Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird

 

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Title Data on geographic locations, sex, microsatellites, CHD markers, sequences and bioclimatic variables
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Download Eopsaltria_australis_genetics_bioclim.txt (216.6 Kb)
Download README.txt (3.565 Kb)
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Title Presence points used for Species Distribution Models
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Download Eopsaltria_australis_presence_points_for_SDM.txt (77.94 Kb)
Download README.txt (1.335 Kb)
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Title Unphased AB4 sequences
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Description Unphased AB4 (aldolase B gene) sequences in FASTA format
Download AB4.fas (18.12 Kb)
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Title Genebank flatfile for AB4
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Description Genebank flatfile for AB4 sequences (aldolase B gene); because sequences are <200bp they are not deposited to Genbank
Download AB4_Genbank_flatfile_no_numbers.txt (101.4 Kb)
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Title Aligned sequences of sex-linked CHDZ and CHDW
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Description Aligned sequences of sex-linked loci CHD-Z and CHD-W. ANWC44930 is a sequence of two alleles of equal length and identical sequence for a male, ANWC43508 is a sequence of two alleles of equal length alleles that differ by one bp of another male, the remaining entries are sequences of a single allele cut from the agarose gel. Alleles codes are: w1-362bp, w2-366bp, z1- 329bp, z3-332bp (Supplementary material S3). Only females have w alleles.
Download CHDZ_CHDWaligned.meg (5.498 Kb)
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Title Input file for TESS analysis of 11 autosomal loci
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Description This file is an input file for TESS analysis of 11 autosomal loci, AB4, GAPDH, GTP, RI2, TGFb, Cpi3, Cpi8, Escmu6, HrU2, Pocc6, Smm7 (Suplementary Material S5). Genotypes for sequenced loci were assigned as haplotype number +100 for the two phased haplotypes of each individual. EYR056 was excluded from analysis restricted to 5 sequenced loci (AB4, GAPDH, GTP, RI2, TGFb).
Download Eopsaltria_australis_11autosomal_loci_TESS_input (5.407 Kb)
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Title Input file for IMa2 analysis of nuclear loci
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Download Eopsaltria_australis_nuclear_loci_IMa2_input (89.87 Kb)
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Title Haplotype alignment of mitochondrial ND2
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Description Aligned mitochondrial sequences of 100 Eastern Yellow Robins in NEXUS format
Download Eopsaltria_australis_ND2.nex (101.6 Kb)
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Title Phased haplotypes AB4
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Description Phased AB4 haplotypes of 44 Eastern Yellow Robins in NEXUS format
Download AB4_EYR44_196bp_phased.nex (20.67 Kb)
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Title Phased haplotypes GAPDH
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Description Phased GAPDH haplotypes of 46 Eastern Yellow Robins in NEXUS format
Download GAPDH_EYR46_317bp_phased.nex (33.05 Kb)
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Title Phased haplotypes GTP
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Description Phased GTP haplotypes of 43 Eastern Yellow Robins in NEXUS format
Download GTP_EYR43_456bp_phased.nex (42.26 Kb)
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Title Phased haplotypes MUSK-I3z
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Description Phased MUSK-I3 haplotypes of 31 Eastern Yellow Robins in NEXUS format; second allele is removed for females, who are hemizygotic for this Z-linked locus
Download MUSK-I3z_EYR31_519bp_phased0.75.nex (29.20 Kb)
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Title Phased haplotypes Rl2
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Description Phased RI2 haplotypes of 47 Eastern Yellow Robins in NEXUS format
Download Rl2_EYR47_292bp_phased.nex (31.42 Kb)
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Title Phased haplotypes TGFb
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Description Phased TGFb haplotypes of 39 Eastern Yellow Robins in NEXUS format
Download TGFb_EYR39_595bp_phased.nex (50.42 Kb)
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When using this data, please cite the original publication:

Pavlova A, Amos N, Joseph L, Loynes K, Austin JJ, Keogh S, Stone GN, Nicholls JA, Sunnucks P (2013) Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird. Evolution 67(12): 3412-3428. http://dx.doi.org/10.1111/evo.12107

Additionally, please cite the Dryad data package:

Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nicholls JA, Sunnucks P (2013) Data from: Perched at the mito-nuclear crossroads: divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.f5q32
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