Abstract
The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project‐dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up‐and‐coming technologies that may help propel the field even further.
Highlights
The past decade has seen a major breakthrough in our ability to and inexpensively sequence genome-scale data from diverse lineages
With rapidly evolving new tools and the caveats that they bring, choosing an optimal strategy that takes into consideration cost, available plant tissue, and short- and long-term research goals can be a daunting task, especially for people who are new to the field of phylogenomics
If polyploidy event is old enough that homeologs can be separated during transcriptome assembly When detecting genome duplication and gene family evolution are of interest beyond reconstructing species relationship Yes, fully reusable aCosts are given in U.S dollars (US$) as of 2018
Summary
We draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up-a nd-coming technologies that may help propel the field even further. A number of analytical approaches have been developed to detect polyploidy and dissect heterogeneity within phylogenetic data sets (Li et al, 2015; Smith et al, 2015; McKain., 2016b; Gompert and Mock, 2017; Gregg et al, 2017), making it easier to address polyploidy and reticulate evolution using genome-scale data. McKain et al.—Practical considerations for plant phylogenomics 2 of 15 which requires distinguishing homeologous gene copies; reticulate evolution, which requires biparentally inherited loci; and the use of herbarium materials with short and partially degraded DNA— making practical suggestions for each.
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