20 Works

Data from: A genetic demographic analysis of Lake Malawi rock-dwelling cichlids using spatio-temporal sampling

Martin Husemann, Rachel Nguyen, Baoqing Ding & Patrick D. Danley
We estimated the effective population sizes (Ne) and tested for short-term temporal demographic stability of populations of two Lake Malawi cichlids: Maylandia benetos, a micro-endemic, and Maylandia zebra, a widespread species found across the lake. We sampled a total of 351 individuals, genotyped them at 13 microsatellite loci and sequenced their mitochondrial D-loop to estimate genetic diversity, population structure, demographic history and effective population sizes. At the microsatellite loci, genetic diversity was high in all...

Data from: From a line in the sand to a landscape of decisions: a Hierarchical Diversity Decision Framework (HiDDeF) for estimating and communicating biodiversity loss along anthropogenic gradients

Kristofor A. Voss, Ryan S. King & Emily S. Bernhardt
1. In setting water quality criteria, managers must choose thresholds for stressors that are protective of aquatic biodiversity. Setting such thresholds requires making implicit judgments about the degree of biodiversity loss that managers are willing to accept. 2. We present a new modeling approach, the Hierarchical Diversity Decision Framework model (HiDDeF) that explicitly communicates the sensitivity of water quality benchmarks to these implicit judgements. We apply HiDDeF to a dataset of stream macroinvertebrate abundances across...

Data from: Predicting nitrate retention at the groundwater- surface water interface in sandplain streams

Robert S Stelzer & J. Thad Scott
Groundwater-surface water ecotones present opportunities for nitrate retention because changes in organic carbon availability, redox potential and nitrate demand often occur at these locations. Although there have been many measurements of nitrate retention and denitrification at the groundwater-surface water interface few investigators have quantitatively predicted where nitrogen transformation occurs in this zone. Our main objective was to describe and predict spatial variation in nitrate retention and removal in shallow groundwater among and within streams in...

Data from: \"De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

Wolfgang Arthofer, Francesco Cicconardi, Nicola Palmieri, Viola Nolte, Christian Schlötterer, Birgit C. Schlick-Steiner, Florian M. Steiner, Marcelo Vallinoto, David A. Weese, B. L. Banbury, R. B. Harris, David S. Kang, Cheolho Sim, Thomas F. Duda, A. D. Leaché, Miguel Carneiro, Coralie Nourisson & Fernando Sequeira
Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to the European montane/alpine zone (Bächli 2008). Mountain biodiversity is considered highly vulnerable to ongoing climate warming (IPCC 2013), and organisms at high altitudes have only limited possibility to shift to cooler habitats at elevations above (Pertoldi & Bach 2007). For such species, rapid evolution may offer a solution for long-term survival. We are establishing D. nigrosparsa as a model system to test the extent and tempo...

Echinoid Associated Traces (EAT)

Elizabeth Petsios, Roger Portell, Shamindri Tennakoon, Tobias Grun, Michal Kowalewski, Lyndsey Farrar & Carrie Tyler
Predation traces found on fossilized prey remains can be used to quantify the evolutionary history of biotic interactions. Fossil mollusk shells bearing these types of traces provided key evidence for the rise of predation during the Mesozoic Marine Revolution (MMR), an event which is thought to have reorganized global marine ecosystems. However, predation pressure on prey groups other than mollusks has not been explored adequately. Consequently, the ubiquity, tempo, and synchronicity of the MMR cannot...

Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny

Kathryn Uckele, Robert Adams, Thomas Parchman & Andrea Schwarzbach
Juniper (Juniperus) is an ecologically important conifer genus of the Northern Hemisphere, the members of which are often foundational tree species of arid regions. The serrate leaf margin clade is native to topologically variable regions in North America, where hybridization has likely played a prominent role in their diversification. Here we use a reduced-representation sequencing approach (ddRADseq) to generate a phylogenomic data set for 68 accessions representing all 22 species in the serrate leaf margin...

Data for: Freeze tolerance influenced forest cover and hydrology during the Pennsylvanian

William Matthaeus, Sophia I. Macarewich, Jon D. Richey, Jonathan P. Wilson, Jennifer C. McElwin, Isabel P. Montañez, William A. DiMichele, Michael T. Hren, Christopher J. Poulsen & Joseph D. White
Global forest cover affects the Earth system by altering surface mass and energy exchange. Physiology determines plant environmental limits and influences geographical vegetation distribution. Ancient plant physiology, therefore, likely affected vegetation-climate feedbacks. We combine climate modeling and ecosystem-process modeling to simulate arboreal vegetation in the late Paleozoic ice age. Using GENESIS V3 GCM simulations, varying pCO2, pO2, and ice extent for the Pennsylvanian, and fossil-derived leaf C:N, maximum stomatal conductance, and specific conductivity for several...

Data from: Compensatory dynamics of lotic algae break down nonlinearly with increasing nutrient enrichment

Stephen Cook
One important mechanism governing the temporal maintenance of biodiversity is asynchrony in cooccurring competitors due to fluctuating environments (i.e. compensatory dynamics). Temporal niche partitioning has evolved in response to predictable oscillations in environmental conditions so that species may offset competition, but we do not yet have a clear understanding of how novel anthropogenic stressors alter seasonal patterns of succession. Many primary producers are nutrient-limited, and enrichment may decrease the importance of environmental fluctuations that govern...

Data from: Evolution of body shape in differently colored sympatric congeners and allopatric populations of Lake Malawi’s rock-dwelling cichlids

Martin Husemann, Michael Tobler, Cagney McCauley, Baoqing Ding & Patrick D. Danley
The cichlid fishes of Lake Malawi represent one of the most diverse adaptive radiations of vertebrates known. Among the rock-dwelling cichlids (mbuna), closely related sympatric congeners possess similar trophic morphologies (i.e. cranial and jaw structures), defend overlapping or adjacent territories, but can be easily distinguished based on male nuptial coloration. The apparent morphological similarity of congeners, however, leads to an ecological conundrum: theory predicts that ecological competition should lead to competitive exclusion. Hence, we hypothesized...

Data from: First evidence for allotriploid hybrids between Juniperus thurifera and J. sabina in a sympatric area in the French Alps

Perla Farhat, Najat Takvorian, Maria Avramidou, Luc Garraud, Robert P. Adams, Sonja Siljak-Yakovlev, Magda Bou Dagher Kharrat & Thierry Robert
At Saint Crépin location (French Alps), where sympatry between the tetraploid Juniperus thurifera and the diploid Juniperus sabina occurs, three individuals with an atypical morphology, have been observed. AFLP markers were used to unravel hybridization and potential introgression events in this population. In total, 147 polymorphic loci remained after the process of peak selection. This dataset demonstrates hybrids originated from a cross between J. sabina and J. thurifera and suggests that back-cross at least to...

Data from: Biomechanical and leaf-climate relationships: a comparison of ferns and seed plants

Daniel J. Peppe, Casee R. Lemons, Dana L. Royer, Scott L. Wing, Ian J. Wright, Christopher H. Lusk & Chazelle H. Rhoden
Premise of the study: Relationships of leaf size and shape (physiognomy) with climate have been well characterized for woody non-monocotyledonous angiosperms (dicots), allowing the development of models for estimating paleoclimate from fossil leaves. More recently, petiole width of seed plants has been shown to scale closely with leaf mass. By measuring petiole width and leaf area in fossils, leaf mass per area (MA) can be estimated and an approximate leaf life span inferred. However, little...

Data from: \"Transcriptomic resources for three populations of Conus miliaris (Mollusca: Conidae) from Easter Island, American Samoa and Guam\" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014

David A. Weese & Thomas F. Duda
Species interactions represent fundamental ecological processes that can have significant impacts on the evolutionary trajectories of species. However, the contribution of predator-prey interactions to genetic and phenotypic divergence within and between species remains largely unknown. In this context, predatory marine snails of the genus Conus exhibit considerable variation in venom composition, a phenomenon that may be due to the evolution of conotoxins in response to predator-prey interactions. It has been hypothesized that geographic differences in...

Data from: Freshwater eutrophication drives sharp reductions in temporal beta diversity

Stephen C. Cook, Lauren Housley, Jeffrey A. Back & Ryan S. King
Eutrophication has become one of the most widespread anthropogenic forces impacting freshwater biological diversity. One potentially important mechanism driving biodiversity changes in response to eutrophication is the alteration of seasonal patterns of succession, particularly among species with short, synchronous life cycles. We tested the hypothesis that eutrophication reduces seasonally driven variation in species assemblages by focusing on an understudied aspect of biodiversity: temporal beta diversity . We estimated the effect of eutrophication on by sampling...

