11 research outputs found
Bayesian majority-rule consensus phylogeny of <i>Pgi</i>.
<p>Sequences are labeled according to sample site, individual number, and allozyme class (slow, medium-slow, medium, fast denoted by the colored shapes).</p
Log-likelihood surface plot of ancestral population size (<i>N</i><sub>e</sub><i>A</i>) versus contemporary population size (<i>N</i><sub>e</sub>).
<p>Estimates are based upon temporal changes in allozyme allele frequencies at <i>Pgi</i> in San Diego, Pescadero, and Site 10. The highest log-likelihood values are indicated by the white shaded contours.</p
<i>Pgi</i> allozyme allele and genotype frequencies in <i>Tigriopus californicus</i>.
a<p>Data from dates prior to 2004 were compiled from published and unpublished sources <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040035#pone.0040035-Burton1" target="_blank">[12]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040035#pone.0040035-Burton3" target="_blank">[14]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040035#pone.0040035-Ganz1" target="_blank">[18]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0040035#pone.0040035-Burton5" target="_blank">[20]</a>.</p><p>
<b>Deviations of samples (of size N) from Hardy-Weinberg proportions shown as </b><b><i>p</i></b><b>-value, non-significant or not-applicable.</b></p
Comparison of codon substitution models using likelihood-ratio tests and amino acid sites showing elevated non-synonymous substitution ratios (ω).
<p><b>DF</b> degrees of freedom; <b><i>LnL</i></b> log-likelihood; <b>NEB</b> naïve empirical Bayes test; <b>BEB</b> Bayes empirical Bayes test; <b>SE</b> standard error.</p><p>
<b>Significant tests are indicated with an asterisk.</b></p
Site frequency tests of recombination, linkage disequilibrium and neutrality at <i>Pgi</i>.
<p><b>N</b> sample size; <b><i>R</i></b> recombination rate per gene; <b><i>Rm</i></b> min. no. recombination events; <b><i>ZnS</i></b> average LD; <b><i>Za</i></b> average LD between adjacent sites; <b><i>ZZ</i></b>  =  <i>Za</i>- <i>ZnS</i>; <b><i>B</i></b> LD among segregating sites; <b><i>Q</i></b> LD among unique partitions; <b><i>D</i></b> Tajima’s D for all sites, non-synonymous sites (<b><i>D<sub>NS</sub></i></b>) and synonymous sites (<b><i>D<sub>S</sub></i></b>); <b><i>D<sub>FL</sub></i></b> Fu and Li’s D; <b><i>F</i></b> Fu and Li’s F; <b><i>HKA</i></b> neutrality test of <i>Pgi</i> compared to RISP gene.</p
Site frequency tests of interpopulation genetic structure, gene flow and neutrality at <i>Pgi</i>.
<p><b><i>F<sub>ST</sub></i></b> among-population genetic differentiation; <b><i>Nm</i></b> gene flow rate between populations; <b><i>S</i></b> number of segregating sites; <b><i>NS</i></b> number of non-synonymous sites; <b><i>MK</i></b> McDonald-Kreitman neutrality test.</p
Athaliana_Isothermal_Array_Probe_Sequence
All custom-designed probes featured on the A.thaliana Isothermal SNP array. The array was manufactured by Agilent Biotech in CGH 8*60K format. The mean Tm value of the probes is 55 degree Celsius. The nomenclature of the probes follows the "Allele source_Chromosome_Position" format. The two alternatives of the allele source are "C" stands for Col-0 allele, and "NC" stands for non-Col-0 allele. The position information of the probes follows TAIR 8 coordinate
TimeSeries_GerminationCohort_ArrayGenotype
Raw microarray genotyping data derived by the Agilent feature extraction software, with built-in rank invariant normalization. Data from the manufacturer-supplied quality-control probes are not included. Cohorts (early, medium, late, and all germinants) are genotyped in two biologcal replicates (rep1 and rep2), and with dye-swap hybridization replicates (Cy3 and Cy5)
STS sequence alignments for O.rufipogon
There are 42 STS sequence alignments in FASTA format in the zip file. Each alignment include an outgroup sequence and 96 ingroup sequences (missing ones are not included). Name of each sequence start with a flow number and followed by sts number, organism/group annotation by IRRI, country of origin, IRGC number and chromosome number. Additional sample and loci information can be found in Table S1 and S2 of the supplementary information on Molecular Ecology website
Supplementary Data set 5
Genes with nonsense SNPs and the corresponding genotypes in field isolates and laboratory reference strains of C. reinhardtii