131,870 Works

Sample_data

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
New sequence data and sequence data retrieved from GenBank for all loci analysed. Details on sampling locality are given for each specimen analysed. Haplotype names as well as GenBank accession numbers are detailed for each loci per specimen, as well as source of previously published data. Information on where samples are held in is also displayed.

DBX5_haplotype_alignment

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
Alignment of DBX5 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.

CYTB_genotype_alignment

Joana Paupério, Jeremy S. Herman, José Melo-Ferreira, Maarit Jaarola, Paulo C. Alves & Jeremy B. Searle
Alignment of cytochrome b sequences of all individuals used for species tree inference.

Maximum likelihood phylograms and their alignment files for ectomycorrhizal fungi associated with Salix arctica and Dryas integrifolia across the North American Arctic.

Ina Timling, Anders Dahlberg, Donald Arthur Walker, Monique Gardes, Jean-Yves Charcosset, Jeffrey M. Welker & Donald Lee Taylor
Maximum-likelihood phylograms (pdf) of (1) Tomentella1, (2) Tomentella 2, (3) Pseudotomentella, (4) Inocybe 1, (5) Inocybe 2, (6) Inocybe 3, (7) Inocybe 4, (8) Inocybe 5, (9) Sebacina 1, (10) Sebacina 2, (11) Sebacina 3, (12) Cortinarius 1, (13) Cortinarius 2, (14) Cortinarius 3, (15) Cortinarius 4, (16) Clavulina, (17) Russula, (18) Tulasnella, (19) Ceratobasidium, (20) Entoloma, (21) Hebeloma, (22) Lactarius, (23) Laccaria, (24) Pyronemataceae, (25) Tuber, (26) Tuberaceae, (27) Sordariaceae, (28) Phialocephala, (29) Cenococcum,...

Data table

Moriaki Yasuhara, Gene Hunt, Denise Breitburg, Akira Tsujimoto & Kota Katsuki
Data table for the global analyses of microfossil data in the present study. AN: Australia and New Zealand. SA: South America. AF: Africa. ASIA: Asia. NAMER: North America. EU: Europe. O: Other.

110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.001

Astrid T. Groot, Heike Staudacher, Andrea Barthel, Olive Inglis, Richard G. Santangelo, Steffi Gebauer-Jung, Heiko Vogel, Jennifer Emerson, Coby Schal, David G. Heckel, Fred Gould & Gerhard Schoefl

110506_SN365_A_s_8_2_seq_GKW-36.txt.gz.003

Astrid T. Groot, Heike Staudacher, Andrea Barthel, Olive Inglis, Richard G. Santangelo, Steffi Gebauer-Jung, Heiko Vogel, Jennifer Emerson, Coby Schal, David G. Heckel, Fred Gould & Gerhard Schoefl

Goldin_Zvonok_Ukraine_Supplemental_Data_File_4_age_data_for_phylogeny_20120913

Pavel Goldin & Evgenij Zvonok

Tropheus moorii male courtship data

Peter Zoppoth, Stephan Koblmüller & Kristina M. Sefc

All data

Tamara S. Haselkorn, Sarah N. Cockburn, Phineas T. Hamilton, Steve Perlman & John Jaenike
This is an Excel workbook containing spreadsheets on restoration of fertility (female egg count), Spiroplasma density (qPCR-Spiroplasma), Howardula motherworm size (Motherworm size), and maternal transmission (Maternal transmission). These data were collected in either the Perlman (University of Victoria) or Jaenike (University of Rochester), as indicated in the file.

Sobralieae matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Nexus matrix of matK sequences of various Sobralieae (Orchidaceae)

Vandeae matK

Kurt M. Neubig, W. Mark Whitten, Barbara S. Carlsward, Mario A. Blanco, Lorena Endara, Norris H. Williams & Michael Moore
Nexus matrix of matK sequences of various Vandeae (Orchidaceae)

Fork length Salvelinus fontinalis / File S1

Louis Bernatchez, Céline Audet & Bérénice Bougas
Data includes the fork length measurement for L♀D♂, D♀L♂, L♀R♂ and R♀L♂ offspring and parents

file 11 - R code for simulated bottleneck in the N=10 x5 population

Stephen P. Robinson, Leigh W. Simmons & W. Jason Kennington
This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Once the bottleneck is simulated, only the allele frequencies are used to generate the subsequent pedigree so variance in individual IBD generated during the bottleneck is not retained. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This...

file 13 - R code for simulated bottleneck in the N=10 x5 population with variance in individual IBD retained

Stephen P. Robinson, Leigh W. Simmons & W. Jason Kennington
This code runs a simulation of the bottleneck and subsequent pedigree used for the N=10 x5 population. Variance in individual IBD generated during the bottleneck retained through the pedigree. This method takes linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates as well as number of alleles per locus. This code links to the following files, which must be in the working directory: files 16 –...

file 15 - R code for simulations with null alleles introduced to three loci or three loci removed

Stephen P. Robinson, Leigh W. Simmons & W. Jason Kennington
This code runs simulations based on observed allele frequencies in the control population but with null alleles artificially introduced to three randomly selected loci at a frequency of 0.05 or these same three loci removed from the data set. This method does not take linkage into account. The output will include mean and 95% confidence intervals for both relatedness and inbreeding estimates. This code links to the following files, which must be in the working...

file 17 - x0 data for MasterBayes cr3 only

Stephen P. Robinson, Leigh W. Simmons & W. Jason Kennington
Microsatellite genotypes for markers residing on chromosome three observed in the experimental control population formatted for the MasterBayes package in R. This file must be in the working directory of R for many of the simulations above to run.

file 25 - expected_f

Stephen P. Robinson, W. Leigh Simmons & Jason W. Kennington
List of inbreeding coefficients for each final generation individual in the pedigree.

file 26 - pedigree for founder simulation

Stephen P. Robinson, Leigh W. Simmons & W. Jason Kennington
Pedigree used in simulation of bottlenecks.

file 28 - bottleneck pedigree for x5 founder simulation

Stephen P. Robinson, Leigh W. Simmons & W. Jason Kennington
Pedigree needed as part of simulate the n = 10 x 5 bottleneck while maintaining variance in individual IBD.

Supplemental Table 2

Alycia L. Stigall & Hannah-Maria R. Brame
Occurrence data by time-slice.

Supplemental Table 6

Alycia L. Stigall & Hannah-Maria R. Brame
Overlap calculations for percent geographic overlap between Maxent models. The weighting scheme and percent overlap calculations are described in Supplemental Text.

Supplemental Table 7

Alycia L. Stigall & Hannah-Maria R. Brame
ENMtools I and D values relative to the 95% confidence interval. Both of these metrics are measured from 0 (complete dissimilarity) to 1 (identity). I/D values that fall within the 95% C.I. (“in”) indicate models that are no more/less similar than random and are interpreted as evidence of niche conservatism. I/D values that fall above the 95% C.I. (“out, high”) and indicate statistical niche conservatism. I/D values that fall below the 95% C.I. (“out, low”)...

BEAST input file for COI

Svante Martinsson, Ainara Achurra, Marcus Svensson & Christer Erséus

run_314

Josep Piñol, Victoria San Andrés, Elizabeth L. Clare, Gisela Mir & William O. C. Symondson
Raw data in fastq format from the sequencing of the Oedothorax fuscus sample using a 314 Ion Torrent chip

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