Biology and Ecology of Abundant Protists (BEAP) Lab
@beaplab.bsky.social
The BEAP Lab is at the Institute of Evolutionary Biology (IBE) in Barcelona. Our goal is to culture and then characterize the cell biology, behavior and ecosystem relevance of abundant protists. PI: Daniel J. Richter. Web: https://www.beaplab.org/
Next, we compared Dollo (A) to ML (B) on a real dataset of Pfam domains. Dollo’s LECA has more domains than any extant eukaryote followed by widespread losses; ML’s has fewer LECA domains and balanced gains/losses. Which to trust? Our results suggest caution with Dollo parsimony.
November 22, 2023 at 10:19 AM
Next, we compared Dollo (A) to ML (B) on a real dataset of Pfam domains. Dollo’s LECA has more domains than any extant eukaryote followed by widespread losses; ML’s has fewer LECA domains and balanced gains/losses. Which to trust? Our results suggest caution with Dollo parsimony.
With Paschalis Natsidis and Max Telford’s simulated sets of 5,000 orthologs with no gains or losses, we tested our suspicion together. We compared Dollo to maximum likelihood (with Laurent Guégen), finding that Dollo consistently overestimates ancestral gene content towards the root.
November 22, 2023 at 10:18 AM
With Paschalis Natsidis and Max Telford’s simulated sets of 5,000 orthologs with no gains or losses, we tested our suspicion together. We compared Dollo to maximum likelihood (with Laurent Guégen), finding that Dollo consistently overestimates ancestral gene content towards the root.