Biology subjects

Ellison, A. M.

Publications and source records attributed to Ellison, A. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Herbarium specimens reliably track plant phenological responses to climate change in understudied montane biomes

Long-term field observations typically are the "gold-standard" for inferences of phenological sensitivities in montane systems but are spatially limited. Herbarium specimens provide broader spatial coverage, but their utility to accurately capture montane phenology remains poorly known. We compared flowering phenology of 45 species inferred from herbarium specimens with comparable data from nearly 50 years of direct observations at the Rocky Mountain Biological Laboratory. Estimates of flowering time and phenological sensitivity to snow density were consistent between herbarium specimens and observations, but observations revealed secondary flowering peaks. Herbarium specimens additionally yielded shallower estimates of phenological sensitivity to spring temperature than did field observations. Across co-occurring species, "early" flowering individuals inferred from herbarium specimens, rather than the mean response across all individuals, may better approximate community-level phenological responses to temperature changes. We conclude that herbarium specimens are reliable resources for closing gaps in understanding phenological variation along elevational gradients of montane systems.

ecology↗

bioRxiv2025

A Novel Three-Layer Methodology for Heterogeneity Analysis: from metrics, through statistical tests and modeling to applications

O_LIDiversity and heterogeneity are related but distinct and often conflated concepts. Diversity quantifies the number or relative abundance of discrete objects (e.g. species), whereas heterogeneity includes interactions among them (i.e. in networks) and between them and their environments. Although estimation, testing, and inference of diversity is well established and understood in ecology, comparable methods for heterogeneity are themselves diverse and rarely applied consistently or coherently. C_LIO_LIWe propose a consistent and coherent methodology for estimation, testing, and inference of heterogeneity of ecological networks. Estimation of heterogeneity is scalable from individuals to populations using the variance-to-mean (V/M) ratio and extensions of Taylors power law (TPL) to analyzing networks. Bootstrapping is used to partition heterogeneous and random clusters, whereas permutation tests are used to compare individual- and network-level heterogeneity. Inference includes the identification of "important" (e.g. dominant, foundation, keystone) species and "rich clubs" in heterogeneous networks, detection of biomarkers, and analysis of heterogeneity-stability relationships. C_LIO_LIWe demonstrate this methodology using the global Earth Microbiome Project dataset. The method could reliably distinguish heterogeneous nodes and networks; identified significant differences in heterogeneity among microbial assemblages in different habitats and in specific sites within habitats; and supported established principles of host filtering, species sorting, and niche partitioning. C_LIO_LIOur methods for estimation, testing, and inference of heterogeneity are modular, scalable, and applicable to a wide range of ecological systems. They also provide a quantitative method for understanding how evolutionary and ecological forces jointly shape both topology and heterogeneity in ecological networks. C_LI

ecology↗

bioRxiv2023

Phenologically-informed species distribution models (SDMs) forecast less species loss and turnover versus standard SDMs

Species distribution models (SDMs) have been central for documenting the relationship between species geographic ranges and environmental conditions for more than two decades. However, the vast majority of SDMs rarely consider functional traits, such as phenology, which strongly affect species demography and fitness. Using >120,000 herbarium specimens representing 360 plant species across the eastern United States, we developed a novel "phenology-informed" SDM that integrates dynamic phenological responses to changing climates. Compared to standard SDMs based only on abiotic variables, our phenology-informed SDMs forecast significantly lower species habitat loss and less species turnover within communities under climate change. These results suggest that phenotypic plasticity or local adaptation in phenology may help many species adjust their ecological niches and persist in their habitats during periods of rapid environmental change. By modeling historical data that link phenology, climate, and species distributions, our findings reveal how species reproductive phenology mediates their geographic distributions along environmental gradients and affects regional biodiversity patterns in the face of future climate change. More importantly, our newly developed model also circumvents the need for mechanistic models that explicitly link traits to occurrences for each species, thus better facilitating the deployment of trait-based SDMs across unprecedented spatial and taxonomic scales.

