![]() ![]() This phenomenon is not limited to heterotrophic plants, as several photosynthetic lineages also have notably elevated rates, including the hard-to-place Gnetales (e.g., Sanderson et al., 2000 Graham and Iles, 2009) and Poales in monocots (e.g., Givnish et al., 2010). Elevated substitution rates, sometimes extreme (e.g., Naumann et al., 2016), are typical of many heterotrophic plant lineages and have been shown to introduce systematic error in phylogenetic inference (e.g., Barkman et al., 2004 Nickrent et al., 2004 Merckx et al., 2009 Lam et al., 2015). Highly elevated substitution rates may lead to long-branch attraction, resulting in phylogenetic misinference (Felsenstein, 1978 Hendy and Penny, 1989). The latter phenomena are observed in the plastomes of many heterotrophic (nonphotosynthetic) plants (e.g., Lam et al., 2015 Mennes et al., 2015a Bellot and Renner, 2016 Bellot et al., 2016 Naumann et al., 2016 Wicke et al., 2016). ![]() However, it will take a while to fully integrate some lineages into the plant tree of life-for example, those with highly modified, rapidly evolving, or difficult-to-recover genomes. For example, studies based on whole-plastid genomes of photosynthetic plants have helped to resolve several problematic relationships at broad and recent levels of plant phylogeny, confirmed earlier phylogenetic results based on few-gene data sets, and affirmed the recalcitrance of several hard-to-resolve relationships (e.g., Givnish et al., 2010 Ruhfel et al., 2014 Barrett et al., 2016 Ross et al., 2016 Fishbein et al., 2018 and Gitzendanner et al., 2018). The resulting massive influxes of data will undoubtedly contribute to more refined pictures of plant relationships. Similar rapid advances with the production of transcriptomes and whole genomes for hundreds or even thousands of plant species are taking place, or are anticipated soon (Wickett et al., 2014 Normille, 2017). Improvements in sequencing technologies in the last decade have made it feasible to assemble whole plastid genomes (plastomes) quite cheaply and rapidly (Goodwin et al., 2016), so that over 2000 plastomes are now available on GenBank (NCBI Organellar Genomes December 2017). Burmanniaceae and Thismiaceae should not be combined as a single family in Dioscoreales. Previous predictions of parallel photosynthesis loss within families are supported for Burmanniaceae, Ericaceae, Gentianaceae, and Orchidaceae. Nonetheless, diverse likelihood frameworks provide generally well-supported and mutually concordant phylogenetic placements of mycoheterotrophs, consistent with recent phylogenetic studies and angiosperm-wide classifications. Mycoheterotrophic plastomes provide challenging cases for phylogenomic inference, as substitutional rates can be elevated and genome reduction can lead to sparse gene recovery. In contrast, parsimony analysis is strongly misled by long-branch attraction among many distantly related mycoheterotrophic monocots. Amino-acid-based likelihood placements are broadly consistent with DNA-based inferences, but extremely rate-elevated taxa can have unexpected placements-albeit with weak support. Key Resultsĭespite multiple very long branches that reflect elevated substitution rates, and frequently patchy gene recovery due to genome reduction, inferred phylogenetic placements of most mycoheterotrophic lineages in DNA-based likelihood analyses are both well supported and congruent with other studies. We used parsimony and likelihood analysis of protein-coding gene sets from published and newly completed plastomes to infer the phylogenetic placement of taxa from the 10 angiosperm families in which mycoheterotrophy evolved. ![]() Mycoheterotroph plastomes therefore provide excellent test cases for investigating how extreme conditions impact phylogenomic inference. Nonphotosynthetic plants such as mycoheterotrophs (which rely on root-associated fungi for essential nutrients, including carbon) tend to have highly elevated rates of plastome evolution, substantial genome reduction, or both. Phylogenomic studies employing large numbers of genes, including those based on plastid genomes (plastomes), are becoming common. ![]()
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