The mismatch between current statistical practice and doctoral training in ecology

Ecologists are studying increasingly complex and important issues such as climate change and ecosystem services. These topics often involve large data sets and the application of complicated quantitative models. We evaluated changes in statistics used by ecologists by searching nearly 20,000 published articles in ecology from 1990 to 2013. We found that there has been a rise in sophisticated and computationally intensive statistical techniques such as mixed effects models and Bayesian statistics and a decline in reliance on approaches such as ANOVA or t tests. Similarly, ecologists have shifted away from software such as SAS and SPSS to the open source program R. We also searched the published curricula and syllabi of 154 doctoral programs in the United States and found that despite obvious changes in the statistical practices of ecologists, more than one-third of doctoral programs showed no record of required or optional statistics classes. Approximately one-quarter of programs did require a statistics course, but most of those did not cover contemporary statistical philosophy or advanced techniques. Only one-third of doctoral programs surveyed even listed an optional course that teaches some aspect of contemporary statistics. We call for graduate programs to lead the charge in improving training of future ecologists with skills needed to address and understand the ecological challenges facing humanity.ECU Open Access Publishing Support Fun

Interactions between competition and predation shape early growth and survival of two Neotropical hylid tadpoles [poster]

Background/Question/Methods Recent literature reviews reveal that competition typically has stronger effects on growth than the presence of predators, while predation has larger effects on survival. Further, past studies show that predators typically lessen the negative effect of competition on growth and also make interspecific competition beneficial for the survival of focal species. We examine the independent and combined effects of competition and predation for survival and growth of the tadpoles of two co-occurring Neotropical hylid frogs (Agalychnis callidryas and Dendropsophus ebraccatus). Our experiment crossed tadpole species composition (single and mixed at single total density) with the presence or absence of a free-roaming predator (Anax sp. dragonfly larva) using a 3x2 factorial design. Six replicates were conducted in 300 L mesocosms at the Smithsonian Tropical Research Center, Gamboa, Panama. Results/Conclusions Dragonfly larvae were effective predators of both species, but had larger effects on A. callidryas survival. A. callidryas grew faster in the presence of D. ebraccatus, suggesting it is a more effective competitor. A. callidryas reduced D. ebraccatus growth in the absence of dragonflies; however, this effect disappeared when predators were present. Though our results are largely consistent with similar previous studies, one interesting difference did emerge. Not only did predation have larger effects on survival than competition, but predator presence resulted in a much larger reduction in tadpole growth than competition – even though predation increased per capita resource levels. This can be attributed to either changes in feeding behavior or metabolic costs of alteration of phenotypically plastic traits. Thus, in our study, predator effects dominated survival and growth and highlight the importance of top-down effects, as well as costs associated with phenotypic plasticity, in shaping interactions between these species

Prey Responses to Predator Chemical Cues: Disentangling the Importance of the Number and Biomass of Prey Consumed

To effectively balance investment in predator defenses versus other traits, organisms must accurately assess predation risk. Chemical cues caused by predation events are indicators of risk for prey in a wide variety of systems, but the relationship between how prey perceive risk in relation to the amount of prey consumed by predators is poorly understood. While per capita predation rate is often used as the metric of relative risk, studies aimed at quantifying predator-induced defenses commonly control biomass of prey consumed as the metric of risk. However, biomass consumed can change by altering either the number or size of prey consumed. In this study we determine whether phenotypic plasticity to predator chemical cues depends upon prey biomass consumed, prey number consumed, or both. We examine the growth response of red-eyed treefrog tadpoles (Agalychnis callidryas) to cues from a larval dragonfly (Anax amazili). Biomass consumed was manipulated by either increasing the number of prey while holding individual prey size constant, or by holding the number of prey constant and varying individual prey size. We address two questions. (i) Do prey reduce growth rate in response to chemical cues in a dose dependent manner? (ii) Does the magnitude of the response depend on whether prey consumption increases via number or size of prey? We find that the phenotypic response of prey is an asymptotic function of prey biomass consumed. However, the asymptotic response is higher when more prey are consumed. Our findings have important implications for evaluating past studies and how future experiments should be designed. A stronger response to predation cues generated by more individual prey deaths is consistent with models that predict prey sensitivity to per capita risk, providing a more direct link between empirical and theoretical studies which are often focused on changes in population sizes not individual biomass

Estimating female malaria mosquito age by quantifying Y-linked genes in stored male spermatozoa

