63 Works

Microbiome assembly and maintenance across the lifespan of bumble bee workers

Tobin Hammer, August Easton-Calabria & Nancy A. Moran
How a host’s microbiome changes over its lifespan can influence development and aging. As these temporal patterns have only been described in detail for humans and a handful of other hosts, an important next step is to compare microbiome dynamics across a broader array of host-microbe symbioses, and to investigate how and why they vary. Here we characterize the temporal dynamics and stability of the bumblebee worker gut microbiome. Bumblebees are a useful symbiosis model...

Population-level variation in parasite resistance due to differences in immune initiation and rate of response

Amanda Hund, Lauren Fuess, Mariah Kenney, Meghan Maciejewski, Joseph Marini, Kum Chuan Shim & Dan Bolnick
Closely related populations often differ in resistance to a given parasite, as measured by infection success or failure. Yet, the immunological mechanisms of these evolved differences are rarely specified. Does resistance evolve via changes to the host’s ability to recognize that an infection exists, actuate an effective immune response, or attenuate that response? We tested whether each of these phases of the host response contributed to threespine sticklebacks’ recently evolved resistance to their tapeworm Schistocephalus...

Label-based expectations affect reward perception in bumblebees

Claire Hemingway & Felicity Muth
While classic models of animal decision-making assume that individuals objectively assess the absolute value of options, decades of research have shown that rewards are often evaluated relative to prior experience, creating ‘contrast effects’. Contrast effects are often assumed to be purely sensory, yet consumer psychology tells us that label-based expectations can affect value perception. However, this has rarely been tested in non-model systems. Bumblebees forage on a variety of flower types that vary in their...

Additional file 2 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Additional file 2: Supplementary Table S1. MG_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metagenomes. MG_metadata. Metadata for sequenced metagenomes. MT_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metatranscriptomes. MT_metadata. Metadata for sequenced metatranscriptomes.

Hybodontiform shark remains (Chondrichthyes, Elasmobranchii) from the Lower Triassic of Yunnan Province, China, with comments on hybodontiform diversity across the PTB

Wen Wen, JüRgen Kriwet, Qiyue Zhang, Michael J. Benton, Christopher J. Duffin, Jingyuan Huang, Changyong Zhou, Shixue Hu & Zhixin Ma
Hybodontiform shark teeth, cephalic and fin spines as well as placoid scales are reported here for the first time from the continental, Lower Triassic Dongchuan Formation near the village of Zhaojia (Huize County, Yunnan Province) in south-west China. The isolated teeth are assigned to three unidentified hybodontiforms but also to a new species of Parvodus, P. huizodus sp. nov., the oldest record of this small-toothed lonchidiid shark genus, extending its range well down into the...

BEDMAP2 - Ice thickness, bed and surface elevation for Antarctica - standardised data points

Peter Fretwell, Alice Fremand, Julien Bodart, Hamish Pritchard, David Vaughan, Jonathan Bamber, N. Barrand, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, D. Callens, H Conway, Alison Cook, Hugh Corr, D Damaske, V. Damn, Fausto Ferraccioli, Rene Forsberg, S. Fujita, Y. Gim, P. Gogineni, J. Griggs … & A. Zirizzotti
We present here the Bedmap2 ice thickness, bed and surface elevation standardised CSV data points that were used to create the Bedmap2 gridding products. The data consists of 25 million points coming from 68 individual surveys acquired in Antarctica. The associated datasets consist of: - Bedmap1 standardised CSV data points: https://doi.org/10.5285/f64815ec-4077-4432-9f55-0ce230f46029 - Bedmap3 standardised CSV data points: https://doi.org/10.5285/91523ff9-d621-46b3-87f7-ffb6efcd1847 - Bedmap2 statistically-summarised data points (shapefiles): https://doi.org/10.5285/0f90d926-99ce-43c9-b536-0c7791d1728b - Bedmap2 gridding products: https://doi.org/10.5285/fa5d606c-dc95-47ee-9016-7a82e446f2f2 This work is supported by...

Additional file 26 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 26: Table S4. The Effects of Diabetes on the Proteogenomic Characteristics of PDAC. Table S4A Mutations and arm events information in PDAC patients with or without diabetes history. Table S4B Matrix of differential pathway enrichment in patients with or without diabetes history at mRNA level. Table S4C Matrix of differential pathway enrichment in patients with or without diabetes history at protein level.

Reproductive benefits associated with dispersal in headwater populations of Trinidadian guppies (Poecilia reticulata)

Isabela Lima Borges, Jillian Dangerfield, Lisa Angeloni, Chris Funk & Sarah Fitzpatrick
Theory suggests that the evolution of dispersal is balanced by its fitness costs and benefits, yet empirical evidence is sparse due to the difficulties of measuring dispersal and fitness in natural populations. Here, we use spatially-explicit data from a multi-generational capture-mark-recapture study of two populations of Trinidadian guppies (Poecilia reticulata) along with pedigrees to test whether there are fitness benefits correlated with dispersal. Combining these ecological and molecular datasets allows us to directly measure the...

Can you hear/see me? Multisensory integration of signals does not always facilitate mate choice

Derek Coss, Michael Ryan, Rachel Page, Kimberly Hunter & Ryan Taylor
Females of many species choose mates using multiple sensory modalities. Multimodal noise may arise, however, in dense aggregations of animals communicating via multiple sensory modalities. Some evidence suggests multimodal signals may not always improve receiver decision-making performance. When sensory systems process input from multimodal signal sources, multimodal noise may arise and potentially complicate decision-making due to the demands on cognitive integration tasks. We tested female túngara frog, Physalaemus (=Engystomops) pustulosus, responses to male mating signals...

Data from: Paternal hatching care regulates the timing, synchrony, and success of hatching in a coral reef fish

John Majoris, Fritz Francisco, Corinne Burns, Simon Brandl, Karen Warkentin & Peter Buston
In oviparous species, the timing of hatching is a crucial decision, but for developing embryos, assessing cues that indicate the optimal time to hatch is challenging. In species with parental care, parents can assess environmental conditions and induce their offspring to hatch. We provide the first documentation of parental hatching regulation in a coral reef fish, demonstrating that male neon gobies (Elacatinus colini) directly regulate hatching by removing embryos from the clutch and spitting hatchlings...

Data from 'Water table depth modulates productivity and biomass across Amazonian forests'

Thaiane R. Sousa, Juliana Schietti, Thaise Emílio, Rafael Herrera Fernández, Hans ter Steege, Carolina V Castilho, Adriane Esquivel Muelbert, Timothy Baker, Aline Pontes-Lopes, Camila V. J. Silva, Juliana M. Silveira, Géraldine Derroire, Wendeson Castro, Abel Monteagudo Mendoza, Ademir Ruschel, Agustín Rudas, Adriano José Nogueira Lima, Agustín Rudas, Alejandro Araujo-Murakami, Ana Andrade, Anand Roopsind, Angelo Gilberto Manzatto, Anthony Di Fiore, Armando Torres-Lezama & Aurélie Dourdain

Wild herbivores enhance resistance to invasion by exotic cacti in an African savanna

Harry Wells, Ramiro Crego, Jesse Alston, S. Kimani Ndung'u, Leo Khasoha, Courtney Reed, Abdikadir Hassan, Samson Kurukura, Jackson Ekadeli, Mathew Namoni, Peter Stewart, Duncan Kimuyu, Amelia Wolf, Truman Young, Tyler Kartzinel, Todd Palmer, Jacob Goheen & Robert Pringle
1. Whether wild herbivores confer biotic resistance to invasion by exotic plants remains a key question in ecology. There is evidence that wild herbivores can impede invasion by exotic plants, but it is unclear whether and how this generalises across ecosystems with varying wild herbivore diversity and functional groups of plants, particularly over long-term (decadal) time frames. 2. Using data from three long-term (13- to 26-year) exclosure experiments in central Kenya, we tested the effects...

Additional file 2 of Whole-transcriptome profiles of Chrysanthemum seticuspe improve genome annotation and shed new light on mRNA–miRNA–lncRNA networks in ray florets and disc florets

Daojin Sun, Jing Zhang, Jun He, Zhiqiang Geng, Song Li, Jiali Zhang, Peiling Li, Lingling Zhang, Zhenxing Wang, Likai Wang, Fadi Chen & Aiping Song
Additional file 2.

BEDMAP2 - Ice thickness, bed and surface elevation for Antarctica - standardised shapefiles and geopackages

Peter Fretwell, Hamish Pritchard, David Vaughan, Jonathan Bamber, N. Barrand, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, D. Callens, H Conway, Alison Cook, Hugh Corr, D Damaske, V. Damn, Fausto Ferraccioli, Rene Forsberg, S. Fujita, Y. Gim, P. Gogineni, J. Griggs, Richard Hindmarsh, P. Holmlund … & Julien Bodart
We present here the Bedmap2 ice thickness, bed and surface elevation aggregated points and survey lines. The aggregated points consist of statistically-summarised shapefile points (centred on a continent-wide 500 m x 500 m grid) that reports the average values of ice thickness, bed and surface elevation from the full-resolution survey data and information on their distribution. The points presented here correspond to the additional points to Bedmap1 used for the gridding of Bedmap2. The data...

Additional file 2 of Whole-genome methylation analysis reveals epigenetic variation between wild-type and nontransgenic cloned, ASMT transgenic cloned dairy goats generated by the somatic cell nuclear transfer

Hao Wu, Wendi Zhou, Haijun Liu, Xudai Cui, Wenkui Ma, Haixin Wu, Guangdong Li, Likai Wang, Jinlong Zhang, Xiaosheng Zhang, Pengyun Ji, Zhengxing Lian & Guoshi Liu
Additional file 2: Fig. S2. Methylation sequencing quality and statistical analyses (A, ASMT transgenic cloned goat (K2020); B, control goat (S2); C, Nontransgenic cloned goat (K03)).

Additional file 3 of Whole-genome methylation analysis reveals epigenetic variation between wild-type and nontransgenic cloned, ASMT transgenic cloned dairy goats generated by the somatic cell nuclear transfer

Hao Wu, Wendi Zhou, Haijun Liu, Xudai Cui, Wenkui Ma, Haixin Wu, Guangdong Li, Likai Wang, Jinlong Zhang, Xiaosheng Zhang, Pengyun Ji, Zhengxing Lian & Guoshi Liu
Additional file 3: Fig. S3. Genome-wide distribution of mean methylation rates (A, ASMT transgenic cloned goat (K2020); B, control goat (S2); C, Nontransgenic cloned goat (K03)).

Additional file 23 of Proteogenomic insights into the biology and treatment of pancreatic ductal adenocarcinoma

Yexin Tong, Mingjun Sun, Lingli Chen, Yunzhi Wang, Yan Li, Lingling Li, Xuan Zhang, Yumeng Cai, Jingbo Qie, Yanrui Pang, Ziyan Xu, Jiangyan Zhao, Xiaolei Zhang, Yang Liu, Sha Tian, Zhaoyu Qin, Jinwen Feng, Fan Zhang, Jiajun Zhu, Yifan Xu, Wenhui Lou, Yuan Ji, Jianyuan Zhao, Fuchu He, Yingyong Hou … & Chen Ding
Additional file 23: Table S1. Clinicopathologic Information and Multi-omics Data in PDAC Cohort. Table S1A Multi-omics information of PDAC cohort. Table S1B Clinicopathologic information of the 229 PDAC.

Using GBIF to Demonstrate Colonial Legacies on Biodiversity Data

Ryan S. Mohammed, Melissa Kemp, Michelle J. LeFebvre, Alexis M. Mychajliw, Grace Turner, Kelly Fowler, Michael Pateman, Maria A. Nieves-Colón, Lanya Fanovich, Siobhan B. Cooke, Liliana M. Dávalos, Scott M. Fitzpatrick, Christina M. Giovas, Myles Stokowski & Ashley A. Wrean
Biologists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”, but do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. We discuss two case studies of the Caribbean’s fragmented natural history collections, the effects of differing legislation and governance by the region’s multiple nation states. We use digital natural history specimen data from GBIF to demonstrate how...

Additional file 2 of Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction

Lauren M. Tom, Martina Aulitto, Yu-Wei Wu, Kai Deng, Yu Gao, Naijia Xiao, Beatrice Garcia Rodriguez, Clifford Louime, Trent R. Northen, Aymerick Eudes, Jenny C. Mortimer, Paul D. Adams, Henrik V. Scheller, Blake A. Simmons, Javier A. Ceja-Navarro & Steven W. Singer
Additional file 2: Supplementary Table S1. MG_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metagenomes. MG_metadata. Metadata for sequenced metagenomes. MT_FC_annotations. Table with data for contigs, predicted genes, and feature count values for genes in the metatranscriptomes. MT_metadata. Metadata for sequenced metatranscriptomes.

Dataset: Local hydrological conditions influence tree diversity and composition across the Amazon basin

Manuel J. Marca-Zevallos, Gabriel M. Moulatlet, Thaiane R. Sousa, Juliana Schietti, Luiz De Souza Coelho, José Ferreira Ramos, Diogenes De Andrade Lima Filho, Iêda Leão Amaral, Francisca Dionízia De Almeida Matos, Lorena M. Rincón, Juan David Cardenas Revilla, Marcelo Petratti Pansonato, Rogerio Gribel, Edelcilio Marques Barbosa, Ires Paula De Andrade Miranda, Luiz Carlos De Matos Bonates, Juan Ernesto Guevara, Rafael P. Salomão, Leandro Valle Ferreira, Dário Dantas Do Amaral, Nigel C.A. Pitman, Corine Vriesendorp, Tim R. Baker, Roel Brienen, Marcelo De Jesus Veiga Carim … & Flávia R.C. Costa
Tree diversity and composition in Amazonia are known to be strongly determined by the water supplied by precipitation. Nevertheless, within the same climatic regime, water availability is modulated by local topography and soil characteristics (hereafter referred to as local hydrological conditions), varying from saturated and poorly drained to well-drained and potentially dry areas. While these conditions may be expected to influence species distribution, the impacts of local hydrological conditions on tree diversity and composition remain...

