Data‐driven guidelines for phylogenomic analyses using SNP data

Author:

Suissa Jacob S.1ORCID,De La Cerda Gisel Y.2,Graber Leland C.3ORCID,Jelley Chloe3ORCID,Wickell David24ORCID,Phillips Heather R.2,Grinage Ayress D.25,Moreau Corrie S.35ORCID,Specht Chelsea D.2ORCID,Doyle Jeff J.2ORCID,Landis Jacob B.26ORCID

Affiliation:

1. Department of Ecology and Evolutionary Biology University of Tennessee at Knoxville Knoxville Tennessee USA

2. School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium Cornell University Ithaca New York USA

3. Department of Entomology Cornell University Ithaca New York USA

4. Boyce Thompson Institute Ithaca New York USA

5. Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA

6. BTI Computational Biology Center, Boyce Thompson Institute Ithaca New York USA

Abstract

AbstractPremiseThere 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.MethodsUsing 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.ResultsOur 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.DiscussionUsing 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.

Publisher

Wiley

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