Biology subjects

Rubenstein, D. R.

Publications and source records attributed to Rubenstein, D. R..

11 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

The thermal benefits of a mound-burrow system in a semi-desert Australian landscape: will this pebble fortress provide refuge from climate change?

Deserts are expected to warm and dry more than other ecoregions, making it critical to understand how arid-adapted animals might cope with increasing climate change. Plasticity in microclimatic niches created through the extended phenotype have been hypothesized to buffer desert-dwelling organisms from rapidly changing conditions. A unique example of the extended phenotype is the mound-burrow system of the western pebble mouse (Pseudomys chapmani), a small rodent that survives in one of Australias harshest environments. Here, using thermo-loggers and by obtaining mound measurements, we show that the mound-burrow system provides protection from prevailing desert conditions of both searing heat and freezing cold. We show that burrow depth and the height of the parapet around the entrance help maintain stable temperatures by warming in winter and cooling in spring. Burrows also had stable humidity levels relative to external fluctuations. We conclude that this unique pebble fortress is a critical resource that allows the species to persist in an extreme environment. We then applied modelling to assess how global warming has, and may continue to, influence(d) thermoregulation and behaviour, revealing that future summers in this extreme region may require refuge at an unachievable depth. Our study highlights the limits of the extended phenotype in buffering climate change impacts and raises concerns about the future of desert rodent populations in a rapidly warming world.

ecology↗

bioRxiv2024

Fitness drivers of division of labor in vertebrates

Although division of labor as a means to increase productivity is a common feature in animal social groups, most previous studies have focused almost exclusively on eusocial insects with extreme task partitioning. Empirical evidence of division of labor in vertebrates is scarce, largely because we lack a theoretical framework to explore the conditions under which division of labor is likely to evolve in cooperatively breeding systems where helpers remain capable of breeding throughout their lifetime. By explicitly considering alternative helping tasks with varying fitness costs, we model how individual decisions on task specialization may influence the emergence of division of labor under both direct and indirect fitness benefits. Surprisingly, we find that direct survival benefits of living in larger groups are the primary force driving the evolution of cooperation to enhance group productivity, and that indirect fitness benefits derived from related group members are only a non-essential facilitator of more stable forms of division of labor in cooperative breeders. In addition, we find that division of labor in vertebrates is favored by harsh environments. Ultimately, our model not only makes key predictions that are consistent with existing empirical data, but also proposes novel avenues for new empirical work in vertebrate and invertebrate systems alike.

animal behavior and cognition↗

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↗

bioRxiv2024

Advancing cooperative breeding research with a peer-reviewed and "live" Cooperative-Breeding Database (Co-BreeD)

Research on cooperative breeding (a system with the core characteristic of individuals providing care for the offspring of others) is important for understanding sociality and cooperation. However, large-scale comparative analyses on the drivers and consequences of cooperation frequently use considerably inaccurate datasets (e.g. due to inconsistent definitions and outdated information). To advance comparative research on cooperative breeding, we introduce the Cooperative-Breeding Database (Co-BreeD), a growing database of key socio-biological parameters of birds and mammals. First, we describe Co-BreeDs structure as a (i) sample-based (i.e. multiple samples per species linked to an exact sampling location and period), (ii) peer-reviewed and (iii) updatable resource. Respectively, these curating principles allow for (i) investigating intra- and inter-species variation and linking between fine-scale social and environmental parameters, (ii) accuracy and (iii) continuous correction and expansion with the publication of new data. Second, we present the first Co-BreeD dataset, which estimates the prevalence of breeding events with potential alloparents in 265 samples from 233 populations of 150 species, including 2 human societies (N = 26,366 breeding events). We conclude by demonstrating (i) how Co-BreeD facilitates more accurate comparative research (e.g. increased explanatory power by enabling the study of cooperative breeding as a continuous trait, and statistically accounting for the sampling error probabilities), and (ii) that cooperative breeding in birds and mammals is more prevalent than currently estimated.

