This document discusses methods for inferring ancestor-descendant relationships among fossil taxa using tip-dating phylogenetic analyses. It summarizes research applying Bayesian tip-dating and other methods to datasets involving trilobites, brachiopods, dinosaurs, and other fossil groups. The results generally support more instances of "budding", where new taxa arise within existing lineages, rather than "anagenesis", where taxa gradually transform over time. The analyses also find many earliest occurrences serving as ancestors to later occurrences of the same morphotaxa.

1. Budding or Anagenesis?
Paraphyly and
Ancestor-Descendant Relationships
from Tip-Dating Phylogenies of
Fossil Lineages
David Bapst & Sandra Carlson
University of California Davis
Evolution 2017 Portland
Sunday, June 25th Feel free to
tweet this talk!
@dwbapst

2. The Question of Ancestors
in the Fossil Record
Fortey and Cooper 1986

3. Morphotaxa in
the Fossil Record
• Often, we find specimens
of varying age with similar
morphology
• We use those features to
define morphotaxa
spanning geologic time
Dicellograptus

4. • Interpret occurrences as a
chain of direct ancestor-
descendant relationships
• Central assumption since the
dawn of paleontology, critical
to biostratigraphy
… and rarely tested
Dicellograptus
The Most Fundamental
Assumption in Paleontology?

5. Maletz & Mitchell (1996)
Qualitative Interpretations of
Ancestor-Descendant Relationships
Among Morphotaxa
Kennett and Srinivasan (1983)
from Pearson (1998)
May Read the Fossil Record Too Literally

6. The problem is, very rarely
can we read the fossil
record as literally as this

7. How do we infer the
relationships among
ancestors & their descendants,
given the incompleteness
of the fossil record?

8. Stratocladistic Methods
Attempted To Make This More Rigorous
Bloch et al., 2001
• Treated implied gaps in
the fossil record as
interchangeable with
character changes under
maximum parsimony
(Fisher, 1991; 1994)

9. Bayesian sampled-ancestor tip-dating
• Infer dated phylogenies under a model of morph
character change, and under a formal model of
diversification and incompleteness of rock record:
the Fossilized Birth-Death Model (Heath et al., 2014)
• Taxa, as point occurrences in time, potentially placed
as sampled-ancestors (Gavryushkina et al., 2014)
Gavryushkinaetal.,2014

10. In The Age Of Ancestor Inference…
Beast2
(PP)
MrBayes
(PP)
cal3
(prop)
Bapst&Hopkins,2017,Paleobio.
(cal3 is an off-brand
tip-dating lite)
• Different methods agree on
placing ancestors [dinosaurs]
• Quantitative inferences agree with
previous putative pairs of
ancestor-descendants [trilobites]
Bapst,Wright,Matzke&Lloyd,2016.Biol.Lett.

11. Static Morphotaxa vs. Points in Time
• Morphotaxa in most fossil-rich groups are not
point occurrences in time (even many dinosaurs have
stratigraphic durations)
• Most studies have treated taxa with durations as a single
occurrence in time, usually earliest (first) occurrence
• Despite FBD assuming every sampled occurrence counted
• What happens with datasets where individual
occurrences are the operational taxon units?
• What happens if we treat individual morphotaxa as
multiple operational taxon units?
Allow us to test for a range of ancestral relationships

12. Anagenesis
‘Budding’
Cladogenesis
Previous analyses find more evidence
for budding (Wagner & Erwin, 1995; Bapst & Hopkins, 2017)
No new morphotypes without branching?
Asymmetry of cladogenetic change?

13. ‘Budding’
Cladogenesis
Anagenesis
Budding evidenced by
paraphyly of occurrences
assigned to same morphotaxon

14. ‘Budding’
Anagenesis
Notice that budding can
look like anagenesis
(but not vice versa)
in an incomplete record

15. Individual Occurrences as
Operational Taxon Units
Hunt, 2007
20 Poseidonomicus species

16. Time (Mya)
Tip-Dating Ostracod Occurrences
3 previously defined
morphospecies are
paraphyletic
(budding!)
12 sampled ancestors
Bapst, in prep.

