DOI: 10.5061/dryad.37pvmcvjr
title: Genomic signatures of rapid adaptive divergence in a tropical montane species

description: This dataset contains data from a study described in the paper: Ericson,
 P.G.P., Irestedt, M., She, H., and Qu, Y. (2021) "Genomic signatures
 of rapid adaptive divergence in a tropical montane species". Biology
 Letters (in print). The study investigates allopatric divergence and
 selection in Archbold’s Bowerbird (Amblyornis papuensis), an iconic bird
 living in a tropical mountain region in New Guinea, using a novel
 chromosome-level genome and population genomic comparisons. Our results
 show that the two populations inhabiting the eastern and western Central
 Range became isolated ca 11,800 years ago, probably because the suitable
 habitats for this cold-tolerating bird decreased when the climate got
 warmer. Our genomic scans detect that genes in highly divergent genomic
 regions are over-represented in developmental processes, which is likely
 associated with the observed differences in body size between the
 populations. Overall, our results suggest that environmental differences
 between eastern and western Central Range likely drive adaptive divergence
 between them.
description: We generated a nearly chromosome-level genome of the closely
 related <i>Ailuroedus stonii</i> and extracted DNA from
 toepads of taxonomically well-identified and vouchered museum study skins
 of <i>Amblyornis papuensis</i> collected between 1938 and
 1961. Phylogenetic relationships were inferred by a Bayesian analysis of
 80,157 randomly drawn SNPs and we estimated genetic population structure
 with principal component analysis (PCA). We compared the historical
 demography of the populations and tested for environmental heterogeneity
 between their core distributions in the highlands of New Guinea. We also
 studied the landscape of genomic divergence between the two populations
 and searched for evidence of selective sweeps.
description: <i>readme.txt</i> : contains an explanation of the
 environmental variables used in the excel-file. 
 <i>Ericson_et_al_papuensis_supplement_Dryad.pdf</i> :
 a pdf file with more details about material and methods, figures and
 tables. <em>papuensis_snapp.nex </em>:
 nexus file with 80,157 randomly drawn SNPs used in SNAPP v1.3.0 in BEAST2
 v2.4.8.
 <em>papuensis_16_haplotypes.vcf.gz</em> : 2,467,355
 SNPs used for PopSizeABC and selection analyses (gzipped).
 <em>papuensis_16_haplotypes_q20_Geno</em> and
 <em>papuensis_16_haplotypes_q20_SNP</em> : files resulting
 from running vcf2smartpca.py with vcf-file <em>papuensis_16_haplotypes.vcf.gz</em>. A total of 19,457 SNPs were used in the principal component analysis (PCA) using <i>smartpca</i> in EIGENSOFT v. 6.1.4. <em>papuensis_MD_neutral_jointDAFpop1_0.obs</em> : two-dimensional, unfolded site frequency spectrum (SFS) generated from a 76 Mb region of scaffold 446 and used in Fastsimcoal v2.6. <em>papuensis_MD_neutral.est</em> and <em>papuensis_MD_neutral.tpl</em> : est and tpl files used to run Fastsimcoal v2.6. <em>papuensis_bio_vars_2300m_3300m.xlsx</em> : excel-file with bioclimatic data obtained from 1939 and 2953 randomly distributed, hypothetical localities within the core-areas for the western and eastern populations, respectively. <em>ailuroedus_stonii_MV_Z43608.fasta.gz</em> : Complete genome assembly of <em>Ailuroedus (buccoides) stonii, </em>tissue sample: Museums Victoria Z43608, voucher specimen: Australian National Wildlife Collection ANWC B24961.