ecology↗

bioRxiv2022

Herbarium records provide reliable phenology estimates in the understudied tropics

Plant phenology has been shifting dramatically in response to climate change, a shift that may have significant and widespread ecological consequences. Of particular concern are tropical biomes, which represent the most biodiverse and imperiled regions of the world. However, compared to temperate floras, we know little about phenological responses of tropical plants because long-term observational datasets from the tropics are sparse. Herbarium specimens have greatly increased our phenological knowledge in temperate regions, but similar data have been underutilized in the tropics and their suitability for this purpose has not been broadly validated. Here, we compare phenological estimates derived from field observational data (i.e., plot surveys) and herbarium specimens at various spatial and taxonomic scales to determine whether specimens can provide accurate estimations of reproductive timing and its spatial variation. Here we demonstrate that phenological estimates from field observations and herbarium specimens coincide well. Fewer than 5% of the species exhibited significant differences between flowering periods inferred from field observations versus specimens regardless of spatial aggregation. In contrast to studies based on field records, herbarium specimens sampled much larger geographic and climatic ranges, as has been documented previously for temperate plants, and effectively captured phenological responses across varied environments. Herbarium specimens are verified to be a vital resource for closing the gap in our phenological knowledge of tropical systems. Tropical plant reproductive phenology inferred from herbarium records are widely congruent with field observations, suggesting that they can (and should) be used to investigate phenological variation and their associated environmental cues more broadly across tropical biomes.

ecology↗

bioRxiv2021

Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot

Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010-2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to explore such legacies. The plot includes 108,632 live stems [≥] 1 cm in diameter (2215 individuals/ha) and 7,595 dead stems [≥] 5 cm in diameter. Fifty-one woody plant species were recorded in the plot, but two tree species-- Tsuga canadensis (eastern hemlock) and Acer rubrum (red maple)--and one shrub-- Ilex verticillata (winterberry)--comprised 56% of all stems. Live tree basal area averaged 42.25 m2/ha, of which 84% was represented by T. canadensis (14.0 m2/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), A. rubrum (7.2 m2/ ha) and Pinus strobus (eastern white pine; 4.4 m2/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha, and were significantly clumped at distances up to 50 m within the plot. Spatial distributions of A. rubrum and Q. rubra showed negative intraspecific correlations in diameters up to at least a 150-m spatial lag, likely indicative of competition for light in dense forest patches. Bivariate marked point-pattern analysis showed that T. canadensis and Q. rubra diameters were negatively associated with one another, indicating resource competition for light. Distribution and abundance of the common overstory species are predicted best by soil type, tree neighborhood effects, and two aspects of land-use history: when fields were abandoned in the late 19th century and the succeeding forest types recorded in 1908. In contrast, a history of intensive logging prior to 1950 and a damaging hurricane in 1938 appear to have had little effect on the distribution and abundance of present-day tree species.

ecology↗

bioRxiv2020

Induced drought strongly affects richness and composition of ground-dwelling ants in the eastern Amazon

Environmental change scenarios caused by low precipitation forecast species loss in tropical regions. We use one year of data from a long-term rainwater exclusion experiment in primary Amazonian rainforest to test whether induced water stress and covarying changes in soil moisture, soil respiration, tree species richness, diversity, size, and total biomass affected species richness and composition (relative abundance) of ground-dwelling ants. Induced drought reduced ant richness, whereas increased soil moisture and variability in tree biomass increased it. Species composition differed between control and rainfall-excluded plots. Occurrence of many ant species was strongly reduced by induced drought, but some generalist groups of ants were favored by it. The expected loss of ant species and changes in ant species composition in tropical forests likely will lead to cascading effects on ecosystem processes and the services they mediate.

