140 Works

Animal models to understand the etiology and pathophysiology in polycystic ovary syndrome

Elisabet Stener-Victorin, Vasantha Padmanabhan, Kirsty A Walters, Rebecca E Campbell, Anna Benrick, Paolo Giacobini, Daniel A Dumesic & David H Abbott
More than one out of ten women worldwide are diagnosed with the leading cause of female reproductive and metabolic dysfunction, polycystic ovary syndrome (PCOS). Despite its high prevalence, PCOS and its accompanying morbidities are likely under-diagnosed, averaging >2 years and 3 physicians changes before women are diagnosed. Despite intensive research, the underlying cause(s) of PCOS have yet to be defined. In order to understand PCOS pathophysiology, its developmental origins, and how to predict and prevent...

Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836)

Sara Simmonds, Allison Fritts-Penniman, Samantha Cheng, Ngurah Mahardika & Paul Barber
The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we...

Sex-dimorphic effects of Biogenesis of Lysosome-related Organelles Complex-1 (BLOC-1) deficiency on mouse perinatal brain development

Cristina Ghiani & Esteban Dell'Angelica
The function(s) of the Biogenesis of Lysosome-related Organelles Complex 1 (BLOC-1) during brain development is hitherto largely unknown. Here, we investigated how its absence alters the trajectory of postnatal brain development using as model the pallid mouse. Most of the defects observed early postnatally in the mutant mice were more prominent in males than in females and in the hippocampus. Male mutant mice, but not females, had smaller brains as compared to sex-matching wild-types at...

Multi-species occupancy models as robust estimators of community richness

Morgan W. Tingley, Christopher Nadeau & Manette Sandor
1. Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. In recent years, multi-species occupancy models (MSOM) have been developed as a statistical tool to account for species-specific heterogeneity in detection while estimating true measures of diversity. Although the power of these models has been tested in various ways, their ability to estimate gamma diversity – or true community size, N – is a...

Eurasian pollen data from 21 kiloannum to the present

A. Binney. H., A. Lozhkin, P Anderson, A. Andreev, E. Bezrukova, T. Blyakharchuk, V. Jankovska, I. Khazhina, S. Krivonogov, K. Kremenetski, E. Novenko, N. Ryabogina, N. Solovieva & V. Zernitzkaya
This dataset contains fossil and modern pollen data collated during a workshop held in the UK in 2008 as part of the NERC (Quantifying and Understanding the Earth System) QUEST programme. The 96 sampling sites are located from 24°E (western Ukraine and Belarus) to easternmost Siberia, and lie north of latitude 40°N. The sample ages range from 21ka to present and are assigned to 1,000 year time slices. The dataset has been checked for consistent...

Association of EGLN1 gene with high aerobic capacity of Peruvian Quechua at high altitude

Abigail W. Bigham, Tom D. Brutsaert, Melisa Kiyamu, Gianpietro Elias Revollendo, Jenna L. Isherwood, Frank S. Lee, Maria Rivera-Ch., Fabiola Leon-Velarde & Sudipta Ghosh
Highland native Andeans have resided at altitude for millennia. They display high aerobic capacity (VO2max) at altitude and this may be a reflection of genetic adaptation to chronic hypoxia. Previous genome-wide (GW) scans for natural selection have nominated EGLN1 as a candidate gene. The encoded protein, EGLN1/PHD2, is an O2 sensor that controls levels of the Hypoxia Inducible Factor-a (HIF-a), which regulates the cellular response to hypoxia. From GWAS and ANCOVA performed on a total...

Data from: Physical and social cues shape nest-site preference and prey capture behavior in social spiders

Gabriella Najm, Angelika Pe, Jonathan Pruitt & Noa Pinter-Wollman
Animals often face conflicting demands when making movement decisions. To examine the decision process of social animals, we evaluated nest site preferences of the social spider Stegodyphus dumicola. Colonies engage in collective web building, constructing three-dimensional nests and two-dimensional capture webs on trees and fences. We examined how individuals and groups decide where to construct a nest based on habitat structure and conspecific presence. Individuals had a strong preference for three dimensional-substrates and conspecific presence....

