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Genomic signatures of rapid adaptive divergence in a tropical montane species

Citation

Ericson, Per; Irestedt, Martin; Qu, Yanhua (2021), Genomic signatures of rapid adaptive divergence in a tropical montane species, Dryad, Dataset, https://doi.org/10.5061/dryad.37pvmcvjr

Abstract

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.

Methods

We generated a nearly chromosome-level genome of the closely related Ailuroedus stonii and extracted DNA from toepads of taxonomically well-identified and vouchered museum study skins of Amblyornis papuensis 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.

Usage Notes

readme.txt : contains an explanation of the environmental variables used in the excel-file. 

Ericson_et_al_papuensis_supplement_Dryad.pdf : a pdf file with more details about material and methods, figures and tables.

papuensis_snapp.nex : nexus file with 80,157 randomly drawn SNPs used in SNAPP v1.3.0 in BEAST2 v2.4.8.

papuensis_16_haplotypes.vcf.gz : 2,467,355 SNPs used for PopSizeABC and selection analyses (gzipped).

papuensis_16_haplotypes_q20_Geno and papuensis_16_haplotypes_q20_SNP : files resulting from running vcf2smartpca.py with vcf-file papuensis_16_haplotypes.vcf.gz. A total of 19,457 SNPs were used in the principal component analysis (PCA) using smartpca in EIGENSOFT v. 6.1.4.

papuensis_MD_neutral_jointDAFpop1_0.obs : two-dimensional, unfolded site frequency spectrum (SFS) generated from a 76 Mb region of scaffold 446 and used in Fastsimcoal v2.6.

papuensis_MD_neutral.est and papuensis_MD_neutral.tpl : est and tpl files used to run Fastsimcoal v2.6.

papuensis_bio_vars_2300m_3300m.xlsx : 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.

ailuroedus_stonii_MV_Z43608.fasta.gz : Complete genome assembly of Ailuroedus (buccoides) stonii, tissue sample: Museums Victoria Z43608, voucher specimen: Australian National Wildlife Collection ANWC B24961.

Funding

Vetenskapsrådet, Award: 621-2017-3693

National Natural Science Foundation of China, Award: NSFC32020103005

Magnus Bergvalls Stiftelse

Riksmusei Vänner

Riksmusei Vänner