Posts tagged “Soltis

Which came first? A pivotal position in the plant tree of life

Amborella trichopoda

Amborella trichopoda

The question of which extant angiosperm (flowering plant) lineage “came first” (i.e., is basal in the flowering plant tree of life) has long puzzled biologists. This question is fascinating and important in its own right, but the answer also has potentially profound ramifications including plant gene and genome evolution (which, for example, has implications for crop improvement). Such information is also important for understanding habit and habitat evolution and for the inference of ancestral character states in the angiosperms (e.g., the ancestral flower as well as the ancestral angiosperm genome). Although great 20th century plant taxonomists such as Arthur Cronquist, Armen Takhtajan, and Robert Thorne generally agreed that taxa from the subclass Magnoliidae comprised the “basal” angiosperm lineage, there was no way to “prove”, one way or another, which extant angiosperm lineage came first until the advent of molecular systematics towards the end of the 20th century.Untitled

With the aid of modern molecular phylogenetic techniques it is now known that the major groups they recognized, such as Magnoliidae sensu Cronquist and Takhtajan, are typically polyphyletic. Most research now indicates instead that Amborellaceae, Nymphaeales (water lilies), and Austrobaileyales are the earliest branching extant angiosperm lineages. However, the relative branching order of these three lineages, particularly in regards to Amborella trichopoda (the sole species within Amborellaceae) and Nymphaeales, was, until recently, somewhat contentious.

While most molecular analyses during the past 20 years have recovered Amborella as the earliest-diverging angiosperm lineage, some studies have suggested a clade comprising Amborella + Nymphaeales, or even Nymphaeales alone, as the root of all angiosperms. Recently, at the University of Florida, Soltis lab postdoc Bryan Drew and colleagues (including AVATOL team member Stephen Smith at the University of Michigan) endeavored to definitively answer the longstanding question of which angiosperm came first—that is, what living angiosperm is sister to all other living angiosperms in the angiosperm tree of life. Using a plastid data set consisting of 236 taxa, 78 genes, and ~58,000 nucleotides, Drew et al. performed a myriad of analyses with the express purpose of discerning the first-diverging angiosperm lineage; this study by Drew et al. was just accepted by Systematic Biology and will be viewable online in the coming months. Their results: Virtually every analysis conducted found Amborella as the earliest-diverging living angiosperm lineage with high internal support, and every plastid analysis performed using their original datasets recovered a topology in which Amborella alone is sister to all other living angiosperms.

CaptureThese findings lend strong affirmation to the Amborella sister hypothesis, and should help guide future research regarding angiosperm character (including genomic features) and habitat evolution. Although the “first” angiosperms are long extinct, a better understanding of Amborella will aid in our understanding of angiosperm evolution as a whole. This was the impetus behind the Amborella Genome Project. As a result of this ongoing project, the Amborella nuclear genome has recently been fully sequenced (www.amborella.org; Amborella Genome Project, Science, in press), and this major achievement should lead to unprecedented insights within flowering plants.

 

Doug Soltis is a distinguished professor at the University of Florida.

Bryan Drew is a post-doctoral researcher in the Soltis lab at the University of Florida.


The Soltis lab fills the gaps in green plant phylogeny for the Open Tree of Life

Phylogenetic tree summarizing relationships among major lineages of green plants (Viridiplantae)

Phylogenetic tree summarizing relationships among major lineages of green plants (Viridiplantae)

In the Soltis lab at the University of Florida, Bryan Drew and Jiabin Deng have spent much of the past year collecting trees and alignments of green plants (Viridiplantae) as part of an effort to produce a synthetic tree that represents all of the described organisms on Earth. As part of the tree-gathering process, they have gleaned public database archives and contacted corresponding authors directly to request data. Although these methods were not as successful as had been hoped, they recovered trees from over 1000 publications involving green plants.

As might be expected, some areas of the green plant tree are better resolved than others. For example, within gymnosperms and flowering plants we have authorsubmitted trees that support the monophyly of most major lineages, but for other major lineages of green plants, such as green algae and bryophytes, sampling is not as complete and those parts of the tree are not as well resolved. Fortunately, for green algae at least, help is on the way in the form of the NSF funded “Assembling the Green Algae Tree of Life” project. Although results from this project will not be incorporated into the upcoming Open Tree of Life “Big Bang Tree”, within a few years the green algae portion of the Open Tree will undoubtedly greatly benefit by inclusion of trees from the Green Algae Tree of Life project. Other parts of the green plant tree are shaping up nicely, and the Soltis lab is sending out some last minute requests to authors in an attempt to shore up regions of the tree that are presently underrepresented.

Here we provide a basic summary of what we know about green plant phylogeny, stressing that there is much we still do not know about relationships in this large clade of perhaps 500,000 species. We know from the fossil record that many green plant taxa have gone extinct; these extinctions contribute to “long branches” in the Tree of Life and can make it very difficult to determine relationships between older lineages. In the green plant tree, two main clades have been recovered, the Chlorophyta and the Streptophyta. The chlorophytes contain most of what is traditionally known as green algae, while the streptophytes contain the remaining green algae as well as land plants (Embryophyta). One of the many insights provided by molecular systematics during the past twenty years is that “green algae” as long recognized are not actually a natural group (i.e., they are not monophyletic), and that some traditionally classified “green algae” are actually more closely related to land plants. However, the closest “green algal” relative of land plants remains unclear—some studies suggest Charales whereas others indicate Zygnemetales or Coleochaetales The land plants (embryophytes) include bryophytes (mosses, hornworts, and liverworts) and vascular plants (tracheophytes). There is still some question as to whether the bryophytes are a natural group or comprise separate evolutionary lineages. The vascular plants are comprised of lycophytes (clubmosses and quillworts), monilophytes (e.g., ferns and horsetails), gymnosperms (cycads, Ginkgo, gnetophytes, and conifers), and angiosperms (flowering plants).

Though the relationships of come large clades are uncertain, these uncertainties will be shown in the Big Bang tree given that we possess many of the trees that highlight these different clade placements. In other areas of the green plant tree we are sorely lacking data, and the Soltis lab (in close collaboration with Stephen Smith’s lab at the University of Michigan) is still working hard to fill in the tens of thousands of holes in the tree that remain. This is a beautiful part of the Open Tree of Life: as with the organisms that it represents, the tree is ever growing!

Doug Soltis is a distinguished professor at the University of Florida.