Lateral transfer in Stochastic Dollo models

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the data as the histories of affected traits are mosaics of the overall phylogeny. We control for the effect of lateral transfer in a Stochastic Dollo model and a Bayesian setting. Our likelihood is highly intractable as the parameters are the solution of a sequence of large systems of differential equations representing the expected evolution of traits along a tree. We illustrate our method on a data set of lexical traits in Eastern Polynesian languages and obtain an improved fit over the corresponding model without lateral transfer.Comment: Improvements suggested by reviewer

Nest survival of Tricolored Blackbirds in California\u27s Central Valley

The Tricolored Blackbird (Agelaius tricolor), almost entirely restricted to California, USA, has recently been proposed for listing under the U.S. Endangered Species Act. Tricolored Blackbirds historically nested in wetlands, but a large proportion of the population now nests in agricultural grain fields where the crop is ready to harvest before the young have fledged. Since 1991, federal agencies have paid farmers to delay harvesting in an effort to increase nesting productivity. However, the relative nesting success of Tricolored Blackbirds breeding in agricultural fields versus wetlands is unknown. Our objectives were to estimate daily survival rate (DSR) of nests, identify habitat covariates that influence nest survival, and estimate the number of young produced per nest. During 2011–2012, we monitored 1,323 Tricolored Blackbird nests in 12 colonies using small temperature data loggers. We modeled DSR using Program RMark with combinations of the following variables: site, habitat type, nest initiation date, nest height, water depth, nest density, colony population size, year, and the proportion of nearby nests that failed. Nest survival varied greatly (range: 0.024–0.719) but was not explained by habitat type. Nest height and nest density were positively associated with DSR. DSR was lowest midway through the breeding season and declined with colony population size. Number of young produced per nest varied by site, was lowest in intermediate-sized colonies of 1,000–5,000 birds, and was highest in 2011. DSR and number of young fledged per nest were similar in agricultural fields and in wetlands. Our results suggest that Tricolored Blackbirds benefit from policies that allow them to complete their nesting cycle in agricultural fields

TraitLab: a Matlab package for fitting and simulating binary tree-like data

TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits are simultaneously lost while new ones arise, and borrowing, whereby traits transfer laterally between species as well as through ancestral relationships. The core of the package is a Markov chain Monte Carlo (MCMC) sampling algorithm that enables the user to sample from the Bayesian joint posterior distribution for tree topologies, clade and root ages, and the trait loss, catastrophe and borrowing rates for a given data set. Data can be simulated according to the fitted Dollo model or according to a number of generalized models that allow for heterogeneity in the trait loss rate, biases in the data collection process and borrowing of traits between lineages. Coupled pairs of Markov chains can be used to diagnose MCMC mixing and convergence and to debias MCMC estimators. The raw data, MCMC run output, and model fit can be inspected using a number of useful graphical and analytical tools provided within the package or imported into other popular analysis programs. TraitLab is freely available and runs within the Matlab computing environment with its Statistics and Machine Learning toolbox, no other additional toolboxes are required.Comment: Manual describing the TraitLab software for phylogenetic inferenc

Developing cultural competence in working with Korean immigrant families

The authors provide an in-depth examination of the historical background, cultural values, family roles, and community contexts of Korean Americans as an aid to both researchers and clinicians in developing cultural competence with this particular group. First, the concept of cultural competence is defined. A brief history of Korean immigration patterns to the United States and demographic information about Korean Americans are reviewed. Second, Korean cultural values, family structure, and family roles are examined as they impact relationships in research and clinical contexts. Three indigenous concepts (cf. L. Kim, 1992) that may be useful in developing cultural competence include haan (suppressed anger), jeong (strong feeling of kinship), and noon-chi (ability to evaluate social situations through implicit cues). Clinical case examples and accounts from a community-based research perspective illustrate these cultural values. Third, important community resources in the Korean American context are highlighted. Links between cultural competence and “ecological pragmatism ” (Kelly, Azelton, Burzette, & Mock, 1994) are discussed. © 2006 Wiley Periodicals, Inc

