The deepest divergences in land plants inferred from phylogenomic evidence

Abstract

Phylogenetic relationships among the four major lineages of land plants (liverworts, mosses, hornworts, and vascular plants) remain vigorously contested; their resolution is essential to our understanding of the origin and early evolution of land plants. We analyzed three different complementary data sets: a multigene supermatrix, a genomic structural character matrix, and a chloroplast genome sequence matrix, using maximum likelihood, maximum parsimony, and compatibility methods. Analyses of all three data sets strongly supported liverworts as the sister to all other land plants, and analyses of the multigene and chloroplast genome matrices provided moderate to strong support for hornworts as the sister to vascular plants. These results highlight the important roles of liverworts and hornworts in two major events of plant evolution: the water-to-land transition and the change from a haploid gametophyte generation-dominant life cycle in bryophytes to a diploid sporophyte generation-dominant life cycle in vascular plants. This study also demonstrates the importance of using a multifaceted approach to resolve difficult nodes in the tree of life. In particular, it is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.alternation of generations ͉ hornworts ͉ liverworts ͉ phylogeny ͉ taxon sampling T he origin and early evolution of land plants (embryophytes) during the mid-Ordovician to lower Silurian (480-430 million years ago) initiated the establishment of the modern terrestrial ecosystems and fundamentally altered the course of evolution of life on earth. Two important events marked this period of unprecedented innovation in plant evolution: the massive colonization of the land by plants descended from charophyte algae and the change of the dominant generation in the plant life cycle from a haploid gametophyte to a diploid sporophyte (1-5). The first event opened a vastly underexplored niche of high-intensity solar radiation and abundant CO 2 to photosynthetic life. The second event conferred on plants two abilities to adapt to a life in a water-deficient and UV-abundant terrestrial environment. One is the ability to produce a large number of genetically diverse gametes to ensure fertilization on land where sperm locomotion is hindered, and the other is the ability to mask deleterious mutations through the dominantrecessive interaction of alleles, thus allowing a large number of alleles to persist in the gene pool (2-4). Our understanding of these events hinges on our knowledge of relationships between the organisms involved in these major evolutionary transitions. Despite numerous studies using diverse approaches analyzing morphological and͞or molecular characters, relationships among early land plants remain controversial (5-19). Fossil evidence, although increasingly improved, has not helped to resolve the issues decisively (20,21).A multitude of phenomena characterizing diversification of many major clades o...

Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits

“…Phylogenomic analyses of genome-scale datasets (i.e., whole-genome-derived gene models or RNAseq-derived transcripts) have recently been exploited to resolve a host of longstanding phylogenetic issues Hampl, et al 2009;Qiu, et al 2006). A critical step common to these analyses is the identification of one-to-one orthologs from genome-scale datasets for each taxon, which are then used as data partitions in large supermatrices.…”

Light-harvesting antenna complexes in the moss Physcomitrella patens: implications for the evolutionary transition from green algae to land plants

“…After at least 450 million years [58], the mosses have flourished in almost all terrestrial environments. Being poikilohydric, the characteristics that mosses derived from green algal-lineage genes might have been effective for acclimating to semiaquatic conditions, while the whole-genome duplication and HGT might have led them to acquire the characteristics required for survival in terrestrial conditions.…”

Third-codon transversion rate-based Nymphaea basal angiosperm phylogeny -- concordance with developmental evidence

“…Plant evolutionary biologists have long attempted to reconstruct angiosperm evolutionary history in an effort to determine the root of angiosperms. Since 1999, a series of molecular phylogenetic analyses have identified the monotypic Amborella, followed by Nymphaeales, or Amborella plus Nymphaeales, in the ANITA clade (Amborella, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as representative of the most basal taxa (Mathews and Donoghue 1999;Parkinson, Adams, and Palmer 1999;Qiu et al 1999;Soltis, Soltis, and Chase 1999;Graham and Olmstead 2000;Qiu et al 2000;Zanis et al 2002;Borsch et al 2003;Zanis et al 2003;Stefanovic, Rice, and Palmer 2004;Leebens-Mack et al 2005;Chang et al 2006;Qiu et al 2006). In some cases, monocotbasal trees have also been reported (Goremykin et al 2003;Goremykin et al 2004;Chang et al 2006;Goremykin and Hellwig 2006).…”