Joanna MaselThread: our latest #preprint looks at long-term #proteome #evolution phenomena and asks #macroevolutionary #LevelsOfSelection questions https://biorxiv.org/content/10.1101/2022.10.27.514087v1 1/11 (Repeat for new server).
We wanted to know what caused the extraordinarily #LongTermTrends we previously saw: in #IntrinsicStructuralDisorder and in the degree to which hydrophobic #AminoAcids are clustered, as a function of the time elapsed since a Pfam domain originated. https://elifesciences.org/articles/57347 2/11
We usually think of #DirectionalEvolution via descent with modification (top), but it's hard to imagine it causing that slow a trend. We hypothesized that #DifferentialLoss might be slow enough to explain why the trend kept going for billions of years without yet saturating 3/11
#DifferentialDiversification can explain long-term trends in body size (Cope's rule) https://www.science.org/doi/10.1126/science.1260065. 4/11
But differential #speciation vs. #extinction can be distinguished only via fossil evidence https://www.nature.com/articles/s41586-020-2176-1 Loss from a #proteome is much easier to infer. 5/11
Extant timetrees are consistent with a myriad of diversification histories - Nature
An infinite number of alternative diversification scenarios—which may have markedly different, but equally plausible, dynamics—can underpin a given time-calibrated phylogeny of extant species, suggesting many previous studies have over-interpreted phylogenetic evidence.
We inferred rates of total loss for each Pfam domain in animals, with co-inference to exclude horizontal gene transfers / false positives. Complete genomes only, checking all 6 reading frames for missing hits. Minimal loss rates match the properties of ancient domains. 6/11
The number of instances of a Pfam within a #genome shows the same trend (shown in last toot). This matches #DifferentialDiversification below, shaping the #evolution of #proteome content via how many paralogous copies a given sequence ends up in. 7/11
Older Pfam domain cohorts show less variance within them. The rate of decline matches that expected from simulations of inferred #DifferentialLoss rates. First time in my career that I was happy to get a small effect size! 8/11
Trends in mean properties as a function of #phylostratigraphy age also match those expected from simulations of inferred #LossRates. 9/11
This process is analogous to #CladeSelection, but way easier to study. #DifferentialDuplication and loss are analogous to differential #speciation and #extinction. We hope this opens up new empirical lines of research into #LevelsOfSelection. 10/11
It's more or less common knowledge that most species that ever lived are now extinct. But it's less recognized that the same is true for #ProteinSequences. For #astrobiology, it's important to remember this when thinking about #AncientLife 11/11
Sage@JoannaMasel Never thought about this! How interesting
New paper published at @molbioevol https://doi.org/10.1093/molbev/msad073. See preprint thread ⬆️⬆️⬆️ for details 12/11