Peer-to-peer support on Facebook for caregivers of children and youth with complex care needs in New Brunswick: An environmental scan

This environmental scan aimed to describe the purpose, use, and reach of health-related peer-to-peer support groups on Facebook for caregivers of children and youth with complex care needs in New Brunswick. A total of 3,104 searches on Facebook and consultations with thirty-two stakeholders led to the identification of forty-seven Facebook support groups (twenty-one active). Groups targeted a range of conditions, with autism and related intellectual disabilities appearing most frequently. Content analysis of posts indicated that groups were primarily used to exchange informational support. This study showed that Facebook-based peer-to-peer support groups are available to families of children and youth with complex care needs in the province. This work also lays a foundation for future scans of Facebook-based support groups in other Canadian provinces and beyond.La présente analyse du milieu visait à décrire l’objectif, l’utilisation et la portée des groupes de soutien entre pairs liés à la santé sur Facebook pour les personnes qui s’occupent d’enfants et de jeunes ayant des besoins de soins complexes au Nouveau-Brunswick. En tout, 3 104 recherches sur Facebook et des consultations auprès de 32 intervenants ont permis de repérer 47 groupes de soutien sur Facebook, dont 21 groupes actifs. Des groupes ciblaient un éventail de troubles; l’autisme et les déficiences intellectuelles connexes étaient ceux qui étaient les plus fréquents. Les analyses de contenu des messages ont révélé que les groupes étaient principalement utilisés pour échanger des informations de soutien. Selon cette étude, des groupes de soutien entre pairs sur Facebook sont offerts aux familles d’enfants et de jeunes ayant des besoins de soins complexes dans la province. De plus, ce travail jette les bases de futures analyses de groupes de soutien sur Facebook d’autres provinces canadiennes et d’ailleurs

Does fire influence the landscape-scale distribution of an invasive mesopredator?

Predation and fire shape the structure and function of ecosystems globally. However, studies exploring interactions between these two processes are rare, especially at large spatial scales. This knowledge gap is significant not only for ecological theory, but also in an applied context, because it limits the ability of landscape managers to predict the outcomes of manipulating fire and predators. We examined the influence of fire on the occurrence of an introduced and widespread mesopredator, the red fox (Vulpes vulpes), in semi-arid Australia. We used two extensive and complimentary datasets collected at two spatial scales. At the landscape-scale, we surveyed red foxes using sand-plots within 28 study landscapes - which incorporated variation in the diversity and proportional extent of fire-age classes - located across a 104 000 km2 study area. At the site-scale, we surveyed red foxes using camera traps at 108 sites stratified along a century-long post-fire chronosequence (0-105 years) within a 6630 km2 study area. Red foxes were widespread both at the landscape and site-scale. Fire did not influence fox distribution at either spatial scale, nor did other environmental variables that we measured. Our results show that red foxes exploit a broad range of environmental conditions within semi-arid Australia. The presence of red foxes throughout much of the landscape is likely to have significant implications for native fauna, particularly in recently burnt habitats where reduced cover may increase prey species\u27 predation risk

Distinct Bacterial Communities in Surficial Seafloor Sediments Following the 2010 Deepwater Horizon Blowout

