218 Works

Data from: Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

Jamie R. Oaks, Jeet Sukumaran, Jacob A. Esselstyn, Charles W. Linkem, Cameron David Siler, Mark T. Holder & Rafe M. Brown
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the...

Data from: Pan-African phylogeography of a model organism, the African clawed frog “Xenopus laevis”

Ben L.S. Furman, Adam J. Bewick, Tia L. Harrison, Eli Greenbaum, Václav Gvoždík, Chifundera Kusamba, Ben Evans, Benjamin L. S. Furman & Ben J. Evans
The African clawed frog Xenopus laevis has a large native distribution over much of sub-Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group. Here we report an analysis of molecular variation of this clade based on 17 loci (one mitochondrial, 16 nuclear) in up...

Data from: Evolution of niche preference in Sphagnum peat mosses

Matthew G. Johnson, Gustaf Granath, Teemu Tahvanainen, Remy Pouliot, Hans K. Stenøien, Line Rochefort, Håkan Rydin & A. Jonathan Shaw
Peat mosses (Sphagnum) are ecosystem engineers— species in boreal peatlands simultaneously create and inhabit narrow habitat preferences along two microhabitat gradients: an ionic gradient and a hydrological hummock-hollow gradient. In this paper we demonstrate the connections between microhabitat preference and phylogeny in Sphagnum. Using a dataset of 39 species of Sphagnum, with an 18-locus DNA alignment and an ecological dataset encompassing three large published studies, we tested for phylogenetic signal and within-genus changes in evolutionary...

Data from: Rapid and accurate taxonomic classification of insect (Class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

Joel F. Gibson, Shadi Shokralla, G. Brian Golding, Mehrdad Hajibabaei, Teresita M. Porter & Donald J. Baird
Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on difficult to define thresholds of distances, sequence similarity cutoffs, or monophyly. Most methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study is to use a naïve Bayesian classifier (Wang et al., 2007) to automate unsupervised taxonomic assignments for large batches of insect COI sequences such as data obtained...

Data from: The effects of life history and sexual selection on male and female plumage colouration

James Dale, Cody J. Dey, Kaspar Delhey, Bart Kempenaers & Mihai Valcu
Classical sexual selection theory provides a well-supported conceptual framework for understanding the evolution and signalling function of male ornaments. It predicts that males obtain greater fitness benefits than females through multiple mating because sperm are cheaper to produce than eggs. Sexual selection should therefore lead to the evolution of male-biased secondary sexual characters. However, females of many species are also highly ornamented. The view that this is due to a correlated genetic response to selection...

Data from: Evolution of sociability by artificial selection

Andrew M. Scott, Ian Dworkin & Reuven Dukas
There has been extensive research on the ecology and evolution of social life in animals that live in groups. Less attention, however, has been devoted to apparently solitary species even though recent research indicates that they also possess complex social behaviors. To address this knowledge gap, we artificially selected on sociability, defined as the tendency to engage in non-aggressive activities with others, in fruit flies. Our goal was to quantify the factors that determine the...

Data from: Limited genomic consequences of hybridization between two African clawed frogs, Xenopus gilli and X. laevis (Anura: Pipidae)

Benjamin L.S. Furman, Caroline M.S. Cauret, Graham A. Colby, G. John Measey & Ben J. Evans
The Cape platanna, Xenopus gilli, an endangered frog, hybridizes with the African clawed frog, X. laevis, in South Africa. Estimates of the extent of gene flow between these species range from pervasive to rare. Efforts have been made in the last 30 years to minimize hybridization between these two species in the west population of X. gilli, but not the east populations. To further explore the impact of hybridization and the efforts to minimize it,...

Data from: Within-group relatedness is correlated with colony-level social structure and reproductive sharing in a social fish.

Jennifer K. Hellmann, Michael G. Sovic, H. Lisle Gibbs, Adam R. Reddon, Constance M. O'Connor, Isaac Y. Ligocki, Susan Marsh-Rollo, Sigal Balshine & Ian M. Hamilton
In group-living species, the degree of relatedness among group members often governs the extent of reproductive sharing, cooperation and conflict within a group. Kinship among group members can be shaped by the presence and location of neighbouring groups, as these provide dispersal or mating opportunities that can dilute kinship among current group members. Here, we assessed how within-group relatedness varies with the density and position of neighbouring social groups in Neolamprologus pulcher, a colonial and...

Data from: The neuroscience of Romeo and Juliet: an fMRI study of acting

Steven Brown, Peter Cockett & Ye Yuan
The current study represents a first attempt at examining the neural basis of dramatic acting. While all people play multiple roles in daily life – for example “spouse” or “employee” – these roles are all facets of the “self” and thus the first-person (1P) perspective. Compared to such everyday role-playing, actors are required to portray other people and to adopt their gestures, emotions, and behaviors. Consequently, actors must think and behave not as themselves but...

Data from: Collective aggressiveness of an ecosystem engineer is associated with coral recovery

Jonathan N. Pruitt, Carl N. Keiser, Brett T. Banka, John S. Liedle, Andrew J. Brooks, Russ J. Schmitt & Sally J. Holbrook
The ecological impacts of animal groups may be different and predictable depending on their collective behavior. Farmerfish (Stegastes nigricans) live in social groups and collectively defend gardens of palatable algae. These gardens also serve as settlement and nursery habitats for corals because farmerfish mob corallivores that attempt to forage on corals within their gardens. We detected large among-colony differences in farmerfish collective aggression towards intruder fish that persist across years. We further found that the...

Data from: Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events

Laurent A. F. Frantz, Anna Rudzinski, Abang Mansyursyah Surya Nugraha, Allowen Evin, James Burton, Ardern Hulme-Beaman, Anna Linderholm, Ross Barnett, Rodrigo Vega, Evan K. Irving-Pease, James Haile, Richard Allen, Kristin Leus, Jill Shephard, Mia Hillyer, Sarah Gillemot, Jeroen Van Den Hurk, Sharron Ogle, Cristina Atofanei, Mark G. Thomas, Friederike Johansson, Abdul Haris Mustari, John Williams, Kusdiantoro Mohamad, Chandramaya Siska Damayanti … & Greger Larson
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back 40 Myr ago. Recent studies, however, suggest that much of Sulawesi’s fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification, and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions...

Data from: Resolving the phylogenetic position of Darwin’s extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data

Frédéric Delsuc, Melanie Kuch, Gillian C. Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T. Duggan & Hendrik N. Poinar
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12,880 year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within...

Data from: How does human motor cortex regulate vocal pitch in singers?

Michel Belyk, Yune S. Lee & Steven Brown
Vocal pitch is used as an important communicative device by humans, as found in the melodic dimension of both speech and song. Vocal pitch is determined by the degree of tension in the vocal folds of the larynx, which itself is influenced by complex and non-linear interactions among the laryngeal muscles. The relationship between these muscles and vocal pitch has been described by a mathematical model in the form of a set of “control rules”....

Data from: Genetic and environmental canalization are not correlated among altitudinally varying populations of Drosophila melanogaster

Ian Dworkin & Maria Pesevski
Organisms are exposed to environmental and mutational effects influencing both mean and variance of phenotypes. Potentially deleterious effects arising from this variation can be reduced by the evolution of buffering (canalizing) mechanisms, ultimately reducing phenotypic variability. There has been interest regarding the conditions enabling the evolution of canalization. Under some models, the circumstances under which genetic canalization evolves is limited, despite apparent empirical evidence for it. It has been argued that genetic canalization evolves as...

Data from: Better safe than sorry: spider societies mitigate risk by prioritizing caution

Colin M. Wright, James L.L. Lichtenstein, Lauren P. Luscuskie, Graham A. Montgomery, Noa Pinter-Wollman & Jonathan N. Pruitt
Group members often vary in the information that they have about their environment. In this study, we evaluated the relative contribution of information held by the population majority vs. new immigrants to groups in determining group function. To do so we created experimental groups of the social spider Stegodyphus dumicola that were either iteratively exposed to a dangerous predator, the ant Anoplopepis custodiens, or kept in safety. We then seeded these groups (i.e., the population...

The influence of ultraviolet reflectance differs between conspicuous aposematic signals in neotropical butterflies and poison frogs

Justin Yeager & James B. Barnett
Warning signals are often characterized by highly contrasting, distinctive and memorable colors. Both chromatic (hue) and achromatic (brightness) contrast contribute to signal efficacy, making longwave colored signals (red and yellow) that generate both chromatic and achromatic contrast common. Shortwave colors (blue and ultraviolet) do not contribute to luminance perception, yet are also common in warning signals. The presence of UV aposematic signals is paradoxical as UV perception is not universal, and evidence for its utility...

Online learning versus workshops: a rank minimized trial comparing the effect of two knowledge translation strategies designed to alter knowledge, readiness to change, and self-efficacy with respect to rehabilitation outcome measures

Mike Szekeres & Joy C. MacDermid
Traditional face-to-face learning is often replaced by virtual learning because it can be more feasible and cost-effective, and more recently due to the need for social distancing. The objective was to evaluate the effectiveness of two innovative knowledge translation (KT) interventions; in-person stakeholder-hosted, interactive, problem-based seminars (SHIPS) versus online problem-based tutorials (e-PBL) in changing knowledge, readiness to change, and self-efficacy with respect to the use of rehabilitation outcome measures. Physical and occupational therapists (n =...

