17 Works

Data from: Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes

Jason T. Ladner & S. R. Palumbi
The identification of species is one of the most basic, and yet critically important, issues in biology with far-reaching potential implications for fields such as biodiversity conservation, population ecology and epidemiology. Morphology has long been the primary tool biologists have used to categorize life. However, we now know that a significant portion of natural diversity is morphologically hidden, and therefore, we must integrate non-morphological tools into the description of biodiversity. Here, we demonstrate the utility...

Data from: Late Paleozoic fusulinoidean gigantism driven by atmospheric hyperoxia

Jonathan L. Payne, John R. Groves, Adam B. Jost, Thienan Nguyen, Sarah E. Moffitt, Tessa M. Hill & Jan M. Skotheim
Atmospheric hyperoxia, with pO2 in excess of 30%, has long been hypothesized to account for late Paleozoic (360-250 million years ago) gigantism in numerous higher taxa. However, this hypothesis has not been evaluated statistically because comprehensive size data have not been compiled previously at sufficient temporal resolution to permit quantitative analysis. In this study, we test the hyperoxia-gigantism hypothesis by examining the fossil record of fusulinoidean foraminifers, a dramatic example of protistan gigantism with some...

Data from: An assessment of wheat yield sensitivity and breeding gains in hot environments

Sharon M. Gourdji, Ky L. Mathews, Matthew Reynolds, Jose Crossa & David B. Lobell
Genetic improvements in heat tolerance of wheat provide a potential adaptation response to long-term warming trends, and may also boost yields in wheat-growing areas already subject to heat stress. Yet there have been few assessments of recent progress in breeding wheat for hot environments. Here, data from 25 years of wheat trials in 76 countries from the International Maize and Wheat Improvement Center (CIMMYT) are used to empirically model the response of wheat to environmental...

Data from: Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure

Kristen Ruegg, Howard C. Rosenbaum, Eric C. Anderson, Marcia Engel, Anna Rothschild, C. Scott Baker & Stephen R. Palumbi
Once hunted to the brink of extinction, humpback whales (Megaptera novaeangliae) in the North Atlantic have recently been increasing in numbers. However, uncertain information on past abundance makes it difficult to assess the extent of the recovery in this species. While estimates of pre-exploitation abundance based upon catch data suggest the population might be approaching pre-whaling numbers, estimates based on mtDNA genetic diversity suggest they are still only a fraction of their past abundance levels....

Data from: Differences in the regulation of growth and biomineralization genes revealed through long-term common garden acclimation and experimental genomics in the purple sea urchin

Melissa Helen Pespeni, Bryan T. Barney & Stephen R. Palumbi
Across heterogeneous landscapes, populations may have adaptive differences in gene regulation that adjust their physiologies to match local environments. Such differences could have origins in acclimation or in genetically fixed variation between habitats. Here we use common garden experiments to evaluate differences in gene expression between populations of the purple sea urchin, Strongylocentrotus purpuratus, spanning 1700 km and average temperature differences of 5 °C to 8 °C. Across expression profiles from 18,883 genes after three...

Data from: Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

Pierre De Wit & Stephen R. Palumbi
Global climate change is projected to accelerate during the next century, altering oceanic patterns in temperature, pH and oxygen concentrations. Documenting patterns of genetic adaptation to these variables in locations that currently experience geographic variation in them is an important tool in understanding the potential for natural selection to allow populations to adapt as climate change proceeds. We sequenced the mantle transcriptome of 39 red abalone (Haliotis rufescens) individuals from three regions (Monterey Bay, Sonoma,...

Data from: Massive phytoplankton blooms under Arctic sea ice

Kevin R. Arrigo, D. K. Perovich, Z. W. Brown & R. S. Pickart
Phytoplankton blooms over Arctic Ocean continental shelves are thought to be restricted to waters free of sea ice. Here, we document a massive phytoplankton bloom beneath fully consolidated pack ice far from the ice edge in the Chukchi Sea, where light transmission has increased in recent decades because of thinning ice cover and proliferation of melt ponds. The bloom was characterized by high diatom biomass and rates of growth and primary production. Evidence suggests that...

Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping

Bruce E. Deagle, Felicity C. Jones, Devin M. Absher, David M. Kingsley & Thomas E. Reimchen
Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and...

Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction

Jonathan L. Payne, Adam B. Jost, Steve C Wang & Jan M. Skotheim
Size is among the most important traits of any organism, yet the factors that control its evolution remain poorly understood. In this study, we investigate controls on the evolution of organismal size using a newly compiled database of nearly 25,000 foraminiferan species and subspecies spanning the past 400 million years. We find a transition in the pattern of foraminiferan size evolution from correlation with atmospheric pO2 during the Paleozoic (400-250 Mya) to long-term stasis during...

