Biology subjects

DeLong, J. P.

Publications and source records attributed to DeLong, J. P..

12 recordsLinked to original sources

bioRxiv2026

Evolutionary Dynamics of Paramecium Mitochondrial Genomes

Ciliates are a diverse group of single-celled eukaryotes that can exhibit a wide range of genetic diversity within morphologically indistinguishable species. However, they are still not well studied as their mechanisms of speciation and the extent of diversification remain unknown. Mitochondrial genomes offer an effective framework for resolving species relationships and evolutionary changes. Here, we analyzed a globally sampled dataset of Paramecium to understand the evolution of mitochondrial genomes in ciliates. Phylogenetic analysis of linear mitochondrial genomes shows the presence of cryptic diversity beyond the P. aurelia complex, with P. bursaria lineage appearing as a deeply diverging out-group. Protein-coding genes are largely conserved, with limited rearrangements, and some ciliate-specific genes appear to be missing in P. bursaria. Population genetic analysis show little to no evidence of recombination along with substantial differences in effective population size across species. Patterns of molecular evolution also indicate purifying selection as the predominant force, the strength of which is at least as strong as in the nucleus and consistent with mitochondrial effective population sizes that are similar or larger than those of the nucleus. Across the functional groups, the electron transport chain and ribosomal genes are highly constrained, while ciliate-specific ymf genes show reduced efficacy of selection compared to the others. These findings offer a basis for connecting mitochondrial variation to evolutionary divergence, functional constraint, and speciation in microbial eukaryotes.

genomics↗

bioRxiv2026

Shifts in the population-genetic landscape of the ciliate genus Paramecium

Ciliates are one of the most ecologically diverse and morphologically intricate unicellular organisms. Despite their evolutionary significance and their prominence in cell-biological research, the population-genetic processes governing their diversification have received remarkably little attention. A fundamental unresolved problem is the existence of geographic isolation among free-living protists and its consequences for species richness. We addressed this issue in the model ciliate Paramecium by sequencing genomes of hundreds of isolates collected worldwide, capturing multiple morphological and cryptic species, with multiple populations each. Contrary to previous reports, we found evidence of geographic differentiation in the majority of species. In a few cases, geographic structure became evident when deeply diverging clades in a species were treated separately. This suggests that the biogeographical patterns of Paramecium have been shaped by periods of genetic isolation leading to speciation, with rare events of global dispersal realized over its long evolutionary history. Despite being largely isolated, populations were remarkably similar in their effective population size, recombination rate, and efficacy of natural selection. Across species, selection appears to be least effective in Paramecium aurelia lineages, and most effective in P. bursaria, presumably due to differences in their breeding characteristics. Despite differences among species in the population-genetic environment, patterns of variation across the genome remained consistent. Selective constraints on a core set of genes seemed to have gradually diverged across the species phylogeny. Genes with multiple copies retained from whole-genome duplication events in P. aurelia were found to be under relatively relaxed purifying selection. Moving forward, this dataset will serve to test hypotheses on the ecological and cellular complexity of Paramecium and beyond.

evolutionary biology↗

bioRxiv2026

The OS-Prey (Omnibus Study of Prey) database: A compilation of diet records for birds of prey.

MotivationThe diet composition of a predator is a direct reflection of its role in a food web, resulting from interactions with prey species. Raptors (including hawks, owls, and falcons) are ubiquitous predators with diverse diets, yet there is no comprehensive database of raptor diet composition. We present a database of over 3500 raw raptor diet records, compiled from more than 1000 studies and representing 173 raptor species from across the world. Our dataset complements existing qualitative summaries of species diets by compiling thousands of quantitative diet "samples" over time and space to present diet data at a uniquely fine resolution. Main types of variable containedThe database comprises published records of raptor diets from pellets, prey remains, direct or photographic observations, prey DNA, and raptor gut or gullet contents. For each diet, we present the taxonomic identity and amounts of consumed prey. We additionally present various metadata for each diet such as location, habitat, and season. Spatial location and grainThe study incorporates diet records collected worldwide, with each record assigned geographic coordinates corresponding to the location where the diet information was obtained. Time period and grainThe database includes diet records from 1893 to 2025. We report a year for each diet record. Major taxa and level of measurementWe recorded raptor diet at the species level, including raptors from three orders: Strigiformes, Falconiformes and Accipitriformes excluding vultures. Most prey are identified to species, but prey taxonomic level varies depending on the extent to which they could be identified. Software formatDiet records and metadata are provided in two files with comma-separated value (.csv) format.

