An assessment of sampling biases across studies of diel activity patterns in marine ray-finned fishes (Actinopterygii)

Author Posting. © University of Miami - Rosenstiel School of Marine and Atmospheric Science, 2016. This article is posted here by permission of University of Miami - Rosenstiel School of Marine and Atmospheric Science for personal use, not for redistribution. The definitive version was published in Bulletin of Marine Science 93 (2017): 611-639, doi:10.5343/bms.2016.1016.Understanding the promotion and regulation of circadian rhythms in marine fishes is important for studies spanning conservation, evolutionary biology, and physiology. Given numerous challenges inherent to quantifying behavioral activity across the full spectrum of marine environments and fish biodiversity, case studies offer a tractable means of gaining insights or forecasting broad patterns of diel activity. As these studies continue to accumulate, assessing whether, and to what extent, the cumulatively collected data are biased in terms of geography, habitat, or taxa represents a fundamentally important step in the development of a broad overview of circadian rhythms in marine fish. As such investigations require a phylogenetic framework, general trends in the phylogenetic sampling of marine fishes should be simultaneously assessed for biases in the sampling of taxa and trait data. Here, we compile diel activity data for more than 800 marine species from more than five decades of scientific studies to assess general patterns of bias. We found significant geographic biases that largely reflect a preference toward sampling warm tropical waters. Additionally, taxonomic biases likewise reflect a tendency toward conspicuous reef associated clades. Placing these data into a phylogenetic framework that includes all known marine fishes revealed significant under-dispersion of behavioral data and taxon sampling across the whole tree, with a few subclades exhibiting significant over-dispersion. In total, our study illuminates substantial gaps in our understanding of diel activity patterns and highlights significant sampling biases that have the potential to mislead evolutionary or ecological analyses.Partial funding was provided by the North Carolina Museum of Natural Sciences

RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses

Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets. RWTY is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface.This work was funded in part by Australian Research Council fellowship awards to D.L.W. and R.L

The effects of climate change on Australia’s only endemic Pokémon: Measuring bias in species distribution models

1. Species distribution models (SDMs) are frequently used to predict the effects of climate change on species of conservation concern. Biases inherent in the process of constructing SDMs and transferring them to new climate scenarios may result in undesirable conservation outcomes. We explore these issues and demonstrate new methods to estimate biases induced by the design of SDM studies. We present these methods in the context of estimating the effects of climate change on Australia\u27s only endemic Pokémon.2. Using a citizen science dataset, we build species distribution models for Garura kangaskhani to predict the effects of climate change on the suitability of habitat for the species. We demonstrate a novel Monte Carlo procedure for estimating the biases implicit in a given study design, and compare the results seen for Pokémon to those seen from our Monte Carlo tests as well as previous studies in the same region using both simulated and real data.3. Our models suggest that climate change will impact the suitability of habitat for G. kangaskhani, which may compound the effects of threats such as habitat loss and their use in blood sport. However, we also find that using SDMs to estimate the effects of climate change can be accompanied by biases so strong that the data themselves have minimal impact on modelling outcomes. 4. We show that the direction and magnitude of bias in estimates of climate change impacts are affected by every aspect of the modelling process, and suggest that bias estimates should be included in future studies of this type. Given the widespread use of SDMs, systemic biases could have substantial financial and opportunity costs. By demonstrating these biases and presenting a novel statistical tool to estimate them, we hope to provide a more secure future for G. kangaskhani and the rest of the world\u27s biodiversity

The squirrel is in the detail: Anatomy and morphometry of the tail in Sciuromorpha (Rodentia, Mammalia)

In mammals, the caudal vertebrae are certainly among the least studied elements of their skeleton. However, the tail plays an important role in locomotion (e.g., balance, prehensility) and behavior (e.g., signaling). Previous studies largely focused on prehensile tails in Primates and Carnivora, in which certain osteological features were selected and used to define tail regions (proximal, transitional, distal). Interestingly, the distribution pattern of these anatomical characters and the relative proportions of the tail regions were similar in both orders. In order to test if such tail regionalization can be applied to Rodentia, we investigated the caudal vertebrae of 20 Sciuridae and six Gliridae species. Furthermore, we examined relationships between tail anatomy/morphometry and locomotion. The position of selected characters along the tail was recorded and their distribution was compared statistically using Spearman rank correlation. Vertebral body length (VBL) was measured to calculate the proportions of each tail region and to perform procrustes analysis on the shape of relative vertebral body length (rVBL) progressions. Our results show that tail regionalization, as defined for Primates and Carnivora, can be applied to almost all investigated squirrels, regardless of their locomotor category. Moreover, major locomotor categories can be distinguished by rVBL progression and tail region proportions. In particular, the small flying squirrels Glaucomys volans and Hylopetes sagitta show an extremely short transitional region. Likewise, several semifossorial taxa can be distinguished by their short distal region. Moreover, among flying squirrels, Petaurista petaurista shows differences with the small flying squirrels, mirroring previous observations on locomotory adaptations based on their inner ear morphometry. Our results show furthermore that the tail region proportions of P. petaurista, phylogenetically more basal than the small flying squirrels, are similar to those of bauplan-conservative arboreal squirrels

Conclusions about Niche Expansion in Introduced Impatiens walleriana Populations Depend on Method of Analysis

Determining the degree to which climate niches are conserved across plant species' native and introduced ranges is valuable to developing successful strategies to limit the introduction and spread of invasive plants, and also has important ecological and evolutionary implications. Here, we test whether climate niches differ between native and introduced populations of Impatiens walleriana, globally one of the most popular horticultural species. We use approaches based on both raw climate data associated with occurrence points and ecological niche models (ENMs) developed with Maxent. We include comparisons of climate niche breadth in both geographic and environmental spaces, taking into account differences in available habitats between the distributional areas. We find significant differences in climate envelopes between native and introduced populations when comparing raw climate variables, with introduced populations appearing to expand into wetter and cooler climates. However, analyses controlling for differences in available habitat in each region do not indicate expansion of climate niches. We therefore cannot reject the hypothesis that observed differences in climate envelopes reflect only the limited environments available within the species' native range in East Africa. Our results suggest that models built from only native range occurrence data will not provide an accurate prediction of the potential for invasiveness if applied to areas containing a greater range of environmental combinations, and that tests of niche expansion may overestimate shifts in climate niches if they do not control carefully for environmental differences between distributional areas

Disentangling the influence of urbanization and invasion on endemic geckos in tropical biodiversity hot spots : a case study of Phyllodactylus martini (Squamata: Phyllodactylidae) along an Urban Gradient in Curaçao

Author Posting. © Peabody Museum of Natural History, 2016. This article is posted here by permission of Peabody Museum of Natural History for personal use, not for redistribution. The definitive version was published in Bulletin of the Peabody Museum of Natural History 57(2016): 147–164, doi:10.3374/014.057.0209.Predicting the response of endemic species to urbanization has emerged as a fundamental challenge in 21st century conservation biology. The factors that underlie population declines of reptiles are particularly nebulous, as these are often the least understood class of vertebrates in a given community. In this study, we assess correlations between feeding ecology and phenotypic traits of the Lesser Antillean endemic Dutch leaf-toed gecko, Phyllodactylus martini, along an urban gradient in the Caribbean island of Curaçao. There has been a marked decline of this species in developed habitats associated with the invasive tropical house gecko Hemidactylus mabouia. We find a correlation between aspects of locomotor morphology and prey in undeveloped habitats that is absent in developed habitats. Analyses of stomach contents further suggest that Phyllodactylus martini alters primary prey items in developed areas. However, changes in prey promote the overlap in foraging niches between Phyllodactylus martini and Hemidactylus mabouia, suggesting that direct resource competition is contributing to the decline of Phyllodactylus martini. In addition to competitive exclusion, we suggest that the urban extirpation of Phyllodactylus martini could also be attributed to a top-down control on population growth by Hemidactylus mabouia. Colonizations of walls put Phyllodactylus martini in direct contact with Hemidactylus mabouia increasing the chances for predation events, as evidenced by our observation of a predation event on a Phyllodactylus martini juvenile by an adult Hemidactylus mabuoia. In total, our results add to a growing body of literature demonstrating the threat that invasive synanthropic reptiles pose to endemics that might otherwise be able to cope with increased urbanization pressures

Reevaluating claims of ecological speciation in Halichoeres bivittatus

Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep divergence in a single mitochondrial locus between the northern and southern Gulf of Mexico, combined with a finding that these two haplotypes were associated with different habitat types (“tropical” vs. “subtropical”) in the Florida Keys and Bermuda, where they overlap. Here, we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study. We find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations in the Keys. These results undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. Future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences

ENMTools 1.0: an R package for comparative ecological biogeography

The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionality was later added for model selection and simulation from ENMs, and the software package has been quite widely used. ENMTools was initially implemented as a Perl script, which was also compiled into an executable file for various platforms. However, the package had a number of significant limitations; it was only designed to fit models using Maxent, it relied on a specific Perl distribution to function, and its internal structure made it difficult to maintain and expand. Subsequently, the R programming language became the platform of choice for most ENM studies, making ENMTools less usable for many practitioners. Here we introduce a new R version of ENMTools that implements much of the functionality of its predecessor as well as numerous additions that simplify the construction, comparison and evaluation of niche models. These additions include new metrics for model fit, methods of measuring ENM overlap, and methods for testing evolutionary hypotheses. The new version of ENMTools is also designed to work within the expanding universe of R tools for ecological biogeography, and as such includes greatly simplified interfaces for analyses from several other R packages

The Rapidly Flaring Afterglow of the Very Bright and Energetic GRB 070125

We report on multi-wavelength observations, ranging from the X-ray to radio wave bands, of the IPN-localized gamma-ray burst GRB 070125. Spectroscopic observations reveal the presence of absorption lines due to O I, Si II, and C IV, implying a likely redshift of z = 1.547. The well-sampled light curves, in particular from 0.5 to 4 days after the burst, suggest a jet break at 3.7 days, corresponding to a jet opening angle of ~7.0 degrees, and implying an intrinsic GRB energy in the 1 - 10,000 keV band of around E = (6.3 - 6.9)x 10^(51) erg (based on the fluences measured by the gamma-ray detectors of the IPN network). GRB 070125 is among the brightest afterglows observed to date. The spectral energy distribution implies a host extinction of Av < 0.9 mag. Two rebrightening episodes are observed, one with excellent time coverage, showing an increase in flux of 56% in ~8000 seconds. The evolution of the afterglow light curve is achromatic at all times. Late-time observations of the afterglow do not show evidence for emission from an underlying host galaxy or supernova. Any host galaxy would be subluminous, consistent with current GRB host-galaxy samples. Evidence for strong Mg II absorption features is not found, which is perhaps surprising in view of the relatively high redshift of this burst and the high likelihood for such features along GRB-selected lines of sight.Comment: 50 pages, 9 figures, 5 tables Accepted to the Astrophysical Journa

Lifespan extension and the doctrine of double effect

Recent developments in biogerontology—the study of the biology of ageing—suggest that it may eventually be possible to intervene in the human ageing process. This, in turn, offers the prospect of significantly postponing the onset of age-related diseases. The biogerontological project, however, has met with strong resistance, especially by deontologists. They consider the act of intervening in the ageing process impermissible on the grounds that it would (most probably) bring about an extended maximum lifespan—a state of affairs that they deem intrinsically bad. In a bid to convince their deontological opponents of the permissibility of this act, proponents of biogerontology invoke an argument which is grounded in the doctrine of double effect. Surprisingly, their argument, which we refer to as the ‘double effect argument’, has gone unnoticed. This article exposes and critically evaluates this ‘double effect argument’. To this end, we first review a series of excerpts from the ethical debate on biogerontology in order to substantiate the presence of double effect reasoning. Next, we attempt to determine the role that the ‘double effect argument’ is meant to fulfil within this debate. Finally, we assess whether the act of intervening in ageing actually can be justified using double effect reasoning