406 Works

Phonotactic learning with neural language models

Connor Mayer & Max Nelson
Computational models of phonotactics share much in common with language models, which assign probabilities to sequences of words. While state of the art language models are implemented using neural networks, phonotactic models have not followed suit. We present several neural models of phonotactics, and show that they perform favorably when compared to existing models. In addition, they provide useful insights into the role of representations on phonotactic learning and generalization. This work provides a promising...

Solutions to BAS-PRO model runs for Modelling 1-10MeV Proton Phase Space Density

Alexander Lozinski, Richard Horne, Sarah Glauert, Giulio Del Zanna & Seth Claudepierre
This dataset contains solution data produced by the BAS-PRO proton radiation belt model for the study "Modelling Inner Proton Belt Variability at Energies 1 to 10MeV using BAS-PRO". The solution data is in the form of 3D grids describing phase space density computed during dynamic simulations of Earth's proton belt over the modelling period 2014 to 2018. Three model runs are included: SA19, J81 and S16. Files were produced in May 2021. This work was...

Data from: Site-specific structural order in Alzheimer’s Aβ42 fibrils

Hongsu Wang, Yoon Kyung Lee, Christine Xue & Zhefeng Guo
Deposition of amyloid fibrils is a pathological hallmark of Alzheimer’s disease. Aβ42 is the major protein whose aggregation leads to the formation of these fibrils. Understanding the detailed structure of Aβ42 fibrils is of particular importance for delineating the mechanism of Aβ42 aggregation and developing specific amyloid-targeting drugs. Here we use site-directed spin labeling and electron paramagnetic resonance spectroscopy to study the site-specific structural order at each and every residue position in Aβ42 fibrils. Strong...

Data from: Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (Didelphis virginiana).

Sergio F. Nigenda-Morales, Yibo Hu, James Beasley, Hugo A. Ruiz-Piña, David Valenzuela-Galván, Robert K. Wayne & James C. Beasley
Skin and coat pigmentation are two of the best-studied examples of traits under natural selection given their quantifiable fitness interactions with the environment (e.g. camouflage) and signaling with other organisms (e.g. warning coloration). Previous morphological studies have found that skin pigmentation variation in the Virginia opossum (Didelphis virginiana) is associated with variation in precipitation and temperatures across its distribution range following Gloger’s rule (lighter pigmentation in temperate environments). To investigate the molecular mechanism associated with...

Data from: Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences

Matthew A. Campbell, Michael E. Alfaro, Max Belasco & J. Andrés López
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the...

Data from: 1970s and ‘Patient 0’ HIV-1 genomes illuminate early HIV/AIDS history in North America

Michael Worobey, Thomas D. Watts, Richard A. McKay, Marc A. Suchard, Timothy Granade, Dirk E. Teuwen, Beryl A. Koblin, Walid Heneine, Philippe Lemey & Harold W. Jaffe
The emergence of HIV-1 group M subtype B in North American men who have sex with men was a key turning point in the HIV/AIDS pandemic. Phylogenetic studies have suggested cryptic subtype B circulation in the United States (US) throughout the 1970s1, 2 and an even older presence in the Caribbean2. However, these temporal and geographical inferences, based upon partial HIV-1 genomes that postdate the recognition of AIDS in 1981, remain contentious3, 4 and the...

Data from: An inexpensive and open-source method to study large terrestrial animal diet and behavior using time-lapse video and GPS

Carlos A. De La Rosa
1. The behavior of free-ranging animals is difficult to study, especially on the large spatial and temporal scales relevant to long-lived large species. Animal-borne video and environmental data collection systems (AVEDs) record behavior and other data in real time as animals conduct daily activities. However, few studies have combined systematically collected, long term AVED foraging data with environmental and movement data to test hypotheses on animal foraging. Additionally, AVEDs are often either prohibitively expensive, or...

Data from: Natural selection interacts with recombination to shape the evolution of hybrid genomes

Molly Schumer, Chenling Xu, Daniel L Powell, Arun Durvasula, Laurits Skov, Chris Holland, John C Blazier, Sriram Sankararaman, Peter Andolfatto, Gil G Rosenthal & Molly Przeworski
To investigate the consequences of hybridization between species, we studied three replicate hybrid populations that formed naturally between two swordtail fish species, estimating their fine-scale genetic map and inferring ancestry along the genomes of 690 individuals. In all three populations, ancestry from the “minor” parental species is more common in regions of high recombination and where there is linkage to fewer putative targets of selection. The same patterns are apparent in a reanalysis of human...

Data from: Biting disrupts integration to spur skull evolution in eels

David C. Collar, Peter C. Wainwright, Michael E. Alfaro, Liam J. Revell & Rita S. Mehta
The demand that anatomical structures work together to perform biological functions is thought to impose strong limits on morphological evolution. Breakthroughs in diversification can occur, however, when functional integration among structures is relaxed. Although such transitions are expected to generate variation in morphological diversification across the tree of life, empirical tests of this hypothesis are rare. Here we show that transitions between suction-based and biting modes of prey capture, which require different degrees of coordination...

Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary

Michael E. Alfaro, Brant C. Faircloth, Richard C. Harrington, Laurie Sorenson, Matt Friedman, Christine E. Thacker, Carl H. Oliveros, David Černý & Thomas J. Near
The Cretaceous–Palaeogene (K–Pg) mass extinction is linked to the rapid emergence of ecologically divergent higher taxa (for example, families and orders) across terrestrial vertebrates, but its impact on the diversification of marine vertebrates is less clear. Spiny-rayed fishes (Acanthomorpha) provide an ideal system for exploring the effects of the K–Pg on fish diversification, yet despite decades of morphological and molecular phylogenetic efforts, resolution of both early diverging lineages and enormously diverse subclades remains problematic. Recent...

Data from: Mechanisms of resilience: empirically quantified positive feedbacks produce alternate stable states dynamics in a model of a tropical reef

Ranjan Muthukrishnan, James O. Lloyd-Smith & Peggy Fong
Alternate stable states (ASS) theory is a dominant conceptual framework for understanding processes that support resilience of ecological communities in the face of multiple anthropogenic disturbances. For decades, coral reefs have been cited as a classic example of ASS, yet this position remains highly controversial, largely because convincing empirical evaluations have been elusive. Using a combination of empirical measurements of positive feedback processes and simulation modelling, we assessed ASS in coral reefs of the Eastern...

Data from: Exploring visual plasticity: dietary carotenoids can change color vision in guppies (Poecilia reticulata)

Benjamin A. Sandkam, Kerry A. Deere-Machemer, Ashley M. Johnson, Gregory F. Grether, F. Helen Rodd & Rebecca C. Fuller
Differences in color vision can play a key role in an organism’s ability to perceive and interact with the environment across a broad range of taxa. Recently, species have been shown to vary in color vision across populations as a result of differences in regulatory sequence and/or plasticity of opsin gene expression. For decades, biologists have been intrigued by among-population variation in color-based mate preferences of female Trinidadian guppies. We proposed that some of this...

Data from: Dry-season decline in tree sapflux is correlated with leaf turgor loss point in a tropical rainforest

Isabelle Maréchaux, Damien Bonal, Megan K. Bartlett, Benoît Burban, Sabrina Coste, Elodie A. Courtois, Maguy Dulormne, Jean-Yves Goret, Eléonore Mira, Ariane Mirabel, Lawren Sack, Clément Stahl & Jerome Chave
1. Water availability is a key determinant of forest ecosystem function and tree species distributions. While droughts are increasing in frequency in many ecosystems, including in the tropics, plant responses to water supply vary with species and drought intensity, and are therefore difficult to model. Based on physiological first principles, we hypothesized that trees with a lower turgor loss point (πtlp), i.e., a more negative leaf water potential at wilting, would maintain water transport for...

Data from: Ephemeral stream reaches preserve the evolutionary and distributional history of threespine stickleback in the Santa Clara and Ventura River Watersheds of southern California

Jonathan Q. Richmond, David K. Jacobs, Adam R. Backlin, Camm C. Swift, Chris Dellith & Robert N. Fisher
Much remains to be understood about the evolutionary history and contemporary landscape genetics of unarmored threespine stickleback in southern California, where populations collectively referred to as Gasterosteus aculeatus williamsoni have severely declined over the past 70+ years and are now endangered. We used mitochondrial sequence and microsatellite data to assess the population genetics and phylogeography of unarmored populations sampled immediately downstream from the type locality of G. a. williamsoni in the upper Santa Clara River,...

Data from: Seasonal polyphenism in wing coloration affects species recognition in rubyspot damselflies (Hetaerina spp.)

Jonathan P. Drury, Christopher N. Anderson & Gregory F. Grether
Understanding how phenotypic plasticity evolves and in turn affects the course of evolution is a major challenge in modern biology. By definition, biological species are reproductively isolated, but many animals fail to distinguish between conspecifics and closely related heterospecifics. In some cases, phenotypic plasticity may interfere with species recognition. Here, we document a seasonal polyphenism in the degree of dark wing pigmentation in smoky rubyspot damselflies (Hetaerina titia) – a shift so pronounced that it...

Data from: RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercus sect. Quercus: Fagaceae)

Bernard Y. Kim, Xinzeng Wei, Sorel Fitz-Gibbon, Kirk E. Lohmueller, Joaquin Ortego, Paul F. Gugger & Victoria L. Sork
A long-term debate in evolutionary biology is the extent to which reproductive isolation is a necessary element of speciation. Hybridizing plants in general are cited as evidence against this notion and oaks specifically have been used as the classic example of species maintenance without reproductive isolation. Here, we use thousands of SNPs generated by RAD sequencing to describe the phylogeny of a set of sympatric white oak species in California and then test whether these...

Data from: Species delimitation with gene flow: a methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs

Kin Onn Chan, Alana M. Alexander, Jesse L. Grismer, Yong-Chao Su, Evan S.H. Quah, Rafe M. Brown, Evan S. H. Quah & L. Lee Grismer
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based...

Data from: A role for migration-linked genes and genomic islands in divergence of a songbird

Kristen Ruegg, Eric C. Anderson, Jason Boone, Jazz Pouls & Thomas B. Smith
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of “genomic islands of divergence” (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson’s thrush, Catharus ustulatus, is a migratory songbird with two genetically-distinct subspecies that differ in a number of traits known to be involved in reproductive isolation...

Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

Owen A. Thompson, L. Basten Snoek, Harm Nijveen, Mark G. Sterken, Rita J. M. Volkers, Rachel Brenchley, Arjen Van't Hof, Roel P. J. Bevers, Andrew R. Cossins, Itai Yanai, Alex Hajnal, Tobias Schmid, Jaryn D. Perkins, David Spencer, Leonid Kruglyak, Erik C. Andersen, Donald G. Moerman, LaDeana W. Hillier, Jan E. Kammenga & Robert H. Waterston
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that...

Data from: Checkerboard score-area relationships reveal spatial scales of plant community structure

Gordon G. McNickle, Eric G. Lamb, Mike Lavender, , Brandon S. Schamp, Steven D. Siciliano, Richard Condit, Stephen P. Hubbell, Jennifer L. Baltzer & James F Cahill
Identifying the spatial scale at which particular mechanisms influence plant community assembly is crucial to understanding the mechanisms structuring communities. It has long been recognized that many elements of community structure are sensitive to area; however the majority of studies examining patterns of community structure use a single relatively small sampling area. As different assembly mechanisms likely cause patterns at different scales we investigate how plant species co-occurrence patterns change with sampling unit scale. We...

Data from: Developmental plasticity affects sexual size dimorphism in an anole lizard

Camille Bonneaud, Erin Marnocha, Anthony Herrel, Bieke Vanhooydonck, Duncan J. Irschick & Thomas B. Smith
While developmental plasticity has been shown to contribute to sexual size dimorphism (SSD) in laboratory studies, its role in shaping SSD variation in wild vertebrate populations is unclear. Here we use a field study and a laboratory experiment to show that resource availability influences the degree of SSD among insular populations of Anolis sagrei lizards in the Bahamas. Total amounts of food biomass explained variation in male, but not female, body size on six Bahamian...

Data from: Forelimb indicators of prey-size preference in the Felidae

Julie Meachen-Samuels & Blaire Van Valkenburgh
The forelimbs, along with the crania, are an essential part of the prey-killing apparatus in cats. Linear morphometrics of the forelimbs were used to determine the morphological differences between felids that specialize on large prey, small prey, or mixed prey. We also compared the scaling of felid forelimbs to those of canids to test whether prey capture strategies affect forelimb scaling. Results suggest that large prey specialists have relatively robust forelimbs when compared with smaller...

Data from: Evaluating the potential for pre-zygotic isolation and hybridization between landlocked and anadromous alewife (Alosa pseudoharengus) following secondary contact

Katherine A. Littrell, David Ellis, Stephen R. Gephard, Andrew D. MacDonald, Eric P. Palkovacs, Katherine Scranton & David M. Post
The recent increase of river restoration projects is altering habitat connectivity for many aquatic species, increasing the chance that previously isolated populations will come into secondary contact. Anadromous and landlocked alewife (Alosa pseudoharengus) are currently undergoing secondary contact as a result of a fishway installation at Rogers Lake in Old Lyme, Connecticut. To determine the degree of pre-zygotic isolation and potential for hybridization between alewife life history forms, we constructed spawning time distributions for two...

Data from: Effects of temperature on consumer-resource interactions

Priyanga Amarasekare
1. Understanding how temperature variation influences the negative (e.g., self-limitation) and positive feedback (e.g., saturating functional responses) processes that characterize consumer-resource interactions is an important research priority. Previous work on this topic has yielded conflicting outcomes with some studies predicting that warming should increase consumer-resource oscillations and others predicting that warming should decrease consumer-resource oscillations. 2. Here I develop a consumer-resource model that both synthesizes previous findings in a common framework and yields novel insights...

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