What else is out there?

[HAL 2.1] To What Extent Current Limits of Phylogenomics Can Be Overcome?

Concept flowchart

Phylogenomic pipeline (HAL 2.1)

What do we know now?

• Motivation: phylogenomics pipeline
  • Reading: HAL 2.1
• Intro Illumina, quality control, assembly, alignment, filtering
• Alignment
  • Reading: HAL 2.2, ClustalW, MUSCLE, T-coffee papers
  • Software: T-coffee, Clustal, Muscle
• Orthology detection
  • Reading: HAL 2.4, Nichio 2017
  • Software: Many options in class google slides!
• Overview of phylogenetic inference: criteria score, search in tree space
• Gene tree estimation
  1. Distance methods
     • Reading (supplemental): HB Ch 5, Baum Ch 8
     • Software: R packages ape, phangorn
  2. Parsimony methods
     • Reading (supplemental): HB Ch 8, Baum Ch 7
     • Software: R packages ape, phangorn
  3. Models of evolution
     • Reading: HAL 1.1
  4. Maximum likelihood
     • Reading: HAL 1.2, RAxML and IQ-Tree papers
     • Software: RAxML (HAL 1.3) and IQ-Tree
  5. Bayesian
     • Reading: HAL 1.4, Mascimento 2017, MrBayes papers
     • Software: MrBayes (HB Ch 7)
  6. Model selection (invited guest: Rob Lanfear developer of IQ-Tree)
• Species tree/network estimation: the coalescent model
  • Reading: HAL 3.1, 3.3, ASTRAL and BUCKy papers
  • Software: PhyloNetworks wiki pipeline (MDL, RAxML, MrBayes, BUCKy, ASTRAL, SNaQ)
• Co-estimation methods
  • Reading: BEAST papers
  • Taming the BEAST slides

Main conclusions

• Phylogenomics is hard
• Importance of data quality and phylogenetic signal
• Importance of clear description of methods used, assumptions and limitations
  • Make sure that you know (in general) what the method you are using does
• Importance of model selection and model fit
• Importance of measures of confidence
  • No desperate quest for 100 bootstrap support values!
• Importance of reproducibility
  • Every choice matters, so keep good track of the choices

Good news

• This was not the class to make you all experts in phylogenetics
• Class notes are publicly available on github forever
• Upcoming: lecture YouTube videos publicly available (Spring 2024)
• You have now your own notes in your personal github repository
• You can continue to have support from phylogenetics student community in slack (if you choose to remain in the workspace)

Jermiin et al 2020

What else is out there?

• Dating
  • Reading: HAL 5.1
  • Supplemental reading: HB Ch 11
  • Bayesian dating: Bromham 2017
  • Software
    • RevBayes
      • HAL 5.2
      • Workshop
      • Tutorial
    • DivTime
    • BEAST
• Reconciliation
  • Reading: HAL 3.2
• Species delimitation
  • Reading: HAL 5.5
  • Software:
    • BPP: HAL 5.6
    • iBPP (morphology and genes): https://github.com/cecileane/iBPP
• SNP methods
  • SVDquartets
  • SNAPP
  • SNAPPnet
  • PhyloNet

Final housekeeping

• Project deadline: May 6th
  • Final project
  • Reproducible script
  • Project guidelines
• Presentations: Apr 30 and May 2
  • 7-minute presentations (very strict!)
  • Please send me your slides at 12pm (or earlier) on the day you are presenting
• Official student evaluations
  • Forward me the email by May 6th to receive HW credit
• Class feedback google form (link on canvas and slack)
  • Highly appreciated
  • Less than 5 minutes to respond
• Advice for future students: slides