Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

Rawlence NJ, Kennedy M, Anderson CNK, Prost S, Till CE, Smith I, Scofield RP, Tennyson AJD, Hamel J, Lalas C, Matisoo-Smith EA, Waters JM

Date Published: July 31, 2015

DOI: http://dx.doi.org/10.5061/dryad.4b3h7

 

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 Translation Table
Downloaded 35 times
Description This table contains the internal laboratory codes used to identify mtDNA control region sequences (in the uploaded sequence alignments), and their corresponding GenBank numbers. Asterisked (*) sequences indicate exemplar sequences used in the 33 haplotype dataset.
Download Translation Table.docx (20.34 Kb)
Details View File Details
Title aDNA optomisation code
Downloaded 6 times
Description Code for implementing the optimisation of ancient-DNA datasets for analysis in BayeSSC.
Download aDNA optomisation code.txt (2.065 Kb)
Details View File Details
Title SISaDNA1perHap33
Downloaded 6 times
Description Nexus file containing one sequence of each haplotype (including out-group sequences) for the 33 haplotype dataset.
Download SISaDNA1perHap33.nex (11.05 Kb)
Details View File Details
Title FoveauxBSPr1
Downloaded 6 times
Description BEAST .xml file for the Bayesian Skyline analysis of L. chalconotus Foveaux Strait.
Download FoveauxBSPr1.xml (32.61 Kb)
Details View File Details
Title OtagoBSPr2
Downloaded 5 times
Description BEAST .xml file for Bayesian Skyline analysis of L. chalconotus Otago.
Download OtagoBSPr2.xml (46.69 Kb)
Details View File Details
Title BayeSSC par files
Downloaded 38 times
Description BayeSSC .par files for joint (Otago and Foveaux Strait) Models 1-6, and Otago only Models 1-3.
Download BayeSSC par files.zip (9.789 Kb)
Details View File Details
Title Randomisation Tests
Downloaded 37 times
Description BEAST .xml files for randomisation tests of estimated substitution rate for L. chalconotus Foveaux Strait (x20) and Otago (x20).
Download Randomisation Tests.zip (162.0 Kb)
Details View File Details
Title BEAST 33 htype
Downloaded 5 times
Description BEAST .xml file for the phylogenetic analysis of the 33 haplotype (including out-group sequences) dataset.
Download BEAST 33 htype.xml (22.42 Kb)
Details View File Details
Title Foveaux_var_rates
Downloaded 39 times
Description BEAST .xml files for testing the effect of variable substitution rates on the Bayesian Skyline Plot of L. chalconotus Foveaux Strait including the use of penguin (Lambert et al. 2002) fixed/prior, Otago fixed/prior, and BayesSSC estimates, and the optimised dataset (from BayeSSC).
Download Foveaux_var_rates.zip (22.42 Kb)
Details View File Details
Title Otago_var_rates
Downloaded 36 times
Description BEAST .xml files for testing the effect of variable substitution rates on the Bayesian Skyline Plot of L. chalconotus Otago including the use of penguin (Lambert et al. 2002) fixed/prior and BayesSSC estimates, and the optimised dataset (from BayeSSC).
Download Otago_var_rates.zip (17.32 Kb)
Details View File Details
Title SIS aDNA Otago alignment
Downloaded 6 times
Description DNA sequence alignment of L. chalconotus Otago.
Download SIS aDNA Otago alignment.fas (23.59 Kb)
Details View File Details
Title SIS aDNA Foveaux alignment
Downloaded 5 times
Description DNA sequence alignment of L. chalconotus Foveaux Strait.
Download SIS aDNA Foveaux alignment.fas (15.13 Kb)
Details View File Details

When using this data, please cite the original publication:

Rawlence NJ, Kennedy M, Anderson CNK, Prost S, Till CE, Smith I, Scofield RP, Tennyson AJD, Hamel J, Lalas C, Matisoo-Smith EA, Waters JM (2015) Geographically contrasting biodiversity reductions in a widespread New Zealand seabird. Molecular Ecology 24(18): 4605–4616. http://dx.doi.org/10.1111/mec.13338

Additionally, please cite the Dryad data package:

Rawlence NJ, Kennedy M, Anderson CNK, Prost S, Till CE, Smith I, Scofield RP, Tennyson AJD, Hamel J, Lalas C, Matisoo-Smith EA, Waters JM (2015) Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4b3h7
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: