DOI: 10.5061/dryad.7pvmcvdvg
title: Data from: Whole-genome phylogeography of the Blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome

description: Whole-genome surveys of genetic diversity and geographic variation often
 yield unexpected discoveries of novel structural variation, which
 long-read DNA sequencing can help clarify. Here we report on whole-genome
 phylogeography of a bird exhibiting classic vicariant geographies across
 Australia and New Guinea, the Blue-faced honeyeater (Entomyzon cyanotis),
 and the discovery and characterization of a novel neo-Z chromosome by
 long-read sequencing. Using short-read genome-wide SNPs, we inferred
 population divergence events within E. cyanotis across the Carpentarian
 and other biogeographic barriers during the Pleistocene (~0.3 – 1.7 MYA).
 Evidence for introgression between non-sister populations supports a
 hypothesis of reticulate evolution around a triad of dynamic barriers
 around Pleistocene Lake Carpentaria between Australia and New Guinea.
 During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z
 chromosome and explore its diversity, divergence and introgression
 landscape. We show that, as in some Sylvioid passerine birds, a fusion
 occurred between chromosome 5 and the Z chromosome to form a neo-Z
 chromosome, with the ancestral pseudoautosomal region (PAR) appearing to
 become non-recombinant between Z and W, along with most of the fused
 chromosome 5 (~37.2 Mbp). The added non-recombinant portion of the neo-Z
 displays reduced heterozygosity and faster population genetic
 differentiation compared with the ancestral Z. Yet, the new PAR shows
 elevated diversity and reduced differentiation compared to autosomes,
 potentially resulting from introgression. In our case, long-read
 sequencing helped clarify the genomic landscape of population divergence
 on autosomes and sex chromosomes in a species where prior knowledge of
 genome structure was still incomplete.
description: We generated VCF files for downstream
 analyses using the GATK pipeline (McKenna et al. 2010) and samtools (Li et
 al. 2009). We generated estimates of heterozygosity and coverage across
 scaffolds with samtools. Sliding window population genetic statistics were
 generated using ANGSD and ngstools (Fumagalli et al. 2013, 2014;
 Korneliussen et al. 2014). pixy was used to calculate population
 statistics across windows (Korunes and Samuk 2021). We used SNAPP to
 generate a coalescent estimate of the population tree using SNPs (Bryant
 et al. 2012). We estimated migration surfaces with EEMS (Petkova et al.
 2016). Satsuma was used to align contigs and scaffolds between species,
 sexes and different assemblies (Grabherr et al. 2010). We generated
 statistics for a phylogenetic network using TreeMix (Pickrell and
 Pritchard 2012). Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., & RoyChoudhury, A. (2012). Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis. <em>Molecular Biology and Evolution</em>, <em>29</em>(8), 1917–1932. https://doi.org/10.1093/molbev/mss086 Fumagalli, M., Vieira, F. G., Korneliussen, T. S., Linderoth, T., Huerta-Sánchez, E., Albrechtsen, A., & Nielsen, R. (2013). Quantifying population genetic differentiation from next-generation sequencing data. <em>Genetics</em>, <em>195</em>(3), 979–992. https://doi.org/10.1534/genetics.113.154740 Fumagalli, M., Vieira, F. G., Linderoth, T., & Nielsen, R. (2014). ngsTools: Methods for population genetics analyses from next-generation sequencing data. <em>Bioinformatics (Oxford, England)</em>, <em>30</em>(10), 1486–1487. https://doi.org/10.1093/bioinformatics/btu041 Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. <em>Bioinformatics</em>, <em>26</em>(9), 1145–1151. https://doi.org/10.1093/bioinformatics/btq102 Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: Analysis of Next Generation Sequencing Data. <em>BMC Bioinformatics</em>, <em>15</em>(1), 356. https://doi.org/10.1186/s12859-014-0356-4 Korunes, K. L., & Samuk, K. (2021). pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. <em>Molecular Ecology Resources</em>, <em>21</em>(4), 1359–1368. https://doi.org/10.1111/1755-0998.13326 Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. <em>Bioinformatics</em>, <em>25</em>(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352 McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110 Petkova, D., Novembre, J., & Stephens, M. (2016). Visualizing spatial population structure with estimated effective migration surfaces. <em>Nature Genetics</em>, <em>48</em>(1), 94–100. https://doi.org/10.1038/ng.3464 Pickrell, J. K., & Pritchard, J. K. (2012). Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. <em>PLoS Genetics</em> <em>8</em>(11), e1002967.
description: See README.txt.