Vector control strategies are among the most effective measures to combat mosquito-borne diseases, such as malaria. These strategies work by altering the mosquito age structure through increased mortality of the older female mosquitoes that transmit pathogens. However, methods to monitor changes to mosquito age structure are currently inadequate for programmatic implementation. Female mosquitoes generally mate a single time soon after emergence and draw down spermatozoa reserves with each oviposition cycle. Here, we demonstrate that measuring spermatozoa quantity in female Anopheles mosquitoes is an effective approach to assess mosquito age. Using multiplexed qPCR targeted at male spermatozoa, we show that Y-linked genes in female mosquitoes are exclusively found in the spermatheca, the organ that houses spermatozoa, and the quantity of these gene sequences significantly declines with age. The method can accurately identify mosquitoes more than 10 days old and thus old enough to potentially transmit pathogens harbored in the salivary glands during blood feeding. Furthermore, mosquito populations that differ by 10% in daily survivorship have a high likelihood of being distinguished using modest sample sizes, making this approach scalable for assessing the efficacy of vector intervention control programs

Data from: A treefrog with reproductive mode plasticity reveals a changing balance of selection for non-aquatic egg-laying

Non-aquatic reproduction has evolved repeatedly, but the factors that select for laying eggs on land are not well understood. The treefrog Dendropsophus ebraccatus has plasticity in reproductive mode, laying eggs that successfully develop in or out of water. This permits the first experimental comparison of the selective agents that shape adult oviposition behavior and embryo developmental capacity. I quantified the sources and strength of arboreal and aquatic egg mortality, how mortality varies with weather patterns, and assessed 39 years of daily rainfall patterns to infer historic levels of egg mortality and effects of climate change on the selective balance between aquatic and non-aquatic egg deposition. Aquatic predators and desiccation were the strongest selective agents in water and air, respectively. Egg mortality varied with weather such that aquatic oviposition was advantageous when rainfall was low, but laying eggs out of water increased survival when rainfall was high. Additionally, I found that since 1972 there have been significant changes in the patterns of rainfall in central Panama, which has altered the selective landscape acting on egg-laying behavior. This work provides insight into both the evolution and maintenance of adaptive phenotypic plasticity as well as historic and current selection on reproduction

Predation and Competition Differentially Affect the Interactions and Trophic Niches of a Neotropical Amphibian Guild

Competition and predation alter individual traits of organisms, and these effects can scale-up to have consequences on community structure and dynamics. The relative importance of competition and predation will depend largely on the local assemblage of species, the type of predators, or the degree of niche segregation. We experimentally investigated the interplay of competition and predation on the structure and trophic level (measured via stable isotope analysis) of a seven-species Neotropical freshwater guild using a mesocosm approach in central Panama. We tested the effect of two types of predators (dragonfly nymphs or adult water bugs) in combination with the presence/absence of a common competitor, the red-eyed treefrog (Agalychnis callidryas), on four core species of tadpoles. We also distinguished between consumptive and non-consumptive effects of each type of predator by presenting them to tadpoles caged or freely roaming. Dragonfly larvae were more efficient predators than water bugs, but these effects were not uniform for all tadpole species. All amphibian species grew bigger when raised in the presence of an uncaged dragonfly nymph, presumably due to reduced competition through thinning, but tadpoles were smaller when exposed to caged dragonfly nymphs indicating the existence of non-consumptive predator effects as well. Predator presence also altered the relative trophic position of the different amphibian species, causing some tadpole species to increase and others to decrease their trophic status. Despite the presumed ecological similarity of tadpole species in the guild, the interplay of competition and predation had varying effects on the trophic status of nearly every species. Our results indicate that community composition can greatly affect the trophic level of larval amphibians, and that predation may have a greater role than competition in structuring Neotropical larval amphibian guilds

TadPlast

Morphological and tail color measurements for 969 Dendropsophus ebraccatus tadpoles raised in one of three predator treatments (fish cues, insect cues or no predator cues [control]). See ReadMe file for a description of the variables

TadPlast.Model_Selection

Code to conduct 'animal models' to estimate sources of additive and non-additive genetic variation. Analyses are Bayesian mixed effects models run in the function MCMCglmm

TadPlast.resample_functions

Code to run bivariate animal models to calculate genetic correlations between the plastic response of families to either insect predation cues or fish predation cues. The code runs a custom function which 1) first randomly sample the degree of plasticity for a given trait, then 2) run the bivariate model to estimate heritability and genetic correlation of plasticity

TadPlast.bivariate_models

Code to run bivariate animal models to calculate genetic correlations between different pairs of aspects of the phenotype of Dendropsophus ebraccatus tadpoles raised in one of three predator treatments for 10 days. The code runs a simple custom function which calculates every pairwise combination of 10 different aspects of the phenotype