Talk given at Evolution 2016 in Austin

1. Combined Analysis of Extant
Rhynchonellida (Brachiopoda) Using
Morphological and Molecular Data
David Bapst
Sandra J. Carlson
Holly A. Schreiber Feel free to
tweet this talk!
@dwbapst

2. Systematics in Paleontology
• Limited to morphological features (almost always)
• Assumes shared morphology reflects shared evolutionary
history (homology)
• But how reliable is that assumption? When is it wrong?
• We know any type of character data can be misleading
• One way to consider reliability of morphology is
compare to independent molecular data for extant taxa
• A fossil-rich group with extant diversity:
• Rhynchonellida: 19 living genera (500+ extinct genera)
• Morphology important to place extinct lineages

3. Rhynchonellida
• Articulated brachiopods with spirolophe lophophores
supported on crura
• 10/19 extant genera live at bathyal or abyssal depths
and are difficult to collect
Crura

4. Compare with tanglegrams via R package phytools
Note: All topologies in this talk are single MPTs
or majority-rule / half-compat summaries
Morphology
(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA
(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Rhynchonellida

5. Morphology
(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA
(3435 base pairs, Bayesian)
Cohen & Bitner 2013

6. Morphology
(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA
(3435 base pairs, Bayesian)
Cohen & Bitner 2013

7. Morphology
(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA
(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Scattered
Superfamilies

8. Differences in:
• Taxonomic coverage
• Outgroups used for rooting
What if we revise the morphological data to include
all rhynchonellides that we have rDNA data for,
and use non-rhynchonellide outgroups?
Revised codings and added ten more characters
Whither Incongruence?

9. • But what about just combining the two datasets?
• Maybe it would support one topology or the other
• Maybe it would find third alternative topology
Whither Incongruence?

10. Phylogenetic Analyses
• Maximum Parsimony (PAUP)
• Unweighted / Equally Weighted
• Bayesian (MrBayes)
• Same model of sequence change as Cohen & Bitner 2013
• Two configurations for morph where we
A. relaxed assumptions
B. made very strict assumptions, to maximize information content
• Combined analyses & with new morph matrix only
• Variants with different sets of taxa (all possible versus
only those with rDNA data from Cohen & Bitner)

11. Phylogenetic Analyses
• Maximum Parsimony (PAUP)
• Unweighted / Equally Weighted
• Bayesian (MrBayes)
• Same model of sequence change as Cohen & Bitner 2013
• Two configurations for morph where we
A. relaxed assumptions
B. made very strict assumptions, to maximize information content
• Combined analyses & with new morph matrix only
• Variants with different sets of taxa (all possible versus
only those with rDNA data from Cohen & Bitner)
…adds up to 12 analyses! How to compare?
(Not to mention with original studies)

12. Contradiction Distance
• Compare summary trees, but polytomies count as
differences in most metrics (e.g. Robinson-Foulds).
• Want to know how much two trees actively contradict
𝐶1 = 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑆𝑝𝑙𝑖𝑡𝑠 𝑖𝑛 𝑇1 𝐶𝑜𝑛𝑡𝑟𝑎𝑑𝑖𝑐𝑡𝑒𝑑 𝐵𝑦 𝑇2
𝐶2 = 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑆𝑝𝑙𝑖𝑡𝑠 𝑖𝑛 𝑇2 𝐶𝑜𝑛𝑡𝑟𝑎𝑑𝑖𝑐𝑡𝑒𝑑 𝐵𝑦 𝑇1
𝐶𝐷12 =
𝐶1 + 𝐶2
2 ∗ (𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑠ℎ𝑎𝑟𝑒𝑑 𝑡𝑖𝑝𝑠 − 2)
• Disagreement between two topologies is fraction of
total possible splits that could disagree, across both
• CD between star tree and fully resolved tree is 0
• CD between two completely contradictory topologies is 1

13. Pairwise Contradiction Distance
Yikes!

14. Pairwise Contradiction Distance
Not surprising…

15. Three Takeaways
• Morph-only analyses disagree with each other, but
all agree with the Bayesian morph-only analysis (a
poorly-resolved ‘compromise’)

16. 18S and 28S rDNA
(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Revised Morphological Matrix
(66 characters, Bayesian)
This Study
CD = 0.41

17. 18S and 28S rDNA
(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Revised Morphological Matrix
(66 characters, Bayesian)
This Study
CD = 0.41
The morph-only analyses aren’t even sure
if the Rhynchonellida is monophyletic

18. Three Takeaways
• Morph-only analyses disagree with each other, but
all agree with the Bayesian morph-only analysis (a
poorly-resolved ‘compromise’)
• Bayesian combined analyses and molecular
analyses had little disagreement among them

19. 18S and 28S rDNA
(3435 base pairs, Bayesian)
Reanalysis in this Study
Combined Analysis
MrBayes, Maximum Information
Shared Taxa Only
 Mostly Agrees with Molecular-Only
CD = 0.06

20.  Disagrees with Morph-Only Topology
Revised Morphological Matrix
(66 characters, Bayesian)
Combined Analysis
MrBayes, Maximum Information
CD = 0.31

21. Three Takeaways
• Morph-only analyses disagree with each other, but
all agree with the Bayesian morph-only analysis (a
poorly-resolved ‘compromise’)
• Bayesian combined analyses and molecular
analyses had little disagreement among them
• Maximum-parsimony combined analyses produced
their own unique topologies, discordant with the
morph-only analyses and the Bayesian combined
analyses

22. So, the molecular signal wins in the
combined analysis…
•But how much of this is due to having
53 times more molecular characters
than morphological?
•Need sensitivity analyses to test if
partition size matters…

23. 1. Repeat morph characters 53 times so
partitions are roughly equal in size
…Won’t converge in MrBayes
Sensitivity Analyses

24. Sensitivity Analyses
2. Simulate 66 binary characters on morph-only
MP majority-rule consensus, with single
transitions, creating data with no homoplasy
• Maximum support possible for morph-only tree
• Recombine with molecular data—which wins?
Actual Data
Bayesian
Combined Analysis
Simulated Data
Almost identical to Bayesian combined/mol trees
CD = 0.25

25. Effect of Missing Data?
• Many of the
differences among
combined analyses
and molecular-only
analyses involve
placement of
Cryptopora and
Acanthobasiliola
• Among the highest in
missing/deleted base
pairs in rDNA data

26. Conclusions
• Morph-only analyses contradicted each other
• Molecular-only and (Bayesian) combined analyses were
congruent with each other
• Sensitivity analyses suggest large size of molecular
partition may be controlling factor
• Still, small number of morph chars did impact the much
larger molecular dataset in combined analyses
• Impacted taxa also missing much of their molecular data
• Is noisy signal of morph data due to long branches?
• Code large fossil taxa within Rhynchonellida crown to test
This research was funded by NSF 1147537.
We thank A. Wright and P. Smits for discussion.

27. Consistency Indices for Morph Data
• CI using Bayesian combined
analysis topology
a) Classic diagnostic traits for
taxa within Rhynch.
b) Characters for
distinguishing articulate
and inarticulate taxa
c) Remainder
• Among the remainder, the
high CI associated with
characters with missing
data