Additional file 1 of Knowledge, attitude and perceptions of medical students towards mental health in a university in Uganda

Raymond Bernard Kihumuro, Mark Mohan Kaggwa, Timothy Mwanje Kintu, Rachael Mukisa Nakandi, David Richard Muwanga, David Jolly Muganzi, Pius Atwau, Innocent Ayesiga, Josephine Nambi Najjuma & Scholastic Ashaba
Supplementary Material 1

Additional file 3 of Knowledge, attitude and perceptions of medical students towards mental health in a university in Uganda

Raymond Bernard Kihumuro, Mark Mohan Kaggwa, Timothy Mwanje Kintu, Rachael Mukisa Nakandi, David Richard Muwanga, David Jolly Muganzi, Pius Atwau, Innocent Ayesiga, Josephine Nambi Najjuma & Scholastic Ashaba
Supplementary Material 3

Determinants of Sedentary Behaviour in Individuals with COPD: A Qualitative Exploration Guided by the Theoretical Domains Framework

Adnan Wshah, Anne-Marie Selzler, Kylie Hill, Dina Brooks & Roger Goldstein
In people with chronic obstructive pulmonary disease (COPD), there is increasing recognition that the prolonged accumulation of sedentary time (ST) is associated with adverse cardio-metabolic health outcomes. Nevertheless, changing this lifestyle, which has evolved over several decades, is likely to be challenging. This study reports the determinants, perceived by individuals with COPD, as being important for reducing ST. An in-depth understanding of this information is essential when planning an intervention to reduce ST. Fourteen individuals...

Additional file 2 of Development and validation of an extended Cox prognostic model for patients with ER/PR+ and HER2− breast cancer: a retrospective cohort study

Yiqun Xie, Xizhou Li, Ying Wu, Wenting Cui & Yang Liu
Additional file 2: Appendix 2. Hazard ratios and their 95% confidence limits of Ki67, PR, ER, and age. Figure 1. Hazard ratios and their 95% confidence limits for a series of binary variables of Ki67. Figure 2. Hazard ratios and their 95% confidence limits for a series of binary variables of ER. Figure 3. Hazard ratios and their 95% confidence limits for a series of binary variables of PR. Figure 4. Hazard ratios and their...

Additional file 3 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 3. Code and data. IPD from co-authors who agreed to share it, results of all analyses presented in the paper, and R code files necessary to reproduce the analysis and figures.

Additional file 5 of Changes in concentrations of cervicovaginal immune mediators across the menstrual cycle: a systematic review and meta-analysis of individual patient data

Sean M. Hughes, Claire N. Levy, Ronit Katz, Erica M. Lokken, Melis N. Anahtar, Melissa Barousse Hall, Frideborg Bradley, Philip E. Castle, Valerie Cortez, Gustavo F. Doncel, Raina Fichorova, Paul L. Fidel, Keith R. Fowke, Suzanna C. Francis, Mimi Ghosh, Loris Y. Hwang, Mariel Jais, Vicky Jespers, Vineet Joag, Rupert Kaul, Jordan Kyongo, Timothy Lahey, Huiying Li, Julia Makinde, Lyle R. McKinnon … & Florian Hladik
Additional file 5: Figure S1. Assessment of publication bias. A Funnel plots. Symbols show the effect of the menstrual cycle (x-axis) and the standard error of that effect (y-axis, reversed). Each symbol shows an individual study. Vertical solid line shows no effect. Vertical dashed line shows the meta-estimate of effect. Diagonal dashed lines enclose the region expected to include 95% of studies based on the estimated meta-effect and the standard errors. B Results of Egger’s...

Data for: New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog, X. borealis

Ben Evans
In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim of further understanding sex chromosome turnover, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog, Xenopus borealis, using genomic data and a new chromosome-scale genome assembly. We confirmed previous findings that 54.1 Mb of chromosome 8L is sex-linked in animals from east Kenya and a lab strain, but most (or...

Additional file 1 of The distribution of bioactive gibberellins along peach annual shoots is closely associated with PpGA20ox and PpGA2ox expression profiles

Mengmeng Zhang, Yangtao Ma, Xianbo Zheng, Bin Tan, Xia Ye, Wei Wang, Langlang Zhang, Jidong Li, Zhiqian Li, Jun Cheng & Jiancan Feng
Additional file 1: Figure S1. Verification of PpKO gene structure using the alignment results of reads obtained from the transcriptome of peach flowers, stems, fruits and pits. Figure S2. Sequence alignment of GA20ox from Arabidopsis and peach. The LPWKET motif are underlined. Figure S3. The phylogenetic trees of CPS (A), KS (B), KO (C), KAO (D) and GA3ox (E). The amino acid sequences were downloaded from Phytozome database and the Gene ID are listed after...

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