From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species

B Wright, KA Farquharson, EA McLennan, K Belov… - BMC genomics, 2019 - Springer
Background Recent advances in genomics have greatly increased research opportunities
for non-model species. For wildlife, a growing availability of reference genomes means that …

Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial

BR Wright, CE Grueber, MJ Lott, K Belov… - Molecular Biology …, 2019 - Springer
Reduced-representation sequencing methods have wide utility in conservation genetics of
non-model species. Several methods are now available that reduce genome complexity to …

A fast, reproducible, high-throughput variant calling workflow for population genomics

CD Mirchandani, AJ Shultz… - Molecular Biology …, 2024 - academic.oup.com
The increasing availability of genomic resequencing data sets and high-quality reference
genomes across the tree of life present exciting opportunities for comparative population …

Reference-free population genomics from next-generation transcriptome data and the vertebrate–invertebrate gap

P Gayral, J Melo-Ferreira, S Glemin, N Bierne… - PLoS …, 2013 - journals.plos.org
In animals, the population genomic literature is dominated by two taxa, namely mammals
and drosophilids, in which fully sequenced, well-annotated genomes have been available …

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga)

JD Manthey, LC Campillo, KJ Burns… - Systematic …, 2016 - academic.oup.com
Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific
genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most …

Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates

J Melville, ML Haines, K Boysen… - Royal Society …, 2017 - royalsocietypublishing.org
Next-generation sequencing (NGS) approaches are increasingly being used to generate
multi-locus data for phylogeographic and evolutionary genetics research. We detail the …

Reference genomes from distantly related species can be used for discovery of single nucleotide polymorphisms to inform conservation management

SJ Galla, NJ Forsdick, L Brown, MP Hoeppner… - Genes, 2018 - mdpi.com
Threatened species recovery programmes benefit from incorporating genomic data into
conservation management strategies to enhance species recovery. However, a lack of …

Estimating and accounting for genotyping errors in RAD‐seq experiments

L Bresadola, V Link, CA Buerkle… - Molecular Ecology …, 2020 - Wiley Online Library
In non‐model organisms, evolutionary questions are frequently addressed using reduced
representation sequencing techniques due to their low cost, ease of use, and because they …

A beginner's guide to low‐coverage whole genome sequencing for population genomics

RN Lou, A Jacobs, AP Wilder… - Molecular …, 2021 - Wiley Online Library
Low‐coverage whole genome sequencing (lcWGS) has emerged as a powerful and cost‐
effective approach for population genomic studies in both model and nonmodel species …

Toward a genome sequence for every animal: Where are we now?

S Hotaling, JL Kelley… - Proceedings of the …, 2021 - National Acad Sciences
In less than 25 y, the field of animal genome science has transformed from a discipline
seeking its first glimpses into genome sequences across the Tree of Life to a global …