Phylogenetic Investigation of the Aliphatic, Non-hydrolyzable Biopolymer Algaenan, with a Focus on Green Algae

Algaenan, an aliphatic biopolymer found in various microalgae, has been implicated as the source of a sizable proportion of the aliphatic refractory organic matter in sedimentary rocks. Because of its recalcitrant nature, algaenan is thought to be preserved selectively in the formation of kerogen and microfossils. Its taxonomic distribution in organisms has not been studied in detail or in a phylogenetic context. Here, we evaluate the distribution and phylogenetic relationships of algaenan-producing organisms from a broad, eukaryote-wide perspective down to the level of genus and species. We focus on the kingdom Plantae, as most described algaenan producers belong to this superkingdom. The phylogenetic distribution of algaenan producers within the Plantae is actually quite limited and a detailed phylogenetic analysis of the two classes that include all green algal algaenan producers suggests that there is no finer-grained pattern of phylogenetic distribution to the production of this biopolymer. Our results suggest that the biopolymer is not widespread ecologically or phylogenetically, is not found abundantly in marine organisms and likely represents a functional description of molecular class, rather than a biomarker for green algae. This adds to a growing body of literature that questions the selective preservation hypothesis for insoluble organic matter and calls for a more detailed chemical and structural analysis of algaenan.Organismic and Evolutionary Biolog

Peat Moss–Like Vegetative Remains from Ordovician Carbonates

Premise of research. Climatically favorable conditions correspond with fossil evidence for dramatic Ordovician marine biodiversification, but coeval terrestrial biodiversity is less well understood. Although diverse Middle and Late Ordovician microfossils are interpreted as reproductive remains of early bryophyte-like land plants (consistent with molecular data indicating pre-Ordovician embryophyte origin), the vegetative structure of Ordovician plants remains mysterious, as do relationships to modern groups. Because distinctive fungal microfossils indicating land plant presence were previously reported from Ordovician carbonate deposits in Wisconsin, we examined another nearby outcrop for additional evidence of terrestrial biodiversification. Methodology. Replicate collections were made from well-understood 455–454 Ma Platteville Formation carbonates of relatively low porosity and hydraulic conductivity. We employed measures to avoid contamination, and organic remains extracted by acid maceration were characterized by light and scanning electron microscopy and energy-dispersive X-ray spectroscopy. Pivotal results. Multicellular organic fragments displayed distinctive cellular features shared with modern vegetative peat mosses but differed from modern materials, e.g., fossil presence of mineral coatings, absence of epibionts. Biometric features of mosslike microfossils isolated from carbonates collected and macerated 12 yr apart by separate investigators did not differ. Putative peat moss remains occurred with foraminifera similar in frequency and thermal maturity to types previously described from the same formation. No diatoms, pollen, or other indicators of post-Ordovician environments were observed. Conclusions. The peat moss–like fragments described here are the oldest-known vegetative remains of land plants and the oldest fossils having distinctive features linking them to a modern plant group. These findings are consistent with peat moss recalcitrance properties that foster fossilization and molecular evidence that the peat moss lineage is 460–607 Ma of age. The new findings suggest that moss-dominated peatlands—recognized for globally significant roles in modern terrestrial biodiversity and C and N cycling—were present hundreds of millions of years earlier than previously thought

Sterols in Red and Green Algae: Quantification, Phylogeny, and Relevance for the Interpretation of Geologic Steranes

Steroids, a class of triterpenoid lipids with high preservation potential, are widely distributed in sedimentary rocks. All eukaryotes have a physiological requirement for these molecules, making steroids important biomarkers for aiding our understanding of eukaryote molecular evolution and geologic history. C-26-C-30 sterols are the molecules most commonly incorporated or synthesized by eukaryotes, and correspond to C-26-C-30 steranes ubiquitously and abundantly preserved in petroleums and sedimentary bitumens. Because these sterols occur in evolutionarily diverse taxa, it can be difficult to associate any particular compound with a single group of organisms. Nevertheless, geochemists have still been able to draw parallels between the empirical patterns in geologic sterane abundances and the age of petroleum source rocks. Paleobiologists have also used sterane data, in particular the patterns in C-29 and C-28 steranes, to support fossil evidence of an early radiation of green algae in latest Proterozoic and Paleozoic and the succession of the major modern phytoplankton groups in the Mesozoic. Although C-29 sterols are found in many eukaryotes, organisms that produce them in proportional abundances comparable to those preserved in Proterozoic and Paleozoic rocks are limited. Based on a large, phylogenetically based survey of sterol profiles from the kingdom Plantae, we conclude that modern ulvophyte and early diverging prasinophyte green algae produce high abundances of C-29 relative to C-27 and C-28 sterols most consistent with the sterane profiles observed in Paleozoic rocks. Our analysis also suggests that ancestral stem groups among the Plantae, including the glaucocystophytes and early divergent red algae are also plausible candidates.Earth and Planetary SciencesOrganismic and Evolutionary Biolog

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

<p>Abstract</p> <p>Background</p> <p>Likelihood-based phylogenetic inference is generally considered to be the most reliable classification method for unknown sequences. However, traditional likelihood-based phylogenetic methods cannot be applied to large volumes of short reads from next-generation sequencing due to computational complexity issues and lack of phylogenetic signal. "Phylogenetic placement," where a reference tree is fixed and the unknown query sequences are placed onto the tree via a reference alignment, is a way to bring the inferential power offered by likelihood-based approaches to large data sets.</p> <p>Results</p> <p>This paper introduces <monospace>pplacer</monospace>, a software package for phylogenetic placement and subsequent visualization. The algorithm can place twenty thousand short reads on a reference tree of one thousand taxa per hour per processor, has essentially linear time and memory complexity in the number of reference taxa, and is easy to run in parallel. <monospace>Pplacer</monospace> features calculation of the posterior probability of a placement on an edge, which is a statistically rigorous way of quantifying uncertainty on an edge-by-edge basis. It also can inform the user of the positional uncertainty for query sequences by calculating expected distance between placement locations, which is crucial in the estimation of uncertainty with a well-sampled reference tree. The software provides visualizations using branch thickness and color to represent number of placements and their uncertainty. A simulation study using reads generated from 631 COG alignments shows a high level of accuracy for phylogenetic placement over a wide range of alignment diversity, and the power of edge uncertainty estimates to measure placement confidence.</p> <p>Conclusions</p> <p><monospace>Pplacer</monospace> enables efficient phylogenetic placement and subsequent visualization, making likelihood-based phylogenetics methodology practical for large collections of reads; it is freely available as source code, binaries, and a web service.</p