26 Works

Response of vegetation to coffee pulp addition

Rebecca Cole & Rakan Zahawi
Applying nutrient-rich agricultural by-products, such as fruit peels and pulp, to degraded land has been proposed as a strategy to overcome a number of barriers to tropical forest recovery. While such linkages between agroindustry and restoration represent win-win scenarios, practical applications remain largely unexplored. In this case study, we tested coffee pulp as an amendment to catalyze forest succession on post-agricultural land in southern Costa Rica. A 0.5-m-deep layer of coffee pulp was deposited across...

Diapause vs. reproductive programs: transcriptional phenotypes in Calanus finmarchicus

Petra H. Lenz, Vittoria Roncalli, Matthew C. Cieslak, Ann M. Tarrant, Ann M. Castelfranco & Daniel K. Hartline
Many arthropods undergo a seasonal dormancy termed “diapause” to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses...

Phylogeny explains why less therapeutically redundant plant species are not necessarily facing greater use pressure

Michael Coe
Understanding which factors influence medicinal plant species selection and harvest or use pressure can provide valuable insights for sustainable management of natural resources and conservation efforts. The utilitarian redundancy model, a theoretical framework in ethnobotany, suggests that species that are therapeutically redundant or fulfill similar therapeutic functions within traditional ethnomedicine are less likely to be under greater use pressure. However, species’ evolutionary relatedness and the preference of certain species over others to treat a given...

Hide ‘n seq: direct versus indirect metabarcoding of coral reef cryptic communities

Patrick Nichols, Molly Timmers & Peter Marko
Ecological patterns in biodiversity are primarily based on conspicuous organisms. Few methods are used to survey the taxonomically rich cryptobiome, which is made up of inhabitants from within microhabitats. One way that cryptic marine biodiversity can be non-invasively surveyed is by analyzing environmental DNA (eDNA) present in seawater. Using coral reefs as a model system, here we compare estimates of cryptic diversity among community biomass and eDNA metabarcoding sampling methods with a broad eukaryotic marker...

Data from: Effectiveness of antifungal treatments during chytridiomycosis epizootics in populations of an endangered frog

Roland Knapp, Maxwell Joseph, Thomas Smith, Ericka Hegeman, Vance Vredenburg, James Erdman, Daniel Boiano, Andrea Jani & Cheryl Briggs
The recently-emerged amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has had an unprecedented impact on global amphibian populations, and highlights the urgent need to develop effective mitigation strategies. We conducted in-situ antifungal treatment experiments in wild populations of the endangered mountain yellow-legged frog during or immediately after Bd-caused mass die-off events. The objective of treatments was to reduce Bd infection intensity ("load") and in doing so alter frog-Bd dynamics and increase the probability of frog population...

Scaling and development of elastic mechanisms: the tiny strikes of larval mantis shrimp

Jacob Harrison, Megan Porter, Matthew McHenry, H. Eve Robinson & Sheila Patek
Latch-mediated spring actuation (LaMSA) is used by small organisms to produce high acceleration movements. Mathematical models predict that acceleration increases as LaMSA systems decrease in size. Adult mantis shrimp use a LaMSA mechanism in their raptorial appendages to produce extremely fast strikes. Until now, however, it was unclear whether mantis shrimp at earlier life-history stages also strike using elastic recoil and latch mediation. We tested whether larval mantis shrimp (Gonodactylaceus falcatus) use LaMSA and, because...

Data for: The paradoxical rarity of a parasitic fruit fly fungus attacking a broad range of hosts

Camiel Doorenweerd, Sebastian Sievert, Walter Rossi & Daniel Rubinoff
Understanding the factors that determine the realized and potential distribution of a species requires knowledge of abiotic, physiological, limitations as well as ecological interactions. Entomopathogenic fungi of the order Laboulbeniales specialize on arthropod hosts and are typically thought to be highly specialized on a single host or closely related group of hosts. Because infections are solely transmitted through direct contact of the hosts, the host ecology to a large extent determines the distribution and occurrence...

Pico-phytoplankton abundance, growth and grazing rates along 110°E in the eastern Indian Ocean

Michael Landry & Selph Karen
Dilution experiments were conducted on R/V Investigator cruise IN2019v03 (17 May to 5 June 2019) on a south-to-north transect along longitude 110°E, west of Australia. Population abundances were measured by flow cytometry. Instantaneous rates of growth and grazing mortality were calculated from 2-treatment dilution incubations at six light levels.

Human impact, climate and dispersal strategies determine plant invasion on islands

Severin D. H. Irl, Andreas H. Schweiger, Manuel J. Steinbauer, Claudine Ah-Peng, José R. Arévalo, Carl Beierkuhnlein, Alessandro Chiarucci, Curtis C. Daehler, José M. Fernández-Palacios, Olivier Flores, Christoph Kueffer, Petr Madera, Rüdiger Otto, Julienne M. I. Schweiger, Dominique Strasberg & Anke Jentsch
Aim: Biological invasions are likely determined by species dispersal strategies as well as environmental characteristics of a recipient region, especially climate and human impact. However, the contribution of climatic factors, human impact and dispersal strategies in driving invasion processes is still controversial and not well embedded in the existing theoretical considerations. Here, we study how climate, species dispersal strategies and human impact determine plant invasion processes on islands distributed in all major oceans in the...

Surface deformation associated with fractures near the 2019 Ridgecrest earthquake sequence

Xiaohua Xu, David T. Sandwell, Lauren A. Ward, Chris W. D. Milliner, Bridget R. Smith-Konter, Peng Fang & Yehuda Bock
Contemporary earthquake hazard models hinge on an understanding of how strain is distributed in the crust and the ability to precisely detect millimeter-scale deformation over broad regions of active faulting. Satellite radar observations revealed hundreds of previously unmapped linear strain concentrations (or fractures) surrounding the 2019 Ridgecrest earthquake sequence. We documented and analyzed displacements and widths of 169 of these fractures. Although most fractures are displaced in the direction of the prevailing tectonic stress (prograde),...

Endothermy makes fishes faster but does not expand their thermal niche

Lucy Harding, Andrew Jackson, Adam Barnett, Ian Donohue, Lewis Halsey, Charlie Huveneers, Carl Meyer, Yannis Papastamatiou, Jayson Semmens, Erin Spencer, Yuuki Watanabe & Nicholas Payne
1. Regional endothermy has evolved several times in marine fishes, and two competing hypotheses are generally proposed to explain the evolutionary drivers behind this trait: thermal niche expansion and elevated cruising speeds. Evidence to support either hypothesis is equivocal, and the ecological advantages conferred by endothermy in fishes remain debated. 2. By compiling published biologging data and collecting precise speed measurements from free-swimming fishes in the wild, we directly test whether endothermic fishes encounter broader...

Distinct impacts of major El Niño events on Arctic temperatures due to differences in eastern tropical Pacific sea surface temperatures

Hyein Jeong, Hyo-Seok Park, Malte Stuecker & Sang-Wook Yeh
The El Niño Southern Oscillation (ENSO) is a climate mode in the tropical Pacific. The ENSO teleconnections are known to affect Arctic temperature, however, the robustness of this relationship remains debated. Here, we find that Arctic surface temperatures during three major El Niño events are remarkably well simulated by a state-of-the-art model when nudged to the observed pan-tropical sea surface temperatures (SSTs). SST perturbation experiments show that the 1982-83 warm pan-Arctic and the 1997-98 cold...

Data for: Phylogeography of an endemic California silkmoth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity

Camiel Doorenweerd, Daniel Rubinoff, Steven McElfresh & Jocelyn Millar
The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from...

Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis

Anthony Barley, James Cordes, James Walker & Robert Thomson
Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events vs....

Data from: Effects of dispersal‐ and niche‐based factors on tree recruitment in tropical wet forest restoration

Leland K. Werden, Karen D. Holl, Juan Abel Rosales, Janelle M. Sylvester & Rakan A. Zahawi
Both dispersal‐ and niche‐based factors can impose major barriers on tree establishment. Our understanding of how these factors interact to determine recruitment rates is based primarily on findings from mature tropical forests, despite the fact that a majority of tropical forests are now secondary. Consequently, factors influencing seed limitation and the seed‐to‐seedling transition (STS) in disturbed landscapes, and how those factors shift during succession, are not well understood. We used a 3.5‐yr record of seed...

Data from: Protection mutualists affect colonization and establishment of host-associated species in a coral reef cryptofauna community

Chelsie Counsell & Megan Donahue
Protection mutualists display territorial behaviors that provide protective services for their host species. To investigate how protection mutualists impact the colonization and establishment of host-associated species, we conducted a two-stage experiment using a coral reef cryptofauna community as our study system. Pocillopora meandrina is a fairly common, branching coral species that forms habitat that is utilized by a variety of marine organisms. There is a guild of protection mutualists that associate with P. meandrina including...

Data from: A global phylogeny of turtles reveals a burst of climate-associated diversification on continental margins

Robert Thomson, Phillip Spinks & H. Bradley Shaffer
Living turtles are characterized by extraordinarily low species diversity given their age. The clade’s extensive fossil record indicates that climate and biogeography may have played important roles in determining their diversity. We investigated this hypothesis by collecting a molecular dataset for 591 individual turtles that together represent 80% of all turtle species, including representatives of all families and 98% of genera, and used it to jointly estimate phylogeny and divergence times. We found that the...

Nitrogen budget data

Tan Zou, Xin Zhang, Luis Lassaletta, Nathaniel Mueller, Francesco Tubiello, Matthew Lisk, Chaoqun Lu, Richard Conant, Christopher Dorich, James Gerber, Hanqin Tian, Tom Bruulsema, Tai Maaz, Kazuya Nishina, Benjamin Bodirsky, Alexander Popp, Lex Bouwman, Arthur Beusen, Jinfeng Chang, Petr Havlík, David Leclère, Josep Canadell, Robert Jackson, Patrick Heffer, Nathan Wanner … & Eric Davidson
Input-output estimates of nitrogen (N) on cropland are essential for improving N management and better understanding the global N cycle. Here, we compare 13 N budget datasets covering 115 countries and regions over 1961-2015. Though most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in Tg N yr-1) and associated min-max ranges were 73 (64-84) for global harvested crop N; 161...

Differential learning by native versus invasive predators to avoid distasteful cleaning mutualists

Lillian Tuttle, Robert Lamb & Allison Stringer
1. Cleaning symbioses on coral reefs are mutually beneficial interactions between two individuals, in which a ‘cleaner’ removes and eats parasites from the surface of a ‘client’ fish. A suite of behavioural and morphological traits of cleaners signal cooperation with co-evolved species, thus protecting the cleaner from being eaten by otherwise predatory clients. However, it is unclear whether cooperation between cleaners and predatory clients is innate or learned, and therefore whether an introduced predator might...

The 'Evil Tribe' spreads across the land: A dated molecular phylogeny provides insight into dispersal, expansion, and biogeographic relationships within one of the largest tribes of the sunflower family (Vernonieae: Compositae)

Sterling C. Keeley, Jason T. Cantley & Timothy J. Gallaher
Premise: With over 1500 species, the globally distributed Vernonieae is one of the most successful members of the Compositae. However, due to its morphological complexity and limited geographic representation in previous studies, subtribal and biogeographic relationships are unclear. Here new DNA sequence data spanning the geographical range of the tribe provides a taxonomically robust time-calibrated phylogeny, an estimation of migration pathways and timing of important biogeographical events and allows inference of environmental factors that have...

