Evolution 2012 Talk: When do we Lack Resolvable Clades?

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A talk presenting my work recently published in PLoS One, at the Evolution meeting in 2012, in Ottawa. Examples of morphological differentiation illustrated with colorful pictures of a group known to many.

You can find the published paper here, without the pocket monsters:

Bapst DW (2013) When Can Clades Be Potentially Resolved with
Morphology? PLoS ONE 8(4): e62312. doi:10.1371/journal.pone.0062312

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062312

Obviously all the Pokemon are copyright of Nintendo of America. But how useful pedagogically they were!

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Evolution 2012 Talk: When do we Lack Resolvable Clades?

  1. 1. When Do We Lack Resolvable Clades? Cladogram from Mitchell et al., 2007 Dave Bapst, University of Chicago The Influence of Morphological Differentiation
  2. 2. Studying the Tree of Life We can use molecular information to work out how living lineages are related…
  3. 3. Studying the Dead Branches …paleontologists are tasked with figuring out the relationships of extinct lineages…
  4. 4. Studying the Dead Branches …generally based on incomplete morphological information.
  5. 5. Paleotrees Sometimes Poorly Resolved Majority Rule Consensus Tree with 87 Graptolite Species (94 Characters) 40 observed nodes 86 possible nodes = 46.5% resolved Cladogram from Mitchell et al., 2007
  6. 6. Paleotrees Sometimes Poorly Resolved Majority Rule Consensus Tree with 87 Graptolite Species (94 Characters) 40 observed nodes 86 possible nodes = 46.5% resolved Cladogram from Mitchell et al., 2007 Strict Consensus Trees from 17 Recent Analyses of Fossil Taxa 31 - 97% resolved Mean of 77% resolved
  7. 7. Polytomies in Morphological Trees • Incomplete datasets • Homoplastic characters • Intrinsically unresolvable relationships – Non-dichotomous branching (Maddison, 1989) – Modes of morphological differentiation and the sampling of ancestors • No synapomorphies to further resolve taxa • Norell, 1992; Smith, 1994; Wagner and Erwin, 1995; Lamboy, 1996 • How often should we expect an intrinsic lack of synapomorphies to group taxa?
  8. 8. Polytomies in Morphological Trees • Incomplete datasets • Homoplastic characters • Intrinsically unresolvable relationships – Non-dichotomous branching (Maddison, 1989) – Modes of morphological differentiation and the sampling of ancestors • No synapomorphies to further resolve taxa • Norell, 1992; Smith, 1994; Wagner and Erwin, 1995; Lamboy, 1996 • How often should we expect an intrinsic lack of synapomorphies to group taxa? …Wait, hold on! Let’s review modes of morphological differentiation…
  9. 9. Morphological divergence rapid on geologic timescales in fossil-rich groups • Temporal lineages static in systematic characters When divergence unassociated with branching events (cladogenesis) that differentiation pattern is termed anagenesis
  10. 10. Morphological Differentiation Patterns with Branching Cryptic Cladogenesis • daughter lineages are not immediately morphologically distinguishable
  11. 11. Budding Cladogenesis • where one daughter lineage immediately diverges morphologically from the ancestor. Wagner and Erwin (1995) found support for this particular pattern.
  12. 12. This morphological pattern can create polytomies. To see this, let’s incompletely sample the fossil record…
  13. 13. …and we would distinguish these four morphotaxa. Yet, no further groups can be formed which would share any derived traits to the exclusion of other taxon units.
  14. 14. Not sampling ancestor does not allow for (Vaporeon, Jolteon) clade to be resolved An intrinsically unresolvable clade would persist in the data as long as future descendants of all three are considered
  15. 15. Cryptic cladogenesis produces unresolvable clades similar to budding
  16. 16. Bifurcating Cladogenesis • Both daughter lineages become morphologically distinct and the ancestral morphotaxon does not persist Relationships among ancestor and descendants are polytomy as long as all three are sampled
  17. 17. Intrinsically Unresolvable Clades • Possible negative effect on morph-based studies – Lack of synapomorphies may lead to falsely inferred relationships based on homeoplasy – Unresolved consensus trees or weakly supported nodes • Misinterpreted as homoplastic or inadequate character data
  18. 18. Intrinsically Unresolvable Clades • Possible negative effect on morph-based studies • How often should we expect intrinsically unresolvable clades in real datasets? – Identifying true polytomies difficult to do robustly – Few empirical analyses: Wagner and Erwin (1995) budding over bifurcation and anagenesis
  19. 19. Intrinsically Unresolvable Clades • Possible negative effect on morph-based studies • How often should we expect intrinsically unresolvable clades in real datasets? • Simulations necessary under a broad range of differentiation patterns and sampling regimes necessary to determine extent of phenomenon
  20. 20. Birth-Death Simulations with paleotree • Modeled branching, extinction, anagenesis and sampling events in the fossil record as Poisson processes – R library paleotree (Bapst, in press, Methods in Ecology and Evolution) • Simulate only shifts in morphology, rather than individual traits – Shifts occur at origination of each morphologically differentiated taxon – Taxa descended from each shift denote each resolvable set of taxa (clade) – Ratio of resolvable clades to potential clades is resolvable proportion • 13 Combinations of Modes of Morphological Differentiation – Branching and extinction rates set equal (λ = μ) – Anagenesis rate equal to diversification rates (= λ = μ) or zero – One, two or three cladogenesis modes (with equal probabilities) – Complexes of cryptic lineages always collapsed