A major fraction of the petroleum hydrocarbons discharged during the 2010 Macondo oil spill became associated with and sank to the seafloor as marine snow flocs. This sedimentation pulse induced the development of distinct bacterial communities. Between May 2010 and July 2011, full-length 16S rRNA gene clone libraries demonstrated bacterial community succession in oil-polluted sediment samples near the wellhead area. Libraries from early May 2010, before the sedimentation event, served as the baseline control. Freshly deposited oil-derived marine snow was collected on the surface of sediment cores in September 2010, and was characterized by abundantly detected members of the marine Roseobacter cluster within the Alphaproteobacteria. Samples collected in mid-October 2010 closest to the wellhead contained members of the sulfate-reducing, anaerobic bacterial families Desulfobacteraceae and Desulfobulbaceae within the Deltaproteobacteria, suggesting that the oil-derived sedimentation pulse triggered bacterial oxygen consumption and created patchy anaerobic microniches that favored sulfate-reducing bacteria. Phylotypes of the polycyclic aromatic hydrocarbon-degrading genus Cycloclasticus, previously found both in surface oil slicks and the deep hydrocarbon plume, were also found in oil-derived marine snow flocs sedimenting on the seafloor in September 2010, and in surficial sediments collected in October and November 2010, but not in any of the control samples. Due to the relative recalcitrance and stability of polycyclic aromatic compounds, Cycloclasticus represents the most persistent microbial marker of seafloor hydrocarbon deposition that we could identify in this dataset. The bacterial imprint of the DWH oil spill had diminished in late November 2010, when the bacterial communities in oil-impacted sediment samples collected near the Macondo wellhead began to resemble their pre-spill counterparts and spatial controls. Samples collected in summer of 2011 did not show a consistent bacterial community signature, suggesting that the bacterial community was no longer shaped by the DWH fallout of oil-derived marine snow, but instead by location-specific and seasonal factors

The relationship between variables in wearable microtechnology devices and cricket fast-bowling intensity

To date, the monitoring of fast-bowling workloads across training and competition environments has been limited to counting total balls bowled. However, bowling at faster velocities is likely to require greater effort while also placing greater load on the bowler. This study investigated the relationship between prescribed effort and microtechnology outputs in fast bowlers to ascertain whether the technology could provide a more refined measure of workload. Twelve high-performing fast bowlers (mean ± SD age 20.3 ± 2.2 y) participated in the study. Each bowler bowled 6 balls at prescribed bowling intensities of 60%, 70%, 85%, and 100%. The relationships between microtechnology outputs, prescribed intensity, and ball velocity were determined using polynomial regression. Very large relationships were observed between prescribed effort and ball velocity for peak PlayerLoad™ (R = .83 ± .19 and .82 ± .20). The PlayerLoad across lower ranges of prescribed effort exhibited a higher coefficient of variation (CV) (60% = 19.0% [17.0–23.0%]), while the CV at higher ranges of prescribed effort was lower (100% = 7.3% [6.4–8.5%]). Routinely used wearable microtechnology devices offer opportunities to examine workload and intensity in cricket fast bowlers outside the normal metrics reported. They offer a useful tool for prescribing and monitoring bowling intensity and workload in elite fast bowlers

A flexible, open, and interactive digital platform to support online and blended experiential learning environments: Thinglink and thin sections

Abstract. This study investigates the potential value of, and provides a method for, the creation of flexible, digital, and asynchronous platforms to create student-centred materials for use in an online and/or blended learning environment. We made use of Thinglink to create a “virtual microscope” resource for geology and associated courses in higher education. This is achieved through the dissemination of a simple learning resource comprising interactive imagery and audio. The visual analysis of rocks under the microscope, termed thin-section petrography, is a fundamental component in geology programmes in higher education, with key skills which are transferable with other fields such as material science, biology, and forensic science. However, learning environments and activities in this field are often dictated by the requirement for access to microscope facilities and supplementary resources which are highly variable in their academic level, availability, design, and scale, ranging from traditional textbooks to online resources. A resource was created which allows individuals to experience some of the aspects of petrographic microscopy in a digital manner. In particular, specific features of the materials observed and how microscopes work were included. The resource was disseminated to a population of learners and educators, who provided responses to a questionnaire. Responses were overwhelmingly positive and indicate considerable interest from learner and teacher alike. Critical areas for improvement include the need for clarity in the user interface and the inclusion of a recorded human voice rather than automated text narration. This study highlights the need for, and benefits of, interactive online learning resources in petrology and associated fields. This type of resource has positive implications for the flexibility, inclusivity, and accessibility of teaching materials. Such resources may prove particularly valuable when distance learning is unavoidable (e.g. the COVID-19 crisis) and/or hybrid, blended learning environments are being deployed. The method and platform used in this study are highly transferable to other subject areas (or other areas of the geosciences)