Source data and code for: Climate change transforms the functional identity of Mediterranean coralligenous assemblages

Daniel Gómez-Gras, Cristina Linares, Maria Dornelas, Joshua S. Madin, Viviana Brambilla, Jean-Baptiste Ledoux, Nathaniel Bensoussan, Paula López-Sendino & Joaquim Garrabou
We used five long-term (>10 years) records of Mediterranean coralligenous assemblages in a multi-taxa, trait-based analysis to investigate MHW-driven changes in functional structure. We show that, despite stability in functional richness (i.e., the range of species functional traits), MHW-impacted assemblages experienced long-term directional changes in functional identity (i.e., their dominant trait values). Declining traits included large sizes, long lifespans, arborescent morphologies, filter feeding strategies or calcified skeletons. These traits, which were mostly supported by few...

A shift to shorter cuticular hydrocarbons accompanies sexual isolation among Drosophila americana group populations

Jeremy S Davis, Matthew Pearcy, Joanne Yew & Leonie Moyle
Because sensory signals often evolve rapidly, they could be instrumental in the emergence of reproductive isolation between species. However, pinpointing their specific contribution to isolating barriers, and the mechanisms underlying their divergence, remains challenging. Here we demonstrate sexual isolation due to divergence in chemical signals between two populations of Drosophila americana (SC and NE) and one population of D. novamexicana, and dissect its underlying phenotypic and genetic mechanisms. Mating trials revealed strong sexual isolation between...

Proximity and abundance of mother trees affects recruitment patterns in a long-term tropical forest restoration study

Rakan Zahawi, Leland Werden, Miriam San-José, Juan Abel Rosales, Jeffry Flores & Karen Holl
Remnant trees and forest fragments in agricultural landscapes can be important sources of propagules to facilitate forest recovery. However, many studies simply quantify forest cover in the surrounding landscape as a percentage, with little attention given to species composition, and subsequently fail to detect an effect on recruitment patterns. We assessed the relative importance of the spatial distribution and life-history traits of 77 tree species on recruitment patterns at a landscape scale in a well-replicated...

Clinging performance on natural substrates predicts habitat use in anoles and geckos

Amber Wright, Stevie Kennedy-Gold, Emily Naylor, Robyn Screen, Carla Piantoni & Timothy Higham
1. For arboreal lizards, the ability to cling or adhere to the substrate is critical for locomotion during prey capture, predator escape, thermoregulation, and social interactions. Thus, selection on traits related to clinging is likely strong. 2. Correlations between morphology, performance, and habitat use have been documented in arboreal lizards, providing a framework for using functional traits to predict habitat use in the field. 3. We tested the hypothesis that clinging performance predicts habitat use...

DNA metabarcoding marker choice skews perception of marine eukaryotic biodiversity

Jordan M Casey, Emma Ransome, Allen G Collins, Angka Mahardini, Eka M Kurniasih, Andrianus Sembiring, Nina M D Schiettekatte, Ni Kadek Dita Cahyani, Aji Wahyu Anggoro, Mikaela Moore, Abby Uehling, Mahdi Belcaid, Paul H Barber, Jonathan B Geller & Christopher P Meyer
DNA metabarcoding is an increasingly popular technique to investigate biodiversity; however, many methodological unknowns remain, especially concerning the biases resulting from marker choice. Regions of the cytochrome c oxidase subunit I (COI) and 18S rDNA (18S) genes are commonly employed “universal” markers for eukaryotes, but the extent of taxonomic biases introduced by these markers and how such biases may impact metabarcoding performance is not well quantified. Here, focusing on macro-eukaryotes, we use standardized sampling from...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Hawaii at Manoa
  • University of California Los Angeles
  • University of La Réunion
  • University of Hohenheim
  • Stanford University
  • The University of Texas at Austin
  • Food and Agriculture Organization of the United Nations
  • Duke University
  • University of Bologna
  • PSL Research University