Early branching events in the diversification of land plants and closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. by conjugation. No analysis provided strong support for a sister relationship between Coleochaetales and embryophytes, and most analyses rejected a sister relationship between Charales and embryophytes (Fig. 4 and Fig. S4). Analyses of nucleotide data that included third positions offered weak support for Charales sister to embryophytes, but as mentioned above, this is likely an artifact of among-lineage variation in nucleotide frequencies at the third codon position (Fig. S2). The results presented here provide strong IKK-16 manufacture support for a sister group relationship between Zygnematophyceae and embryophytes in analyses of amino acids and first and second codon positions (Figs. 2C4), a relationship that has been inferred in recent analyses of plastomes (8, 36) and a smaller set of nuclear gene sequences (27, 29). Whereas most individual gene trees did not provide strong support for any of the hypotheses illustrated in Fig. 1, a small proportion of gene trees did exhibit well-supported conflict with each hypothesis (Figs. 2 and ?and3,3, and Fig. S3). This discordance was not unexpected and may be because of incomplete sorting of ancestral variation between speciation events represented by short internodes in the species phylogeny (63, 64) (Fig. 2). ASTRAL analyses (61) of gene trees estimated from amino acid alignments recovered strong support for Zygnematophyceae as sister to land plants (Fig. 4). ASTRAL analyses of in-frame nucleotide data, when first and second positions alone are considered, recovered the same relationship but with weaker support (Figs. 3 and ?and4);4); after filtering fragmentary sequences to improve gene tree resolution, we again recovered this relationship with high support (Fig. 4). As seen in our supermatrix and supertree analyses, ASTRAL analyses of nucleotide data including all codon positions recovered trees with weak support for as the sister lineage to land plants. Again, this result is interpreted as an artifact of among-lineage variation in character-state frequencies. Zygnematophyceae are a group of unicellular or filamentous streptophyte algae that sexually reproduce by conjugation, rather than flagellate cells (65). The absence of motile cells and plasmodesmata in Zygnematales may be interpreted as secondary reduction of morphological complexity following divergence from a common ancestor shared IKK-16 manufacture with Charales and Coleochaetales, which is consistent with their mode of reproduction (29). Phragmoplast presence and structure is also consistent with this interpretation of secondary loss, as they seem to be absent from most Zygnematophyceae, but simplified phragmoplasts have been characterized for the filamentous (31, 66), (33), and likely (67). Fowke and Pickett-Heaps (31) suggested that the rudimentary phragmoplast seen in may represent an ancestral form, but placement IKK-16 manufacture of Zygnematophyceae as sister to land plants implies that a simplified (rather than ancestral) phragmoplast existed in the zygnematophycean stem lineage and was independently lost within the two major zygnematalean clades (Figs. 2 and ?and3).3). The possibility of independent origins of phragmoplasts in multiple streptophyte lineages appears unlikely; however, the phycoplast, a collection of microtubules serving a similar IKK-16 manufacture function in cytokinesis relative to the phragmoplast but forming parallel to the division plane (in contrast to the phragmoplast), did evolve independently in the lineage leading to the core chlorophytes (68, 69). Reports on the occurrence of phragmoplast-mediated cytokinesis in the ulvophycean chlorophytes and (70), however, should be interpreted with caution, as functional studies are lacking and structurally this system is more reminiscent of a rudimentary telophase spindle than a genuine streptophyte phragmoplast. Bryophyte Relationships. Whereas the monophyly of each bryophyte lineageBryophyta (mosses), Anthocerotophyta (hornworts), and Marchantiophyta (liverworts)is strongly supported here (Figs. 2C4), most of our results reject the current, widely accepted hypothesis that liverworts are sister to all other land plants (38, 42, 71). Furthermore, the widely accepted view that liverworts, mosses, and hornworts are, respectively, successive sister groups to vascular plant life (25, 42, 43)which is normally strongly backed by parsimony mapping of mitochondrial intron increases (42) and latest mitochondrial phylogenomic analyses (72)isn’t recovered in virtually any of our analyses. Prior analyses of protein-coding genes extracted from entire plastome sequences acquired suggested which the three bryophyte divisions (Bryophyta, Anthocerotophyta, and Marchantiophyta) type a clade (41, 73; but find ref. 71). Bryophytes are solved as monophyletic in a number of analyses right here, including 3 of 12 amino acidity supermatrix analyses and everything ASTRAL analyses predicated on GNGT1 either amino acidity data or in-frame nucleotide data with no addition of third positions (Figs. 2C4). Supertree analyses of ML gene trees and shrubs estimated from second and initial codon position.