Project notes 2024

name	project
Alissa	Do fossil ages improve trees impacted by taphonomic biases?
Christian	Constraining the evolution of photosynthetic pathways (CAM)
Jordan	Assessing the impact of taxon sampling on PCMs
Katie	Redating the origins of horseshoe crabs - implications for habitat transitions
Matias	The impact of model choice on the phylogenetic history of sabre tooth tigers
Max	The impact of model choice on the phylogenetic history of spinosaurs
Meghan	A simulation pipeline for assessing the impact of clock model violation
Victoria	Constraining the evolution of manatees

Status update

Alissa

• Does fossil age information “prevent” stemward slippage?
• https://www.nature.com/articles/nature08745 (data not available)
• Try getting data from here: https://royalsocietypublishing.org/doi/full/10.1098/rspb.2023.0333
  • Suggest selecting one representative per extant taxa
• Status update: investigating the data

Christian

• Aim: to date the evolution of photosynthetic systems
• Inspiration: https://www.nature.com/articles/ng.3435 (see Fig. 3a)
• Unclear whether the data is readily available from this paper
• Note gene trees distinct from the species tree
• Some papers on dating gene / genome duplication:
  • https://royalsocietypublishing.org/doi/10.1098/rspb.2017.0912
  • https://www.sciencedirect.com/science/article/pii/S1360138518301596
• Try this paper for CAM gene IDs and trees:
  • https://link.springer.com/article/10.1007/s13258-022-01263-8
• Update: not related to photosynthesis! (the genes are called CaM, but they’re not part of the CAM pathway) But we’ll move forward with this data anyway!
  • Note the sequence data isn’t provided in the supplement but we’ll just pick 15 accession number!

Jordan

• Ichthyosaurs

• Aim: switching from the impact of branch lengths on PCMs to taxon sampling (e.g., taxon from different environments)

• Data: https://www.science.org/doi/10.1126/science.abf5787

• Some other inspiration: https://royalsocietypublishing.org/doi/epdf/10.1098/rspb.2017.0546

• Status update: trying to reproduce the PCM output / run the scripts from the previous study

Katie

• Horseshoe crabs

• Aim: Rebuild the trees: what are the implications for habitat transitions

• getting age data; later revisit how to incorporate long ranging taxa

• Analysis running!

• Status update: constant rate analysis looks good but skyline didn’t converge

• Next: simplify the skyline set up - vary psi only, compare trees

Matias

• Sabre tooth tigers

• Do models change the previously inferred topology?

• Matrix available here: https://onlinelibrary.wiley.com/doi/full/10.1111/cla.12008 (but only in the PDF)

• Suggest checking papers that have cited this one, to see if anyone has used (or extended) the same matrix

• Status update: going through the set, using Laura’s tutorial as a guide

Max

• Spinosaurs (or broader)

• Do models change the previously inferred topology?

• Run the analysis under different models - done!

• Issue running model adequacy - resolved

• Next steps: compare trees, use model adequacy to select the best model

Meghan

• Simulations to investigate the impact of clock model misspecification (partitions simulated under different rates)

• Option: simulate morphological partitions under different rates

• Check out papers by Simon Ho

• Note: to simulated characters under a clock model you need to transform branches = time into branches = rate x time

• Simclock: https://github.com/dosreislab/simclock

• Status update: workflow established

• Next: inference using multiple replicates

Victoria

• Reconstructing an evolutionary timeline for Sirenians (manatees / dugongs)
• https://www.sciencedirect.com/science/article/pii/S0895981121001231
• In the process of getting age data
• Age data data obtained. FBD set up in progress!
• -> FBD analysis is complete!
• Next: compare to existing trees, examine distribution of traits
• ASR?