De novoassembly of a chromosome-scale reference genome for the northern flickerColaptes auratus

Abstract

The northern flicker, Colaptes auratus, is a widely distributed North American woodpecker and a long-standing focal species for the study of ecology, behavior, phenotypic differentiation, and hybridization. We present here a highly contiguous de novo genome assembly of C. auratus, the first such assembly for the species and the first published chromosome-level assembly for woodpeckers (Picidae). The assembly was generated using a combination of short-read Chromium 10× and long-read PacBio sequencing, and further scaffolded with chromatin conformation capture (Hi-C) reads. The resulting genome assembly is 1.378 Gb in size, with a scaffold N50 of 11 and a scaffold L50 of 43.948 Mb. This assembly contains 87.4–91.7% of genes present across four sets of universal single-copy orthologs found in tetrapods and birds. We annotated the assembly both for genes and repetitive content, identifying 18,745 genes and a prevalence of ∼28.0% repetitive elements. Lastly, we used fourfold degenerate sites from neutrally evolving genes to estimate a mutation rate for C. auratus, which we estimated to be 4.007 × 10−9 substitutions/site/year, about 1.5× times faster than an earlier mutation rate estimate of the family. The highly contiguous assembly and annotations we report will serve as a resource for future studies on the genomics of C. auratus and comparative evolution of woodpeckers.

Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

“…Stairway Plot 2 uses the site frequency spectrum (SFS) to fit a flexible multi-epoch model of changes in population size. For all demographic analyses, we used the folded SFS and specified a mutation rate of 4.007 × 10 −9 mutations per site per generation and a generation time of one year for both species [57]. Changes in effective population size over time were generally consistent between both species, being characterized by recurrent episodes of bottleneck followed by population expansion (Figure 4a–b).…”

“…For each population, we used the default 67% sites for training, and calculated median estimates and 95% pseudo-CI based on 200 replicates. We assumed a mutation rate of 4.007 × 10 −9 mutations per site per generation, as estimated from coding regions of the Northern Flicker’s genome [57] and a generation time of one year for both species. We then utilized the estimates of N e from Stairway Plot 2 across the past 500 kya to calculate the harmonic mean on linear-stepped time points, representing each population’s long-term N e .…”

“…We used the SNP dataset with maf > 0.02 and ran the analysis with default settings. Because ReLERNN is robust to demographic model misspecification [63], we simulated an equilibrium model considering a mutation rate of 4.007 x 10 -9 mutations per generation [57] and assuming a generation time of one year. Finally, we explored the recombination history of each population by analyzing their patterns of linkage disequilibrium (LD) decay using PopLDdecay [120].…”

Demography and linked selection interact to shape the genomic landscape of codistributed woodpeckers during the Ice Age

“…For each population, we used the default 67% sites for training, and calculated median estimates and 95% pseudo‐CI based on 200 replicates. We assumed a mutation rate of 4.007 × 10 −9 mutations per site per generation, as estimated from synonymous sites of the Northern Flicker's genome (Hruska & Manthey, 2021) and a generation time of 1 year for both species. We then utilized the estimates of N e from stairway plot 2 across the past 500 kya to calculate the harmonic mean on linear‐stepped time points, representing each population's long‐term N e .…”

“…For each population, we used the SNP data set with maf > 0.02 and ran the analysis with default settings. Because ReLERNN is robust to demographic model misspecification (Adrion et al, 2020), we simulated an equilibrium model considering a mutation rate of 4.007 × 10 −9 mutations per generation (Hruska & Manthey, 2021) and assuming a generation time of 1 year. Finally, we explored the recombination history of the individuals in each sampling region by analysing their patterns of linkage disequilibrium (LD) decay using PopLDdecay (Zhang et al, 2018).…”