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Dating Plastid Endosymbiosis and Diversification in Eukaryotic Algae

Periodic Reporting for period 1 - AlgDates (Dating Plastid Endosymbiosis and Diversification in Eukaryotic Algae)

Reporting period: 2016-07-01 to 2018-06-30

During the eukaryote evolutionary history, the acquisition of plastids and the evolution of algae is one of the major transitions that has heavily shaped the earth and its biosphere as it is today. Still, few is known about the ancient endosymbiotic events, the evolution of these algal lineages and the correlation with the earth geological past conditions. One of the main problems, is that we lack molecular data for key extant species with good fossil record, which is fundamental to date the speciation events and help to resolve phylogenetic relationships between extant living species an reconstruct the evolution through the geological time scale. In the current situation of rapid climate change, we need to understand the adaptation and diversification of algae, which are of fundamental ecological importance. We addressed this issue by obtaining molecular data of calcareous algae with a high quality fossil record (Corallinales and Dasycladales) and including them in a plastid-wide phylogenomics study, including all known lineages of Cyanobacteria (the lineage that gave rise to the chloroplast in eukaryotes), the primary algae (Glaucophyta, Rhodophyta and Chloroplastida) and complex algae derived from secondary eukaryotic endosymbiotic events (Haptophyta, Ochrophyta, Cryptophyta, Euglenozoa and Chlorarachnophyta). The results include 2 newly sequenced algal genomes of calcareous red algae including its whole chloroplast genome, a state-of-the-art phylogenomic dataset including over 80 plastid markers (~20,000 amino acid positions) for a wide taxon sampling of more than 300 species, and 10 highly confident calibration points, and a timed tree with narrower time estimates than previous eukaryote-wise studies including diversification rates of each lineage and correlation with paleoclimatic data.
During the period of two years, we have sampled several algal specimens. I have performed multiple protocols and tests in order to obtain high quality molecular data from diverse calcareous species. I have characterized them molecularly by the use of metatranscriptomics and metagenomics. I obtained two high quality genomes after cleaning the genomes using bioinformatic tools; taking advantage of the excellent infrastructure and collaborating with workers in the Ecologie, Systématique et evolution lab. In collaboration with experts on the fossil record of red algae and a PhD student focused on plastid phylogenomics, we have performed phylogenomic analyses: we have curated a high quality plastid gene-based amino acidic dataset, we have collected all needed taxonomic sampling and established the proper calibration points to date the speciation events in the geological scale. We have obtained a plastid-wise timed tree with narrower confidence intervals compared to previous studies at an eukaryotic level. We have also performed diversification analyses that correlate the rates of evolution of the algal lineages with paleoclimatic data. Preliminary results have been disseminated through talks and posters in international and local scientific meetings as well as though social media and through an outreach activity with the general public. This results and the data generated have been or will be published soon in Open Access as the EU requires, using online platforms such Biorxiv, Figshare and Researchgate.
Our results are providing an accurate timed phylogeny of plastid evolution to the whole evolutionary community. Also, we provide to the scientific community a couple of high quality red calcareous algal genomes that will help to understand the biology of this ecologically important lineage, who are important carbonate producers in northern reefs, important ecological niches for marine biodiversity; including microscopic eukaryotes and larvae of macroscopic species. Overall, the data resulted from this project can be used by other scientists working in distinct disciplines: from specific red algae to macroevolutionary studies, and also can be used to understand the evolution of our seas in rapid climate change situations.
Plastid evolution