17. Tip-Dating with
First and Last Occurrences
• A kludge: Duplicate character data for each taxon, put
separate uniform age priors for first and last occurrences
• thus doubling the number of tips
• Genus-level analyses for three groups of mid-Paleozoic
brachiopods: Terebratulides, Pentamerides, and
Stenoscismatoids (Carlson & Fitzgerald, 2008; Carlson, unpub.)
• Wrote R functions for automating and streamlining
creating NEXUS files with MrBayes blocks for tip-dating,
including analyses with empty matrices and topological
constraints
• https://github.com/dwbapst/paleotree

18. Outgroups
MCCT
MCCT for
Devonian
Terebratulides
• 9 paraphyletic
genera among 72
• 21 sampled anc.
(all first occs.
ancestral to last)
How does this
vary across the
posterior?

19. 10-50% of OTUs as Sampled Ancestors
Values Across the Post-Burnin Posteriors
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.

20. About 25% of SA are Last Occurrences:
10-22% Upper Limit on Anagenesis
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.

21. Majority of SA are First Occ. As Ancestors
to Last Occ. (Especially in Pentamerides)
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.

22. Budding (Paraphyletic Taxa) 2-4x More Common
Among Terebratulides and Stenoscismatoids
Terebr: 67 char, 78 gen
Pentam: 65 char, 84 gen
Steno: 30 char, 26 gen Bapst & Carlson, in prep.

23. A New Era of Ancestors on Trees
• Treating fossil morphotaxa as more than single OTUs sheds
light on patterns of ancestor-descendant relationships
• Earliest occurrences are frequently sampled ancestors to
their last occurrence, reaffirming that morphotaxa are often
ancestor-descendant sequences (but maybe not always)
• Budding likely more common than anagenesis:
10-22% of last occ. as SA (= maximum anagenesis), but
paraphyletic taxa mostly as common (= minimum budding)
• Ancestor-descendant relationships varied in pattern
(esp. Pentam. vs other groups)
This research was funded by
NSF grant EAR-1147537.
Thanks for listening! Questions?

26. Gaps in Densely-Sampled
Fossil Records
Maletz and Zhang, 2003; Vandenberg, 2003; C.E. Mitchell
• Closest relatives separated by a 15 to 20 million year gap in
this lineage:
• Were the intermediates living somewhere else? Open ocean?
Bergstromgraptus
Middle Darrwillian
Sinoretiograptus
Latest Katian

27. The Question of Ancestors
in the Fossil Record
?

28. Tip-Dating with Mesozoic Theropods
• We used a somewhat infamous dataset to compare
tip-dating methods with cal3, for ancestor-
descendant relationships, divergence dating,
estimating evolutionary rates, etc...
• Do the methods agree?
• The support for particular taxa to be probable
ancestors were fairly correlated across methods
• So… Is Archaeopteryx really the ancestral bird?
Bapst, Wright, Matzke
& Lloyd, 2016; Biol. Lett.2. Ancestor-Descendants in the Fossil Record
with
April Wright Graeme LloydNick Matzke

29. • Significant rank-order pair-
wise correlations of
ancestral placement
between methods
• Strongest between MrBayes
and BEAST2
• Considerable differences
despite similar model
• Median # of ancestors per
tree for tip-dating = 1-2
• With cal3 (using entire
taxon durations) = 17
• Always buddingBeast2
(PP)
MrBayes
(PP)
cal3
(prop)
Bapst, Wright, Matzke & Lloyd, 2016

30. Whither the Ancestral Bird?
• Archaeopteryx rarely placed as a sampled ancestor
• Never placed as ancestor on lineage leading to
extant birds, but rather as a sampled ancestor to its
sister taxon / possible synonym Wellnhoferia
Bapst, Wright, Matzke & Lloyd, 2016

31. Case 1:
Cambrian pterocephaliid trilobites
• Hopkins (2011) did a cladistic analysis and reviewed
a number of (qualitative) ancestor-descendant
pairs previously suggested for this group
• Does cal3 find support for those pairs, and does it
match the mode inferred by previous authors?
• Apply cal3 to the single maximum-parsimony topology &
100 CONOP solutions from Hopkins (2011)
• Obtained 100 dated phylogenies, quantified support for
a given AD pair as the proportion of trees
Bapst & Hopkins, now in press at Paleobiology!

32. Each pair is a
stacked barplot
Dots indicate
putative pairs
Evidence for all
a priori AD pairs,
& a few extra
cal3 finds very
little support for
anagenesis
Given biases,
perhaps entirely
budding?

33. • Each pair is a
stacked barplot
• Dots indicate
putative pairs
• Support for all
a priori AD pairs,
& a few extra
• cal3 finds very
little support for
anagenesis
• Support for budding
suggests globally
instantaneous origins
of new morphotaxa
2. Ancestor-Descendants in the Fossil Record