Age and location influence the costs of compensatory and accelerated growth in a hibernating mammal

Sarah Heissenberger, Gabriela Pinho, Julien Martin & Daniel Blumstein
The increase of structural growth rates to compensate for a poor initial body condition, defined as compensatory growth, may have physiological costs, but little is known about its effects on individual fitness in the wild. Yellow-bellied marmots (Marmota flaviventer) are obligate hibernators and depend on fat accumulation acquired during an approximately 4-month summer to survive overwinter. We investigated the costs to survival and longevity of rapid growth in a wild population of yellow-bellied marmots. We...

Data from: The legacy effects of keystone individuals on collective behavior scale to how long they remain within a group

Jonathan N. Pruitt & Noa Pinter-Wollman
The collective behaviour of social groups is often strongly influenced by one or few individuals, termed here ‘keystone individuals’. We examined whether the influence of keystone individuals on collective behaviour lingers after their departure and whether these lingering effects scale with their tenure in the group. In the social spider, Stegodyphus dumicola, colonies' boldest individuals wield a disproportionately large influence over colony behaviour. We experimentally manipulated keystones' tenure in laboratory-housed colonies and tracked their legacy...

Data from: Specifying high-altitude electrons using low-altitude LEO systems: the SHELLS model

Seth Claudepierre
The dataset includes a tarball of all of the data shown in the figures in the manuscript, along with the neural network coefficients as described in the Appendix of the manuscript.

Разбор трех разборов. Автоэвристические заметки

Александр Жолковский
В статье разбираются три недавние работы автора: разборы трех очень разных текстов – «Темных аллей» Бунина, «Двух капитанов» Каверина и «Личной жизни» Зощенко, – между которыми обнаруживаются интересные сходства. Одно состоит в том, как долго автору открывалась некая, теперь представляющаяся окончательной, разгадка структуры каждого из текстов. Другое, более неожиданное, – в том, что эти произведения объединяет общая черта: «авторский» мотив, встроенный в три совершенно несходных нарратива. Заключительный раздел статьи посвящен теоретическим выводам из выявленных аналогий....

Seedling response to water stress in valley oak (Quercus lobata) is shaped by different gene networks across populations

Alayna Mead, Juan Peñaloza Ramirez, Megan Bartlett, Jessica Wright, Lawren Sack & Victoria Sork
Drought is a major stress for plants, creating a strong selection pressure for traits that enable plant growth and survival in dry environments. Many drought responses are conserved species-wide responses while others vary among populations distributed across heterogeneous environments. We tested how six populations of the widely-distributed California valley oak (Quercus lobata) sampled from contrasting climates would differ in their response to soil drying relative to well-watered controls in a common environment by measuring ecophysiological...

Extending adaptor grammars to learn phonological alternations

Canaan Breiss & Colin Wilson

Phonotactic learning with neural language models

Connor Mayer & Max Nelson

Beyond the landscape: resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Sophia Kimmig, Joscha Beninde, Myriam Brandt, Anna Schleimer, Stephanie Kramer-Schadt, Heribert Hofer, Konstantin Börner, Christoph Schulze, Ulrich Wittstatt, Mike Heddergott, Tania Halczok, Christoph Staubach & Alain Frantz
Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual-based sampling across an urban-rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding...

Assessing seasonal demographic covariation to understand environmental-change impacts on a hibernating mammal

Maria Paniw, Dylan Childs, Kenneth Armitage, Daniel Blumstein, Julien Martin, Madan Oli & Arpat Ozgul
Natural populations are exposed to seasonal variation in environmental factors that simultaneously affect several demographic rates (survival, development, reproduction). The resulting covariation in these rates determines population dynamics, but accounting for its numerous biotic and abiotic drivers is a significant challenge. Here, we use a factor-analytic approach to capture partially unobserved drivers of seasonal population dynamics. We use 40 years of individual-based demography from yellow-bellied marmots (Marmota flaviventer) to fit and project population models that...