Data from: Genomic basis for coral resilience to climate change

Daniel J. Barshis, Jason T. Ladner, Thomas A. Oliver, François O. Seneca, Nikki Traylor-Knowles & Stephen R. Palumbi
Recent advances in DNA-sequencing technologies now allow for in-depth characterization of the genomic stress responses of many organisms beyond model taxa. They are especially appropriate for organisms such as reef-building corals, for which dramatic declines in abundance are expected to worsen as anthropogenic climate change intensifies. Different corals differ substantially in physiological resilience to environmental stress, but the molecular mechanisms behind enhanced coral resilience remain unclear. Here, we compare transcriptome-wide gene expression (via RNA-Seq using...

Data from: Genetic signature of adaptive peak shift in threespine stickleback

Sean M. Rogers, Patrick Tamkee, Brian Summers, Sarita Balabahadra, Melissa Marks, David E. Kingsley & Dolph Schluter
Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution...

Data from: Patterns and controlling factors of species diversity in the Arctic Ocean

Moriaki Yasuhara, Gene Hunt, Gert Van Dijken, Kevin R. Arrigo, Thomas M. Cronin & Jutta E. Wollenburg
AIM: The Arctic Ocean is one of the last near-pristine regions on Earth and although human activities are expected to impact on Arctic ecosystems, we know very little about baseline patterns of Arctic Ocean biodiversity. This paper aims to describe Arctic Ocean-wide patterns of benthic biodiversity and to explore factors related to the large-scale species diversity patterns. LOCATION: Arctic Ocean. METHODS: We used large ostracode and foraminiferal datasets to describe the biodiversity patterns and apply...

Data from: Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus)

Fabian Staubach, Anna Lorenc, Philipp W. Messer, Kun Tang, Dmitri A. Petrov & Diethard Tautz
General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and extensive genome information is available. We have used high-density single nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection...

Data from: Diversification and phylogeographic structure in widespread Azteca plant-ants from the northern Neotropics

Elizabeth G. Pringle, Timothy C. Bonebrake, Santiago R. Ramírez, Deborah M. Gordon & Rodolfo Dirzo
The Neotropical myrmecophytic tree Cordia alliodora hosts symbiotic Azteca ants in most of its widespread range. The taxonomy of the genus Azteca is notoriously difficult, which has frequently obscured species identity in ecological studies. We used sequence data from one mitochondrial and four nuclear loci to infer phylogenetic relationships, patterns of geographic distribution, and timing of diversification for 181 colonies of Azteca from Mexico to Colombia. We identified at least eight lineages of C. alliodora-dwelling...

Data from: Long-term differences in extinction risk among the seven forms of rarity

Paul G. Harnik, Carl Simpson & Jonathan L. Payne
Rarity is widely used to predict the vulnerability of species to extinction. Species can be rare in markedly different ways, but the relative impacts of these different forms of rarity on extinction risk are poorly known and cannot be determined through observations of species that are not yet extinct. The fossil record provides a valuable archive with which we can directly determine which aspects of rarity lead to the greatest risk. Previous paleontological analyses confirm...

Data from: Nectar bacteria, but not yeast, weaken a plant-pollinator mutualism

Rachel L. Vannette, Marie-Pierre L. Gauthier, Tadashi Fukami & M.-P. L. Gauthier
Mutualistic interactions are often subject to exploitation by species that are not directly involved in the mutualism. Understanding which organisms act as such ‘third-party’ species and how they do so is a major challenge in the current study of mutualistic interactions. Here, we show that even species that appear ecologically similar can have contrasting effects as third-party species. We experimentally compared the effects of nectar-inhabiting bacteria and yeasts on the strength of a mutualism between...

Data from: Adaptive morphological shifts to novel habitats in marine sculpin fishes

Matthew L. Knope & Jeffrey A. Scales
Sculpin fishes of the North American Pacific Coast provide an ideal opportunity to examine whether adaptive morphological character shifts have facilitated occupation of novel habitat types because of their well-described phylogeny and ecology. In this group, the basal-rooted species primarily occupy the subtidal habitat, whereas the species in the most distal clades are found in the intertidal. We tested multiple evolutionary models to determine whether changes in body size and changes in number of scales...

Registration Year

  • 2012

Resource Types

  • Dataset


  • Stanford University
  • National Museum of Natural History
  • Oregon State University
  • Shanghai Institutes for Biological Sciences
  • Swarthmore College
  • University of California, Berkeley
  • University of Hawaii at Manoa
  • University of Northern Iowa
  • University of Hong Kong
  • Alfred Wegener Institute for Polar and Marine Research