Rare species biodiversity, socio-demographics and local and landscape characteristics in Northern California community urban gardens

Theresa Ong, Brenda Lin, Azucena Lucatero, Hamutahl Cohen, Peter Bichier, Monika Egerer, Alana Danieu, Shalene Jha & Stacy Philpott
Cities are sometimes characterized as homogenous with species assemblages composed of abundant, generalist species having similar ecological functions. Under this assumption, rare species, or species observed infrequently, would have especially high conservation value in cities for their potential to increase functional diversity. Management to increase the number of rare species in cities could be an important conservation strategy in a rapidly urbanizing world. However, most studies of species rarity define rarity in relatively pristine environments...

Evolutionary gain and loss of a pathological immune response to parasitism

Daniel Bolnick, Jesse Weber, Natalie Steinel, Stephen De Lisle, Lauren Fuess, Foen Peng, Kum Chuan Shim, Brian Lohman & Swapna Subramanian
Parasites impose fitness costs on their hosts. Biologists often assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests selection may instead favor loss of resistance. Intraspecific variation in immune costs are rarely surveyed in a manner that tests evolutionary patterns, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes they gained resistance to the freshwater-associated...

Hybodontiform shark remains (Chondrichthyes, Elasmobranchii) from the Lower Triassic of Yunnan Province, China, with comments on hybodontiform diversity across the PTB

Wen Wen, JüRgen Kriwet, Qiyue Zhang, Michael J. Benton, Christopher J. Duffin, Jingyuan Huang, Changyong Zhou, Shixue Hu & Zhixin Ma
Hybodontiform shark teeth, cephalic and fin spines as well as placoid scales are reported here for the first time from the continental, Lower Triassic Dongchuan Formation near the village of Zhaojia (Huize County, Yunnan Province) in south-west China. The isolated teeth are assigned to three unidentified hybodontiforms but also to a new species of Parvodus, P. huizodus sp. nov., the oldest record of this small-toothed lonchidiid shark genus, extending its range well down into the...

BEDMAP3 - Ice thickness, bed and surface elevation for Antarctica - standardised shapefiles and geopackages

Peter Fretwell, Hamish Pritchard, Alice Fremand, Julien Bodart, A. Aitken, Jonathan Bamber, R.E. Bell, C Bianchi, Robert Bingham, Donald Blankenship, G. Casassa, Ginny Catania, K Christianson, H Conway, Hugh Corr, X. Cui, D Damaske, V. Damn, R. Drews, G. Eagles, O. Eisen, H. Eisermann, F Ferraccioli, Rene Forsberg, S Franke … & A. Zirizzotti
We present here the Bedmap3 ice thickness, bed and surface elevation aggregated points and survey lines. The aggregated points consist of statistically-summarised shapefile points (centred on a continent-wide 500 m x 500 m grid) that reports the average values of Antarctic ice thickness, bed and surface elevation from the full-resolution survey data and information on their distribution. The points presented here correspond to the added points since the last release of Bedmap2. The data comes...

Quality Improvement Center for Adoption and Guardianship Support and Preservation

Rowena Fong & Nancy Rolock
The Children’s Bureau, Administration for Children and Families, Department of Health and Human Service established the National Quality Improvement Center for Adoption and Guardianship Support and Preservation (QIC-AG). In October 2014, the QIC-AG was awarded to Spaulding for Children in partnership with The University of Texas at Austin, The University of Wisconsin at Milwaukee, and The University of North Carolina at Chapel Hill. The QIC-AG was designed to promote permanence, when reunification is no longer...

Registration Year

  • 2022
    63

Resource Types

  • Dataset
    63

Affiliations

  • The University of Texas at Austin
    57
  • Fudan University
    28
  • Sun Yat-sen University
    24
  • Capital Medical University
    23
  • First Affiliated Hospital of Xi'an Jiaotong University
    23
  • Tongji University
    23
  • Second Affiliated Hospital of Harbin Medical University
    23
  • Nanjing Agricultural University
    23
  • Sichuan University
    21
  • Shanghai Jiao Tong University
    21