ecology↗

bioRxiv2020

Phenological displacement is uncommon among sympatric angiosperms

Interactions between species can influence access to resources and successful reproduction. One possible outcome of such interactions is reproductive character displacement. Here, the similarity of reproductive traits - such as flowering time - among close relatives growing in sympatry differ more so than when growing apart. However, evidence for the overall prevalence and direction of this phenomenon, or the stability of such differences under environmental change, remains untested across large taxonomic and spatial scales. We apply data from tens of thousands of herbarium specimens to examine character displacement in flowering time across 110 animal-pollinated angiosperm species in the eastern USA. We demonstrate that the degree and direction of phenological displacement among co-occurring closely related species pairs varies tremendously. Overall, flowering time displacement in sympatry is not common. However, displacement is generally greater among species pairs that flower close in time, regardless of direction. We additionally identify that future climate change may alter the nature of phenological displacement among many of these species pairs. On average, flowering times of closely related species were predicted to shift further apart by the mid-21st century, which may have significant future consequences for species interactions and gene flow.

ecology↗

bioRxiv2020

A new method for counting reproductive structures in digitized herbarium specimens using Mask R-CNN

Phenology-the timing of life-history events-is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from > 3000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with > 87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with [≥] 90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant response to ongoing climatic change.

ecology↗

bioRxiv2020

Towards a unifying diversity-area relationship (DAR) of species- and gene-diversity

AimThe microbiome as a biogeographic entity can be investigated, to the minimum, from two perspectives: one is the spatial/temporal distribution of species (or any level of the operational taxonomic unit or OTU) diversity, and another is the spatial/temporal distribution of metagenomic gene diversity. Both are necessary for comprehensive understanding of the taxonomical, ecological, evolutionary and functional aspects of the microbiome biogeography. Here we propose to investigate the metagenomic diversity-area relationship (m-DAR), which is a transformation of the species-DAR (s-DAR) that extended the classic SAR (species-area relationship) by replacing the species richness with general species diversity measured in Hill numbers. InnovationThe m-DAR and s-DAR, using the same mathematical models, offer a unifying tool for investigating the biogeography of microbiome from ecological, metagenomic and functional perspectives. Specifically, we investigate m-DAR of the human gut metagenome in terms of the MG (metagenomic gene) and MFGC (metagenome functional gene cluster) respectively, by sketching out the DAR-profile, PDO (pair-wise diversity overlap) profile, MAD (maximal accrual diversity) profile, and RIP (ratio of individual- to population-diversity) profile at each scale. These profiles constitute our unifying DAR toolset and can be applied to any microbiomes beyond the human gut microbiome. Main conclusionsWe demonstrate the construction and applications of the m-DAR and its associated four profiles with six large datasets of the human gut metagenomes including three microbiome-associated diseases (obesity, diabetes, IBD) and their healthy controls, supported with randomization tests to determine the differences between healthy and diseased treatments in their m-DAT parameters. Theoretically, our study presents a successful case to demonstrate the feasibility of unifying systematic biogeography vs. evolutionary biogeography, of an inclusive biogeography of plants, animal and microbes. Practically, our approach offers an important tool for investigating the spatial scaling of human metagenome diversity in a population (cohort) and its relationship with individual-level diversity.

ecology↗

bioRxiv2020

Regulation by the pitcher plant Sarracenia purpurea of the structure of its inquiline food web

AO_SCPLOWBSTRACTC_SCPLOWPhytotelmata, the water-filled habitats in pitcher plants, bromeliad tanks, and tree-holes, host multitrophic food webs that are model experimental systems for studying food-web structure and dynamics. However, the plant usually is considered simply as an inert container, not as an interacting part of the food web. We used a manipulative field experiment with a response-surface design to determine effects of nutrient enrichment (multiple levels of NH4NO3, PO4, and captured prey), top predator (removed or present), and the plant itself (with or without plastic tubes inserted into the pitchers to isolate the food web from the plant) on the macrobial food web within the modified leaves ("pitchers") of the carnivorous pitcher plant Sarracenia purpurea. Connection to the plant, addition of NH4NO3 and removal of the top predator significantly increased the food webs saturation, defined as its trophic depth and number of interactions. No effects on food-web saturation resulted from addition of PO4 or supplemental prey. Plants such as S. purpurea that create phytotelmata are more than inert containers and their inhabitants are more than commensal inquilines. Rather, both the plant and the inquilines are partners in a complex network of interactions.

ecology↗

bioRxiv2020

Clockwise and counterclockwise hysteresis characterize state changes in the same aquatic ecosystem

Incremental increases in a driver variable, such as nutrients or detritus, can trigger abrupt shifts in aquatic ecosys-tems. Once these ecosystems change state, a simple reduction in the driver variable may not return them to their original state. Because of the long time scales involved, we still have a poor understanding of the dynamics of ecosys-tem recovery after a state change. A model system for understanding ecosystem recovery is the aquatic microecosystem that inhabits the cup-shaped leaves of the pitcher plant Sarracenia purpurea. With enrichment of organic matter, this system flips within 1 to 3 days from an oxygen-rich state to an oxygen-poor (hypoxic) state. In a replicated green-house experiment, we enriched pitcher plant leaves at different rates with bovine serum albumin (BSA), a molecular substitute for detritus. Changes in dissolved oxygen ([O2]) and undigested BSA concentration were monitored during enrichment and recovery phases. At low enrichment rates, ecosystems showed a substantial lag in the recovery of [O2] (clockwise hysteresis). At intermediate enrichment rates, [O2] tracked the levels of undigested BSA with the same profile during the enrichment and recovery phases (no hysteresis). At high enrichment rates, we observed a novel response: changes in [O2] were proportionally larger during the recovery phase than during the enrichment phase (counter-clockwise hysteresis). These experiments demonstrate that detrital enrichment rate can modulate a diversity of hysteretic responses in a single aquatic ecosystem. With counter-clockwise hysteresis, rapid reduction of a driver variable following high enrichment rates may be a viable restoration strategy.

ecology↗

bioRxiv2020

Foundation species across a latitudinal gradient in China

AbstractFoundation species play important roles in structuring forest communities and ecosystems. Foundation species are difficult to identify without long-term observations or experiments and their foundational roles rarely are identified before they are declining or threatened. We used new statistical criteria based on size-frequency distributions, species diversity, and spatial codispersion among woody plants to identify potential ("candidate") foundation species in 12 large forest dynamics plots spanning 26 degrees of latitude in China. We used these data to identify a suite of candidate foundation species in Chinese forests; test the hypothesis that foundation woody plant species are more frequent in the temperate zone than in the tropics; and compare these results with comparable data from the Americas to suggest candidate foundation genera in Northern Hemisphere forests. We identified more candidate foundation species in temperate plots than in subtropical or tropical plots, and this relationship was independent of the latitudinal gradient in overall species richness. Two species of Acer, the canopy tree Acer ukurunduense and the shrubby treelet Acer barbinerve were the only two species that met both criteria in full to be considered as candidate foundation species. When we relaxed the diversity criteria, Acer, Tilia, and Juglans spp., and Corlyus mandshurica were frequently identified as candidate foundation species. In tropical plots, the tree Mezzettiopsis creaghii and the shrubs or treelets Aporusa yunnanensis and Ficus hispida had some characteristics associated with foundation species. Species diversity of co-occurring woody species was negatively associated with basal area of candidate foundation species more frequently at 5- and 10-m spatial grains (scale) than at a 20-m grain. Conversely, Bray-Curtis dissimilarity was positively associated with basal area of candidate foundation species more frequently at 5-m than at 10- or 20-m grains. Our data support the hypothesis that foundation species should be more common in temperate than in tropical or boreal forests, and suggest that in the Northern Hemisphere that Acer be investigated further as a foundation tree genus.

