109 Works

Data from: Robust inference on large-scale species habitat use with interview data: the status of jaguars outside protected areas in Central America

Lisanne S. Petracca, Jacqueline L. Frair, Jonathan B. Cohen, Ana Patricia Calderón, Javier Carazo-Salazar, Franklin Castañeda, Daniel Corrales-Gutiérrez, Rebecca J. Foster, Bart Harmsen, Sandra Hernández-Potosme, Luis Herrera, Melva Olmos, Sandy Pereira, Hugh S. Robinson, Nathaniel Robinson, Roberto Salom-Pérez, Yahaira Urbina, Kathy A. Zeller & Howard Quigley
Evaluating range-wide habitat use by a target species requires information on species occurrence over broad geographic regions, a process made difficult by species rarity, large spatiotemporal sampling domains, and imperfect detection. We address these challenges in an assessment of habitat use for jaguars (Panthera onca) outside protected areas in Central America. Occurrence records were acquired within 12 putative corridors using interviews with knowledgeable corridor residents. We developed a Bayesian hierarchical occupancy model to gain robust...

Data from: Density dependence and population regulation in marine fish: a large-scale, long-term field manipulation

Mark A. Hixon, Todd W. Anderson, Kevin L. Buch, Darren W. Johnson, J. Brock McLeod & Christopher Derek Stallings
Do small-scale experiments showing spatial density dependence in marine fishes scale-up to temporal density dependence and regulation of relatively large local populations? If so, what are the causative mechanisms and their implications? We conducted an 8-year multi-generation study of population dynamics of bicolor damselfish (Stegastes partitus) inhabiting four large coral reefs in the Bahamas. After a 4-year baseline period, it was clear that two populations naturally received very few settlement-stage larvae, so recruitment of recently...

Data from: Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae

James Starrett, Marshal Hedin, Nadia Ayoub & Cheryl Y. Hayashi
Hemocyanins are multimeric copper-containing hemolymph proteins involved in oxygen binding and transport in all major arthropod lineages. Most arachnids have seven primary subunits (encoded by paralogous genes a–g), which combine to form a 24-mer (4 × 6) quaternary structure. Within some spider lineages, however, hemocyanin evolution has been a dynamic process with extensive paralog duplication and loss. We have obtained hemocyanin gene sequences from numerous representatives of the spider infraorders Mygalomorphae and Araneomorphae in order...

Data from: Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution

Jason E. Bond, Nicole L. Garrison, Chris A. Hamilton, Rebecca L. Godwin, Marshal Hedin & Ingi Agnarsson
Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider “backbone” phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis...

Numerical responses of omnivorous terrestrial arthropods to plant alternative resources suppress prey populations: a meta-analysis

Shelby Rinehart & Jeremy Long
Omnivory is ubiquitous in ecological communities. Yet, we lack a consensus of how plant alternative resources impact the ability of omnivores to suppress prey populations. Previous work suggests that plant alternative resources can increase, decrease, or have no effect on the magnitude of omnivore-prey interactions. This discrepancy may arise from 1) the ability of omnivores to numerically respond to plant alternative resources and 2) identity-specific effects of plant alternative resources. We used a meta-analysis to...

Phylogenomics and biogeography of leptonetid spiders (Araneae : Leptonetidae)

Jason Bond, Joel Ledford & Marshal Hedin
Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number...

2D and 3D coral models imaged in Curaçao: George, Mullinix, et al PeerJ 2021

Emma E. George, James A. Mullinix, Fanwei Meng, Barbara A. Bailey, Clinton Edwards, Ben Felts, Andreas F. Haas, Aaron Hartmann, Benjamin Mueller, Ty F. Roach, Peter Salamon, Cynthia Silveira, Mark Vermeij, Forest Rohwer & Antoni Luque
Abstract from the article associated with the dataset: George, Mullinix, et al PeerJ 2021. Reef-building corals are ecosystem engineers that compete with other benthic or- ganisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the...

Data from: The effects of temperature on the kinematics of rattlesnake predatory strikes in both captive and field environments

Malachi Whitford, Grace Freymiller, Timothy Higham & Rulon Clark
The outcomes of predator-prey interactions between endotherms and ectotherms can be heavily influenced by environmental temperature, owing to the difference in how body temperature affects locomotor performance. However, as elastic energy storage mechanisms can allow ectotherms to maintain high levels of performance at cooler body temperatures, detailed analyses of kinematics are necessary to fully understand how changes in temperature might alter endotherm-ectotherm predator-prey interactions. Viperid snakes are widely distributed ectothermic mesopredators that interact with endotherms...

Global biogeography of fungal and bacterial biomass carbon in topsoil

Liyuan He, Jorge Rodrigues, Nadejda Soudzilovskaia, Milagros Barceló, Pål Axel Olsson, Changchun Song, Leho Tedersoo, Fenghui Yuan, Fengming Yuan, David Lipson & Xiaofeng Xu
Bacteria and fungi, representing two major soil microorganism groups, play an important role in global nutrient biogeochemistry. Biogeographic patterns of bacterial and fungal biomass are of fundamental importance for mechanistically understanding nutrient cycling. We synthesized 1323 data points of phospholipid fatty acid-derived fungal biomass C (FBC), bacterial biomass C (BBC), and fungi:bacteria (F:B) ratio in topsoil, spanning 11 major biomes. The FBC, BBC, and F:B ratio display clear biogeographic patterns along latitude and environmental gradients...

The population genetics of non-migratory Allen's Hummingbird (Selasphorus sasin sedentarius) following a recent mainland colonization

Brian Myers, Kevin Burns, Christopher Clark & Alan Brelsford
Allen's Hummingbird comprises two subspecies, one migratory (Selasphorus sasin sasin) and one non-migratory (S. s. sedentarius). The non-migratory subspecies, previously endemic to the California Channel Islands, apparently colonized the California mainland on the Palos Verdes Peninsula some time before 1970, and now breeds throughout coastal southern California. We sequenced and compared populations of mainland non-migratory Allen's Hummingbird to Channel Island populations from Santa Catalina, San Clemente, and Santa Cruz Island. We found no evidence of...

Reintroduced grazers and prescribed fire effects on beetle assemblage structure and function in restored grasslands

Nicholas Barber, Melissa Nelson, Sheryl Hosler, Fabian Boetzl & Holly Jones
Ecological restoration seeks to re-establish functioning ecosystems, but planning and evaluation often focus on taxonomic community structure and neglect consumers and their functional roles. The functional trait composition of insect assemblages, which make up the majority of animal diversity in many systems, can reveal how they are affected by restoration management and the consequences for ecosystem function. We sampled ground beetle (Coleoptera: Carabidae) assemblages in restored tallgrass prairies varying in management with prescribed fire and...

An Exploratory Study of the Experiences of Gay, Lesbian and Bisexual Fraternity and Sorority Members Revisited

Douglas N. Case, Grahaeme A. Hesp & Charles G. Eberly

Project Report NOAA Ship Hi'ialakai, Project HA-18-01 (Legs 1, 2, and 3)

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PIFSC project report ; Project HA-18-01 (Legs 1, 2, and 3)

Allometric modelling of plant biomass from drone-acquired photographs: drone images, ground control marker coordinates and biomass data from 36 sites, 2016-2020

A. Cunliffe, K. Anderson, F. Boschetti, H. Graham, R. Brazier, I. Myers-Smith, T. Astor, M. Boer, L. Calvo, P. Clark, M. Cramer, M. Encinas-Lara, S. Escarzaga, J. Fernández-Guisuraga, A. Fisher, K. Gdulová, B. Gillespie, A. Griebel, N. Hanan, M. Hanggito, S. Haselberger, C. Havrilla, W. Ji, J. Karl, M. Kirchhoff … & R. Wojcikiewicz
This dataset contains RGB photographs acquired from drone surveys. There are 741 harvest plots from 38 surveys at 36 sites around the world. Each site was approximately 1 ha in area. Included with the photographic images are the coordinates of ground control markers, biomass, taxonomic and location data for harvest plots and ancillary metadata. The observations can be used to obtain allometric size-biomass models. This work was supported by the Natural Environment Research Council award...

Data from: Sierra Nevada mountain lake microbial communities are structured by temperature, resources, and geographic location

Marika Schulhof, Andrew Allen, Eric Allen, Natalie Mladenov, John McCrow, Natalie Jones, Jessica Blanton, Hamanda Badona Cavalheri, Drishti Kaul, Celia Symons & Jonathan Shurin
Warming, eutrophication (nutrient fertilization) and brownification (increased loading of allochthonous organic matter) are three global trends impacting lake ecosystems. However, the independent and synergistic effects of resource addition and warming on autotrophic and heterotrophic microorganisms are largely unknown. In this study, we investigate the independent and interactive effects of temperature, dissolved organic carbon (DOC, both allochthonous and autochthonous), and nitrogen (N) supply, in addition to the effect of spatial variables, on the composition, richness, and...

Data from: Flowering plant composition shapes pathogen infection intensity and reproduction in bumble bee colonies

Nicholas Barber, Lynn Adler, Olivia Biller & Rebecca Irwin
Pathogens pose significant threats to pollinator health and food security. Pollinators can transmit diseases during foraging, but the consequences of plant species composition for infection is unknown. In agroecosystems, flowering strips or hedgerows are often used to augment pollinator habitat. We used canola as a focal crop in tents, and manipulated flowering strip composition using plant species we had previously shown to result in higher or lower bee infection in short-term trials. We also manipulated...

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Paul A. Maier, Amy G. Vandergast, Steven M. Ostoja, Andres Aguilar & Andrew J. Bohonak
Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus) Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this “glacial pulse” model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including...

Data from: The effects of temperature on the defensive strikes of rattlesnakes

Malachi D. Whitford, Grace A. Freymiller, Timothy E. Higham & Rulon W. Clark
Movements of ectotherms are constrained by their body temperature owing to the effects of temperature on muscle physiology. As physical performance often affects the outcome of predator–prey interactions, environmental temperature can influence the ability of ectotherms to capture prey and/or defend themselves against predators. However, previous research on the kinematics of ectotherms suggests that some species may use elastic storage mechanisms when attacking or defending, thereby mitigating the effects of sub-optimal temperature. Rattlesnakes (Crotalus spp.)...

Data matrices for: Phylogenomics of peacock spiders and their kin (Salticidae, Maratus), with implications for the evolution of male courtship displays

Damian Elias & Marshal Hedin
Understanding diversity has been a pursuit in evolutionary biology since its inception. A challenge arises when sexual selection has played a role in diversification. Questions of what constitutes a “species”, homoplasy versus synapomorphy, and whether sexually-selected traits show phylogenetic signal have hampered work on many systems. Peacock spiders are famous for sexually selected male courtship dances and peacock-like abdominal ornamentation. This lineage of jumping spiders currently includes over 90 species classified into two genera, Maratus...

Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Eric Ekdale & Thomas Deméré
Extant baleen whales (Mysticeti) have a deciduous foetal dentition, but are edentulous at birth. Fossils reveal that the earliest mysticetes possessed an adult dentition. Aetiocetids, a diverse clade of Oligocene toothed mysticetes, have a series of small palatal foramina and associated sulci medial to the postcanine dentition. The openings have been homologized with lateral palatal foramina that transmit neurovascular structures to baleen in extant mysticetes, thereby implying a co-occurrence of teeth and baleen in aetiocetids....

Pairing functional connectivity with population dynamics to prioritize corridors for Southern California spotted owls

Erin Conlisk, Emily Haeuser, Alan Flint, Rebecca Lewison & Megan Jennings
Aim: Land use change, climate change, and shifts to disturbance regimes make successful wildlife management challenging, particularly when ongoing urbanization constrains habitat and movement. Preserving and maintaining landscape connectivity is a potential strategy to support wildlife responding to these stressors. Using a novel model framework, we determined the population-level benefit of a set of identified potential corridors for spotted owl population viability. Location: Southern California, United States. Methods: Combining habitat suitability and dynamic metapopulation models,...

Data from: When one phenotype is not enough - divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

Giulia Zancolli, Juan J. Calvete, Michael D. Cardwell, Harry W. Greene, William K. Hayes, Matthew J. Hegarty, Hans-Werner Herrmann, Andrew T. Holycross, Dominic I. Lannutti, John F. Mulley, Libia Sanz, Zachary D. Travis, Joshua R. Whorley, Catharine E. Wüster & Wolfgang Wuster
Understanding the origin and maintenance of phenotypic variation, particularly across a continuous spatial distribution, represents a key challenge in evolutionary biology. For this, animal venoms represent ideal study systems: they are complex, variable, yet easily quantifiable molecular phenotypes with a clear function. Rattlesnakes display tremendous variation in their venom composition, mostly through strongly dichotomous venom strategies, which may even coexist within single species. Here, through dense, widespread population-level sampling of the Mojave rattlesnake, Crotalus scutulatus,...

Data from: A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements

Shahan Derkarabetian, James Starrett, Nobuo Tsurusaki, Darrell Ubick, Stephanie Castillo & Marshal Hedin
Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe....

Data from: New insights into New World biogeography: an integrated view from the phylogeny of blackbirds, cardinals, sparrows, tanagers, warblers, and allies

F. Keith Barker, Kevin J. Burns, John Klicka, Scott M. Lanyon & Irby J. Lovette
Understanding the biogeographic origins and temporal sequencing of groups within a region or of lineages within an ecosystem can yield important insights into evolutionary dynamics and ecological processes. Fifty years ago, Ernst Mayr generated comprehensive—if limited—inferences about the origins of the New World avifaunas, including the importance of pre-Isthmian dispersal between North and South America. Since then, methodological advances have improved our ability to address many of the same questions, but the phylogenies upon which...

Data from: Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae)

Jared A. Grummer, , Tod W. Reeder & Robert W. Bryson
Current molecular methods of species delimitation are limited by the types of species delimitation models and scenarios that can be tested. Bayes factors allow for more flexibility in testing non-nested species delimitation models and hypotheses of individual assignment to alternative lineages. Here, we examined the efficacy of Bayes factors in delimiting species through simulations and empirical data from the Sceloporus scalaris species group. Marginal likelihood scores of competing species delimitation models, from which Bayes factor...

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