451 Works

Data from: Competing influences on morphological modularity in biomechanical systems: a case study in mantis shrimp

Philip S. L. Anderson, Danielle C. Smith & S. N. Patek
Andersonetal2016_Evo&Dev_dataZip file containing the raw tps and centroid size files used for morphometric analyses in the paper.

Data from: Tuning Geometric Morphometrics: an R tool to reduce information loss caused by surface smoothing

Antonio Profico, Alessio Veneziano, Alessandro Lanteri, Paolo Piras, Gabriele Sansalone & Giorgio Manzi
The application of Geometric Morphometrics has remarkably increased since 3D imaging techniques have become widespread, such as high-resolution computerised tomography, laser scanning and photogrammetry. Acquisition, 3D rendering and simplification of virtual objects produce faceting and topological artefacts, which can be counteracted by applying decimation and smoothing algorithms. Nevertheless, smoothing algorithms can have detrimental effects. This work aims at developing a method to assess the amount of information loss or recovery after the application of 3D...

Data from: Point of impact: the effect of size and speed on puncture mechanics

Philip S. L. Anderson, Jeff LaCosse & Mark Pankow
The use of high-speed puncture mechanics for prey capture has been documented across a wide range of organisms, including vertebrates, arthropods, molluscs and cnidarians. These examples span four phyla and seven orders of magnitude difference in size. The commonality of these puncture systems offers an opportunity to explore how organisms at different scales and with differentmaterials,morphologies and kinematics performthe same basic function. However, there is currently no framework for combining kinematic performance with cutting mechanics...

Data from: Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon

Carolyn A. Wessinger, Craig C. Freeman, Mark E. Mort, Mark D. Rausher & Lena C. Hileman
Premise of the study: Evolutionary radiations provide opportunities to examine large-scale patterns in diversification and character evolution, yet are often recalcitrant to phylogenetic resolution due to rapid speciation events. The plant genus Penstemon has been difficult to resolve using Sanger sequence-based markers, leading to the hypothesis that it represents a recent North American radiation. The present study demonstrates the utility of multiplexed shotgun genotyping (MSG), a style of Restriction site-associated DNA sequencing (RADseq), to infer...

Data from: Female and male life tables for seven wild primate species

Anne M. Bronikowski, Marina Cords, Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Linda M. Fedigan, Anne Pusey, Tara Stoinski, Karen B. Strier & William F. Morris
We provide male and female census count data, age-specific survivorship, and female age-specific fertility estimates for populations of seven wild primates that have been continuously monitored for at least 29 years: sifaka (Propithecus verreauxi) in Madagascar; muriqui (Brachyteles hypoxanthus) in Brazil; capuchin (Cebus capucinus) in Costa Rica; baboon (Papio cynocephalus) and blue monkey (Cercopithecus mitis) in Kenya; chimpanzee (Pan troglodytes) in Tanzania; and gorilla (Gorilla beringei) in Rwanda. Using one-year age-class intervals, we computed point...

Data from: A collection of non-human primate computed tomography scans housed in MorphoSource, a repository for 3D data

Lynn E. Copes, Lynn M. Lucas, James D. Thostenson, Hopi E. Hoekstra & Douglas M. Boyer
A dataset of high-resolution microCT scans of primate skulls (crania and mandibles) and certain postcranial elements was collected to address questions about primate skull morphology. The sample consists of 489 scans taken from 431 specimens, representing 53 species of most Primate families. These data have transformative reuse potential as such datasets are necessary for conducting high power research into primate evolution, but require significant time and funding to collect. Similar datasets were previously only available...

Data from: The effects of quantitative fecundity in the haploid stage on reproductive success and diploid fitness in the aquatic peat moss Sphagnum macrophyllum

Matthew G. Johnson & A. Jonathan Shaw
A major question in evolutionary biology is how mating patterns affect the fitness of offspring. However, in animals and seed plants it is virtually impossible to investigate the effects of specific gamete genotypes. In bryophytes, haploid gametophytes grow via clonal propagation and produce millions of genetically identical gametes throughout a population. The main goal of this research was to test whether gamete identity has an effect on the fitness of their diploid offspring in a...

Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Polly Y. Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J. Rothfels, Uwe Ohler & Philip N. Benfey
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main...

Data from: Costs and benefits of group living in primates: an energetic perspective

A. Catherine Markham & Laurence R. Gesquiere
Group size is a fundamental component of sociality, and has important consequences for an individual's fitness as well as the collective and cooperative behaviours of the group as a whole. This review focuses on how the costs and benefits of group living vary in female primates as a function of group size, with a particular emphasis on how competition within and between groups affects an individual's energetic balance. Because the repercussions of chronic energetic stress...

