2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics.

ABSTRACT: Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort,

SUBMITTER: Chambers EA 

PROVIDER: S-EPMC9994478 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature