Data from: Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell

Grealy A, Phillips M, Miller G, Gilbert MTP, Rouillard J, Lambert D, Bunce M, Haile J

Date Published: January 12, 2017

DOI: http://dx.doi.org/10.5061/dryad.6h3q7

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title RaxML_inputs
Downloaded 15 times
Description Input phylip files (.phy) and partition files (_part.txt) used for maximum likelihood tree generation in RaxML for various data sets (mt=mitochondrial, nuc=nuclear, ry=ry-coded, m3=mitochondrial third codon positions, loops=mitochondrial rRNA loops). Note that RY coded bases are given by a 0 (R) or 1 (Y).
Download RaxML_inputs.zip (1.115 Mb)
Details View File Details
Title MrBayes_inputs
Downloaded 18 times
Description Input nexus files (.nex) used for Bayesian phylogenetic inference for various datasets (mt=mitochondrial, nuc=nuclear, nt=standard coded (nucleotide), ry=ry-coded, m3=mitochondrial third codon positions, loops=mitochondrial rRNA loops)
Download MrBayes_inputs.zip (758.1 Kb)
Details View File Details
Title Nuclear_sequence_alignments
Downloaded 18 times
Description Non-partitioned multiple sequence alignments for various nuclear loci in FASTA format (.fasta).
Download Nuclear_sequence_alignments.zip (37.90 Kb)
Details View File Details
Title MCMCTree_inputs
Downloaded 16 times
Description Inputs in phylip format (.phy) for molecular dating analysis conducted in MCMCTree for several datasets (mt=mitochondrial, nuc=nuclear, nt=standard coded (nucleotide), ry=ry-coded, m3=mitochondrial third codon positions). Note that RY-coded data are represented by R and Y. Tree topologies (.trees) used as input are shown: for mitochondrial and combined mitochondrial/nuclear datasets, two topologies were tested, one in which moa/tinamous are sister to the remaining notopalaeognathae, and one where rheas are sister to the remaining notopalaeognathae. For the nuclear dataset, the topology derived from phylogenetic inference on the nuclear data alone was used. MCMCTree control files (.ctl) are not shown as parameters used are described in text.
Download MCMCTree_inputs.zip (455.7 Kb)
Details View File Details
Title FASTQ
Downloaded 15 times
Description Total shotgun NGS (combined Ion Torrent Proton, Ion Torrent PGM, and MiSeq data as well as enriched and non-enriched libraries) reads (trimmed, quality filtered and unfiltered) in FASTQ format (.fastq).
Download FASTQ.zip (1.009 Gb)
Details View File Details

When using this data, please cite the original publication:

Grealy A, Phillips M, Miller G, Gilbert MTP, Rouillard J, Lambert D, Bunce M, Haile J (2017) Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Molecular Phylogenetics and Evolution 109: 151-163. http://dx.doi.org/10.1016/j.ympev.2017.01.005

Additionally, please cite the Dryad data package:

Grealy A, Phillips M, Miller G, Gilbert MTP, Rouillard J, Lambert D, Bunce M, Haile J (2017) Data from: Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.6h3q7
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: