Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations

Rawlence NJ, Collins CJ, Anderson CNK, Maxwell JJ, Smith IWG, Robertson BC, Knapp M, Horsburgh KA, Stanton JL, Scofield RP, Tennyson AJD, Matisoo-Smith EA, Waters JM

Date Published: June 13, 2016

DOI: http://dx.doi.org/10.5061/dryad.118vg

 

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Title BEAST Dloop phylogenetic analysis with Birth Death speciation prior
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Download Chatham_sealions_Dloop_Birth_Death.xml (17.57 Kb)
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Title BEAST Dloop phylogenetic analysis with Yule speciation prior
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Download Chatham_sealions_Dloop_Yule.xml (17.04 Kb)
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Title Individual Based Model for anthropogenic mortality estimates
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Download IBM script.r (7.192 Kb)
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Title Sequence alignment of Chatham Island sea lions
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Description Sequence alignment of Chatham Island sea lion mtDNA D-loop including all Chatham Islands individuals (NRO number, location, haplotype - C1 to 9), exemplar haplotype sequences of subantarctic individuals (SA1-3), exemplar haplotype sequences of prehistoric New Zealand individuals (NZ1-14), and outgroups (Australian sea lion, South American sea lion, New Zealand furseal). Please see Suppl. Info. Table S1 for numbers of New Zealand and subantarctic individuals for each haplotype.
Download Chatham Island sealions_final.fas (10.07 Kb)
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Title BEAST mitogenome phylogenetic analysis with birth-death speciation prior
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Download mitogenome_birth_death.xml (396.1 Kb)
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Title BEAST mitogenome phylogenetic analysis with Yule speciation prior
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Download mitogenome_Yule.xml (395.6 Kb)
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Title Chatham Island mitogenome Ion Torrent NGS raw sequences
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Download CHI.sff.raw.fastq.zip (15.84 Mb)
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Title Prehistoric mainland New Zealand sea lion mitogenome Ion Torrent NGS raw sequences
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Download DEB.sff.raw.fastq.zip (23.09 Mb)
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Title BayeSSC .par files
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Download BayeSSC .par files.zip (7.004 Kb)
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Title Pinniped whole mitogenome phylogenetic alignment
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When using this data, please cite the original publication:

Rawlence NJ, Collins CJ, Anderson CNK, Maxwell JJ, Smith IWG, Robertson BC, Knapp M, Horsburgh KA, Stanton JL, Scofield RP, Tennyson AJD, Matisoo-Smith EA, Waters JM (2016) Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations. Molecular Ecology 25(16): 3950–3961. http://dx.doi.org/10.1111/mec.13726

Additionally, please cite the Dryad data package:

Rawlence NJ, Collins CJ, Anderson CNK, Maxwell JJ, Smith IWG, Robertson BC, Knapp M, Horsburgh KA, Stanton JL, Scofield RP, Tennyson AJD, Matisoo-Smith EA, Waters JM (2016) Data from: Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.118vg
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