Data from: Fertilizer legacies meet saltwater incursion: challenges and constraints for coastal plain wetland restoration

Marcelo Ardón, Ashley M. Helton, Mark D. Scheuerell & Emily S. Bernhardt
Coastal wetland restoration is an important tool for climate change adaptation and excess nutrient runoff mitigation. However, the capacity of restored coastal wetlands to provide multiple ecosystem services is limited by stressors, such as excess nutrients from upstream agricultural fields, high nutrient legacies on-site, and rising salinities downstream. The effects of these stressors are exacerbated by an accelerating hydrologic cycle, expected to cause longer droughts punctuated by more severe storms. We used seven years of...

Data from: Differential adaptation to a harsh granite outcrop habitat between sympatric Mimulus species

Kathleen Gray Ferris & John H. Willis
Understanding which environmental variables and traits underlie adaptation to harsh environments is difficult since many traits evolve simultaneously as populations or species diverge. Here we investigate the ecological variables and traits that underlie Mimulus laciniatus’ adaptation to granite outcrops compared to its sympatric, mesic-adapted progenitor M. guttatus. We use fine scale measurements of soil moisture and herbivory to examine differences in selective forces between the species’ habitats, and measure selection on flowering time, flower size,...

Data from: Smashing mantis shrimp strategically impact shells

R. L. Crane, S. M. Cox, S.A. Kisare & S. N. Patek
Many predators fracture strong mollusk shells, requiring specialized weaponry and behaviors. The current shell fracture paradigm is based on jaw- and claw-based predators that slowly apply forces (high impulse, low peak force). However, predators also strike shells with transient intense impacts (low impulse, high peak force). Toward the goal of incorporating impact fracture strategies into the prevailing paradigm, we measured how mantis shrimp (Neogonodactylus bredini) impact snail shells, tested whether they strike shells in different...

Data from: Sizing ocean giants: patterns of intraspecific size variation in marine megafauna

Craig R. McClain, Meghan A. Balk, Mark C. Benfield, Trevor A. Branch, Catherine Chen, James Cosgrove, Alistair D. M. Dove, Leo C. Gaskins, Rebecca Helm, Frederick G. Hochberg, Frank B. Lee, Andrea Marshall, Steven E. McMurray, Caroline Schanche, Shane N. Stone, Andrew D. Thaler & Rebecca R. Helm
What are the greatest sizes that the largest marine megafauna obtain? This is a simple question with a difficult and complex answer. Many of the largest-sized species occur in the world’s oceans. For many of these, rarity, remoteness, and quite simply the logistics of measuring these giants has made obtaining accurate size measurements difficult. Inaccurate reports of maximum sizes run rampant through the scientific literature and popular media. Moreover, how intraspecific variation in the body...

Data from: Mechanical sensitivity reveals evolutionary dynamics of mechanical systems

Philip S. L. Anderson & Sheila N. Patek
A classic question in evolutionary biology is how form–function relationships promote or limit diversification. Mechanical metrics, such as kinematic transmission (KT) in linkage systems, are useful tools for examining the evolution of form and function in a comparative context. The convergence of disparate systems on equivalent metric values (mechanical equivalence) has been highlighted as a source of potential morphological diversity under the assumption that morphology can evolve with minimal impact on function. However, this assumption...

Data from: Exaggerated sexual swellings and male mate choice in primates: testing the reliable indicator hypothesis in the Amboseli baboons

Courtney L. Fitzpatrick, Jeanne Altmann & Susan C. Alberts
The paradigm of competitive males vying to influence female mate choice has been repeatedly upheld, but, increasingly, studies also report competitive females and choosy males. One female trait that is commonly proposed to influence male mate choice is the exaggerated sexual swelling displayed by females of many Old World primate species. The reliable indicator hypothesis posits that females use the exaggerated swellings to compete for access to mates, and that the swellings advertise variation in...

Data from: Variation in the impact of non-native seaweeds along gradients of habitat degradation: a meta-analysis and an experimental test

Laura Tamburello, Elena Maggi, Lisandro Benedetti-Cecchi, Giuseppe Bellistri, Alex James Rattray, Chiara Ravaglioli, Luca Rindi, Jason Roberts & Fabio Bulleri
Biological invasions are acknowledged among the main drivers of global changes in biodiversity. Despite compelling evidence of species interactions being strongly regulated by environmental conditions, there is a dearth of studies investigating how the effects of non-native species vary among areas exposed to different anthropogenic pressures. Focusing on marine macroalgae, we performed a meta-analysis to test whether and how the direction and magnitude of their effects on resident communities and species varies in relation to...

