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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. Using genotyping‐by‐sequencing data from 22Glycinespecies, 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. 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. 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. 

Abstract As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.