Journal
Nature Communications
Publication Date
2016
Volume
7
Inclusive Pages
10474
Document Type
Open Access Publication
DOI
10.1038/ncomms10474
Rights and Permissions
W.C. Warren, P. Minx, et al. 25 January 2016. Evolutionary signals of selection on cognition from the great tit genome and methylome. Nature communications. Art. No. 10474. DOI: 10.1038/ncomms10474. http://www.nature.com/ncomms/2016/160125/ncomms10474/full/ncomms10474.html
Recommended Citation
Warren, Wesley C.; Minx, Patrick; and et al, "Evolutionary signals of selection on cognition from the great tit genome and methylome." Nature Communications. 7, 10474. (2016).
https://digitalcommons.wustl.edu/open_access_pubs/4520
ncomms10474-s1.pdf (4213 kB)
Supplementary Figures 1-10, Supplementary Methods and Supplementary References
ncomms10474-s2.xlsx (25 kB)
Scaffolds
ncomms10474-s3.xlsx (11 kB)
Sampling locations, sex, sample volumes and DNA concentrations of the 29 re-sequenced great tits
ncomms10474-s4.xlsx (8 kB)
The pairwise FST values for five sample sites. EU samples exclude samples from Spain, Estonia and France individuals
ncomms10474-s5.xlsx (39 kB)
Chromosomal locations of sweep areas, along with their summed composite likelihood ratio (CLR) score from the SweepFinder analysis.
ncomms10474-s6.xlsx (17 kB)
Results of an enrichment test conducted for GO terms associated with the genes found from selective sweep and that were positively selected by using human orthologs (a and b) and chicken orthologs (c and d). From the random gene set test, the GO term groups appeared no more than three times except for phosphatidylinositol-mediated signalling GO group which appeared seven times.
ncomms10474-s7.xlsx (8 kB)
Species from which EGR1 sequences were obtained.
ncomms10474-s8.xlsx (8 kB)
The amount of RNA reads before and after filtering done by Fastq-Mcf.
ncomms10474-s9.xlsx (9 kB)
Repeat content of the great tit genome identified by RepeatMasker
ncomms10474-s10.xlsx (10 kB)
Chromosome wide diversity estimates (measured as Watterson's θ) from 29 birds (called with ANGSD) and from the reference bird ABEL (called with Platypus). The ratio of the two diversity estimates per chromosome is given along with the Spearman correlation coefficient of per chromosome diversity (measured in sliding windows of size 50 kb).
ncomms10474-s11.xlsx (10 kB)
Supplementary Figures 1-10, Supplementary Methods and Supplementary References
ncomms10474-s2.xlsx (25 kB)
Scaffolds
ncomms10474-s3.xlsx (11 kB)
Sampling locations, sex, sample volumes and DNA concentrations of the 29 re-sequenced great tits
ncomms10474-s4.xlsx (8 kB)
The pairwise FST values for five sample sites. EU samples exclude samples from Spain, Estonia and France individuals
ncomms10474-s5.xlsx (39 kB)
Chromosomal locations of sweep areas, along with their summed composite likelihood ratio (CLR) score from the SweepFinder analysis.
ncomms10474-s6.xlsx (17 kB)
Results of an enrichment test conducted for GO terms associated with the genes found from selective sweep and that were positively selected by using human orthologs (a and b) and chicken orthologs (c and d). From the random gene set test, the GO term groups appeared no more than three times except for phosphatidylinositol-mediated signalling GO group which appeared seven times.
ncomms10474-s7.xlsx (8 kB)
Species from which EGR1 sequences were obtained.
ncomms10474-s8.xlsx (8 kB)
The amount of RNA reads before and after filtering done by Fastq-Mcf.
ncomms10474-s9.xlsx (9 kB)
Repeat content of the great tit genome identified by RepeatMasker
ncomms10474-s10.xlsx (10 kB)
Chromosome wide diversity estimates (measured as Watterson's θ) from 29 birds (called with ANGSD) and from the reference bird ABEL (called with Platypus). The ratio of the two diversity estimates per chromosome is given along with the Spearman correlation coefficient of per chromosome diversity (measured in sliding windows of size 50 kb).
ncomms10474-s11.xlsx (10 kB)