ecology↗

bioRxiv2018

Multivariate methods for testing hypotheses of temporal community dynamics

For ecological research to make important contributions towards understanding and managing temporally-variable global change processes, such as responses to land-use and climatic change, we must have effective and comparable ways to quantify and analyse compositional change over time in biological communities. These changes are the sum of local colonisation and extinction events, or changes in the biomass and relative abundance of taxa within and among samples. We conducted a quantitative review of currently available methods for the analysis of multivariate datasets collected at temporal intervals. This review identified the need for the application of quantitative, hypothesis-based approaches to understand temporal change in community composition, particularly for small datasets with less than 15 temporal replicates. To address this gap, we: (1) conceptually present how temporal patterns in community dynamics can be framed as specific, testable hypotheses; (2) provide three fully-worked case-studies, complete with R code, demonstrating multivariate analysis methods for temporal hypothesis testing and pattern visualisation; and (3) present a road map for testing specific, quantitative hypotheses relating to the underlying mechanisms of temporal community dynamics.

ecology↗

bioRxiv2018

Expanded view of the ecological genomics of ant responses to climate change

Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of > 16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genus Aphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species: A. ashmeadi, A. floridana, A. fulva, A. miamiana, A. picea, and A. rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8 to 396.0 Mb) and flow cytometry estimates (210.7 to 690.4 Mb). In an analysis of currently sequenced ant genomes and the new Aphaenogaster sequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature showed the strongest correlation with genome size, with ants from locations with colder minimum temperatures having larger genomes. These results suggest that temperature extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.

genomics↗

bioRxiv2017

Widespread sampling biases in herbaria revealed from large-scale digitization

O_LINon-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases.\nC_LIO_LIWe determined spatial, temporal, trait, phylogenetic, and collector biases in [~]5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England (NE).\nC_LIO_LIWe identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via founder effects.\nC_LIO_LIStudies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.\nC_LI

plant biology↗

bioRxiv2017

Selfing species exhibit diminished niche breadth over time.

Self-pollinating plants (\"selfers\") have larger geographic ranges and inhabit higher latitudes than their outcrossing relatives. This finding has led to the hypothesis that selfers also have broader climatic niches. It is possible that the increased likelihood of successful colonization into new areas and the initial purging of deleterious mutations may offset selfers inability to adapt to new environments due to low heterozygosity. Here, for the first time, we examine the climatic niches and mutation accumulation rates of hundreds of closely related selfing and outcrossing species. Contrary to expectations, selfers do not have wider climatic niche breadths than their outcrossing sister taxa despite selfers greatly expanded geographic ranges. Selfing sister pairs also exhibit greater niche overlap than outcrossing sisters, implying that climatic niche expansion becomes limited following the transition to selfing. Further, the niche breadth of selfers is predicted to decrease significantly faster than that of closely-related outcrossers. In support of these findings, selfers also display significantly higher mutation accumulation rates than their outcrossing sisters, implying decreased heterozygosity, effective population size, and adaptive potential. These results collectively suggest that while the release from mate limitation among selfing species may result in initial range expansion, range size and niche breadth are decoupled, and the limitations of an increasingly homogeneous genome will constrict selfers climatic niches and over time reduce their geographic ranges.

ecology↗

bioRxiv2017

Ecological Network Metrics: Opportunities For Synthesis

Network ecology provides a systems basis for approaching ecological questions, such as factors that influence biological diversity, the role of particular species or particular traits in structuring ecosystems, and long-term ecological dynamics (e.g. stability). Whereas the introduction of network theory has enabled ecologists to quantify not only the degree, but also the architecture of ecological complexity, these advances have come at the cost of introducing new challenges, including new theoretical concepts and metrics, and increased data complexity and computational intensity. Synthesizing recent developments in the network ecology literature, we point to several potential solutions to these issues: integrating network metrics and their terminology across sub-disciplines; benchmarking new network algorithms and models to increase mechanistic understanding; and improving tools for sharing ecological network research, in particular \"model\" data provenance, to increase the reproducibility of network models and analyses. We propose that applying these solutions will aid in synthesizing ecological subdisciplines and allied fields by improving the accessibility of network methods and models.

ecology↗

bioRxiv2017

Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test

Ecological studies aim to better understand the distribution and abundances of organisms. Yet ecological works often are subjected to unintentional biases thus an improved framework for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants (Formica rufa, RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 meters of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE-SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research.

ecology↗