorhynchus formosanus), now restricted to a handful of high-mountain headwaters in Taiwan. We estimate that this lineage has diverged from Japanese masu salmon over one million years ago and has no detectable gene flow for [~]50,000 years. It has accumulated extensive chromosome fusions and expansions of cold-adaptation gene families, qualifying it as a new species rather than a subspecies of Japanese masu salmon. Whole-stream sampling reveals an overlooked Hehuan-Creek population that retains high heterozygosity and has gained unique alleles. Life-table simulations show that the Hehuan population has a notably lower extinction risk and can persist or even grow under low-to-moderate typhoon frequency, whereas Qijiawan-Creek population would decline precipitously under the same or higher frequency . These findings contradict the notion that peripheral populations are likely genetically depleted and support stream-specific "precision conservation" in place of broad, untargeted translocations that could erode local adaptation potential. Thus, our genomic-ecological analysis has uncovered hidden strong resilience in a critically endangered, climate-threatened salmonid lineage.

genomics↗

bioRxiv2024

Circadian Activity Predicts Breeding Phenology in the Asian Burying Beetle Nicrophorus nepalensis

Climate change continues to alter breeding phenology in a range of plant and animal species across the globe. Traditional methods for assessing when organisms reproduce often rely on time-intensive field observations or destructive sampling, creating an urgent need for efficient, non-invasive approaches to assess reproductive timing. Here, we examined three populations of the Asian burying beetle Nicrophorus nepalensis from subtropical Okinawa (500 m) and Taiwan mountains (1100-3200 m) that were reared under contrasting photoperiods in order to develop a predictive framework linking circadian activity to breeding phenology. Using automated activity monitors, we quantified adult circadian rhythms and employed machine learning to predict breeding phenology (seasonal versus year-round breeders) from behavior alone. Our model achieved 95% accuracy under long-day conditions using just three behavioural features, and notably, maintained 76% accuracy under short-day conditions when both types are reproductively active, revealing persistent behavioural differences between breeding strategies. These results demonstrate how integrating behavioural monitoring with machine learning can provide both a rapid, scalable method for tracking population responses to climate change and novel insights into species adaptive responses to shifting seasonal cues across different elevational gradients in their native range.

animal behavior and cognition↗

bioRxiv2022

Allee effects mediate the impact of land-use change on the thermal niche of social species

Land-use change not only affects habitat availability, it can also reduce population density and limit opportunities for interactions with conspecifics, further influencing species resilience to environmental challenges. For social species whose conspecific interactions are typically cooperative in nature, little is known about how land-use change influences demography and social behavior, and how this interaction impacts a species climatic niche. Here, we develop a spatially explicit, individual-based model to explore how land-use changes influence population size and niche width in social organisms through the Allee effect, the positive impact of higher population density on individual fitness. We then empirically test key model predictions by studying the distribution and cooperative behavior of burying beetles (Nicrophorus nepalensis) along elevational gradients in Taiwan. In support of our model predictions, we find that beetle densities are lower in areas of greater land-use change, making it harder for individuals in these hotter environments to form cooperative groups to compete against blowflies, their primary interspecific competitor. Consequently, the beetles lower distributional boundary is higher in areas with greater land-use change, indicating that the beetles thermal niche is reduced via Allee effects in human-altered landscapes. Ultimately, land-use change not only reduces habitat availability, it also shrinks the thermal niche of social species, making them more vulnerable to climate change.

ecology↗

bioRxiv2022

Niche hypervolume analysis revealed that water pollution reduces reproductive success of endangered landlocked salmon but does not directly impact their population density

The critical information for conserving endangered species is to identify how different niche dimensions affect key life history stages of a population. However, it is often difficult to quantify how each ecological niche dimension affects different life history stages because environmental factors may affect each fitness component of organisms to various degrees. Here, we applied the recently developed hypervolume method that follows the idea of Hutchinsons n-dimensional hypervolume. We analyzed the niche space of different life history stages of the endangered landlocked salmon Oncorhynchus masou formosanus, the most southerly distributed of all salmonoids. We found no direct effect of water pollution on salmon population density but a significant negative effect on salmon reproductive success. Surprisingly, the niche hypervolume analysis showed that the size of hatching success niche hypervolume was only 17.9% and 18.4% of the natural redd site density or population density, respectively. This result demonstrates a much higher environmental requirement for salmon during the egg stage than that affecting population density or nesting environment. Our results suggest that understanding the behavioral and physiological mechanisms that influence crucial life history stages in the wild is critical to developing effective conservation programs, and the niche hypervolume is a valuable method to achieve this.

ecology↗

bioRxiv2020

Antagonistic Effects of Intraspecific Cooperation and Interspecific Competition on Thermal Performance

Understanding how climate-mediated biotic interactions shape thermal niche width is critical in an era of global change. Yet, most previous work on thermal niches has ignored detailed mechanistic information about the relationship between temperature and organismal performance, which can be described by a thermal performance curve. Here, we develop a model that predicts the width of thermal performance curves will be narrower in the presence of interspecific competitors, causing a species optimal breeding temperature to diverge from that of a competitor. We test this prediction in the Asian burying beetle Nicrophorus nepalensis, confirming that the divergence in actual and optimal breeding temperatures is the result of competition with blowflies. However, we further show that intraspecific cooperation enables beetles to outcompete blowflies by recovering their optimal breeding temperature. Ultimately, linking direct (abiotic factors) and indirect effects (biotic interactions) on niche width will be critical for understanding species-specific responses to climate change.

ecology↗

bioRxiv2018

Biological adaptation under fluctuating selection

Bet-hedging--an evolutionary strategy that reduces fitness variance at the expense of lower mean fitness--is the primary explanation for most forms of biological adaptation to environmental unpredictability. However, most applications of bet-hedging theory to biological problems have largely made unrealistic demographic assumptions, such as non-overlapping generations and fixed population sizes. Consequently, the generality and applicability of bet-hedging theory to real world phenomena remains unclear. Here we use continuous-time, stochastic Lotka-Volterra models to relax overly restrictive demographic assumptions and explore a suite of biological adaptations to fluctuating environments. We discover a novel \"rising-tide strategy\" that--unlike the bet-hedging strategy--generates both a higher mean and variance in fitness. The positive fitness effects of the rising-tide strategys specialization to good years can overcome any negative effects of higher fitness variance in unpredictable environments. Moreover, we show not only that the rising-tide strategy will be selected for over a much broader range of environmental conditions than the bet-hedging strategy, but also under more realistic demographic circumstances. Ultimately, our model demonstrates that there are likely to be a wide range of ways that organisms respond to environmental unpredictability.

ecology↗

bioRxiv2018

A Chemically-triggered Transition from Conflict to Cooperation in Burying Beetles

Although interspecific competition has long been recognized as a major driver of trait divergence and adaptive evolution1-3, relatively little effort has focused on how it influences the evolution of intraspecific cooperation4-6. Here we identify the mechanism by which the perceived pressure of interspecific competition influences the transition from intraspecific conflict to cooperation in a facultative cooperatively breeding species, the Asian burying beetle Nicrophorus nepalensis. In their natural environment in central Taiwan, N. nepalensis are typically aggressive to conspecifics and only cooperate with others of their own species at critical carcass resources in the presence of blowflies, their primary competitors7. We demonstrate that beetles form larger groups and are more cooperative in carcass preparation in warmer environments where the pressure of interspecific competition with blowflies is highest8. To test the hypothesis that the presence of blowflies promotes beetle cooperation and to identify the mechanism by which this occurs, we manipulated blowfly larvae on carcasses in the lab. We not only found that beetles are more cooperative at carcasses when blowfly maggots have begun to digest the tissue, but that this social cooperation appears to be triggered by a single chemical cue-- dimethyl disulfide (DMDS)--emitted from carcasses consumed by blowflies but not from control carcasses lacking blowflies. Our results provide experimental evidence that interspecific competition promotes the transition from intraspecific conflict to cooperation in N. nepalensis via a surprisingly simple social chemical cue that is a reliable indicator of interspecific competition. This finding helps bridge the gap between the proximate and ultimate factors regulating the transition between cooperation and conflict and moves toward a more comprehensive understanding of the evolution of mechanisms governing intraspecific variation in social behaviour.

evolutionary biology↗

bioRxiv2017

Response to Qian et al (2017): Daily and seasonal climate variations are both critical in the evolution of species’ elevational range size

In their recent critique, Qian et al. (2017) claimed that the results of structural equation modeling analysis (SEM) in Chan et al. (2016) were flawed. Here, we show that the source of the difference in their re-analysis is that Qian et al. did not follow the standard, iterative process of SEM, which allows researchers to evaluate which model offers the best account of the data in both absolute and relative senses. Here, we provide step-by-step instructions to reproduce our published results. All of Qian et al.s concerns regarding SEM can be put to rest. Moreover, in our original paper we used three distinct statistical methods--hierarchical partitioning, SEM, and stationary bootstrap--to show that different temporal scales of environmental variability can differentially impact the elevational range size (ERS) of species. It is time to move on to probing the pressing issue of how and why climatic variability impacts ERS.

ecology↗