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- 1.0539495 - ÚBO DATA Scientific data 2021
Bryja, Josef
Genomic ddRAD datasets of Ethiopian Lophuromys - raw data.
Description: The files contain pair-end reads that were submitted to ipyrad (Eaton & Overcast, 2020) for denovo assembly of ddRAD loci. The reads were demultiplexed and barcodes removed in Skewer (Jiang, Lei, Ding & Zhu, 2014) and pre-processing of read ends in PEAR (Zhang, Kobert, Flouri & Stamatakis, 2014). Every pair of reads was merged (with minimum required overlap of 10 nucleotides) and cut in two halves. If they were not successfully merged, we trimmed off the last 10 nucleotides from the reverse read. The PEAR-treatment was necessary to avoid poor quality mergers in a substantial proportion of loci. The data are used and analysed in Komarova et al., submitted to Molecular Ecology.
Keywords : ddRAD * Lophuromys * Ethiopia
OECD category: Zoology
DOI: https://doi.org/10.57680/asep.0539495
Handle: http://hdl.handle.net/11104/0317292
Depositor: Bryja, Josef
Date of release: 15.2.2021
License: BY-NC
File Download Size Commentary Access Lophuromys_melanonyx.zip File list 14 1.2 GB open-access Lophuromys_simensis_northII.zip File list 7 533.6 MB open-access Lophuromys_simensis_menageshae.zip File list 11 1.5 GB open-access Lophuromys_simensis_northI.zip File list 10 2 GB open-access Lophuromys_chercherensis.zip File list 11 923.3 MB open-access Lophuromys_flavopunctatus.zip File list 11 487.2 MB open-access Lophuromys_chrysopus.zip File list 10 970.6 MB open-access Lophuromys_pseudosikapusi.zip File list 10 609.5 MB open-access Lophuromys_brunneus.zip File list 10 1.2 GB open-access Lophuromys_outgroups.zip File list 12 180.4 MB open-access Lophuromys_menageshae.zip File list 13 83.1 MB open-access Lophuromys_brevicaudus.zip File list 12 975.6 MB open-access R&D Projects: GA ČR(CZ) GA18-17398S
Institutional support: RVO:68081766 - 2.0534139 - ÚBO DATA Scientific data 2020
Bryja, Josef
Anchored phylogenomics data used for phylogenomic analysis of Arvicanthini rodents.
Description: The files represent datasets used in the paper: Mikula et al.: Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Molecular Phylogenetics and Evolution, under review.
Arvicanthini_40sp_377loci.nex = alignments of 377 nuclear loci obtained by anchored phylogenomic approach in 40 species of Arvicanthini rodents (partitioned nexus format)
Arvicanthini_40sp_377loci_genetrees.nwk = Bayesian gene trees (for 377 genes) used as input for the ASTRAL analysis (newick format)
Keywords : anchored phylogenomics * Arvicanthini rodents * alignments
OECD category: Zoology
DOI: https://doi.org/10.57680/asep.0537176
Handle: http://hdl.handle.net/11104/0312390
Depositor: Bryja, Josef
Date of release: 9.11.2020
ASEP publication:
Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini)
License: BY-NC-ND
File Download Size Commentary Access Arvicanthini_40sp_377loci_genetrees.nwk 18 367.6 KB open-access Arvicanthini_40sp_377loci.nexus 14 23.3 MB open-access R&D Projects: GA ČR(CZ) GA18-17398S
Institutional support: RVO:68081766 - 3.0533584 - ÚBO DATA Scientific data 2020
Bryja, Josef
Genomické ddRAD datasety etiopských Lophuromys.
[Genomic ddRAD datasets of Ethiopian Lophuromys.]
Description: (1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals.
(2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci present in 90% of genotyped ingroup individuals.
The data are used and analysed in Komarova et al., submitted to Molecular Ecology.
[(1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals.
(2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci present in 90% of genotyped ingroup individuals.
The data are used and analysed in Komarova et al., submitted to Molecular Ecology.]
Keywords : ddRAD * Lophuromys * Ethiopia
OECD category: Zoology
DOI: https://doi.org/10.57680/asep.0533584
Handle: http://hdl.handle.net/11104/0311955
Depositor: Bryja, Josef
Date of release: 28.10.2020
License: BY-NC
File Download Size Commentary Access Lophuromys_sNMF30.nex 18 119.3 MB open-access Lophuromys_sNMF30.geno 9 58.5 MB open-access Lophuromys_sNMF90.nexus 13 7.9 MB open-access Lophuromys_sNMF90.geno 10 4.2 MB open-access Lophuromys_Phylip_71341snps.phy 10 19.3 MB open-access Lophuromys_Phylip_13184snps.phy 11 3.6 MB open-access Lophuromys_Phylip_699snps.phy 13 189.8 KB open-access R&D Projects: GA ČR(CZ) GA18-17398S
Institutional support: RVO:68081766