Data from: The evolution of highly variable immunity genes across a passerine bird radiation.

O'Connor E, Strandh M, Hasselquist D, Nilsson J, Westerdahl H

Date Published: January 6, 2016

DOI: http://dx.doi.org/10.5061/dryad.2q8c2

 

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Title Evolutionary Models Script
Downloaded 5 times
Description R script containing the code used to run the evolutionary models and test for phylogentic signal
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Title HNalla_RV_454_Raw_20120507_1525_1_2
Downloaded 5 times
Description Raw (unfiltered) 454 sequence data for Primer Pair 1. Demultiplexed using the software jMHC (2011).
Download HNalla_RV_454_Raw_20120507_1525_1_2.txt (228.9 Kb)
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Title Short_RV_454_Raw_20120507_1115_1_2
Downloaded 11 times
Description Raw (unfiltered) 454 sequence data for Primer Pair 3. Demultiplexed using the software jMHC (2011).
Download Short_RV_454_Raw_20120507_1115_1_2.txt (2.303 Mb)
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Title HNalla46_Raw_Data_20151119_1740_1
Downloaded 7 times
Description Raw (unfiltered) 454 sequence data for Primer Pair 2. Demultiplexed using the software jMHC (2011).
Download HNalla46_Raw_Data_20151119_1740_1.txt (7.601 Mb)
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Title Phylogenetic tree of species
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Description Maximum clade credibility tree summarising the phylogenetic relationships between the bird species studied (rooted using Gallus gallus).
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Title Samples Info
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Description Details of of the samples included in the study. The column "Sample Name" specifies the unique name of each sample. The column "Species" indicates which species each sample is from. The column "Location" provides information on the location the sample was collected at.
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Title All Spp Final Aligned Variants
Downloaded 13 times
Description Alignment of all 536 alleles identified. Alignment performed manually using BioEdit V.7.2.5 Sequence Alignment Editor (Hall 1999). In FASTA format.
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Title Key to final allele names
Downloaded 12 times
Description This file provides a key to the allele names that links the names they have been allocated in the manuscript to the original names of the raw sequences (these numbers match the sequence numbers in the raw sequence files provided). "Species" denotes the species in which the allele was found. "Old Seq Name" refers to the names in the raw sequence files (sequence number). "New Name" refers to the allele name used in the manuscript. "Seq" is the aligned sequence. The alleles which were detected by more than one primer pair are identifiable as their "Old Seq Name" is comprised of more than one sequence number adjoined by a colon.
Download Key to allele names.txt (164.3 Kb)
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Title All Final Variants
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Description All variants found (unaligned) in FASTA format.
Download All Variants.txt (148.1 Kb)
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When using this data, please cite the original publication:

O'Connor E, Strandh M, Hasselquist D, Nilsson J, Westerdahl H (2016)The evolution of highly variable immunity genes across a passerine bird radiation. Molecular Ecology, 25(4):977–989 http://dx.doi.org/10.1111/mec.13530

Additionally, please cite the Dryad data package:

O'Connor E, Strandh M, Hasselquist D, Nilsson J, Westerdahl H (2016) Data from: The evolution of highly variable immunity genes across a passerine bird radiation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2q8c2
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