108 Works

Anthropogenic noise alters parental behavior and nestling development, but not fledging condition

Meelyn Mayank Pandit, James Eapen, Gabriela Pineda-Sabilon, Margaret Caulfield, Alexander Moreno, Jay Wilhelm, Jessica Ruyle, Eli Bridge & Darren Proppe
Anthropogenic noise is a ubiquitous feature of the American landscape, and is a known stressor for many bird species, leading to negative effects in behavior, physiology, reproduction, and ultimately fitness. While a number of studies have examined how anthropogenic noise affects avian fitness, there are few that simultaneously examine how anthropogenic noise impacts the relationship between parental care behavior and nestling fitness. We conducted Brownian noise playbacks for six hours a day during the nesting...

Data from: Genome reduction and microbe-host interactions drive adaptation of a sulfur-oxidizing bacterium associated with a cold seep sponge

Ren-Mao Tian, Weipeng Zhang, Lin Cai, Yue-Him Wong, Wei Ding & Pei-Yuan Qian
As the most ancient metazoan, sponges have established close relationships with particular microbial symbionts. However, the characteristics and physiology of thioautotrophic symbionts in deep-sea sponges are largely unknown. Using a tailored “differential coverage binning” method on 22-Gb metagenomic sequences, we recovered the nearly complete genome of a sulfur-oxidizing bacterium (SOB) that dominates the microbiota of the cold seep sponge Suberites sp. Phylogenetic analyses suggested that this bacterium (an unclassified gammaproteobacterium termed “Gsub”) may represent a...

Data from: A carbohydrate-rich diet increases social immunity in ants

Adam D. Kay, Abbie J. Bruning, Andy Van Alst, Tyler T. Abrahamson, William O. H. Hughes & Michael Kaspari
Increased potential for disease transmission among nest-mates means living in groups has inherent costs. This increased potential is predicted to select for disease resistance mechanisms that are enhanced by cooperative exchanges among group members, a phenomenon known as social immunity. One potential mediator of social immunity is diet nutritional balance because traits underlying immunity can require different nutritional mixtures. Here, we show how dietary protein–carbohydrate balance affects social immunity in ants. When challenged with a...

Data from: Invasion facilitates hybridization with introgression in the Rattus rattus species complex

Justin B. Lack, Daniel U. Greene, Chris John Conroy, Meredith J. Hamilton, Janet K. Braun, Michael A. Mares & Ronald A. Van Den Bussche
Biological invasions result in novel species interactions, which can have significant evolutionary impacts on both native and invading taxa. One evolutionary concern with invasions is hybridization among lineages that were previously isolated, but make secondary contact in their invaded range(s). Black rats, consisting of several morphologically very similar but genetically distinct taxa that collectively have invaded six continents, are arguably the most successful mammalian invaders on the planet. We used mitochondrial cytochrome b sequences, two...

Data from: Archipelago-wide survey of Philippine forest dragons (Agamidae: Gonocephalus): multilocus phylogeny uncovers unprecedented levels of genetic diversity in a biodiversity hotspot

Luke J. Welton, Cameron D. Siler, L. L. Grismer, Arvin C. Diesmos, Jack W. Sites & Rafe M. Brown
We utilize robust geographical genetic sampling, a multilocus dataset, and coalescent-based species delimitation statistics to provide the first phylogenetic inferences of relationships of Philippine Gonocephalus, combined with estimates of putative species diversity in this virtually unknown island radiation. Our results reveal startling levels of undocumented diversity, genetically partitioned at a number of geographic levels across the archipelago. In this paper we present the first survey of genetic lineage diversity, coupled with an archipelago-wide elucidation of...

Data from: Maternal effects are no match for stressful conditions: a test of the maternal match hypothesis in a common zooplankter.

Jessica E. Beyer & K. David Hambright
1. Maternal effects modulate population responses to environmental conditions and so are predicted to play a large role in the responses of organisms to global change. 2. In response to one such aspect of global change, the eutrophication of freshwaters and associated blooms of the toxin-producing cyanobacteria species Microcystis aeruginosa, the rotifer Brachionus calyciflorus produces larger offspring. 3. We hypothesized that rotifers exposed to Microcystis may be adaptively increasing offspring investment and offspring fitness (i.e....

Divergence, gene flow, and speciation in eight lineages of trans-Beringian birds

Kevin Winker, Jessica McLaughlin, Travis Glenn & Brant Faircloth
Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans-Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks,...

Bottom-up when it is not top-down: Predators and plants control biomass of grassland arthropods

Ellen Welti, Rebecca Prather, Nate Sanders, Kirsten De Beurs & Michael Kaspari
1) We investigate where bottom-up and top-down control regulates ecological communities as a mechanism linking ecological gradients to the geography of consumer abundance and biomass. We use standardized surveys of 54 North American grasslands to test alternate hypotheses predicting 100-fold shifts in the biomass of four common grassland arthropod taxa—Auchenorrhyncha, sucking herbivores, Acrididae, chewing herbivores, Tettigoniidae, omnivores, and Araneae, predators. 2) Bottom-up models predict that consumer biomass tracks plant quantity (e.g. productivity and standing biomass)...

Data from: Parallel Pleistocene amphitropical disjunctions in a parasitic plant and its host

Adam C. Schneider & Abigail J. Moore
PREMISE OF THE STUDY: Aphyllon is a clade of holoparasites that includes closely related North American and South American species parasitic on Grindelia. Both Aphyllon (Orobanchaceae) and Grindelia (Asteraceae) have amphitropical disjunctions between North America and South America; however, the timing of these patterns and the processes to explain them are unknown. METHODS: Chronograms for the Orobanchaceae and Grindelia and their relatives were constructed using fossil and secondary calibration points, one of which was based...

The seventh macronutrient: how sodium shortfall ramifies through populations, food webs, and ecosystems

Michael Kaspari
Of the 25 elements required to build most organisms, sodium has a unique set of characteristics that ramify through terrestrial ecology. In plants, sodium is found in low concentrations and has little metabolic function; in plant consumers, particularly animals, sodium is essential to running costly Na-K ATPases. Here I synthesize a diverse literature from physiology, agronomy, and ecology, toward identifying sodium’s place as the “7th macronutrient”, one whose shortfall targets two trophic levels—herbivores and detritivores....

Data from: Drought mildly reduces plant dominance in a temperate prairie ecosystem across years

Karen Castillioni, Kevin Wilcox, Lifen Jiang, Chang Gyo Jung, Yiqi Luo & Lara Souza
1. Shifts in dominance and species reordering can occur in response to global change. However, it is not clear how altered precipitation and disturbance regimes interact to affect species composition and dominance. 2. We explored community-level diversity and compositional similarity responses, both across and within years, to a manipulated precipitation gradient and annual clipping in a mixed-grass prairie in Oklahoma, USA. We imposed seven precipitation treatments (five water exclusion levels [-20%, -40%, -60%, -80%, and...

Supplementary material for: Phylogenomics and historical biogeography of seahorses, dragonets, goatfishes, and allies (Teleostei: Syngnatharia): Assessing factors driving uncertainty in biogeographic inferences

Ricardo Betancur-R
The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes—the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon...

Data from: Salty, mild, and low plant biomass grasslands increase top-heaviness of invertebrate trophic pyramids

Ellen Welti, Lucie Kuczynski, Katharine Markse, Nathan Sanders, Kirsten De Beurs & Michael Kaspari
Aim Multiple hypotheses predict how gradients of nutrient availability, plant biomass, and temperature shape trophic pyramids. We aim to disentangle the simultaneous influence of those different factors and their indirect effects on trophic structure and individual trophic levels. Location United States Time period 2017 Major taxa studied Invertebrates Methods To examine differences in trophic pyramid shape and abundance within trophic levels across ecological gradients, we used a structural equation modeling approach to analyze 54 standardized...

Rice genome-scale network integration reveals transcriptional regulators of grass cell wall synthesis

Laura Bartley & Kangmei Zhao
Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases....

Double-tagging scores of seabirds reveals that light-level geolocator accuracy is limited by species idiosyncrasies and equatorial solar profiles

Luke Halpin, Jeremy Ross, Raül Ramos, Rowan Mott, Nicholas Carlile, Nick Golding, José Manuel Reyes-González, Teresa Militão, Fernanda De Felipe, Zuzana Zajková, Marta Cruz Flores, Sarah Saldanha, Virginia Morera-Pujol, Leia Navarro-Herrero, Laura Zango, Jacob Gonzalez-Solis & Rohan Clarke
Light-level geolocators are popular bio-logging tools, with advantageous sizes, longevity, and affordability. Biologists tracking seabirds often presume geolocator spatial accuracies between 186-202 km from previously-innovative, yet taxonomically, spatially, and computationally limited, studies. Using recently developed methods, we investigated whether assumed uncertainty norms held across a larger-scale, multispecies study. We field-tested geolocator spatial accuracy by synchronously deploying these with GPS loggers on scores of seabirds across five species and 11 Mediterranean Sea, East Atlantic and South...

Data from: Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution

Richard E. Broughton, Ricardo Betancur-R., Chenhong Li, Gloria Arratia & Guillermo Orti
Over half of all vertebrates are “fishes”, which exhibit enormous diversity in morphology, physiology, behavior, reproductive biology, and ecology. Investigation of fundamental areas of vertebrate biology depend critically on a robust phylogeny of fishes, yet evolutionary relationships among the major actinopterygian and sarcopterygian lineages have not been conclusively resolved. Although a consensus phylogeny of teleosts has been emerging recently, it has been based on analyses of various subsets of actinopterygian taxa, but not on a...

