Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Lineage diversification and morphological evolution in a large-scale continental radiation: The neotropical ovenbirds and woodcreepers (aves: furnariidae)

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution

Optical properties of polymeric materials for concentrator photovoltaic systems

a b s t r a c t As part of our research on materials for concentrator photovoltaics (CPV), we are evaluating the optical properties and solar radiation durability of a number of polymeric materials with potential in CPV applications. For optical materials in imaging or non-imaging optical systems, detailed knowledge of the wavelength-dependent complex index of refraction is important for system design and performance, yet optical properties for many polymeric systems are not available in the literature. Here we report the index of refraction, optical absorbance, haze, and Urbach edge analysis results of various polymers of interest for CPV systems. These values were derived from ellipsometry and from using a VUV-VASE and transmission based absorbance spectroscopy on thick film samples. Fluoropolymers such as poly(tetrafluoroethylene-co-hexafluoropropylene) (Teflon s FEP), poly(tetrafluoroethylene-co-perfluoropropyl vinyl ether) (Teflon s PFA) and poly(ethylene-co-tetrafluoroethylene) (Teflon s ETFE Film) have desirable optical and physical properties for optical applications in CPV. Ethylene backbone polymers such as polyvinylbutyral (PVB) sheet (e.g., DuPont TM PV5200), and ethylene co-polymers such as poly(ethylene-co-vinyl acetate) (EVA) (e.g., DuPont TM Elvax s PV1400), and poly(ethylene-co-methacrylic acid metal salt) ionomer sheet (e.g., DuPont TM PV5300) have applications as encapsulants in crystalline silicon (c-Si) and other flat plate PV applications. These materials are available with both a wide variety of polymer compositions and additive packages which affect their optical properties such as the UV absorption edge. Even materials such as DuPont's Kapton s polyimide films, which are used behind the PV cell for their electrically insulating properties, have optical requirements, and we have also characterized these materials. The detailed optical properties of these materials will be useful in the design of the geometrical optics of a CPV system and optimization of the system's optical throughput. This information will also provide insights into the system's optical absorption. This is important, for example in the UV, where this absorption can impact the radiation durability of the materials

The Evolution Of A Tropical Biodiversity Hotspot

The tropics are the source of most biodiversity yet inadequate sampling obscures answers to fundamental questions about how this diversity evolves. We leveraged samples assembled over decades of fieldwork to study diversification of the largest tropical bird radiation, the suboscine passerines. Our phylogeny, estimated using data from 2389 genomic regions in 1940 individuals of 1287 species, reveals that peak suboscine species diversity in the Neotropics is not associated with high recent speciation rates but rather with the gradual accumulation of species over time. Paradoxically, the highest speciation rates are in lineages from regions with low species diversity, which are generally cold, dry, unstable environments. Our results reveal a model in which species are forming faster in environmental extremes but have accumulated in moderate environments to form tropical biodiversity hotspots

Spreading the sparing: Against a limited-capacity account of the attentional blink.

The identification of the second of two targets presented in close succession is often impaired-a phenomenon referred to as the attentional blink. Extending earlier work (Di Lollo, Kawahara, Ghorashi, and Enns, in Psychological Research 69:191-200, 2005), the present study shows that increasing the number of targets in the stream can lead to remarkable improvements as long as there are no intervening distractors. In addition, items may even recover from an already induced blink whenever they are preceded by another target. It is shown that limited memory resources contribute to overall performance, but independent of the attentional blink. The findings argue against a limited-capacity account of the blink and suggest a strong role for attentional control processes that may be overzealously applied. © 2005 Springer-Verlag

Understanding within-session loss-chasing: an experimental investigation of the impact of stake size on cognitive control

Loss-chasing is a central feature of problematic gambling, yet it remains a poorly conceived and understood concept. Loss-chasing is believed to stem from an ero- sion of cognitive control when gambling. The opportunity to gamble at significantly dis- parate stake sizes on a gambling activity is considered to be a risk factor for loss-chasing. This study investigated the impact of gambling at disparate stake sizes on executive processes integral to maintaining cognitive control when gambling, namely response inhibition and reflection impulsivity. Frequent adult non-problem gamblers (n = 32) participated in a repeated measures experiment; and gambled at three disparate stake sizes (£20, £2 and no stake per bet) on a simulated gambling task. Participants’ response inhibition performance and reflection impulsivity levels after gambling at various stake sizes were compared via a go/no-go task and information sampling task, respectively. Quality of decision-making i.e. the evaluation of available information to make probability judgements was impaired after gambling at higher stakes in comparison to lower stakes, indicating an increase in reflection impulsivity. No effect on response inhibition was observed. Although exploratory, this suggests that the opportunity for participants to substantially increase stake size on a gambling activity may be a risk factor for impaired cognitive performance when gambling, and perhaps create vulnerability for within-session loss-chasing in some players. Keywords Problem gambling - Cognitive control - Loss-chasing - Response inhibition - Reflection impulsivit