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

Target-enriched enzymatic methyl sequencing: flexible, scalable and inexpensive hybridization capture for quantifying DNA methylation

The increasing interest in studying DNA methylation to understand how traits or diseases develop requires new and flexible approaches for quantifying DNA methylation in a diversity of organisms. In particular, we need efficient yet cost-effective ways to measure CpG methylation states over large and complete regions of the genome. Here, we develop TEEM-Seq (target-enriched enzymatic methyl sequencing), a method that combines enzymatic methyl sequencing with a custom-designed hybridization capture bait set that can be scaled to reactions including large numbers of samples in any species for which a reference genome is available. Using DNA from a passerine bird, the superb starling (Lamprotornis superbus), we show that TEEM-Seq is able to quantify DNA methylation states similarly well to the more traditional approaches of whole-genome and reduced-representation sequencing. Moreover, we demonstrate its reliability and repeatability, as duplicate libraries from the same samples were highly correlated. Importantly, the downstream bioinformatic analysis for TEEM-Seq is the same as for any sequence-based approach to studying DNA methylation, making it simple to incorporate into a variety of workflows. We believe that TEEM-Seq could replace traditional approaches for studying DNA methylation in candidate genes and pathways, and be effectively paired with other whole-genome or reduced-representation sequencing approaches to increase project sample sizes. In addition, TEEM-Seq can be combined with mRNA sequencing to examine how DNA methylation in promoters or other regulatory regions is related to the expression of individual genes or gene networks. By maximizing the number of samples in the hybridization reaction, TEEM-Seq is an inexpensive and flexible sequence-based approach for quantifying DNA methylation in species where other capture-based methods are unavailable or too expensive, particularly for non-model organisms.

genetics↗

bioRxiv2021

Prenatal environmental variation, alternative reproductive tactics and the formation of a mixed-kin cooperative society

Although animal societies often evolve due to limited natal dispersal that results in kin clustering and facilitates cooperation among relatives, many species form cooperative groups with low and variable kin structure. Groups in such mixed-kin societies often comprise residents and immigrants of the same sex that compete for breeding opportunities. To understand how such mixed-kin societies form despite their potential for social conflict, we investigated the environmental causes and subsequent fitness consequences of dispersal decisions in male cooperatively breeding superb starlings (Lamprotornis superbus) that live in a climatically unpredictable environment. We show that the two alternative reproductive tactics--natal dispersal or philopatry--exhibit reproductive tradeoffs resulting in equal lifetime inclusive fitness. The tactic an individual adopts is governed by the environment its parents experience prior to laying rather than the environment it experiences during its juvenile stage. When individuals adopt the tactic not predicted by early life environmental conditions, their fitness is reduced. Ultimately, climate-driven oscillating selection may help stabilize mixed-kin animal societies, despite their reduced kin structure and potential for social conflict.

evolutionary biology↗

bioRxiv2020

Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps

Eusocial animals often achieve ecological dominance in the ecosystems where they occur, a process that may be linked to their demography. That is, reproductive division of labor and high reproductive skew in eusocial species is predicted to result in more stable effective population sizes that may make groups more competitive, but also lower effective population sizes that may make groups more susceptible to inbreeding and extinction. We examined the relationship between demography and social organization in one of the few animal lineages where eusociality has evolved recently and repeatedly among close relatives, the Synalpheus snapping shrimps. Although eusocial species often dominate the reefs where they occur by outcompeting their non-eusocial relatives for access to sponge hosts, many eusocial species have recently become extirpated across the Caribbean. Coalescent-based historical demographic inference in 12 species found that across nearly 100,000 generations, eusocial species tended to have lower but more stable effective population sizes through time. Our results are consistent with the idea that stable population sizes may enable eusocial shrimps to be more competitively dominant, but they also suggest that recent population declines are likely caused by eusocial shrimps heightened sensitivity to anthropogenically-driven environmental changes as a result of their low effective population sizes and localized dispersal, rather than to natural cycles of inbreeding and extinction. Thus, although the unique life histories and demography of eusocial shrimps has likely contributed to their persistence and ecological dominance over evolutionary timescales, these social traits may also make them vulnerable to contemporary environmental change.

evolutionary biology↗

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

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↗