Maximizing ecological and evolutionary insight in bisulfite sequencing data sets.

Genome-scale bisulfite sequencing approaches have opened the door to ecological and evolutionary studies of DNA methylation in many organisms. These approaches can be powerful. However, they introduce new methodological and statistical considerations, some of which are particularly relevant to non-model systems. Here, we highlight how these considerations influence a study's power to link methylation variation with a predictor variable of interest. Relative to current practice, we argue that sample sizes will need to increase to provide robust insights. We also provide recommendations for overcoming common challenges and an R Shiny app to aid in study design.

Behavioral Plasticity and the Origins of Novelty: The Evolution of the Rattlesnake Rattle.

Environmentally induced behavior (behavioral plasticity) has long been hypothesized to promote the origins of novel morphological traits, but this idea remains controversial. One context in which this hypothesis can be evaluated is animal communication, where behavior and morphology are often linked. Here, we examined the evolution of one of nature's most spectacular communication signals: the rattlesnake rattle. We specifically evaluated whether rattlesnake rattling behavior-and, hence, the rattle-originated from a simple behavior: vibrating the tail when threatened. By reconstructing the ancestral state of defensive tail vibration, we show that this behavior is nearly ubiquitous in the Viperidae (the family that includes rattlesnakes) and widespread in the Colubridae (the largest snake family, nearly all of which are nonvenomous), suggesting a shared origin for the behavior between these families. After measuring tail vibration in 56 species of Viperidae and Colubridae, we show that the more closely related a species was to rattlesnakes, the more similar it was to rattlesnakes in duration and rate of tail vibration. Thus, the rattlesnake rattle might have evolved via elaboration of a simple behavior. These data thereby support the long-standing hypothesis that behavioral plasticity often precedes-and possibly instigates-the evolution of morphological novelty.

Mainland size variation informs predictive models of exceptional insular body size change in rodents.

The tendency for island populations of mammalian taxa to diverge in body size from their mainland counterparts consistently in particular directions is both impressive for its regularity and, especially among rodents, troublesome for its exceptions. However, previous studies have largely ignored mainland body size variation, treating size differences of any magnitude as equally noteworthy. Here, we use distributions of mainland population body sizes to identify island populations as 'extremely' big or small, and we compare traits of extreme populations and their islands with those of island populations more typical in body size. We find that although insular rodents vary in the directions of body size change, 'extreme' populations tend towards gigantism. With classification tree methods, we develop a predictive model, which points to resource limitations as major drivers in the few cases of insular dwarfism. Highly successful in classifying our dataset, our model also successfully predicts change in untested cases.

Unravelling the determinants of insular body size shifts.

The island rule, a pattern of size shifts on islands, is an oft-cited but little understood phenomenon of evolutionary biology. Here, we explore the evolutionary mechanisms behind the rule in 184 mammal species, testing climatic, ecological and phylogenetic hypotheses in a robust quantitative framework. Our findings confirm the importance of species' ecological traits in determining both the strength and the direction of body size changes on islands. Although the island rule pattern appears relatively weak overall, we find strongest support for models incorporating trait, climatic and geographical factors in a phylogenetic context, lending support to the idea that the island rule is a complex phenomenon driven by interacting intrinsic and extrinsic mechanisms. Overall, we find that different clades may be evolutionarily predisposed to dwarfism or gigantism, but the magnitude of size changes depends more on adaptation to the novel island environment.

Classification tree methods provide a multifactorial approach to predicting insular body size evolution in rodents.

Many hypotheses have been proposed to explain size changes in insular mammals, but no single variable suffices to explain the diversity of responses, particularly within Rodentia. Here in a data set on insular rodents, we observe strong consistency in the direction of size change within islands and within species but (outside of Heteromyidae) little consistency at broader taxonomic scales. Using traits of islands and of species in a classification tree analysis, we find the most important factor predicting direction of change to be mainland body mass (large rodents decrease, small ones increase); other variables (island climate, number of rodent species, and area) were significant, although their roles as revealed by the classification tree were context dependent. Ecological interactions appear relatively uninformative, and on any given island, the largest and smallest rodent species converged or diverged in size with equal frequency. Our approach provides a promising framework for continuing examination of insular body size evolution.

Fluticasone and food allergen elimination reverse sub-epithelial fibrosis in children with eosinophilic esophagitis.

BACKGROUND: Symptoms of vomiting and dysphagia in children with eosinophilic esophagitis may be related to the development of mucosal fibrosis. AIM: Our aims were to (1) investigate esophageal fibrosis in children with EoE compared to patients with gastroesophageal reflux disease and normal individuals, and (2) to assess the degree of mucosal fibrosis in patients with EoE before and after medical treatment. METHODS: A retrospective analysis of esophageal biopsies from patients with EoE, GERD, and normal mucosa was performed. Demographic data, clinical information, eosinophil number, and sub-epithelial fibrosis was compared among the groups. A similar comparison was performed in EoE patients, before and after therapy. RESULTS: Esophageal biopsies from 53 children were included, of which 17 with EoE, 17 GERD, and 19 were normal. A significantly higher number of eosinophils and greater fibrosis was found in EoE patients vs. GERD and normal (fibrosis grade 2: 13 patients in the EoE group vs. one patient for each control group; p=0.0001). After therapy, a significant decrease in fibrosis and eosinophils number was noted in EoE patients [fibrosis grade 2: 10 (71.5%) patients vs. one (7.1%) patient, and eosinophil count was 35.5/HPF vs. 13.4/HPF, pre- and post-therapy, respectively; p<0.05]. The decrease in esophageal fibrosis paralleled the improvement in the related clinical symptoms. CONCLUSION: A higher degree of esophageal fibrosis was found in patients with EoE compared to GERD or normal esophagus. Conventional therapy in EoE improved obstructive symptoms, decreased eosinophils count, and reversed the degree of fibrosis. We suggest that appropriate therapy in patients with EoE will improve clinical symptoms and histology.

Eosinophilic esophagitis disease in children from West Virginia: a review of the last decade (1995-2004).

BACKGROUND: Eosinophilic esophagitis (EoE) is a newly established disease in adults and children. The incidence and prevalence of the disease among children from the United States are largely unknown. We examined the endoscopy reports of children who attended our gastroenterology clinic in the last 10 yr. MATERIALS A AND METHODS: retrospective review of all diagnostic upper endoscopy procedures was executed between 1995-2004, of which a quarter (25%) per each year was randomly selected for pathological reevaluation of the number of Eos. The diagnosis of EoE was established when higher than 15 Es/hpf was detected in the esophageal biopsy; and the prevalence of EoE was calculated. The clinical symptoms, endoscopic presentation, and treatment of the patients with EoE disease were also reviewed. RESULTS: A total of 1,424 procedures were reviewed, of which 355 esophageal samples were reevaluated. During the study period, 44 patients were diagnosed with EoE. The prevalence rate of EoE disease was 0.73/10,000 children during the study period. Similar results were found when the number of Eos was established at >20 Es/hpf. Abdominal pain (55%), vomiting (43%), and heartburn (39%) were the most common symptoms, and characteristic mucosal appearance was found in only 11% of the patients. CONCLUSION: The rate of EoE in our pediatric patient population is low. Prospective studies are needed to establish the incident and prevalence of EoE disease in children living in the United States.