Data from: Critically endangered island endemic or peripheral population of a widespread species? Conservation genetics of Kikuchi’s gecko and the global challenge of protecting peripheral oceanic island endemic vertebrates

Cameron D. Siler, Jamie R. Oaks, Kerry Cobb, Hidetoshi Ota & Rafe M. Brown
Aim: To highlight the significant conservation challenge of evaluating peripheral endemic vertebrates in island archipelago systems and to assess empirically the complexities of approaches to conservation genetic studies across political and biogeographic boundaries. To demonstrate the poignant need for international collaboration and coordination when species delimitation problems with high conservation concern involve island endemics with biogeographically peripheral ranges. Location: Southeast Asia, Lanyu Island, Taiwan, and the Philippines. Methods: Genetic samples were collected and sequenced for...

Data from: A Flippase-mediated GAL80/GAL4 intersectional resource for dissecting appendage development in Drosophila

Brittany N. Smith, Arash M. Ghazanfari, Rudolf A. Bohm, William P. Welch, Bing Zhang & John P. Masly
Drosophila imaginal discs provide an ideal model to study processes important for cell signaling and cell specification, tissue differentiation, and cell competition during development. One challenge to understanding genetic control of cellular processes and cell interactions is the difficulty in effectively targeting a defined subset of cells in developing tissues in gene manipulation experiments. A recently developed Flippase-induced intersectional GAL80/GAL4 repression method incorporates several gene manipulation technologies in Drosophila to enable such fine-scale dissection in...

Data from: Agricultural intensification and the functional capacity of soil microbes on smallholder African farms

Stephen A. Wood, Mark A. Bradford, Jack A. Gilbert, Krista L. McGuire, Cheryl A. Palm, Katherine L. Tully, Jizhong Zhou & Shahid Naeem
1. Fertilization may impact ecosystem processes that sustain agriculture, such as nutrient cycling, by altering the composition of soil microbial communities that regulate such processes. These processes are crucial to low-input, smallholder tropical agriculture, which supports 900 million of the world's poorest people. Yet little is known about how efforts to increase crop yield on such farms will affect the capacity of soil microbial communities to carry out ecosystem processes. 2. We studied the diversity...

Data from: Brain transcriptional profiles of male alternative reproductive tactics and females in bluegill sunfish

Charlyn G. Partridge, Matthew D. MacManes, Rosemary Knapp & Bryan D. Neff
Bluegill sunfish (Lepomis macrochirus) are one of the classic systems for studying male alternative reproductive tactics (ARTs) in teleost fishes. In this species, there are two distinct life histories: parental and cuckolder, encompassing three reproductive tactics, parental, satellite, and sneaker. The parental life history is fixed, whereas individuals who enter the cuckolder life history transition from sneaker to satellite tactic as they grow. For this study, we used RNAseq to characterize the brain transcriptome of...

Data from: Mechanical and tactile incompatibilities cause reproductive isolation between two young damselfly species

Alexandra A. Barnard, Ola M. Fincke, Mark A. McPeek & John P. Masly
External male reproductive structures have received considerable attention as a cause of reproductive isolation (RI), because the morphology of these structures often evolves rapidly between populations. This rapid evolution presents the potential for mechanical incompatibilities with heterospecific female structures during mating and could thus prevent interbreeding between nascent species. Although such mechanical incompatibilities have received little empirical support as a common cause of RI, the potential for mismatch of reproductive structures to cause RI due...

Data from: Host species of a sexual-parasite do not differentiate between clones of Amazon mollies

Amber M. Makowicz, Darrshini S. Muthurajah & Ingo Schlupp
A major mechanism of pre-zygotic isolation is the ability for individuals to recognize conspecifics. In gynogenetic species complexes, the sexual host species occur in syntopy with the unisexual species that relies on the sexuals’ sperm for reproduction, which provide an excellent opportunity for the evolution of fine-tuned species recognition capabilities. Here, we examined if males and females from both parental species (sailfin molly, Poecilia latipinna, and Atlantic molly, P. mexicana) can distinguish between different clonal...

Data from: Toward a geography of omnivory: omnivores increase carnivory when sodium is limiting

Natalie A. Clay, Richard J. Lehrter & Michael Kaspari
1. Toward understanding the geography of omnivory, we tested three hypotheses that predict the proportion of animal tissue consumed: The Sodium Limitation Hypothesis predicts that omnivores increase animal consumption in Na-poor environments because Na bioaccumulates from plants to predators; thus, heterotrophs are Na-rich sources. The Nitrogen Limitation and Habitat Productivity Hypotheses use the same logic to predict more animal consumption in N-poor and productive environments respectively. 2. Omnivory is a common trophic strategy, but what...

Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)

Abigail J. Moore, Jurriaan M. De Vos, Lillian P. Hancock, Eric Goolsby & Erika J. Edwards
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny...

Data from: Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska

Jie Deng, Yunfu Gu, Jin Zhang, Kai Xue, Yujia Qin, Mengting Yuan, Huaqun Yin, Zhili He, Liyou Wu, Edward Schuur, James Tiedje, Jizhong Zhou, James M. Tiedje & Edward A. G. Schuur
Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and...

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