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

Data from: Leaf drought tolerance cannot be inferred from classic leaf traits in a tropical rainforest

Isabelle Maréchaux, Laurent Saint-André, Megan K. Bartlett, Lawren Sack & Jérôme Chave
Plants are enormously diverse in their traits and ecological adaptation, even within given ecosystems, such as tropical rainforests. Accounting for this diversity in vegetation models poses serious challenges. Global plant functional trait databases have highlighted general trait correlations across species that have considerably advanced this research program. However, it remains unclear whether trait correlations found globally hold within communities, and whether they extend to drought tolerance traits. For 134 individual plants spanning a range of...

Data from: Evidence of host-associated divergence from coral-eating snails (genus Coralliophila) in the Coral Triangle

Sara E. Simmonds, Vincent Chou, Samantha H. Cheng, Rita Rachmawati, Hilconida P. Campulong, Paul H. Barber, Hilconida P. Calumpong & G. Ngurah Mahardika
We studied how host-associations and geography shape the genetic structure of sister species of marine snails Coralliophila radula (A. Adams, 1853) and C. violacea (Kiener, 1836). These obligate ectoparasites prey upon corals and are sympatric throughout much of their ranges in coral reefs of the tropical and subtropical Indo-Pacific. We tested for population genetic structure of snails in relation to geography and their host corals using mtDNA (COI) sequences in minimum spanning trees and AMOVAs....

High-frequency measurements of aeolian saltation flux: time series data

Raleigh L. Martin, Jasper F. Kok, Chris H. Hugenholtz, Thomas E. Barchyn, Marcelo Chamecki & Jean T. Ellis
High-frequency (25-50 Hz) coupled observations of wind speed and aeolian saltation flux (i.e, the wind-blown movement of sand) were measured at three field sites: Jericoacoara, Brazil; Rancho Guadalupe, California; and Oceano, California. The dataset provided here contains the full record of raw and processed time series of saltation flux and wind speed measured at multiple heights above the sediment surface.

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Paul A Maier, Amy G Vandergast, Steve M Ostoja, Andres Aguilar & Andrew J Bohonak
Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this “glacial pulse” model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including novel admixed (“fused”) lineages. We tested for patterns of glacial pulse lineage diversification in...

Data from: Safety cues can give prey more valuable information than danger cues

Barney Luttbeg, Maud C O Ferrari, Daniel T Blumstein & Douglas P Chivers
The ability of prey to assess predation risk is fundamental to their success. It is routinely assumed predator cues do not vary in reliability across levels of predation risk. We propose that cues can differ in how precisely they indicate different levels of predation risk. What we call danger cues precisely indicate high risk levels, while safety cues precisely indicate low risk levels. Using optimality modeling, we find that prey fitness is increased when prey...

Data from: A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

Matthew Friedman, Kara Feilich, Hermione Beckett, Michael Alfaro, Brant Faircloth, David Černý, Masaki Miya, Thomas Near & Richard Harrington
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide...

Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions

Jonathan Chang, Daniel L. Rabosky & Michael E. Alfaro
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread...

Data from: Globally consistent impact of tropical cyclones on the structure of tropical and subtropical forests

Thomas Ibanez, Gunnar Keppel, Christophe Menkes, Thomas W. Gillespie, Matthieu Lengaigne, Morgan Mangeas, Gonzalo Rivas-Torres & Philippe Birnbaum
1. Tropical cyclones (TCs) are large-scale disturbances that regularly impact tropical forests. Although long-term impacts of TCs on forest structure have been proposed, a global test of the relationship between forest structure and TC frequency and intensity is lacking. We test on a pantropical scale whether TCs shape the structure of tropical and subtropical forests in the long-term. 2. We compiled forest structural features (stem density, basal area, mean canopy height and maximum tree size)...

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  • University of California, Los Angeles
  • University of California System
  • Princeton University
  • University of Georgia
  • Smithsonian Tropical Research Institute
  • Field Museum of Natural History
  • University of Cambridge
  • Louisiana State University of Alexandria
  • University of Antwerp
  • University of Liège
  • University of Washington
  • University of Michigan–Ann Arbor
  • National Institutes of Health
  • University of Chicago
  • McMaster University