Data‐driven guidelines for phylogenomic analyses using SNP data

• Published in: Applications in plant sciences Vol. 12; no. 6; pp. e11611 - n/a
• Main Authors: Suissa, Jacob S., De La Cerda, Gisel Y., Graber, Leland C., Jelley, Chloe, Wickell, David, Phillips, Heather R., Grinage, Ayress D., Moreau, Corrie S., Specht, Chelsea D., Doyle, Jeff J., Landis, Jacob B.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.11.2024; John Wiley and Sons Inc; Wiley
• Subjects: Accuracy; ancestral state reconstructions; Application; data collection; Datasets; Divergence; divergence time estimation; Genes; Genomes; Genotyping; genotyping by sequencing; genotyping‐by‐sequencing (GBS); Glycine; Glycine (Fabaceae); loci; locus; Missing data; phylogenetic comparative methods; Phylogenetics; Phylogeny; risk reduction; Single-nucleotide polymorphism; single‐nucleotide polymorphism (SNP) filtering; topology; Trees; Australia; United States > US; genotyping‐by‐sequencing (GBS); ancestral state reconstructions; divergence time estimation; phylogenetic comparative methods; locus; Glycine; single‐nucleotide polymorphism (SNP) filtering
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11611

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%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution. Discussion Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.