Data from: Comparative and population mitogenomic analyses of Madagascar’s extinct, giant ‘subfossil’ lemurs

Logan Kistler, Aakrosh Ratan, Laurie R. Godfrey, Brooke E. Crowley, Cris E. Hughes, Runhua Lei, Yinqui Cui, Mindy L. Wood, Kathleen M. Muldoon, Haingoson Andriamialison, John J. McGraw, Lynn P. Tomsho, Stephan C. Schuster, Webb Miller, Edward E. Louis, Anne D. Yoder, Ripan S. Malhi, George H. Perry & Yinqiu Cui
Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct ‘subfossil’ lemur species, all of which were substantially larger (body mass ∼11–160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study...

Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).

Laurence R. Gesquiere, Toni E. Ziegler, Patricia A. Chen, Katherine A. Epstein, Susan C. Alberts & Jeanne Altmann
The development of non-invasive methods, particularly fecal determination, has made possible the assessment of hormone concentrations in wild animal populations. However, measuring fecal metabolites needs careful validation for each species and for each sex. We investigated whether radioimmunoassays (RIAs) previously used to measure fecal testosterone (fT) in male baboons and fecal estrogens (fE) in female baboons were well suited to measure these hormones in the opposite sex. We compared fE and fT concentrations determined by...

Data from: Incorporating thresholds into understanding salinity tolerance: a study using salt-tolerant plants in salt marshes

Qiang He, Brian R. Silliman & Baoshan Cui
Although salinity in many ecosystems such as salt marshes can be extremely high, an asymmetry in salinity range between experimental studies (relatively narrow) and field conditions (potentially broad) has strongly affected current understanding of plant salinity tolerance. To improve understanding, it is thus important to examine plant tolerances over a broad range of salinities and identify potential tolerance thresholds. We examine tolerances of two widely-distributed marsh plants, Suaeda salsa and Salicornia europaea, to salinities ranging...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Environmental controls on canopy foliar N distributions in a neotropical lowland forest

Christopher S. Balzotti, Gregory P. Asner, Philip G. Taylor, Cory C. Cleveland, Rebecca Cole, Roberta E. Martin, Megan Nasto, Brooke B. Osborne, Stephen Porder & Alan R. Townsend
Distributions of foliar nutrients across forest canopies can give insight into their plant functional diversity and improve our understanding of biogeochemical cycling. We used airborne remote sensing and Partial Least Squares Regression (PLSR) to quantify canopy foliar nitrogen (N) across ~164 km2 of wet lowland tropical forest in the Osa Peninsula, Costa Rica. We determined the relative influence of climate and topography on the observed patterns of canopy foliar N using a gradient boosting model...

Data from: Postcrania of the most primitive euprimate and implications for primate origins

Doug M. Boyer, Séverine Toussaint & Marc Godinot
The fossil record of early primates is largely comprised of dentitions. While teeth can indicate phylogenetic relationships and dietary preferences, they say little about hypotheses pertaining to the positional behavior or substrate preference of the ancestral crown primate. Here we report the discovery of a talus bone of the dentally primitive fossil euprimate Donrussellia provincialis. Our comparisons and analyses indicate that this talus is more primitive than that of other euprimates. It lacks features exclusive...

Data from: Genetics of incipient speciation in Drosophila mojavensis. III. Life history divergence in allopatry and reproductive isolation

William J. Etges, Cássia Cardoso De Oliveira, Mohamed A. F. Noor & Michael G. Ritchie
We carried out a three-tiered genetic analysis of egg-to-adult development time and viability in ancestral and derived populations of cactophilic D. mojavensis to test the hypothesis that evolution of these life history characters has shaped premating reproductive isolation in this species. First, a common garden experiment with 11 populations from Baja California and mainland Mexico and Arizona reared on two host cacti revealed significant host plant X region and population interactions for viability and development...

Data from: Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change

Jill T. Anderson, David W. Inouye, Amy M. McKinney, Robert I. Colautti & Thomas Mitchell-Olds
Anthropogenic climate change has already altered the timing of major life history transitions, such as the initiation of reproduction. Both phenotypic plasticity and adaptive evolution can underlie rapid phenological shifts in response to climate change but their relative contributions are poorly understood. Here, we combine a continuous 38-year field survey with quantitative genetic field experiments to assess adaptation in the context of climate change. We focused on Boechera stricta (Brassicaeae), a mustard native to the...

Data from: Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

Heather M. Hines, Riccardo Papa, Mayte Ruiz, Alexie Papanicolaou, Charles Wang, H. Frederik Nijhout, W. Owen McMillan & Robert D. Reed
BACKGROUND: Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of...

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