DOI: 10.5061/dryad.f5q32
title: 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

description: Relationships among multi-locus genetic variation, geography and
 environment can reveal how evolutionary processes affect genomes. We
 examined the evolution of an Australian bird, the eastern yellow robin
 Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA)
 genetic markers, and bioclimatic variables. In southeastern Australia, two
 divergent mtDNA lineages occur east and west of the Great Dividing Range,
 perpendicular to latitudinal nDNA structure. We evaluated alternative
 scenarios to explain this striking discordance in landscape genetic
 patterning. Stochastic mtDNA lineage sorting can be rejected because the
 mtDNA lineages are essentially distinct geographically for &gt;1500
 km. Vicariance is unlikely: the Great Dividing Range is neither a current
 barrier nor was it at the Last Glacial Maximum according to species
 distribution modeling; nuclear gene flow inferred from coalescent analysis
 affirms this. Female philopatry contradicts known female-biased dispersal.
 Contrasting mtDNA and nDNA demographies indicate their evolutionary
 histories are decoupled. Distance-based redundancy analysis, in which
 environmental temperatures explain mtDNA variance above that explained by
 geographic position and isolation-by-distance, favors a non-neutral
 explanation for mitochondrial phylogeographic patterning. Thus, observed
 mito-nuclear discordance accords with environmental selection on a
 female-linked trait, such as mtDNA, mtDNA-nDNA interactions or genes on
 W-chromosome, driving mitochondrial divergence in the presence of nuclear
 gene flow.
description: Data on geographic
 locations, sex, microsatellites, CHD markers, sequences and bioclimatic
 variablesEopsaltria_australis_genetics_bioclim.txtPresence points used for Species Distribution ModelsEopsaltria_australis_presence_points_for_SDM.txtUnphased AB4 sequencesUnphased AB4 (aldolase B gene) sequences in FASTA formatAB4.fasGenebank flatfile for AB4Genebank flatfile for AB4 sequences (aldolase B gene); because sequences are &lt;200bp they are not deposited to GenbankAB4_Genbank_flatfile_no_numbers.txtAligned sequences of sex-linked CHDZ and CHDWAligned 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.CHDZ_CHDWaligned.megInput file for TESS analysis of 11 autosomal lociThis 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).Eopsaltria_australis_11autosomal_loci_TESS_inputInput file for IMa2 analysis of nuclear lociEopsaltria_australis_nuclear_loci_IMa2_inputHaplotype alignment of mitochondrial ND2Aligned mitochondrial sequences of 100 Eastern Yellow Robins in NEXUS formatEopsaltria_australis_ND2.nexPhased haplotypes AB4Phased AB4 haplotypes of 44 Eastern Yellow Robins in NEXUS formatAB4_EYR44_196bp_phased.nexPhased haplotypes GAPDHPhased GAPDH haplotypes of 46 Eastern Yellow Robins in NEXUS formatGAPDH_EYR46_317bp_phased.nexPhased haplotypes GTPPhased GTP haplotypes of 43 Eastern Yellow Robins in NEXUS formatGTP_EYR43_456bp_phased.nexPhased haplotypes MUSK-I3zPhased MUSK-I3 haplotypes of 31 Eastern Yellow Robins in NEXUS format; second allele is removed for females, who are hemizygotic for this Z-linked locusMUSK-I3z_EYR31_519bp_phased0.75.nexPhased haplotypes Rl2Phased RI2 haplotypes of 47 Eastern Yellow Robins in NEXUS formatRl2_EYR47_292bp_phased.nexPhased haplotypes TGFbPhased TGFb haplotypes of 39 Eastern Yellow Robins in NEXUS formatTGFb_EYR39_595bp_phased.nex