32 Works

Data from: The loss of hemoglobin and myoglobin does not minimize oxidative stress in Antarctic icefishes

Kristin M. O'Brien, Elizabeth L. Crockett, Jacques Philip, Corey A. Oldham, Megan Hoffman, Donald E. Kuhn, Ronald Barry & Jessica McLaughlin
The unusual pattern of expression of hemoglobin (Hb) and myoglobin (Mb) among Antarctic notothenioid fishes provides an exceptional model system for assessing the impact of these proteins on oxidative stress. We tested the hypothesis that the lack of oxygen-binding proteins may reduce oxidative stress. Levels and activity of pro-oxidants, small-molecule and enzymatic antioxidants, and levels of oxidized lipids and proteins in liver, oxidative skeletal muscle, and heart ventricle were quantified in five species of notothenioid...

Data from: Increased reproductive investment associated with greater survival and longevity in Cassin’s auklets

Michael E. Johns, Pete Warzybok, Russell W. Bradley, Jaime Jahncke, Mark Lindberg & Greg A. Breed
Individuals increase lifetime reproductive output through a trade-off between investment in future survival and immediate reproductive success. This pattern may be obscured in certain higher quality individuals that possess greater reproductive potential. The Cassin’s auklet (Ptychoramphus aleuticus) is a long-lived species where some individuals exhibit greater reproductive ability through a behavior called double brooding. Here, we analyze 32 years of breeding histories from marked known-age auklets to test whether double brooding increases lifetime fitness despite...

Data from: Recommendations for using msBayes to incorporate uncertainty in selecting an ABC model prior: a response to Oaks et al.

Michael James Hickerson, Graham N. Stone, Konrad Lohse, Terrence C. Demos, Xiaoou Xie, Cedric Landerer & Naoki Takebayashi
Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that...

A target enrichment probe set for resolving the flagellate land plant tree of life

Jesse W. Breinholt, Sarah B. Carey, George P. Tiley, E. Christine Davis, Lorena Endara, Stuart F. McDaniel, Leandro Neves, Emily B. Sessa, Matt Von Konrat, Susan Fawcett, Stefanie M. Ickert-Bond, Paulo H. Labiak, Juan Larraín, Marcus Lehnert, Lily R. Lewis, Nathalie S. Nagalingum, Nikisha Patel, Stefan A. Rensing, Weston Testo, Alejandra Vasco, Juan Carlos Villarreal, Evelyn Webb Williams, J. Gordon Burleigh, Sahut Chantanaorrapint, Leandro G. Neves … & Stefanie M. Ickert‐Bond
Premise of the Study: New sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. Methods and Results: We leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target...

Data from: Strong maternal fidelity and natal philopatry shape genetic structure in North Pacfic humpback whales

C. Scott Baker, Debbie Steel, John Calambokidis, Erin A. Falcone, Ursula Gozález-Peral, Jay Barlow, Alexander M. Burdin, Phillip J. Clapham, John K. B. Ford, Christine M. Gabriele, David Mattila, Janice M. Straley, Barbara L. Taylor, Jorge Urbán, Paul R. Wade, David Weller, Briana H. Witteveen, Manami Yamaguchi, CS Baker, BH Witteveen, E Falcone, BL Taylor, JKB Ford, AM Burdin, PJ Clapham … & JM Straley
We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds in humpback whales based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. For 2,193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions during the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. From sequences of the mtDNA...

Speciation and gene flow in two sympatric small mammals from Madagascar, Microgale fotsifotsy and M. soricoides (Mammalia: Tenrecidae)

Kathryn M Everson, Link E Olson & Steven M Goodman
Madagascar’s shrew tenrecs (Mammalia: Tenrecidae: Microgale, Nesogale) form an excellent system for studying speciation. Most species are endemic to the island’s eastern moist evergreen forest, a region renowned for high levels of biodiversity and a high rate of in situ diversification. We set out to understand the speciation dynamics in a clade of recently described taxa: Microgale fotsifotsy and M. soricoides, which have nearly identical distributions in the moist evergreen forest, and M. nasoloi, which...

Data from: Euglossine bees mediate only limited long-distance gene flow in a tropical vine

Øystein H. Opedal, Mohsen Falahati-Anbaran, Elena Albertsen, W. Scott Armbruster, Rocío Pérez-Barrales, Hans K. Stenøien & Christophe Pélabon
Euglossine bees (Apidae: Euglossini) have long been hypothesized to act as long-distance pollinators of many low-density tropical plants. We tested this hypothesis by the analysis of gene flow and genetic structure within and among populations of the euglossine bee-pollinated vine Dalechampia scandens. Using microsatellite markers, we assessed historical gene flow by the quantification of regional-scale genetic structure and isolation by distance among 18 populations, and contemporary gene flow by the estimation of recent migration rates...

Data from: Compositional and functional shifts in arctic fungal communities in response to experimentally increased snow depth

Tatiana A. Semenova, Luis N. Morgado, Jeffrey M. Welker, Marilyn D. Walker, Erik Smets & József Geml
Climate warming leads to more intensive evaporation from the Arctic sea resulting in increased precipitation in the low Arctic, e.g., higher snowfall during winter. Deeper snow keeps the arctic soils warmer and alters soil attributes and vegetation, e.g., increase in nitrogen availability, expansion of shrubs and decline in shade-intolerant lichens and bryophytes. Changes in soil properties and vegetation are expected to influence on saprotrophic and plant-symbiotic fungi, but how increased snow depth affects their community...

Data from: Drought intensification drives turnover of structure and function in stream invertebrate communities

Thomas W.H. Aspin, Thomas J. Matthews, Kieran Khamis, Alexander M. Milner, Zining Wang, Matthew J. O'Callaghan, Mark E. Ledger & Thomas W. H. Aspin
Climatic extremes are becoming more frequent and intense across much of the globe, potentially transforming the biodiversity and functioning of affected ecosystems. In freshwaters, hydrological extremes such as drought can regulate beta diversity, acting as powerful environmental filters to dictate the complement of species and functional traits found at local and landscape scales. New methods that enable beta diversity and its functional equivalent to be partitioned into turnover (replacement of species/functions) and nestedness-resultant (gain/loss of...

Data from: Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic

Ina Timling, Anders Dahlberg, Donald Arthur Walker, Monique Gardes, Jean-Yves Charcosset, Jeffrey M. Welker & Donald Lee Taylor
Ectomycorrhizal fungi (EMF) form symbioses with a few plant species that comprise a large fraction of the arctic vegetation. Despite their importance, the identity, abundance and distribution of EMF in the Arctic, as well as the key drivers controlling their community composition are poorly understood. In this study, we investigated the diversity and structure of EMF communities across a bioclimatic gradient spanning much of the North American Arctic. We collected roots from two principal arctic...

Data from: Quantifying the dark data in museum fossil collections as palaeontology undergoes a second digital revolution

Charles R. Marshall, Seth Finnegan, Erica C. Clites, Patricia A. Holroyd, Nicole Bonuso, Crystal Cortez, Edward Davis, Gregory P. Dietl, Patrick S. Druckenmiller, Ron C. Eng, Christine Garcia, Kathryn Estes-Smargiassi, Austin Hendy, Kathy A. Hollis, Holly Little, Elizabeth A. Nesbitt, Peter Roopnarine, Leslie Skibinski, Jann Vendetti & Lisa D. White
Large-scale analysis of the fossil record requires aggregation of palaeontological data from individual fossil localities. Prior to computers these synoptic datasets were compiled by hand, a laborious undertaking that took years of effort and forced palaeontologists to make difficult choices about what types of data to tabulate. The advent of desktop computers ushered in palaeontology’s first digital revolution – online literature-based databases, such as the Paleobiology Database (PBDB). However, the published literature represents only a...

Data from: Biogeographic and anthropogenic correlates of Aleutian Islands plant diversity: a machine-learning approach

Monte Garroutte, Falk Huettmann, Campbell O. Webb & Stefanie M. Ickert-Bond
This is the first comprehensive analysis of vascular plant diversity patterns in the Aleutian Islands to identify and quantify the impact of Aleutian Island distance dispersal barriers, geographical, ecological and anthropogenic factors. Data from public Open Access databases, printed floristic accounts, and from collections made by the primary author were used to develop an Aleutian floristic database. The most common plant distribution pattern was ‘an eastern origin community’, though it compared similarly to the ‘Western’...

Data from: Does multiple paternity affect seed mass in angiosperms? An experimental test in Dalechampia scandens

C. Pélabon, E. Albertsen, M. Falahati-Anbaran, J. Wright, W. S. Armbruster & W.S. Armbruster
Flowers fertilized by multiple fathers may be expected to produce heavier seeds than those fertilized by a single father. However, the adaptive mechanisms leading to such differences remain unclear, and the evidence inconsistent. Here, we first review the different hypotheses predicting an increase in seed mass when multiple paternity occurs. We show that distinguishing between these hypotheses requires information about average seed mass, but also about within-fruit variance in seed mass, bias in siring success...

Data from: Apex predators and the facilitation of resource partitioning among mesopredators

Kelly J. Sivy, Casey B. Pozzanghera, Kassidy E. Colson, Matthew A. Mumma & Laura R. Prugh
Apex predators may influence carnivore communities through the suppression of competitively dominant mesopredators, however they also provide carrion subsidies that could influence foraging and competition among sympatric mesopredators when small prey is scarce. We assessed coyote Canis latrans and red fox Vulpes vulpes winter diet overlap and composition from scats collected in two study areas with >3-fold difference in grey wolf Canis lupus density due to a wolf control program. We hypothesized that differences in...

Data from: The contemporary genetic pattern of European moose is shaped by postglacial recolonization, bottlenecks, and the geographical barrier of the Baltic Sea

Magdalena Niedziałkowska, Kris J. Hundertmark, Bogumiła Jędrzejewska, Vadim E. Sidorovich, Hanna Zalewska, Rauno Veeroja, Erling J. Solberg, Sauli Laaksonen, Håkan Sand, Vyacheslav A. Solovyev, Andrey Sagaydak, Juha Tiainen, Rimvydas Juškaitis, Gundega Done, Vadim A. Borodulin, Evgenii A. Tulandin & Krzysztof Niedziałkowski
To investigate genetic diversity and the population structure of the European moose (Alces alces), we analyzed 14 microsatellite loci for 694 samples collected across 16 localities. The highest genetic diversity was detected in Belarus and Russia and the lowest was found in Scandinavia. Two major genetic clusters existed, Scandinavian and continental, and some further spatial structure was detected. There was high concordance between the spatial distribution of microsatellite clusters analyzed in the present study and...

Data from: Interpreting the FLOCK algorithm from a statistical perspective

Eric C. Anderson & Patrick D. Barry
We show that the algorithm in the program FLOCK (Duchesne & Turgeon 2009) can be interpreted as an estimation procedure based on a model essentially identical to the STRUCTURE (Pritchard et al. 2000) model with no admixture and non-correlated allele frequency priors. Rather than using MCMC, the FLOCK algorithm searches for the maximum-a-posteriori estimate of this STRUCTURE model via a simulated annealing algorithm with a rapid cooling schedule (namely, the exponent on the objective function...

Data from: Blossom colour change after pollination provides carbon for developing seeds

Christophe Pélabon, Lauriane Hennet, Richard Strimbeck, Hansen Johnson & William Scott Armbruster
1. We tested the hypothesis that greening of the floral (involucral) bracts of Dalechampia scandens blossoms after pollination (when bracts are white) increases carbon assimilation and provides photosynthate to developing seeds. 2. We investigated the importance of the involucral bracts for the process of seed development in two ways. First, we removed or shaded bracts of hand-pollinated blossoms to prevent their photosynthesis and tested the effects of these manipulations on seed development. Secondly, we measured...

Data from: Are flatfishes (Pleuronectiformes) monophyletic?

Matthew A. Campbell, Wei-Jen Chen & J. Andrés López
All extant species of flatfish (order Pleuronectiformes) are thought to descend from a common ancestor, and therefore to represent a monophyletic group. This hypothesis is based largely on the dramatic bilateral asymmetry and associated ocular migration characteristics of all flatfish. Yet, molecular-based phylogenetic studies have been inconclusive on this premise. Support for flatfish monophyly has varied with differences in taxonomic and gene region sampling schemes. Notably, the genus Psettodes has been found to be more...

Data from: Heteropatric speciation in a duck, Anas crecca

Kevin Winker, Kevin G. McCracken, Daniel D. Gibson & Jeffrey L. Peters
Heteropatric differentiation is a mode of speciation with gene flow in which divergence occurs between lineages that are in sympatry and allopatry at different times during cyclic spatial movements. Empirical evidence suggests that heteropatric differentiation may prove to be common among seasonally migratory organisms. We examined genetic differentiation between the sedentary Aleutian Islands population of green-winged teal (Anas crecca nimia) and its close migratory relative, the Eurasian, or Old World (OW), Anas c. crecca population,...

Data from: Effect of pyric herbivory on source-sink dynamics in grassland birds

Craig A. Davis, Roy T. Churchwell, Samuel D. Fuhlendorf, David M. Engle & Torre J. Hovick
Grasslands world-wide provide a host of ecosystem services. In particular, these grasslands serve as biodiversity repositories for a myriad of imperilled animal species. One such group is grassland birds, which have experienced significant declines, predominantly caused by extensive loss and degradation of native grasslands. Rangeland management that promotes increasing and sustaining livestock production through reducing the inherent, disturbance-driven variability that historically occurred in grasslands is considered a major contributing factor to these declines. An alternative...

Data from: Intra-population variation in the natal origins and wing morphology of overwintering western monarch butterflies Danaus plexippus

Louie H. Yang, Dmitry Ostrovsky, Matthew C. Rogers, Jeffrey M. Welker & Jeffery M. Welker
Understanding the natal origins of migratory animals is critical for understanding their population dynamics and conservation. However, quantitative estimates of population recruitment from different natal habitats can be difficult to assess for many species, especially those with large geographic ranges. These limitations hinder the evaluation of alternative hypotheses about the key movements and ecological interactions of migratory species. Here, we quantitatively investigated intra-population variation in the natal origins of western North American monarch butterflies Danaus...

Data from: Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus.

Gregory O’Corry-Crowe, Tom Gelatt, Lorrie Rea, Carolina Bonin, Michael Rehberg & Greg O'Corry-Crowe
Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density-dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n=1,106) and 16 microsatellite loci...

Data from: Does functional trait diversity predict aboveground biomass and productivity of tropical forests? Testing three alternative hypotheses

Bryan Finegan, Marielos Peña-Claros, Alexandre De Oliveira, Nataly Ascarrunz, M. Syndonia Bret-Harte, Geovana Carreño-Rocabado, Fernando Casanoves, Sandra Díaz, Paul Eguiguren Velepucha, Fernando Fernandez, Juan Carlos Licona, Leda Lorenzo, Beatriz Salgado Negret, Marcel Vaz & Lourens Poorter
1. Tropical forests are globally important, but it is not clear whether biodiversity enhances carbon storage and sequestration in them. We tested this relationship focusing on components of functional trait biodiversity as predictors. 2. Data are presented for three rain forests in Bolivia, Brazil and Costa Rica. Initial above-ground biomass and biomass increments of survivors, recruits and survivors + recruits (total) were estimated for trees ≥10 cm d.b.h. in 62 and 21 1.0-ha plots, respectively....

Data from: Migratory culture, population structure and stock identity in North Pacific beluga whales (Delphinapterus leucas)

Greg O'Corry-Crowe, Robert Suydam, Lori Quakenbush, Brooke Potgieter, Lois Harwood, Dennis Litovka, Tatiana Ferrer, John Citta, Vladimir Burkanov, Kathy Frost, Barbara Mahoney & Greg O’Corry-Crowe
The annual return of beluga whales, Delphinapterus leucas, to traditional seasonal locations across the Arctic may involve migratory culture, while the convergence of discrete summering aggregations on common wintering grounds may facilitate outbreeding. Natal philopatry and cultural inheritance, however, has been difficult to assess as earlier studies were of too short a duration, while genetic analyses of breeding patterns, especially across the beluga's Pacific range, have been hampered by inadequate sampling and sparse information on...

Data from: The evolutionary history of polycotylid plesiosaurians

Valentin Fischer, Roger B J Benson, Patrick S Druckenmiller, Hilary F Ketchum & Nathalie Bardet
Polycotylidae is a clade of plesiosaurians that appeared during the Early Cretaceous and became speciose and abundant early in the Late Cretaceous. However, this radiation is poorly understood. Thililua longicollis from the Middle Turonian of Morocco is an enigmatic taxon possessing an atypically long-neck and, as originally reported, a series of unusual cranial features that cause unstable phylogenetic relationships for polycotylids. We reinterpret the holotype specimen of Thililua longicollis and clarify its cranial anatomy. Thililua...

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