ecology↗

bioRxiv2024

Integrating predator energetic balance, risk-taking behavior and microhabitat in functional response: Untangling indirect interactions in a multispecies vertebrate community

1O_LIPredator-prey interactions in natural communities are complex, with predators often exploiting multiple prey types and generating indirect interactions among them. Ecological theory has traditionally modeled these interactions using functional responses models which are based on foraging rates, not energy transfers. This approach overlooks how the energy acquisition rate of a predator can alter its behavior and, in turn, the strength of species interactions. C_LIO_LIHere, we integrate predator energetics into a functional response model to represent trade-offs predators face when foraging on prey that vary in risk and abundance across heterogeneous landscapes. We compared model predictions to 20 years of prey species density and reproductive success data. The mechanistic model was parameterized for an Arctic tundra vertebrate community, where the Arctic fox feeds on cyclic lemmings and eggs of sandpipers (non-risky prey) and gulls (risky prey that often nest in partial refuge like islands). In this system, predator-mediated interactions generate apparent mutualism between lemmings and birds, but its strength varies between species, and the mechanisms underlying this interaction remain unclear. C_LIO_LIWe found that fox energetic balance was highly related to lemming density, with a threshold of 89 lemmings per km2 required for a positive energetic balance. Model-predicted gull nest acquisition rates were lowest on islands when the energetic balance of foxes was positive, and highest for nests on the shore when foxes were in deficit. The model that incorporated predator risk-taking behavior and energetic balance produced variation in gull hatching success that most closely matched empirical observations. C_LIO_LIWe documented for the first time that a shift in predator energetic balance, triggering changes in attack and capture probabilities on a risky prey, can be a key mechanism underlying the apparent mutualism between lemmings and gulls. In contrast, for non-risky prey, the indirect effect can be essentially driven by changes in predator movement. These findings highlight how prey characteristics can lead to different mechanisms behind similar indirect interactions. C_LIO_LITaken together, our results indicate that mechanistic models integrating species traits, landscape features, and energy-dependent behavioral adjustments can improve our ability to quantify interaction strengths in natural communities. C_LI

ecology↗

bioRxiv2024

Simple, universal rules predict trophic interaction strengths

Many drivers of ecological systems exhibit regular scaling relationships, yet the mechanisms explaining these relationships are often unknown. Trophic interaction strengths are no exception, exhibiting scaling relationships with predator and prey traits that lack evolutionary explanations. We propose two rules to explain the scaling of trophic interaction strengths through the relationship between a predators feeding rate and its preys density -- the so-called predator functional response. First, functional responses allow predators to meet their energetic demands when prey are rare. Second, functional responses approach their maxima near the highest prey densities predators experience. We show that equations derived from these rules predict functional response parameters across over 2,100 functional response experiments and make additional predictions such as their allometric scaling. The two rules thereby offer a potential ultimate explanation for the determinants of trophic interaction strengths, revealing ecologically realized constraints to the complex, adaptive nature of functional response evolution.

ecology↗

bioRxiv2024

In defense of the Type I functional response: The frequency and population-dynamic effects of feeding on multiple prey at a time

Ecologists differ in the degree to which they consider the linear Type I functional response to be an unrealistic versus sufficient representation of predator feeding rates. Empiricists tend to consider it unsuitably non-mechanistic and theoreticians tend to consider it necessarily simple. Hollings original rectilinear Type I response is dismissed by satisfying neither desire, with most compromising on the smoothly saturating Type II response for which searching and handling are assumed to be mutually exclusive activities. We derive a "multiple-prey-at-a-time" response and a generalization that includes the Type III to reflect predators that can continue to search when handling an arbitrary number of already-captured prey. The multi-prey model clarifies the empirical relevance of the linear and rectilinear models and the conditions under which linearity can be a mechanistically-reasoned description of predator feeding rates, even when handling times are long. We find support for linearity in 35% of 2,591 compiled empirical datasets and support for the hypothesis that larger predator-prey body-mass ratios permit predators to search while handling greater numbers of prey. Incorporating the multi-prey response into the Rosenzweig-MacArthur population-dynamics model reveals that a non-exclusivity of searching and handling can lead to coexistence states and dynamics that are not anticipated by theory built on the Type I, II, or III response models. In particular, it can lead to bistable fixed-point and limit-cycle dynamics with long-term crawl-by transients between them under conditions where abundance ratios reflect top-heavy food webs and the functional response is linear. We conclude that functional response linearity should not be considered empirically unrealistic but also that more cautious inferences should be drawn in theory presuming the linear Type I to be appropriate.

