19 Works

Data from: A generalist brood parasite modifies use of a host in response to reproductive success

Matthew I. M. Louder, Wendy M. Schelsky, Amber N. Albores & Jeffrey P. Hoover
Avian obligate brood parasites, which rely solely on hosts to raise their young, should choose the highest quality hosts to maximize reproductive output. Brown-headed cowbirds (Molothrus ater) are extreme host generalists, yet female cowbirds could use information based on past reproductive outcomes to make egg-laying decisions thus minimizing fitness costs associated with parasitizing low-quality hosts. We use a long-term (21 years) nest-box study of a single host, the prothonotary warbler (Protonotaria citrea), to show that...

Data from: aTRAM - automated Target Restricted Assembly Method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

Julie M Allen, Daisie I. Huang, Quentin C Cronk & Kevin P Johnson
Background: Assembling genes from next-generation sequencing data is not only time consuming but computationally difficult, particularly for taxa without a closely related reference genome. Assembling even a draft genome using de novo approaches can take days, even on a powerful computer, and these assemblies typically require data from a variety of genomic libraries. Here we describe software that will alleviate these issues by rapidly assembling genes from distantly related taxa using a single library of...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles

Courtney L. Cox, James R. Doroghazi & Douglas A. Mitchell
Background: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a burgeoning class of natural products with diverse activity that share a similar origin and common features in their biosynthetic pathways. The precursor peptides of these natural products are ribosomally produced, upon which a combination of modification enzymes installs diverse functional groups. This genetically encoded peptide-based strategy allows for rapid diversification of these natural products by mutation in the precursor genes merged with unique combinations of...

Data from: Genomic diversity and differentiation of a managed island wild boar population

Laura Iacolina, Massimo Scandura, Daniel J. Goedbloed, Panoraia Alexandri, Richard P. M. A. Crooijmans, Greger Larson, Alan Archibald, Marco Apollonio, Lawrence B. Schook, Martien A. Groenen & Hendrik-Jan Megens
The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and...

Data from: Scale-dependent role of demography and dispersal on the distribution of populations in heterogeneous landscapes

Benjamin T. Martin, Sergiusz Czesny, David H. Wahl & Volker Grimm
Both dispersal and local demographic processes determine a population's distribution among habitats of varying quality, yet most theory, experiments, and field studies have focused on the former. We use a generic model to show how both processes contribute to a population's distribution, and how the relative importance of each mechanism depends on scale. In contrast to studies only considering habitat-dependent dispersal, we show that predictions of ideal free distribution (IFD) theory are relevant even at...

Data from: Serum amyloid A protein concentration in blood is influenced by genetic differences in the cheetah (Acinonyx jubatus)

Ashley D. Franklin, Anne Schmidt-Küntzel, Karen A. Terio, Laurie L. Marker & Adrienne E. Crosier
Systemic amyloid A (AA) amyloidosis is a major cause of morbidity and mortality among captive cheetahs. The self-aggregating AA protein responsible for this disease is a byproduct of serum amyloid A (SAA) protein degradation. Transcriptional induction of the SAA1 gene is dependent on both C/EBPβ and NF-κB cis-acting elements within the promoter region. In cheetahs, 2 alleles exist for a single guanine nucleotide deletion in the putative NF-κB binding site. In this study, a novel...

Data from: Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology

Andres Gomez, Klara Petrzelkova, Carl J. Yeoman, Klara Vlckova, Jakub Mrázek, Ingrid Koppova, Franck Carbonero, Alexander Ulanov, David Modry, Angelique Todd, Manolito Torralba, Karen Nelson, H. Rex Gaskins, Brenda Wilson, Rebecca M. Stumpf, Bryan A. White, Steven R. Leigh & Karen E. Nelson
The metabolic activities of gut microbes significantly influence host physiology; thus, characterizing the forces that modulate this micro-ecosystem is key to understanding mammalian biology and fitness. To investigate the gut microbiome of wild primates and determine how these microbial communities respond to the host's external environment, we characterized faecal bacterial communities and, for the first time, gut metabolomes of four wild lowland gorilla groups in the Dzanga-Sangha Protected Areas, Central African Republic. Results show that...

Data from: Differential responses of marine communities to natural and anthropogenic changes

Michal Kowalewski, Jacelyn M. Wittmer, Troy A. Dexter, Alessandro Amorosi & Daniele Scarponi
Responses of ecosystems to environmental changes vary greatly across habitats, organisms, and observational scales. The Quaternary fossil record of the Po Basin demonstrates that marine communities of Northern Adriatic reemerged unchanged following the most recent glaciation, which lasted ~100,000 years. The Late Pleistocene and Holocene interglacial ecosystems were both dominated by the same species, species turnover rates approximated predictions of resampling models of a homogenous system, and comparable bathymetric gradients in species composition, sample-level diversity,...

Data from: A novel landscape genetics approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum)

Maria Jose Ruiz-Lopez, Claudia Barelli, Francesco Rovero, Keith Hodges, Christian Roos, William E. Peterman & Nelson Ting
A comprehensive understanding of how human disturbance affects tropical forest ecosystems is critical for the mitigation of future losses in global biodiversity. Although many genetic studies of tropical forest fragmentation have been conducted to provide insight into this issue, relatively few have incorporated landscape data to explicitly test the effects of human disturbance on genetic differentiation among populations. In this study, we use a newly developed landscape genetic approach that relies on a genetic algorithm...

Data from: Evolution of the assassin’s arms: insights from a phylogeny of combined transcriptomic and ribosomal DNA data (Heteroptera: Reduvioidea)

Junxia Zhang, Eric R. L. Gordon, Michael Forthman, Wei Song Hwang, Kim Walden, Daniel R. Swanson, Kevin P. Johnson, Rudolf Meier & Christiane Weirauch
Assassin bugs (Reduvioidea) are one of the most diverse (>7,000 spp.) lineages of predatory animals and have evolved an astounding diversity of raptorial leg modifications for handling prey. The evolution of these modifications is not well understood due to the lack of a robust phylogeny, especially at deeper nodes. We here utilize refined data from transcriptomes (370 loci) to stabilize the backbone phylogeny of Reduvioidea, revealing the position of major clades (e.g., the Chagas disease...

Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms

Niv Sabath, Emma E. Goldberg, Lior Glick, Moshe Einhorn, Tia-Lynn Ashman, Ray Ming, Sarah P. Otto, Jana Vamosi, Itay Mayrose & Jana C. Vamosi
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious...

Data from: Fat, fibre and cancer risk in African Americans and rural Africans

Stephen J. D. O’Keefe, Jia V. Li, Leo Lahti, Junhai Ou, Franck Carbonero, Mohammed Khaled, Joram M. Posma, James Kinross, Elaine Wahl, Elizabeth Ruder, Kishore Vipperla, Vasudevan Naidoo, Lungile Mtshali, Sebastian Tims, Philippe G. B. Puylaert, James DeLany, Alyssa Krasinskas, Ann C. Benefiel, Hatem O. Kaseb, Keith Newton, Jeremy K. Nicholson, Willem M. De Vos, H. Rex Gaskins & Erwin G. Zoetendal
Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in...

Data from: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

Tong Geon Lee, Indrajit Kumar, Brian W. Diers & Matthew E. Hudson
The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of...

Data from: Disentangling environmental drivers of metabolic flexibility in birds: the importance of temperature extremes versus temperature variability

Maria Stager, Henry S. Pollock, Phred M. Benham, Nicholas D. Sly, Jeffrey D. Brawn & Zachary A. Cheviron
Examining physiological traits across large spatial scales can shed light on the environmental factors driving physiological variation. For endotherms, flexibility in aerobic metabolism is especially important for coping with thermally challenging environments and recent research has shown that aerobic metabolic scope [the difference between maximum thermogenic capacity (Msum) and basal metabolic rate (BMR)] increases with latitude in mammals. One explanation for this pattern is the climatic variability hypothesis, which predicts that flexibility in aerobic metabolism...

Data from: Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis

William P. Wysocki, Lynn G. Clark, Eduardo Ruiz-Sanchez, Lakshmi Attigala & Melvin R. Duvall
Background: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae. Results: Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13...

Data from: Identification of the Minimal Cytolytic Unit for Streptolysin S and an Expansion of the Toxin Family

Evelyn M. Molloy, Sherwood R. Casajens, Courtney L. Cox, Tucker Maxson, Nicole A. Ethridge, Gabriele Margos, Volker Fingerle & Douglas A. Mitchell
Background: Streptolysin S (SLS) is a cytolytic virulence factor produced by the human pathogen Streptococcus pyogenes and other Streptococcus species. Related “SLS-like” toxins have been characterized in select strains of Clostridium and Listeria, with homologous clusters bioinformatically identified in a variety of other species. SLS is a member of the thiazole/oxazole-modified microcin (TOMM) family of natural products. The structure of SLS has yet to be deciphered and many questions remain regarding its structure-activity relationships. Results:...

Data from: A female’s past experience with predators affects male courtship and the care her offspring will receive from their father

Katie McGhee, Sally Feng, Sagan Leasure, Alison Bell & Alison M. Bell
Differential allocation occurs when individuals adjust their reproductive investment based on their partner's traits. However, it remains unknown whether animals differentially allocate based on their partner's past experiences with predation risk. If animals can detect a potential mate’s experience with predators, this might inform them about the stress level of their potential mate, the likelihood of parental effects in offspring, and/or the dangers present in the environment. Using threespined stickleback (Gasterosteus aculeatus), we examined whether...

Data from: Shedding light on a cryptic cavernicole: a second species of Zenkevitchia Birstein (Crustacea: Amphipoda: Typhlogammaridae) discovered via molecular techniques

Dmitry A. Sidorov, Andrey A. Gontcharov, Dmitry M. Palatov, Steven J. Taylor, Alexander A. Semenchenko, Steven Taylor & Dmitry Palatov
The Abkhazian region, in the southern foothills of the Caucasus Mountain Range, comprises a unique natural environment containing numerous subterranean habitats with relict and endemic lineages of obligate stygofauna. We aimed to assess the molecular phylogenetic relationships of Typhlogammaridae species from Balkan and Transcaucasian caves using the mitochondrial cytochrome c oxidase I (COI) in hopes of discovering previously undetected biodiversity. Our results showed molecular divergence within the genus Zenkevitchia Birstein, with two distinct groups located...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Illinois at Urbana Champaign
  • University of Pittsburgh
  • Wageningen University & Research
  • Helmholtz Centre for Environmental Research
  • Federal Institute of São Paulo
  • University of Montana
  • Sao Paulo State University
  • University of Hohenheim
  • Ghent University
  • Federal University of São Carlos