GEOL2317: Frontiers in palaeontology

Getting up to speed

Before reading this paper you should brush up on some key phylogenetics concepts. Berkley's primer articles are a good place to start; in particular the sections "Evolutionary trees: A primer" and "How to build a tree". The canonical reference for the enthusiastic is Felsenstein's comprehensive Inferring phylogenies (2004).

You should have a loose idea of:

• How fossils are preserved
• Refresher: Taphonomy
• How to read a phylogenetic tree
• Refresher: Baum et al. 2005
• Phylogenetic terminology: stem groups, sister groups, clades, paraphyly…
• Refresher: Higher Classification
• What sorts of data underpin phylogenetic analysis
• How phylogenetic trees are constructed and 'scored'
• How optimal trees are found (or approximated)

Reading the paper

You should use this course as an opportunity to develop the skill of scientific reading. Many people recommend reading only the abstract, introduction and conclusion on a first pass, then looking through the figures, and only then reading the paper in sequence. I have had some success with the "Morse Code method". Discuss techniques with others in your group, and with your demonstrator.

After reading the paper, ask yourself a few questions to see how well you understood it.

• What's the overall topic that the study is trying to address?
• What were the major views on this topic before this work?
• What are the authors trying to argue? What is their evidence?
• What assumptions do the authors make?
• What do you have to assume to get to the results from the conclusions? Do these assumptions hold?
• What aspects of the argument did you find most convincing? Least convincing?
• How did you feel when reading the paper?
• How has the paper moved on our understanding? What new questions does it raise – and what practical implications does it have? How might its results be tested or developed further?

Discussing the paper

In the in-class session, your group and one other will discuss the paper's strengths and weaknesses and implications for the larger question of whether fossils are reliable. Besides reading the paper individually, you might also want to quickly look at some related papers to get a broader context for the work and for how it has been received. Perhaps you could identify three or four key papers as a group, and skim one or two each?

Some easy ways to find related literature are:

• Use Google Scholar to search for the article. Look at the citing articles ("Cited by 123"), or use the "Related articles" link.
• Search for the article in Connected papers. Use the "Prior works" and "Derivative works" links to see a list of previous or subsequent papers related to the article (but not necessarily linked by citations).

Preparation

Your group of three or four will be assigned to argue for or against the motion "Fossils help us to interpret the evolutionary origins of living groups", or to act as ’active listeners‘. Working in groups allows you to sample a broader selection of the literature than you could alone.

As a team, identify a list of papers that look relevant to the question. Dividing these among yourselves, try to understand and then summarise the key arguments on both sides of the debate. What will each team assert, and what are the counter-arguments? What is the strongest evidence in favour of each position? How might this evidence be challenged, and how might these challenges be rebuffed?

Finding papers

• Plenty of ink has been spilt on this topic, and you shouldn't struggle to find arguments on both sides of the topic. But if you get stuck, you may click here to reveal some Google Scholar searches that might point you in the right direction.
• • I would start by searching:
    • Fossils phylogenetic analysis
    • Fossil decay phylogeny
    • missing data phylogeny
    • palaeontological bias evolutionary tree
    • incompleteness phylogeny
  • Suggestions from the demonstrators:

    • AD: I would perhaps start with 'blind' searches perhaps with the terms: fossils enrich; fossil bias; fossils mislead; "fossils are essential to"; fossils inadequate. I would probably follow these search queries with the same terms but with "origin of" (including the "'s which tell google to search for the exact phrase) if the terms did not lead to papers that are pertinent to the question which addresses the evolutionary origins of living groups.

      The title and abstract should be sufficient to figure out if the paper is worth reading at all (many will not be).

      It is also worth considering if the paper you're reading is 'seminal' or at the periphery of a topic. The citation count may indicate this but reading the introduction is useful to gauge similar work, and should cite the most important papers in that sub-field.

    • AB: For either side of the motion, I would think consider an initial case or argument that I could make. For the proposer, I would think “where have fossils been useful”, using a case study as a reference point. My mind would go to “transition fossil”, as these provide a type of evidence unavailable elsewhere. For the opposer, I would reflect on what the/an alternative would be if not fossils, i.e. molecular data. Hence, as an initial reference point I would search for “morphological vs molecular data” (or “fossil vs genetic data”), aiming to find pre-existing literature that makes comparisons from a quality-of-data perspective, and refine terminology as appropriate.

      In both cases, I would also put a general “use of fossils” to see how they are used in studies and what information is derived from them, and consider the case for/against using them from there (again refining as appropriate). A further, perhaps more technical, phrase could be “fossils tree resolution” to see if fossils help with this in particular as this could be relevant for questions of group origins (evidence on both sides).