ecology↗

bioRxiv2024

Heritable intraspecific variation among prey in size and movement interact to shape predation risk and potential natural selection

O_LIPredator and prey traits are important determinants of the outcomes of trophic interactions. In turn, the outcomes of trophic interactions shape the evolution of predator and prey traits. How species traits are likely to respond to selection from trophic interactions depends crucially on whether and how heritable species traits are and their genetic correlations. Of the many traits potentially influencing the outcomes of trophic interactions, body size and movement traits have emerged as universally key traits. Yet, how these traits shape and are shaped by trophic interactions is generally unclear, as few studies have simultaneously measured the impacts of these traits on the outcomes of trophic interactions, their heritability, and their correlations within the same system. C_LIO_LIWe used outcrossed and then clonally propagated lines of the ciliate protist Paramecium caudatum from natural populations to examine variation in morphology and movement behavior, the extent to which this variation was heritable, and how intraspecific differences among lines altered Paramecium susceptibility to predation by the copepod Macrocyclops albidus. C_LIO_LIWe found that the Paramecium lines exhibited heritable variation in body size and movement traits. In contrast to expectations from interspecific allometric relationships, body size and movement speed showed little covariance among clonal lines. The proportion of Paramecium consumed by copepods was positively associated with Paramecium body size and velocity, however, we also found evidence of an interaction such that greater velocities led to greater predation risk for large body-sized paramecia but did not alter predation risk for smaller body-sized paramecia. The proportion of paramecia consumed was not related to copepod body size. These patterns of predation risk and heritable trait variation in paramecia suggest that copepod predation may act as a selective force operating independently on movement and body size and generating the strongest selection against large, high-velocity paramecia. C_LIO_LIOur results illustrate how the interactions between ecology and genetics can shape the potential natural selection on prey traits through the outcomes of trophic interactions. Further simultaneous measures of predation outcomes, traits, and their quantitative genetic characteristics will provide insights into the evolutionary ecology of species interactions and their eco-evolutionary consequences. C_LI

ecology↗

bioRxiv2022

Ecological boundaries and constraints on viable eco-evolutionary pathways

Evolutionary dynamics are subject to constraints ranging from limitations on what is physically possible to limitations on the pathways that evolution can take. One set of evolutionary constraints, known as demographic constraints, constrain what can occur evolutionarily due to the population demographic or population dynamical consequences of evolution leading to conditions that make populations susceptible to extinction. These demographic constraints can limit the strength of selection or rates of environmental change populations can experience while remaining extant and the trait values a population can express. Here we further hypothesize that the population demographic and population dynamical consequences of evolution also can constrain the eco-evolutionary pathways that populations can traverse by defining ecological boundaries represented by areas of likely extinction. We illustrate this process using a model of predator evolution. Our results show that the populations that persist over time tend to be those whose eco-evolutionary dynamics have avoided ecological boundaries representing areas of likely extinction due to stochastic deviations from a deterministic eco-evolutionary expectation. We term this subset of persisting pathways viable eco-evolutionary pathways. The potential existence of ecological boundaries constraining evolutionary pathways has important implications for predicting evolutionary dynamics, interpreting past evolution, and understanding the role of stochasticity and ecological constraints on eco-evolutionary dynamics.

ecology↗

bioRxiv2022

Predator feeding rates may often be unsaturated under typical prey densities

Predator feeding rates (described by their functional response) must saturate at high prey densities. Although thousands of manipulative functional response experiments show feeding rate saturation at high densities under controlled conditions, it is unclear how saturated feeding rates are at natural prey densities. The general degree of feeding rate saturation has important implications for the processes determining feeding rates and how they respond to changes in prey density. To address this, we linked two databases - one of functional response parameters and one on mass-abundance scaling - through prey mass to calculate a feeding rate saturation index. We find that: 1) feeding rates may commonly be unsaturated and 2) the degree of saturation varies with predator and prey taxonomic identities and body sizes, habitat, interaction dimension, and temperature. These results reshape our conceptualization of predator-prey interactions in nature and suggest new research on the ecological and evolutionary implications of unsaturated feeding rates.

ecology↗

bioRxiv2021

Quantifying predator functional responses under field conditions reveals interactive effects of temperature and interference with sex and stage.

