22 Works

Data from: Improving HybrID: how to best combine indirect and direct encoding in evolutionary algorithms

Lucas Helms & Jeff Clune
Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot...

Data from: Restoration of native mangrove wetlands can reverse diet shifts of benthic macrofauna caused by invasive cordgrass

Jianxiang Feng, Qian Huang, Hui Chen, Jiemin Guo & Guanghui Lin
1. Ecological replacement using native mangrove species combined with physical treatments has become an effective method in controling the spread of invasive Spartina alterniflora. To re-establish ecosystem functions, trophic interactions between macrofauna and their potential food resources must be considered during the restoration process. 2. Here we examined the changes in the diets of macrofauna in three restored mangrove ecosystems with different invasion histories following the removal of S. alterniflora in southern China. Carbon and...

Data from: Habitat filtering determines the functional niche occupancy of plant communities worldwide

Yuanzhi Li, Bill Shipley, Jodi N. Price, Vinícius De L. Dantas, Riin Tamme, Mark Westoby, Andrew Siefert, Brandon S. Schamp, Marko J. Spasojevic, Vincent Jung, Daniel C. Laughlin, Sarah J. Richardson, Yoann Le Bagousse-Pinguet, Christian Schöb, Antonio Gazol, Honor C. Prentice, Nicolas Gross, Jacob Overton, Marcus V. Cianciaruso, Frédérique Louault, Chiho Kamiyama, Tohru Nakashizuka, Kouki Hikosaka, Takehiro Sasaki, Masatoshi Katabuchi … & Marco A. Batalha
How the patterns of niche occupancy vary from species-poor to species-rich communities is a fundamental question in ecology that has a central bearing on the processes that drive patterns of biodiversity. As species richness increases, habitat filtering should constrain the expansion of total niche volume, while limiting similarity should restrict the degree of niche overlap between species. Here, by explicitly incorporating intraspecific trait variability, we investigate the relationship between functional niche occupancy and species richness...

Data from: Inconsistent reproductive isolation revealed by interactions between Catostomus fish species

Elizabeth Mandeville, Thomas Parchman, Kevin Thompson, Robert Compton, Kevin Gelwicks, Se Jin Song, C. Alex Buerkle, Thomas L. Parchman & Elizabeth G. Mandeville
Interactions between species are central to evolution and ecology, but we do not know enough about how outcomes of interactions between species vary across geographic locations, in heterogeneous environments, or over time. Ecological interactions between species are known to vary, but evolutionary interactions such as reproductive isolation are often assumed to be consistent. Hybridization among Catostomus fish species occurs over a large and heterogeneous geographic area and across taxa with distinct evolutionary histories, and allows...

Data from: When perception reflects reality: non-native grass invasion alters small mammal risk landscapes and survival

Joseph P. Ceradini & Anna D. Chalfoun
1. Modification of habitat structure due to invasive plants can alter the risk landscape for wildlife by, for example, changing the quality or availability of refuge habitat. Whether perceived risk corresponds with actual fitness outcomes, however, remains an important open question. We simultaneously measured how habitat changes due to a common invasive grass (cheatgrass, Bromus tectorum) affected the perceived risk, habitat selection, and apparent survival of a small mammal, enabling us to assess how well...

Data from: Plasticity contributes to a fine-scale depth gradient in sticklebacks’ visual system

Thor Veen, Chad Brock, Diana Rennison & Daniel Bolnick
The light environment influences an animal’s ability to forage, evade predators, and find mates, and consequently is known to drive local adaptation of visual systems. However, the light environment may also vary over fine spatial scales at which genetic adaptation is difficult. For instance, in aquatic systems the available wavelengths of light change over a few meters depth. Do animals plastically adjust their visual system to such small-scale environmental light variation? Here, we show that...

Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use

Ryan A. Long, Alois Wambua, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey...

Data from: A single migrant enhances the genetic diversity of an inbred puma population

Kyle C. Gustafson, T. Winston Vickers, Walter M. Boyce, Holly B. Ernest & Kyle D. Gustafson
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east...

Data from: Humans permanently occupied the Andean highlands by at least 7 ka

Randall Haas, Ioana C. Stefenescu, Alex Garcia-Putnam, Mark S. Aldenderfer, Mark T. Clementz, Melissa S. Murphy, Carlos Viviano Llave, James T. Watson, Alexander Garcia-Putnam & Ioana C. Stefanescu
High-elevation environments above 2500 metres above sea level (m.a.s.l.) were among the planet's last frontiers of human colonization. Research on the speed and tempo of this colonization process is active and holds implications for understanding rates of genetic, physiological and cultural adaptation in our species. Permanent occupation of high-elevation environments in the Andes Mountains of South America tentatively began with hunter–gatherers around 9 ka according to current archaeological estimates, though the timing is currently debated....

Data from: Phenotypic plasticity drives a depth gradient in male conspicuousness in threespine stickleback, Gasterosteus aculeatus

Chad D. Brock, Molly E. Cummings & Daniel I. Bolnick
Signal evolution is thought to depend on both a signal's detectability or conspicuousness (signal design) as well as any extractable information it may convey to a potential receiver (signal content). While theoretical and empirical work in sexual selection has largely focused on signal content, there has been a steady accrual of evidence that signal design is also important for trait evolution. Despite this, relatively little attention has been paid to spatial variation in the conspicuousness...

Data from: Heterospecific eavesdropping in ant-following birds of the Neotropics is a learned behaviour

Henry S. Pollock, Ari E. Martinez, J.P. Kelley, Janeene M. Touchton, Corey E. Tarwater & J. Patrick Kelley
Animals eavesdrop on other species to obtain information about their environments. Heterospecific eavesdropping can yield tangible fitness benefits by providing valuable information about food resources and predator presence. The ability to eavesdrop may therefore be under strong selection, although extensive research on alarm-calling in avian mixed-species flocks has found only limited evidence that close association with another species could select for innate signal recognition. Nevertheless, very little is known about the evolution of eavesdropping behaviour...

Data from: Internet blogs, polar bears, and climate-change denial by proxy

Jeffrey A. Harvey, Daphne Van Den Berg, Jacintha Ellers, Remko Kampen, Thomas W. Crowther, Peter Roessingh, Bart Verheggen, Rascha J. M. Nuijten, Eric Post, Stephan Lewandowsky, Ian Stirling, Meena Balgopal, Steven C. Amstrup & Michael E. Mann
Increasing surface temperatures, Arctic sea-ice loss, and other evidence of anthropogenic global warming (AGW) are acknowledged by every major scientific organization in the world. However, there is a wide gap between this broad scientific consensus and public opinion. Internet blogs have strongly contributed to this consensus gap by fomenting misunderstandings of AGW causes and consequences. Polar bears (Ursus maritimus) have become a “poster species” for AGW, making them a target of those denying AGW evidence....

Data from: Demographic drivers of a refugee species: large-scale experiments guide strategies for reintroductions of hirola

Abdullahi H. Ali, Matthew J. Kauffman, Rajan Amin, Amos Kibara, Juliet King, David Mallon, Charles Musyoki & Jacob R. Goheen
Effective reintroduction strategies require accurate estimates of vital rates and the factors that influence them. We estimated vital rates of hirola (Beatragus hunteri) populations exposed to varying levels of predation and rangeland quality from 2012 to 2015, and then built population matrices to estimate the finite rate of population change (λ) and demographic sensitivities. Mean survival for all age classes and population growth was highest in the low predation/high-rangeland quality setting (λ = 1.08 ±...

Data from: Mitogenomes and relatedness do not predict frequency of tool-use by sea otters

Kathy Ralls, Nancy Rotzel McInerney, Roderick B. Gagne, Holly B. Ernest, M. Tim Tinker, Jessica Fujii, Jesus Maldonado & Katherine Ralls
Many ecological aspects of tool-use in sea otters are similar to those in Indo-Pacific bottlenose dolphins. Within an area, most tool-using dolphins share a single mitochondrial haplotype and are more related to each other than to the population as a whole. We asked whether sea otters in California showed similar genetic patterns by sequencing mitogenomes of 43 otters and genotyping 154 otters at 38 microsatellite loci. There were six variable sites in the mitogenome that...

Data from: Quantifying the similarity between genes and geography across Alaska's alpine small mammals

L. Lacey Knowles, Rob Massatti, Qixin He, Link E. Olson & Hayley C. Lanier
Aim: Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species-specific or shared manner. Location: Alaska and adjacent north-western Canada. Methods: For each taxon we generated 3500–7500 single-nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between...

Data from: The greenscape shapes surfing of resource waves in a large migratory herbivore

Ellen O. Aikens, Matthew J. Kauffman, Jerod A. Merkle, Samantha P.H. Dwinnel, Gary L. Fralick, Kevin L. Monteith & Samantha P. H. Dwinnell
The Green Wave Hypothesis posits that herbivore migration manifests in response to waves of spring green-up (i.e. green-wave surfing). Nonetheless, empirical support for the Green Wave Hypothesis is mixed, and a framework for understanding variation in surfing is lacking. In a population of migratory mule deer (Odocoileus hemionus), 31% surfed plant phenology in spring as well as a theoretically perfect surfer, and 98% surfed better than random. Green-wave surfing varied among individuals and was unrelated...

Data from: Constraints on trait combinations explain climatic drivers of biodiversity: the importance of trait covariance in community assembly

John M. Dwyer & Daniel C. Laughlin
Trade-offs maintain diversity and structure communities along environmental gradients. Theory indicates that if covariance among functional traits sets a limit on the number of viable trait combinations in a given environment, then communities with strong multidimensional trait constraints should exhibit low species diversity. We tested this prediction in winter annual plant assemblages along an aridity gradient using multilevel structural equation modelling. Univariate and multivariate functional diversity measures were poorly explained by aridity, and were surprisingly...

Data from: State-dependent behavior alters endocrine-energy relationship: implications for conservation and management

Brett R. Jesmer, Jacob R. Goheen, Kevin L. Monteith & Matthew J. Kauffman
Glucocorticoids (GC) and triiodothyronine (T3) are two endocrine markers commonly used to quantify resource limitation, yet the relationships between these markers and the energetic state of animals has been studied primarily in small-bodied species in captivity. Free-ranging animals, however, adjust energy intake in accordance with their energy reserves, a behavior known as state-dependent foraging. Further, links between life-history strategies and metabolic allometries cause energy intake and energy reserves to be more strongly coupled in small...

Data from: Founder events, isolation, and inbreeding: Intercontinental genetic structure of the domestic ferret

Kyle D. Gustafson, Michelle G. Hawkins, Tracy L. Drazenovich, Robert Church, Susan A. Brown & Holly B. Ernest
Domestication and breeding for human-desired morphological traits can reduce population genetic diversity via founder events and artificial selection, resulting in inbreeding depression and genetic disorders. The ferret (Mustela putorius furo) was domesticated from European polecats (M. putorius), transported to multiple continents, and has been artificially selected for several traits. The ferret is now a common pet, a laboratory model organism, and feral ferrets can impact native biodiversity. We hypothesized global ferret trade resulted in distinct...

Data from: Circadian rhythms vary over the growing season and correlate with fitness components

Matthew J. Rubin, Marcus T. Brock, Amanda M. Davis, Zachary M. German, Mary Knapp, Stephen M. Welch, Stacey L. Harmer, Julin N. Maloof, Seth J. Davis & Cynthia Weinig
Circadian clocks have evolved independently in all three domains of life, suggesting that internal mechanisms of time-keeping are adaptive in contemporary populations. However, the performance consequences of either discrete or quantitative clock variation have rarely been tested in field settings. Clock sensitivity of diverse segregating lines to the environment remains uncharacterized as do the statistical genetic parameters that determine evolutionary potential. In field studies with Arabidopsis thaliana, we found that major perturbations to circadian cycle...

Data from: Endemic chronic wasting disease causes mule deer population decline in Wyoming

Melia T. DeVivo, David R. Edmunds, Matthew J. Kauffman, Brant A. Schumaker, Justin Binfet, Terry J. Kreeger, Bryan J. Richards, Hermann M. Schätzl & Todd E. Cornish
Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting white-tailed deer (Odocoileus virginianus), mule deer (Odocoileus hemionus), Rocky Mountain elk (Cervus elaphus nelsoni), and moose (Alces alces shirasi) in North America. In southeastern Wyoming average annual CWD prevalence in mule deer exceeds 20% and appears to contribute to regional population declines. We determined the effect of CWD on mule deer demography using age-specific, female-only, CWD transition matrix models to estimate the population growth...

Data from: ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability

Miguel Arenas, Claudia C. Weber, David A. Liberles & Ugo Bastolla
The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we present ProtASR,...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of Wyoming
  • University of California, Davis
  • Colorado State University
  • The University of Texas at Austin
  • University of Florida
  • Helmholtz Centre for Environmental Research
  • Universidade Federal de Goiás
  • VU University Amsterdam
  • Ghent University
  • Princeton University