Interpreting the γ Statistic in Phylogenetic Diversification Rate Studies: A Rate Decrease Does Not Necessarily Indicate an Early Burst

Background Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the γ statistic. Methodology Using simulations under varying conditions, I examine the sensitivity of γ to the distribution of the most recent branching times. Using an exploratory data analysis tool for lineages through time plots, tree deviation, I identified trees with a significant γ statistic that do not appear to have the characteristic early accumulation of lineages consistent with an early, rapid rate of cladogenesis. I further investigated the sensitivity of the γ statistic to recent diversification by examining the consequences of failing to simulate the full time interval following the most recent cladogenic event. The power of γ to detect rate decrease at varying times was assessed for simulated trees with an initial high rate of diversification followed by a relatively low rate. Conclusions The γ statistic is extraordinarily sensitive to recent diversification rates, and does not necessarily detect early bursts of diversification. This was true for trees of various sizes and completeness of taxon sampling. The γ statistic had greater power to detect recent diversification rate decreases compared to early bursts of diversification. Caution should be exercised when interpreting the γ statistic as an indication of early, rapid diversification

Selaginella and the Satyr: Euptychia westwoodi (Lepidoptera: Nymphalidae) Oviposition Preference and Larval Performance

Members of the plant genus Selaginella (de Beauvois 1805) have few known insect herbivores even though they are considered by some to be ‘living fossils’, with extant taxa virtually indistinguishable from 300 Mya fossils. Butterflies are well-known herbivores, and the satyrs are among the most speciose of them despite having radiated ∼35 Mya ago. Nearly all satyrs feed on grass or sedges, but members of the Neotropical genus Euptychia Hübner 1818 feed on Selaginella; little is known about the degree to which this butterfly favors this ancient plant over those that its close relatives utilize. To advance our knowledge of Euptychia natural history, we conducted a series of experiments to examine oviposition preference and growth rates across a series of potential host plants on a Euptychia westwoodi population in Costa Rica. We found that Euptychia westwoodi Butler 1867 exhibit a strong preference to oviposit on Selaginella eurynota over the sympatric Selaginella arthritica, though they perform equally well as larvae on both plants. We did not observe oviposition on a sympatric grass that is commonly consumed by close relatives of E. westwoodi, and when larvae were offered the grass they refused to eat. These results suggest thatE. westwoodi in Costa Rica exhibit a strong preference for Selaginella and may have lost the ability to feed on a locally abundant grass commonly used by other Satyrinae

A complete record from colonization to extinction reveals density dependence and the importance of winter conditions for a population of the silvery blue, Glaucopsyche lygdamus.

Butterflies in the family Lycaenidac are often the focus of conservation efforts. However, our understanding of lycaenid population dynamics has been limited to relatively few examples of long-term monitoring data that have been reported. Here, factors associated with population regulation are investigated using a complete record of a single population of the silvery blue, Glaucopsyche lygdamus Doubleday (Lepidoptera: Lycaenidae). Adults of G. lygdamus were first observed in an annual grassland near Davis, California, in 1982 and were last seen in 2003. Relationships between inter-annual variation in abundance and climatic variables were examined, accounting for density dependent effects. Significant effects of both negative density dependence and climatic variation were detected, particularly precipitation and temperature during winter months. Variation in precipitation, the strongest predictor of abundance, was associated directly and positively with butterfly abundance in the same year. Winter temperatures had a negative effect in the same year, but had a lagged, positive effect on abundance in the subsequent year. Mechanistic hypotheses are posed that include climatic effects mediated through both larval and adult plant resources

Not all toxic butterflies are toxic: high intra- and interspecific variation in sequestration in subtropical swallowtails

Many herbivorous insects make use of plant secondary metabolites by consuming and storing these toxic compounds in their body tissue or integument, thereby obtaining chemical defense against their natural enemies. Swallowtail butterflies in the tribe Troidini (Papilionidae) sequester toxic alkaloids (aristolochic acids, AAs) from their host plants in the genus Aristolochia. Troidine butterflies have been a model group for development of theory on host plant chemical sequestration, but most studies on this group have been limited to a single species in North America. These studies have led, in part, to the paradigm that troidine butterflies are toxic, thereby explaining the numerous mimicry relationships that exist throughout most of their range. Herein, we present one of the first comparative studies in a single location of a community of troidine butterflies. We examined the AA content of five co-occurring troidine butterfly species and their two Aristolochia host plants. We found that one Aristolochia species, A. triangularis, was preferred in choice assays and did not possess quantifiable levels of AA. We also found that most troidine butterflies did not possess quantifiable levels of AAs, but larvae have the ability to sequester AAs when it is present in their diet. A larval preference experiment showed that host plant AA concentration did not influence larval feeding choice. A performance experiment showed that higher levels of AAs in the diet increased larval mortality, which might indicate a cost associated with sequestration of the chemical defense and also might shed some light on why so many troidine butterflies in this community have little or no AAs. We propose that automimicry might be operating in this system and many putative models of this paradigmatic system might not possess plant-derived defensive chemistry

iteRates: An R Package for Implementing a Parametric Rate Comparison on Phylogenetic Trees

Patterns of diversification rate variation detected in phylogenetic hypotheses are frequently used to infer historical, ecological, and evolutionary processes. The parametric rate comparison (PRC) is a method for detecting rate variation in trees that models branch lengths as random variables drawn from familiar statistical distributions. iteRates is a library of functions for the R statistical computing environment for implementing PRC on phylogenetic trees. Here, we describe some of the functions in iteRates for subtree identification, tree manipulation, applying the PRC and K-clades PRC analyses, and conducting a whole-tree randomization test

Temporal diversification of Central American cichlids

<p>Abstract</p> <p>Background</p> <p>Cichlid fishes are classic examples of adaptive radiation because of their putative tendency to explosively diversify after invading novel environments. To examine whether ecological opportunity increased diversification (speciation minus extinction) early in a species-rich cichlid radiation, we determined if Heroine cichlids experienced a burst of diversification following their invasion of Central America.</p> <p>Results</p> <p>We first reconstructed the Heroine phylogeny and determined the basal node to use as the root of Central American Heroine diversification. We then examined the influence of incomplete taxon sampling on this group's diversification patterns. First, we added missing species randomly to the phylogeny and assessed deviations from a constant rate of lineage accumulation. Using a range of species numbers, we failed to recover significant deviations from a pure-birth process and found little support for an early burst of diversification. Then, we examined patterns of lineage accumulation as nodes were increasingly truncated. We assumed that as we removed more recently diverged lineages that sampling would become more complete thereby increasing the power to detect deviations from a pure-birth model. However, truncation of nodes provided even less support for an early burst of diversification.</p> <p>Conclusions</p> <p>Contrary to expectations, our analyses suggest Heroine cichlids did not undergo a burst of diversification when they invaded from South America. Throughout their history in Central America, Heroine cichlids appear to have diversified at a constant rate.</p

A Hierarchical Bayesian Approach to Ecological Count Data: A Flexible Tool for Ecologists

Many ecological studies use the analysis of count data to arrive at biologically meaningful inferences. Here, we introduce a hierarchical Bayesian approach to count data. This approach has the advantage over traditional approaches in that it directly estimates the parameters of interest at both the individual-level and population-level, appropriately models uncertainty, and allows for comparisons among models, including those that exceed the complexity of many traditional approaches, such as ANOVA or non-parametric analogs. As an example, we apply this method to oviposition preference data for butterflies in the genus Lycaeides. Using this method, we estimate the parameters that describe preference for each population, compare the preference hierarchies among populations, and explore various models that group populations that share the same preference hierarchy

Measuring Individual-Level Resource Specialization

Many apparently generalized species are in fact composed of individual specialists that use a small subset of the population’s resource distribution. Niche variation is usually established by testing the null hypothesis that individuals draw from a common resource distribution. This approach encourages a publication bias in which negative results are rarely reported, and obscures variation in the degree of individual specialization, limiting our ability to carry out comparative studies of the causes or consequences of niche variation. To facilitate studies of the degree of individual specialization, this paper outlines four quantitative indices of intrapopulation variation in resource use. Traditionally, such variation has been measured by partitioning the population’s total niche width into within- and between-individual, sex, or phenotype components. We suggest two alternative measures that quantify the mean resource overlap between an individual and its population, and we discuss the advantages and disadvantages of all four measures. The utility of all indices depends on the quality of the empirical data. If resources are measured in a coarse-grained manner, individuals may falsely appear generalized. Alternatively, specialization may be overestimated by cross-sectional sampling schemes where diet variation can reflect a patchy environment. Isotope ratios, parasites, or diet–morphology correlations can complement cross-sectional data to establish temporal consistency of individual specialization

Recent Hybrids Recapitulate Ancient Hybrid Outcomes

Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z chromosome in both the old and contemporary hybrids. The same pattern of reduced L. melissa ancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in old or ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection and recombination affect hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown