Data-driven guidelines for phylogenomic analyses using SNP data.

ABSTRACT:

Premise

There is a general lack of consensus on the best practices for filtering of single-nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full "locus") in phylogenomic analyses and subsequent comparative methods.

Methods

Using genotyping-by-sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.

Results

Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90-100%) r

SUBMITTER: Suissa JS 

PROVIDER: S-EPMC11610416 | biostudies-literature | 2024 Nov-Dec

REPOSITORIES: biostudies-literature