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.
Alignment of DBX5 haplotypes inferred by Phase version 2.1 (Stephens et al. 2001; Stephens & Donnelly 2003) and used for gene tree inference.
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 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.
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.
Nexus matrix of matK sequences of various Sobralieae (Orchidaceae)
Nexus matrix of matK sequences of various Vandeae (Orchidaceae)
Data includes the fork length measurement for L♀D♂, D♀L♂, L♀R♂ and R♀L♂ offspring and parents
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 retainedStephen 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 –...
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...
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.
List of inbreeding coefficients for each final generation individual in the pedigree.
Pedigree used in simulation of bottlenecks.
Pedigree needed as part of simulate the n = 10 x 5 bottleneck while maintaining variance in individual IBD.
Occurrence data by time-slice.
Overlap calculations for percent geographic overlap between Maxent models. The weighting scheme and percent overlap calculations are described in Supplemental Text.
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”)...
Raw data in fastq format from the sequencing of the Oedothorax fuscus sample using a 314 Ion Torrent chip