503 Works

Data from: Genetic and phenotypic variation across a hybrid zone between ecologically divergent tree squirrels (Tamiasciurus)

Andreas S Chavez, Carl J Saltzberg & G J Kenagy
A hybrid zone along an environmental gradient should contain a clinal pattern of genetic and phenotypic variation. This occurs because divergent selection in the two parental habitats is typically strong enough to overcome the homogenizing effects of gene flow across the environmental transition. We studied hybridization between two parapatric tree squirrels (Tamiasciurus spp.) across a forest gradient over which the two species vary in coloration, cranial morphology, and body size. We sampled 397 individuals at...

Data from: Improving the efficacy of web-based educational outreach in ecology

Gregory R. Goldsmith, Andrew D. Fulton, Colin D. Witherill & Javier F. Espeleta
Scientists are increasingly engaging the web to provide formal and informal science education opportunities. Despite the prolific growth of web-based resources, systematic evaluation and assessment of their efficacy remains limited. We used clickstream analytics, a widely available method for tracking website visitors and their behavior, to evaluate >60,000 visits over three years to an educational website focused on ecology. Visits originating from search engine queries were a small proportion of the traffic, suggesting the need...

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...

Data from: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

R. Alexander Pyron, Frank T. Burbrink & John J. Wiens
Background: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to clarify their taxonomy. Here, we present the first large-scale phylogenetic estimate for Squamata. Results: The estimated phylogeny contains 4161 species representing all currently recognized families...

Data from: Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

Stacy J. Mantooth, David J. Hafner, , Brett R. Riddle & Robert W. Bryson
We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range-wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil-calibrated and rate-calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using...

Data from: Biogeography of scorpions in the Pseudouroctonus minimus complex (Vaejovidae) from south-western North America: implications of ecological specialization for pre-Quaternary diversification

Robert W. Bryson, Warren E. Savary & Lorenzo Prendini
Aim: The aim of this study was to assess the impact of pre-Quaternary tectonics and orogeny relative to that of Pleistocene climate change on diversification within the Pseudouroctonus minimus complex, a group of vaejovid scorpions with stenotopic habitat requirements. Location: South-western North America (United States and Mexico). Methods: Multilocus sequence data (1899 base pairs from two mitochondrial and two nuclear genes) were generated from 65 samples of scorpions in the minimus complex. Phylogeographical structure within...

Data from: Projected climate-driven faunal movement routes

Joshua J. Lawler, Aaron S. Ruesch, Julian D. Olden & Brad H. McRae
Historically, many species moved great distances as climates changed. However, modern movements will be limited by the patterns of human-dominated landscapes. Here, we use a combination of projected climate-driven shifts in the distributions of 2903 vertebrate species, estimated current human impacts on the landscape, and movement models, to determine through which areas in the western hemisphere species will likely need to move to track suitable climates. Our results reveal areas with projected high densities of...

Data from: How stock of origin affects performance of individuals across a meta-ecosystem: an example from Sockeye salmon

Jennifer R. Griffiths, Daniel E. Schindler & Lisa W. Seeb
Connectivity among diverse habitats can buffer populations from adverse environmental conditions, influence the functioning of meta-ecosystems, and ultimately affect the reliability of ecosystem services. This stabilizing effect on populations is proposed to derive from complementarity in growth and survival conditions experienced by individuals in the different habitats that comprise meta-ecosystems. Here we use the fine scale differentiation of salmon populations between diverse lake habitats to assess how rearing habitat and stock of origin affect the...

Data from: Diversification across the New World within the ‘blue’ cardinalids (Aves: Cardinalidae)

, Jaime Chaves, Brian Tilston Smith, Matthew J. Miller, Kevin Winker, Jorge L. Pérez-Emán, John Klicka & Robert W. Bryson
Aim: To examine the history of diversification of ‘blue’ cardinalids (Cardinalidae) across North and South America. Location: North America (including Middle America) and South America. Methods: We collected 163 individuals of the 14 species of blue cardinalids and generated multilocus sequence data (3193 base pairs from one mitochondrial and three nuclear genes) to infer phylogeographical structure and reconstruct time-calibrated species trees. We then estimated the ancestral range at each divergence event and tested for temporal...

Data from: The future of food from the sea

Tracey Mangin, Christopher Costello, Ling Cao, Stefan Gelcich, Miguel A. Cisneros-Mata, Christopher M. Free, Halley E. Froehlich, Christopher D. Golden, Gakushi Ishimura, Jason Maier, Ilan Macadam-Somer, Michael C. Melnychuk, Masanori Miyahara, Carryn L. De Moor, Rosamond Naylor, Linda Nøstbakken, Elena Ojea, Erin O’Reilly, Ana M. Parma, Andrew J. Plantinga, Shakuntala H. Thilsted & Jane Lubchenco
Global food demand is on the rise and serious questions remain about whether supply can increase sustainably. Land-based expansion is possible, but may exacerbate climate change and biodiversity loss and compromise the delivery of other ecosystem services. As food from the sea represents only 17% of current edible meat production, we ask: How much food can we expect the ocean to sustainably produce by 2050? We examine the main food-producing sectors in the ocean—wild fisheries,...

Data from: Fluid preservation causes minimal reduction of parasite detectability in fish specimens: a new approach for reconstructing parasite communities of the past?

Evan Fiorenza, Katie Leslie, Mark Torchin, Katherine Maslenikov, Luke Tornabene & Chelsea Wood
Long-term datasets are needed to evaluate temporal patterns in wildlife disease burdens, but historical data on parasite abundance are extremely rare. For more than a century, natural history collections have been accumulating fluid-preserved specimens, which should contain the parasites infecting the host at the time of its preservation. However, before this unique data source can be exploited, we must identify the artefacts that are introduced by the preservation process. Here, we experimentally address whether the...

Siderophore concentrations along the North Pacific Gradients 1.0 and 2.0 cruises transect

Jiwoon Park & Randelle Bundy
This dataset includes concentrations of siderophores (strong iron-binding ligands) measured from seawater samples taken during Gradients 1.0 (KOK1606) and 2.0 (MGL1704) cruises, which took place in April-May 2016 and May-June 2017 respectively. Concentrations were measured using a Thermo iCAP RQ ICP-MS coupled to a Dionex Ultimate 3000 HPLC.

Host Factor Experiment (IM006B-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG3/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^4 PFU.

Host Factor Experiment (IM006A-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG3/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 PFU.

Host Factor Experiment (ICL006-R)

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Purpose: To obtain samples from Calu-3 cells infected with A/CA/04/09 (H1N1) for both transcriptional and proteomics analyses. Details: Time Points = 0, 3, 7, 12, 18, 24, 30, 36 and 48 h post infection; Done in triplicate for both RNA and protein; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks done in triplicate from same cell stock as rest of...

Host Factor Experiment (IM004-P)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; doses = 1E4 PFU; Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Host Factor Experiment (SCL008-R)

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Purpose: To obtain samples for transcriptional and proteomic analysis using wild type icSARS CoV and icSARS ExoNI and icSARS dNSP16 mutants in 2B-4 cells/sorted Calu-3 cells with high ACE2 expression. Details: Time Points = 0, 7, 12, 24, 36, 48, 60 and 72h post infection (Note: only 0, 24, 48 and 72hr samples analysed for proteomics); Done in triplicate for RNA and quadruplicate for protein; Replicates are defined as 3 or 4 different wells, plated...

Host Factor Experiment (CA04M001-R)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics. General Design: 20 week-old C57Bl6 mice; Three Doses = 1E3, 1E4, 1E5, 1E6 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Host Factor Experiment (KL001-R)

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Polarized confluent monolayers of Calu-3 cells were infected apically with the avian-origin IAVs A/Anhui/01/2013 (H7N9) [Anhui01], A/Netherland/219/2003 (H7N7) [NL219], A/Vietnam/1203/2004 (H5N1) [VN1203], or a human seasonal virus A/Panama/2007/1999 (H3N2) [Pan99] at an MOI of 1. Time-matched mocks were also included using the same cell stock as the rest of the samples. Culture medium (same as what the virus stock is in) was used for the mock infections. Quadruplicate wells were infected for each virus/timepoint. Measured...

Host Factor Experiment (KL002-R)

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Groups of 6- to 8-week-old BALB/c mice were infected with either A/Anhui/01/2013 (H7N9), A/Netherlands/219/2003 (H7N7), A/Vietnam/1203/2004 (H5N1), or pandemic H1N1 human virus, A/Mexico/4482/2007 (H1N1). Infections were done at 10^5 PFU or time-matched mock infected. Time points were 1, 3 and 5 d.p.i. There were 4-5 infected and 3 mock infected animals/time point. Lung samples were collected for virus load and transcriptional analysis. Weight loss and animal survival were also monitored.

Host Factor Experiment (IM006A-P)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG3/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 PFU.

Host Factor Experiment (SM009-R)

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Purpose: To obtain lung samples from C57BL6 or PLAT knock-out mice infected with SARS MA15 virus for transcriptional analysis. Details: Time Points = 4 and 7 days post-infection; 2-3 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.

Host Factor Experiment (SM003-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with , icSARS, SARS MA15 or SARS BatSRBD mutant viruses for transcriptional analysis. Details: Time Points = 1, 2, 4 and 7 days post-infection; 3-5 replicates for infected and mock mice; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu for icSARS, 10^4 or 10^5pfu for MA15 and 10^4pfu BatSRBD.

How variable is mixing efficiency in the abyss?

Takashi Ijichi, Louis St. Laurent, Kurt L. Polzin & John Toole
This directory contains BBTRE/DoMORE processed data (“all_BBTRE.mat” and “all_DoMORE.mat”) that was used to produce all figures in the above research letter. Each mat file has two structure arrays named “location” and “patch10”. The “location” array includes microstructure profile information used in this study (Table D1). The “patch10” array includes 10-m patch-wise parameter estimates used in this study (Table D2). Note that bulk averaged parameters can be constructed from parameters saved in “patch10” (see the above...

Host Factor Experiment (SM020-R)

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Purpose: To obtain lung samples from ppp1r14c knockout mutant mice infected with SARS MA15 virus for transcriptional analyses. Details: Time Points = days 4 and 7 post-infection; 2-3 replicate mice for each condition; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.

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Affiliations

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