42 Works

Data from: Modeling effects of nonbreeders on population growth estimates

Aline M. Lee, Jane M. Reid & Steven R. Beissinger
Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates. We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms...

Data from: Neuroendocrine profiles associated with discrete behavioural variation in Symphodus ocellatus, a species with male alternative reproductive tactics

Bridget M. Nugent, Kelly A. Stiver, Suzanne H. Alonzo & Hans A. Hofmann
The molecular mechanisms underlying phenotypic plasticity are not well understood. Identifying mechanisms underlying alternative reproductive tactics (ARTs) in species for which the behavioural and fitness consequences of this variation are well characterized provides an opportunity to integrate evolutionary and mechanistic understanding of the maintenance of variation within populations. In the ocellated wrasse Symphodus ocellatus, the behavioural phenotypes of three distinct male morphs (sneakers, satellites and nesting males), which arise from a single genome, have been...

Data from: Invading Africa: a novel transoceanic dispersal by a New World ant parasitoid

Elizabeth A. Murray & John M. Heraty
Aim: An ant parasitoid wasp genus (Eucharitidae: Kapala) common in the New World exhibits the intriguing pattern of having one species distributed widely across tropical Africa and Madagascar. The unusual distribution prompted an investigation of the age, origins and diversification of the Afrotropical Kapala species. We evaluate a previous hypothesis that the species was anthropogenically introduced. Location: Africa and Madagascar and the Neotropics. Methods: Numerous forms of evidence are incorporated to explain the origin of...

Data from: Social selection parapatry in Afrotropical sunbirds

Jay P. McEntee, Joshua V. Peñalba, Chacha Werema, Elia Mulungu, Maneno Mbilinyi, David Moyer, Louis Hansen, Jon Fjeldså & Rauri C. K. Bowie
The extent of range overlap of incipient and recent species depends on the type and magnitude of phenotypic divergence that separates them, and the consequences of phenotypic divergence on their interactions. Signal divergence by social selection likely initiates many speciation events, but may yield niche-conserved lineages predisposed to limit each others’ ranges via ecological competition. Here we examine this neglected aspect of social selection speciation theory in relation to the discovery of a non-ecotonal species...

Data from: High phylogenetic utility of an ultraconserved element probe set designed for Arachnida

James Starrett, Shahan Derkarabetian, Marshal Hedin, , John E. McCormack, Brant C. Faircloth & Robert W. Bryson
Arachnida is an ancient, diverse, and ecologically important animal group that contains a number of species of interest for medical, agricultural, and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic...

Data from: Adaptive evolution of a derived radius morphology in manakins (Aves, Pipridae) to support acrobatic display behavior

Anthony R. Friscia, Gloria D. Sanin, Willow R. Lindsay, Lainy B. Day, Barney A. Schlinger, Josh Tan, Matthew J. Fuxjager & Anthony Friscia
The morphology of the avian skeleton is often studied in the context of adaptations for powered flight. The effects of other evolutionary forces, such as sexual selection, on avian skeletal design are unclear, even though birds produce diverse behaviors that undoubtedly require a variety of osteological modifications. Here, we investigate this issue in a family of passerine birds called manakins (Pipridae), which have evolved physically unusual and elaborate courtship displays. We report that, in species...

Data from: Do thermoregulatory costs limit altitude distributions of Andean forest birds?

Gustavo A. Londono, Mark A. Chappell, Jill E. Jankowski & Scott K. Robinson
Along tropical mountains, species often occupy narrow altitude ranges. Numerous biotic and abiotic factors have been proposed as determinants of altitude occupancy. We measured several aspects of thermal physiology of 215 bird species across a 2·6-km altitude gradient in the Peruvian Andes. We predicted that highland species would show adaptation to the colder high-altitude climate and that energy costs of thermoregulation might limit upslope dispersal of lowland natives. We found reductions in thermal conductance, body...

Data from: A chemical-genomic screen of neglected antibiotics reveals illicit transport of kasugamycin and blasticidin S

Anthony L. Shiver, Hendrik Osadnik, George Kritikos, Bo Li, Nevan Krogan, Athanasios Typas & Carol A. Gross
Fighting antibiotic resistance requires a deeper understanding of the genetic factors that determine the antibiotic susceptibility of bacteria. Here we describe a chemical-genomic screen in Escherichia coli K-12 that was designed to discover new aspects of antibiotic resistance by focusing on a set of 26 antibiotics and other stresses with poorly characterized mode-of-action and determinants of resistance. We show that the screen identifies new resistance determinants for these antibiotics including a common signature from two...

Data from: Phylogenetics support an ancient common origin of two scientific icons: Devils Hole and Devils Hole pupfish

İsmail K. Sağlam, Jason Baumsteiger, Matt J. Smith, Javier Linares-Casenave, Andrew L. Nichols, Sean M. O'Rourke & Michael R. Miller
The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m2 pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an...

Data from: A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna

Henrik Krehenwinkel, Maxene Graze, Dennis Roedder, Tanaka Kazuhiro, Yuki G. Baba, Christoph Muster, Gabriele Uhl & Kazuhiro Tanaka
Aim: The phylogeographical history of wide-ranging Palaearctic species is not well understood. Here, we present a range-wide phylogeographical study of the wasp spider, Argiope bruennichi (Scopoli, 1772), a highly dispersive and widely distributed Palaearctic species. We aim to identify glacial refugia and patterns of interglacial gene flow across the Palaearctic. Location: Palaearctic region, including the Azores, Madeira, Europe, North Africa and Asia. Methods: We conduct a range-wide phylogeographical survey. Our study is based on nuclear...

Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

Data from: Morphological identification and single-cell genomics of marine diplonemids

Ryan M. R. Gawryluk, Javier Del Campo, Noriko Okamoto, Jurgen F. H. Strassert, Julius Lukes, Thomas A. Richards, Alexandra Z. Worden, Alyson E. Santoro & Patrick J. Keeling
Recent global surveys of marine biodiversity have revealed that a group of organisms known as “marine diplonemids” constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2 and 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids,...

Data from: Ants exhibit asymmetric hybridization in a mosaic hybrid zone

Jessica Purcell, Sacha Zahnd, Anouk Athanasiades, Rebecca Türler, Michel Chapuisat & Alan Brelsford
Research on hybridization between species provides unparalleled insights into the pre- and post-zygotic isolating mechanisms that drive speciation. In social organisms, colony-level incompatibilities may provide additional reproductive barriers not present in solitary species, and hybrid zones offer an opportunity to identify these barriers. Here, we use genotyping-by-sequencing to sequence hundreds of markers in a hybrid zone between two socially polymorphic ant species, Formica selysi and Formica cinerea. We characterize the zone, determine the frequency of...

Data from: Herbivore size matters for productivity-richness relationships in African savannas

Deron E. Burkepile, Richard W. S. Fynn, Dave I. Thompson, Nathan P. Lemoine, Sally E. Koerner, Stephanie Eby, Nicole Hagenah, Kevin R. Wilcox, Scott L. Collins, Kevin P. Kirkman, Alan K. Knapp & Melinda D. Smith
1.Productivity and herbivory often interact to shape plant community composition and species richness with levels of production mediating the impact of herbivory. Yet, differences in herbivore traits such as size, feeding guild, and dietary requirements may result in different impacts of diverse herbivore guilds across productivity gradients. 2.We used size-selective herbivore exclosures to separate the effects of herbivory by larger herbivores, such as elephant, Burchell's zebra, and blue wildebeest from those of medium/smaller herbivores, such...

Data from: Post-fire recovery in coastal sage scrub: seed rain and community trajectory

Erin Conlisk, Rebecca Swab, Alejandra Martínez-Berdeja & Matthew P. Daugherty
Disturbance is a primary mechanism structuring ecological communities. However, human activity has the potential to alter the frequency and intensity of natural disturbance regimes, with subsequent effects on ecosystem processes. In Southern California, human development has led to increased fire frequency close to urban areas that can form a positive feedback with invasive plant spread. Understanding how abiotic and biotic factors structure post-fire plant communities is a critical component of post-fire management and restoration. In...

Data from: An evaluation of transcriptome-based exon capture for frog phylogenomics across multiple scales of divergence (Class: Amphibia, Order: Anura)

Daniel M. Portik, Lydia L. Smith & Ke Bi
Custom sequence capture experiments are becoming an efficient approach for gathering large sets of orthologous markers in nonmodel organisms. Transcriptome-based exon capture utilizes transcript sequences to design capture probes, typically using a reference genome to identify intron–exon boundaries to exclude shorter exons (<200 bp). Here, we test directly using transcript sequences for probe design, which are often composed of multiple exons of varying lengths. Using 1260 orthologous transcripts, we conducted sequence captures across multiple phylogenetic...

Data from: Spatiotemporal patterns of duck nest density and predation risk: a multi-scale analysis of 18 years and more than 10 000 nests

Kevin Ringelman, John M. Eadie, Joshua T. Ackerman, Andy Sih, Daniel L. Loughman, Gregory S. Yarris, Shaun L. Oldenburger, M. Robert McLandress, Kevin M. Ringelman & Andrew Sih
Many avian species are behaviorally-plastic in selecting nest sites, and may shift to new locations or habitats following an unsuccessful breeding attempt. If there is predictable spatial variation in predation risk, the process of many individuals using prior experience to adaptively change nest sites may scale up to create shifting patterns of nest density at a population level. We used 18 years of waterfowl nesting data to assess whether there were areas of consistently high...

Data from: Unlinked Mendelian inheritance of red and black pigmentation in snakes: implications for Batesian mimicry

Alison R. Davis Rabosky, Christian L. Cox & Daniel L. Rabosky
Identifying the genetic basis of mimetic signals is critical to understanding both the origin and dynamics of mimicry over time. For species not amenable to large laboratory breeding studies, widespread color polymorphism across natural populations offers a powerful way to assess the relative likelihood of different genetic systems given observed phenotypic frequencies. We classified color phenotype for 2,175 ground snakes (Sonora semiannulata) across the continental United States to analyze morph ratios and test among competing...

Data from: Population structure of a vector-borne plant parasite

Kelsey M. Yule, Jennifer A. H. Koop, Nicolas M. Alexandre, Lauren R. Johnston & Noah K. Whiteman
Parasites are among the most diverse groups of life on Earth, yet complex natural histories often preclude studies of their speciation processes. The biology of parasitic plants facilitates in situ collection of data on both genetic structure and the mechanisms responsible for that structure. Here, we studied the role of mating, dispersal and establishment in host race formation of a parasitic plant. We investigated the population genetics of a vector-borne desert mistletoe (Phoradendron californicum) across...

Data from: Honey bee inhibitory signaling is tuned to threat severity and can act as a colony alarm signal

Ken Tan, Shihao Dong, Xinyu Li, Xiwen Liu, Chao Wang, Jianjun Li & James C. Nieh
Alarm communication is a key adaptation that helps social groups resist predation and rally defenses. In Asia, the world's largest hornet, Vespa mandarinia, and the smaller hornet, Vespa velutina, prey upon foragers and nests of the Asian honey bee, Apis cerana. We attacked foragers and colony nest entrances with these predators and provide the first evidence, in social insects, of an alarm signal that encodes graded danger and attack context. We show that like A....

Data from: Comparing the responses of bryophytes and short-statured vascular plants to climate shifts and eutrophication

Risto Virtanen, Anu Eskelinen & Susan Harrison
Few experimental studies have tested how abundance and diversity of grassland bryophytes respond to global environmental changes such as climate shifts and eutrophication. Because bryophytes in grasslands are low-statured, and because plant height is a key functional trait governing plant responses to resource gradients, their responses to these factors could resemble those of better-studied small vascular plants. Alternatively, traits unique to bryophytes could lead to qualitatively different responses than those of small vascular plants. In...

Data from: Functional homogenization of flower visitor communities with urbanization

Nicolas Deguines, Romain Julliard, Mathieu De Flores & Colin Fontaine
Land-use intensification and resulting habitat loss are put forward as the main causes of flower visitor decline. However, the impact of urbanization, the prime driver of land-use intensification in Europe, is poorly studied. In particular, our understanding of whether and how it affects the composition and functioning of flower visitor assemblages is scant, yet required to cope with increasing urbanization worldwide. Here, we use a nation-wide dataset of plant-flower visitor (Coleoptera, Diptera, Hymenoptera, Lepidoptera) interactions...

Data from: Human–wildlife conflict, benefit sharing and the survival of lions in pastoralist community-based conservancies

Sara Blackburn, J. Grant C. Hopcraft, Joseph O. Ogutu, Jason Matthiopoulos & Laurence Frank
Like many wildlife populations across Africa, recent analyses indicate that African lions are declining rapidly outside of small fenced areas. Community conservancies – privately protected areas that engage community members in conservation – may potentially maintain wildlife populations in unfenced pastoralist regions, but their effectiveness in conserving large carnivores has been largely unknown until now. We identify drivers of lion survival in community conservancies within the Masai Mara ecosystem, Kenya, applying mark–recapture analyses to continuous...

Data from: Estimating resource preferences of a native bumblebee: the effects of availability and use-availability models on preference estimatess

Alexandra N. Harmon-Threatt, Perry De Valpine & Claire Kremen
Identifying resource preference is considered essential for developing targeted conservation plans but, for many species, questions remain about the best way to estimate preference. Resource preferences for bees are particularly difficult to determine as the resources they collect, nectar and pollen, are challenging to estimate availability and collection. Resources are traditionally measured at the flower or inflorescence level, but these measures of availability do not correspond to the resources actually used by bees. Additionally, it...

Data from: Agricultural practices for food safety threaten pest control services for fresh produce

Daniel S. Karp, Rebekah Moses, Sasha Gennet, Matthew S. Jones, Shimat Joseph, Leithen K. M'Gonigle, Lauren C. Ponisio, William E. Snyder & Claire Kremen
Over the past decade, several foodborne disease outbreaks provoked widespread reforms to the fresh produce industry. Subsequent concerns about wildlife vectors and contaminated manures created pressure on growers to discontinue use of manure-based composts and remove nearby semi-natural vegetation. Despite widespread adoption, impacts of these practices on ecosystem services such as pest control have not been assessed. We used a landscape-scale field experiment to quantify associations between compost applications, semi-natural vegetation, pest control services and...

Registration Year

  • 2016
    42

Resource Types

  • Dataset
    42

Affiliations

  • University of California System
    42
  • University of California, Berkeley
    7
  • San Diego State University
    4
  • University of California, Riverside
    4
  • University of California, Davis
    4
  • University of Florida
    3
  • University of North Carolina
    2
  • The University of Texas at Arlington
    2
  • University of Lausanne
    2
  • Australian National University
    2