Biology subjects

Ellison, A. M.

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

8 recordsLinked to original sources

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↗

bioRxiv2017

When a foundation crumbles: forecasting forest community dynamics following the decline of the foundation species Tsuga canadensis

AbstractIn the forests of northeastern North America, invasive insects and pathogens are causing major declines in some tree species and a subsequent reorganization of associated forest communities. Using observations and experiments to investigate the consequences of such declines are hampered because trees are long-lived. Simulation models can provide a means to forecast possible futures based on different scenarios of tree species decline, death, and removal. Such modeling is particularly urgent for species such as eastern hemlock (Tsuga canadensis), a foundation species in many northeast forest regions that is declining due to the hemlock woolly adelgid (Adelges tsugae). Here, we used an individual-based forest simulator, SORTIE-ND, to forecast changes in forest communities in central Massachusetts over the next 200 years under a range of scenarios: a no-adelgid, status-quo scenario; partial resistance of hemlock to the adelgid; adelgid irruption and total hemlock decline over 25 years, adelgid irruption and salvage logging of hemlock trees; and two scenarios of preemptive logging of hemlock and hemlock/white pine.We applied the model to six study plots comprising a range of initial species mixtures, abundances, and levels of hemlock dominance. Simulations indicated that eastern white pine, and to a lesser extent black birch and American beech, would gain most in relative abundance and basal area following hemlock decline. The relative dominance of these species depended on initial conditions and the amount of hemlock mortality, and their combined effect on neighborhood-scale community dynamics. Simulated outcomes were little different whether hemlock died out gradually due to the adelgid or disappeared rapidly following logging. However, if eastern hemlock were to become partially resistant to the adelgid, hemlock would be able to retain its dominance despite substantial losses of basal area. Our modeling highlights the complexities associated with secondary forest succession due to ongoing hemlock decline and loss. We emphasize the need both for a precautionary approach in deciding between management intervention or simply doing nothing in these declining hemlock forests, and for clear aims and understanding regarding desired community- and ecosystem-level outcomes.

ecology↗

bioRxiv2016

Regime shifts, alternative states and hysteresis in the Sarracenia microecosystem

Changes in environmental conditions can lead to rapid shifts in the state of an ecosystem (\"regime shifts\"), which, even after the environment has returned to previous conditions, subsequently recovers slowly to the previous state (\"hysteresis\"). Large spatial and temporal scales of dynamics, and the lack of frameworks linking observations to models, are challenges to understanding and predicting ecosystem responses to perturbations. The naturally-occurring microecosystem inside leaves of the northern pitcher plant (Sarracenia purpurea) exhibits oligotrophic and eutrophic states that can be induced by adding insect prey. Here, we further develop a model for simulating these dynamics, parameterize it using data from a prey addition experiment and conduct a sensitivity analysis to identify critical zones within the parameter space. Simulations illustrate that the microecosystem model displays regime shifts and hysteresis. Parallel results were observed in the plant itself after experimental enrichment with prey. Decomposition rate of prey was the main driver of system dynamics, including the time the system remains in an anoxic state and the rate of return to an oxygenated state. Biological oxygen demand in fluenced the shape of the systems return trajectory. The combination of simulated results, sensitivity analysis and use of empirical results to parameterize the model more precisely demonstrates that the Sarracenia microecosystem model displays behaviors qualitatively similar to models of larger ecological systems.

ecology↗