Low-coverage whole genome sequencing for highly accurate population assignment: Mapping migratory connectivity in the American Redstart (Setophaga ruticilla)

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing methods, such as low-coverage whole genome sequencing (lcWGS), provides new opportunities for improved estimates of migratory connectivity. Here, we use lcWGS to identify fine-scale population structure in a widespread songbird, the American Redstart (Setophaga ruticilla), and accurately assign individuals to genetically distinct breeding populations. Assignment of individuals from the nonbreeding range reveals population-specific patterns of varying migratory connectivity. By combining migratory connectivity results with demographic analysis of population abundance and trends, we consider full annual cycle conservation strategies for preserving num..., Genetic sampling and library preparation
Sample site locations were chosen to maximize sampling coverage across the breeding and nonbreeding ranges of the American Redstart. We used genetic samples from a total of 330 individuals: 182 individuals from 16 locations across the breeding range and 148 individuals from 15 locations in the nonbreeding range (Table S1). Sample collection occurred between 1993 and 2022 and consisted of either blood from brachial venipuncture or feathers. We extracted DNA from blood samples using the standard protocol for Qiagen DNEasy Blood and Tissue Kits and we modified the protocol to maximize DNA yield from feathers. Whole genome sequencing libraries were prepared following modifications of Illumina’s Nextera Library Preparation protocol (Schweizer & DeSaix, 2023). Pooled libraries were sequenced on eight HiSeq 4000 lanes at Novogene Corporation Inc. with a target sequencing depth of 2X per individual.
Bioinformatics
We trimmed the sequence data to remo..., The Beagle files are gzip compressed tab-delimited text files (see the README.md for formatting details) specifying the genotype likelihood data of the sampled American Redstarts (Setophaga ruticilla). Thus, these files can be viewed using any software or utilities that decompress gzip. For example, with the `zcat` utility, a user can open a Terminal window on a OSX system or in Linux, and enter `zcat < amre.combined.47.148.122.ds_2.0x.beagle.gz` to view the entire file. However, it is not recommended to view these files in their entirety due to their large size. Bash shell utilities are recommended as open-source tools for viewing and editing these large gzip compressed text files. The main purpose of the Beagle files is for users to be able to process them with software such as PCangsd and WGSassign, as demonstrated in the corresponding manuscript for this data set.
The remaining files are uncompressed text files.