The Dynamics Of Introgression Across An Avian Radiation

Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson\u27s D-statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur

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)

In pursuit of the dynamic optimality conjecture

In 1985, Sleator and Tarjan introduced the splay tree, a self-adjusting binary search tree algorithm. Splay trees were conjectured to perform within a constant factor as any offline rotation-based search tree algorithm on every sufficiently long sequence---any binary search tree algorithm that has this property is said to be dynamically optimal. However, currently neither splay trees nor any other tree algorithm is known to be dynamically optimal. Here we survey the progress that has been made in the almost thirty years since the conjecture was first formulated, and present a binary search tree algorithm that is dynamically optimal if any binary search tree algorithm is dynamically optimal.Comment: Preliminary version of paper to appear in the Conference on Space Efficient Data Structures, Streams and Algorithms to be held in August 2013 in honor of Ian Munro's 66th birthda

Systematics, biogeography, and diversification of Scytalopus tapaculos (Rhinocryptidae), an enigmatic radiation of Neotropical montane birds

Copyright © American Ornithological Society 2020. All rights reserved. For permissions, e-mail: [email protected]. We studied the phylogeny, biogeography, and diversification of suboscine passerines in the genus Scytalopus (Rhinocryptidae), a widespread, species-rich, and taxonomically challenging group of Neotropical birds. We analyzed nuclear (exons, regions flanking ultraconserved elements) and mitochondrial (ND2) DNA sequence data for a taxonomically and geographically comprehensive sample of specimens collected from Costa Rica to Patagonia and Brazil. We found that Scytalopus is a monophyletic group sister to Eugralla and consists of 3 main clades roughly distributed in (1) the Southern Andes, (2) eastern Brazil, and (3) the Tropical Andes and Central America. The clades from the Southern Andes and eastern Brazil are sister to each other. Despite their confusing uniformity in plumage coloration, body shape, and overall appearance, rates of species accumulation through time in Scytalopus since the origin of the clade in the Late Miocene are unusually high compared with those of other birds, suggesting rapid non-adaptive diversification in the group. We attribute this to their limited dispersal abilities making them speciation-prone and their occurrence in a complex landscape with numerous barriers promoting allopatric differentiation. Divergence times among species and downturns in species accumulation rates in recent times suggest that most speciation events in Scytalopus predate climatic oscillations of the Pleistocene. Our analyses identified various cases of strong genetic structure within species and lack of monophyly of taxa, flagging populations which likely merit additional study to clarify their taxonomic status. In particular, detailed analyses of species limits are due in S. parvirostris, S. latrans, S. speluncae, the S. atratus complex, and the Southern Andes clade

On the role of goal relevance in emotional attention: Disgust evokes early attention to cleanliness

Prior evidence has shown that aversive emotional states are characterised by an attentional bias towards aversive events. The present study investigated whether aversive emotions also bias attention towards stimuli that represent means by which the emotion can be alleviated. We induced disgust by having participants touch fake disgusting objects. Participants in the control condition touched nondisgusting objects. The results of a subsequent dot-probe task revealed that attention was oriented to disgusting pictures irrespective of condition. However, participants in the disgust condition also oriented towards pictures representing cleanliness. These findings suggest that the deployment of attention in aversive emotional states is not purely stimulus driven but is also guided by the goal to alleviate this emotional state

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

Impact of Community-Based Larviciding on the Prevalence of Malaria Infection in Dar es Salaam, Tanzania.

The use of larval source management is not prioritized by contemporary malaria control programs in sub-Saharan Africa despite historical success. Larviciding, in particular, could be effective in urban areas where transmission is focal and accessibility to Anopheles breeding habitats is generally easier than in rural settings. The objective of this study is to assess the effectiveness of a community-based microbial larviciding intervention to reduce the prevalence of malaria infection in Dar es Salaam, United Republic of Tanzania. Larviciding was implemented in 3 out of 15 targeted wards of Dar es Salaam in 2006 after two years of baseline data collection. This intervention was subsequently scaled up to 9 wards a year later, and to all 15 targeted wards in 2008. Continuous randomized cluster sampling of malaria prevalence and socio-demographic characteristics was carried out during 6 survey rounds (2004-2008), which included both cross-sectional and longitudinal data (N = 64,537). Bayesian random effects logistic regression models were used to quantify the effect of the intervention on malaria prevalence at the individual level. Effect size estimates suggest a significant protective effect of the larviciding intervention. After adjustment for confounders, the odds of individuals living in areas treated with larviciding being infected with malaria were 21% lower (Odds Ratio = 0.79; 95% Credible Intervals: 0.66-0.93) than those who lived in areas not treated. The larviciding intervention was most effective during dry seasons and had synergistic effects with other protective measures such as use of insecticide-treated bed nets and house proofing (i.e., complete ceiling or window screens). A large-scale community-based larviciding intervention significantly reduced the prevalence of malaria infection in urban Dar es Salaam