O_LIPredator functional responses describe predator feeding rates and are a core component of predator-prey theory. Although originally defined as the relationship between predator feeding rates and prey densities, it is now well known that predator functional responses are shaped by a multitude of factors. Unfortunately, how these factors interact with one another remains unclear, as widely used laboratory methods for measuring functional responses are generally logistically constrained to examining a few factors simultaneously. Furthermore, it is also often unclear whether laboratory derived functional responses translate to field conditions. C_LIO_LIOur goal was to apply an observational approach for measuring functional responses to understand how sex/stage differences, temperature, and predator interference interact to influence the functional response of zebra jumping spiders on midges under natural conditions. C_LIO_LIWe used field feeding surveys of jumping spiders to infer spider functional responses. We applied a Bayesian model averaging approach to estimate differences among sexes and stages of jumping spiders in their feeding rates and their dependencies on midge densities, temperature, and predator interference. C_LIO_LIWe find that females exhibit the steepest functional responses on midges, followed by juveniles, and then males, despite males being larger than juveniles. We also find that sexes and stages differ in the temperature dependence of their space clearance (aka attack) rates. We find little evidence of temperature dependence in females, whereas we find some evidence for an increase in space clearance rate at high temperatures in males and juveniles. Interference effects on feeding rates were asymmetric with little effect of interference on male feeding rates, and effects of interference on females and juveniles depending on the stage/sex from which the interference originates. C_LIO_LIOur results illustrate the multidimensional nature of functional responses in natural settings and reveal how factors influencing functional responses can interact with one another through behavior and morphology. Further studies investigating the influence of multiple mechanisms on predator functional responses under field conditions will provide an increased understanding of the drivers of predator-prey interaction strengths and their consequences for communities and ecosystems. C_LI

ecology↗

bioRxiv2020

Estimating predator functional responses using the times between prey captures

O_LIPredator functional responses, which describe how predator feeding rates change with prey densities, are a core component of predator-prey theory. Given their importance, ecologists have measured thousands of predator functional responses. However, most of these studies have used a single standard experimental method that is ill-suited to address many current, pressing questions regarding functional responses. C_LIO_LIWe derive a new experimental design and statistical analysis that quantifies the parameters of predator functional responses by using the time between a predators feeding events and can be used with individual predators requiring only one or a few trials. We examine the feasibility of this experimental method and analysis by using simulations to examine the ability of the statistical model to estimate the true functional response parameters from simulated data. We also perform a proof-of-concept experiment estimating the functional responses of two individual jumping spiders feeding on midges. C_LIO_LIOur simulations show that the statistical method is capable of reliably estimating functional response parameters under a wide range of parameter values and sample sizes. Our proof-of-concept experiment illustrates that the experimental design and statistical method provided reasonable estimates of functional response parameters and good fits to the data for individual jumping spiders using only a few trials per individual. C_LIO_LIBy virtue of the fewer number of trials required to measure a functional response, the method derived here promises to expand the questions that can be addressed using functional response experiments and the systems for which functional responses can be measured. For example, this method is well-poised to address questions such as intraspecific variation in predator functional response parameters and the role of predator and prey traits and abiotic conditions on shaping functional responses. We hope, therefore, that this time-between-captures method will refine our understanding of functional responses and thereby our understanding of predator-prey interactions more generally. C_LI

ecology↗

bioRxiv2018

Data paper: FoRAGE (Functional Responses from Around the Globe in all Ecosystems) database: a compilation of functional responses for consumers and parasitoids

Functional responses - the relationships between consumer foraging rate and resource (prey) density - provide key insights into consumer-resource interactions and predation mechanics while also being a major contributor to population dynamics and food web structure. We present a global database of standardized functional response parameters extracted from the published literature. We refit the functional responses with a Type II model using standardized methods and report the fitted parameters along with data on experimental conditions, consumer and resource taxonomy and type, as well as the habitat and dimensionality of the foraging interaction. The consumer and resource species covered here are taxonomically diverse, from protozoans filtering algae to wasps parasitizing moth larvae to wolves hunting moose. The FoRAGE database (doi:10.5063/F17H1GTQ) is a living data set that will be updated periodically as new functional responses are published.

ecology↗