Data from: Nitrogen transformations differentially affect nutrient-limited primary production in lakes of varying trophic state

J. Thad Scott, Mark J. McCarthy & Hans W. Paerl
The concept of lakes “evolving” phosphorus (P) limitation has persisted in limnology despite limited direct evidence. Here, we developed a simple model to broadly characterize nitrogen (N) surpluses and deficits relative to P in lakes, and compared the magnitude of this imbalance to estimates of N gains and losses through biological N transformations. The model suggested that approximately half of oligotrophic lakes in the US had a stoichiometric N deficit, but almost 90% of the...

Data from: Quantitative genetic analyses of male color pattern and female mate choice in a pair of cichlid fishes of Lake Malawi, East Africa

Baoqing Ding, Daniel W. Daugherty, Martin Husemann, Ming Chen, Aimee E. Howe & Patrick D. Danley
The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits...

Data from: Reconstructing the mass and thermal ecology of North American Pleistocene tortoises

Donald A. Esker, Steven L. Forman & Dava K. Butler
Researchers often interpret the presence of tortoises in Pleistocene assemblages as evidence of an interglacial age, based on an assumption that these fossils indicate thermic climates, as modern giant tortoises require. Since the Paleocene, tortoises have been common components of terrestrial fossil assemblages and have repeatedly evolved species of giant size. Whereas extant giant tortoises are found only on islands off the coasts of South America and Africa, at least two species persisted in North...

Data from: Spatial, temporal, and experimental: three study design cornerstones for establishing defensible numeric criteria in freshwater ecosystems

Jason M. Taylor, Jeffrey A. Back, Bryan W. Brooks & Ryan S. King
1.Nutrient over‐enrichment increasingly threatens global water resources. Stressor‐response studies specifically designed to identify levels of nutrients strongly associated with undesirable ecological conditions are needed to inform numeric nutrient criteria that protect inland waters. 2.Diatoms are important components of aquatic life, which support higher trophic levels and are sensitive to nutrient enrichment. We tested a framework that relies on stressor‐response modelling of phosphorus (P) enrichment and stream diatom assemblages across many field locations, multiple years and...

Data from: Estimating infection prevalence: best practices and their theoretical underpinnings

Ian F. Miller, India Schneider-Crease, Charles L. Nunn & Michael P. Muehlenbein
Accurately estimating infection prevalence is fundamental to the study of population health, disease dynamics, and infection risk factors. Prevalence is estimated as the proportion of infected individuals (“individual-based estimation”), but is also estimated as the proportion of samples from which the disease-causing organisms are recovered (“anonymous estimation”). The latter method is often used when researchers lack information on individual host identity, which can occur during noninvasive sampling of wild populations or when the individual that...

Data from: Detrital nutrient content and leaf species differentially affect growth and nutritional regulation of detritivores

Halvor M. Halvorson, Chris L. Fuller, Sally A. Entrekin, J. Thad Scott & Michelle A. Evans-White
Resource nutrient content and identity are common bottom-up controls on organismal growth and nutritional regulation. One framework to study these factors, ecological stoichiometry theory, predicts that elevated resource nitrogen (N) and phosphorus (P) contents enhance organism growth by alleviating constraints on N and P acquisition. However, the regulatory mechanisms underlying this response – including whether responses depend on resource identity – remain poorly understood. In this study, we tested roles of detrital N and P...

The effects of salinity and N:P on N-rich toxins by both an N-fixing and non-N-fixing cyanobacteria

Felicia Osburn, Nicole Wagner, Raegyn Taylor, Kevin Chambliss, Bryan Brooks & Thad Scott
Freshwater ecosystems are experiencing increased salinization. Adaptive management of harmful algal blooms (HABs) contribute to eutrophication/salinization interactions through the hydrologic transport of blooms to coastal environments. We examined how nutrients and salinity interact to affect growth, elemental composition, and cyanotoxin production/release in two common HAB genera. Microcystis aeruginosa (non-nitrogen (N)-fixer and microcystin-LR producer; MC-LR) and Aphanizomenon flos-aquae (N-fixer and cylindrospermopsin producer; CYN) were grown in N:phosphorus (N:P) 4 and 50 (by atom) for 21 and...

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