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- 1.0543554 - ÚBO DATA Scientific data 2021
Bryja, Josef
Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents - data and commands.
Description: Phylogenomic data ("anchored phylogenomics") and commands used for phylogenetic analyses. From: Nicolas et al.: Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: first fully resolved phylogeny, evolutionary history and delimitation of extant genera. Molecular Phylogenetics and Evolution.
Keywords : phylogenomics * African rodents * radiation
OECD category: Zoology
DOI: https://doi.org/10.57680/asep.0543554
Handle: http://hdl.handle.net/11104/0320791
Depositor: Bryja, Josef
Date of release: 2.7.2021
ASEP publication:
Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera
License: BY-NC
File Download Size Commentary Access prao_analyses_inputs.zip File list 28 6.5 MB open-access R&D Projects: GA ČR(CZ) GC20-07091J
Institutional support: RVO:68081766 - 2.0539495 - 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 11 1.2 GB open-access Lophuromys_simensis_northII.zip File list 5 533.6 MB open-access Lophuromys_simensis_menageshae.zip File list 8 1.5 GB open-access Lophuromys_simensis_northI.zip File list 7 2 GB open-access Lophuromys_chercherensis.zip File list 7 923.3 MB open-access Lophuromys_flavopunctatus.zip File list 8 487.2 MB open-access Lophuromys_chrysopus.zip File list 7 970.6 MB open-access Lophuromys_pseudosikapusi.zip File list 6 609.5 MB open-access Lophuromys_brunneus.zip File list 7 1.2 GB open-access Lophuromys_outgroups.zip File list 10 180.4 MB open-access Lophuromys_menageshae.zip File list 11 83.1 MB open-access Lophuromys_brevicaudus.zip File list 8 975.6 MB open-access R&D Projects: GA ČR(CZ) GA18-17398S
Institutional support: RVO:68081766 - 3.0534139 - 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 15 367.6 KB open-access Arvicanthini_40sp_377loci.nexus 12 23.3 MB open-access R&D Projects: GA ČR(CZ) GA18-17398S
Institutional support: RVO:68081766 - 4.0533584 - 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 5 119.3 MB open-access Lophuromys_sNMF30.geno 6 58.5 MB open-access Lophuromys_sNMF90.nexus 7 7.9 MB open-access Lophuromys_sNMF90.geno 6 4.2 MB open-access Lophuromys_Phylip_71341snps.phy 7 19.3 MB open-access Lophuromys_Phylip_13184snps.phy 7 3.6 MB open-access Lophuromys_Phylip_699snps.phy 8 189.8 KB open-access R&D Projects: GA ČR(CZ) GA18-17398S
Institutional support: RVO:68081766