  21. 21. Resolvable Proportion of Clades Fully Extinct Clades Complete Sampling 1000 runs, ~100 taxa • With total sampling of fossil record, low resolvability under budding / bifurcation
  22. 22. Resolvable Proportion of Clades Fully Extinct Clades Complete Sampling 1000 runs, ~100 taxa • As expected, lower resolvability when some cladogenesis is cryptic
  23. 23. Resolvable Proportion of Clades Fully Extinct Clades Complete Sampling 1000 runs, ~100 taxa • Also as expected, increase in resolvability with anagenesis (rate same as div rates)
  24. 24. Resolvable Proportion of Clades Fully Extinct Clades Incomplete Sampling Samp Rate = λ = μ 1000 runs, ~100 taxa • At sampling rate analogous to shelly marine invert records, more clades are resolvable but most patterns predict 1/3rd to 1/5th of observed clades to be intrinsically unresolvable
  25. 25. Resolvable Proportion of Clades Fully Extant Clades Complete Sampling at Present-Day 1000 runs, 50-300 taxa No Fossil Taxa • Even with no sampling in the fossil record, well-sampled extant-only morph datasets will have unresolvable clades (except when all branching is via bifurcation)
  26. 26. Additionally… • Some patterns often produce large intrinsic polytomies when long-lived morphotaxa produce many descendants • Unresolvable clades present at all node depths – Evolutionary history cannot erase deep polytomies – Does selectively sampling among higher taxa change this? • High rates of anagenesis or, paradoxically, poor sampling can increase intrinsic resolvability – Under cryptic cladogenesis, almost no observed durations for morphotaxa in datasets with few unresolvable clades
  27. 27. Conclusions • When should we expect intrinsically unresolvable clades in morphological systematics? – At least in groups where morphotaxa are consistently sampled across geologic time – Present in both fossil and extant analyses • Having partially unresolved relationships may be an expected outcome in morph analyses, rather than a symptom of inadequate data – Need analyses to quantify phylogenetic uncertainty Thanks to M. Foote, D. Jablonski, M. Webster, S. Kidwell, M. Pennell, E. King, A. Krug, J. Brown and C. Belanger for comments…And thanks to all the Pokemon!
  28. 28. As rate of anagenesis increases relative to div rates, number of resolvable clades increases but the mean duration of observed taxon ranges drops, no longer reflecting extinction rate. ~600 extinct clades with ~100 sampled morphotaxa
  29. 29. Under very poor preservation (sampling rate = tenth of div rates), some models predict that almost all clades will be resolvable, but not all models of differentiation.
  30. 30. Inferring Relationships from Morphology: Characters Wings Feathers Bones Does not Meta. Flightless Head Crest Pidgeot 1 1 1 1 0 1 Butterfree 1 0 0 0 0 NA Farfetch’d 1 1 1 1 1 0 Dodrio 0 1 1 1 1 1 • Relationships among fossil taxa are pieced together used shared derived morphological features that are shared by only a portion of taxa • These are called synapomorphies • N.B. the lack of three heads is a plesiomorphy
  31. 31. • Well supported clades are taxa that share many characters to the exclusion of other taxa – The set of relationships that infers the least changes is generally taken as the best solution – Many groups often have multiple best solutions Feathers, bones, loss of metamorphisis Wings, Flight Inferring Relationships from Morphology: Using Parsimony
  32. 32. • Relationships that cannot be resolved become non-bifurcating polytomies – Polytomies are generally seen as a failure of the cladistic analysis (not enough information) – For a roote fully-bifurcating tree of N taxa, there would be N-1 nesting clades/nodes Polytomies: A Failure to Infer Relationships? No clear relationships among these three taxa
  33. 33. Could we resolve the relationships if we don’t sample the ancestor?
  34. 34. Four Legs On Fire Electrified Scaly Flameon 1 1 0 0 Jolteon 1 0 1 0 Vaporeon 1 0 0 1
  35. 35. Let’s incompletely sample this record…
  36. 36. …And we might obtain these three morphotaxa.
  37. 37. Four Legs Shellder on Tail Shellder on Head Slowpoke 1 0 0 Slowbro 1 1 0 Slowking 1 0 1
  38. 38. Note, in practice, the indep. acquisition of bipedality and a commensual Shellder would probably cause Slowbro and Slowking to be incorrectly united as sister taxa -The difficulties of defining homology! If we never sampled the ancestor, we would just have a bifurcation.
  39. 39. Four Legs On Fire Electrified Scaly Evee 1 0 0 0 Flameon 1 1 0 0 Jolteon 1 0 1 0 Vaporeon 1 0 0 1
  40. 40. Four Legs On Fire Electrified Scaly Flameon 1 1 0 0 Jolteon 1 0 1 0 Vaporeon 1 0 0 1 We’d have this problem even if we didn’t sample the ancestor!
  41. 41. Pure Budding Sims: 50-60% of the nodes Bifurcating and Anagenesis most resolved
  42. 42. Wagner and Erwin found support for mixture of budding cladogenesis and anagenesis in forams and gastropods. Here, when rates of budding and anagenesis are equal, 65-75% of clades are resolvable. (Apropos of nothing, W&E’s gastropod tree is ~60% resolved.)
  43. 43. As sampling rates INCREASE, proportion of resolvable clades DECREASE in all scenarios Change strongest with bifurcation Thus, expect well sampled groups to be more poorly resolved in fossil record
  44. 44. Budding cladogenesis drops number of resolvable clades in extant-only analyses
  45. 45. Dave Bapst University of Chicago Geophysical Sciences When Do We Lack Resolvable Clades?

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