Download - UC Davis Talk Bapst 05-11-17
From Cambrian Trilobites to Modern Brachiopods:
New Approaches in Phylogenetic Paleobiology
David Bapst, PhD
University of California Davis
It All Starts With Morphology
Bapst et al., 2012, PNAS
Paleontologist relies primarily on morphology for discriminating taxon units and inferring relationships
• In many groups in the fossil record, we find specimens of different geologic age that share identical or very similar morphological features
Morphology, Taxa, Trees
Morphology, Taxa, Trees
• In many groups in the fossil record, we find specimens of different geologic age that share identical or very similar morphological features
• We use those features to define morphospeciesthat can span millions of years, to infer relationships among lineages (phylogenies)
Systematic Paleontology
• Code taxa for discrete morphological traits (characters)
• Cladistic analyses use maximum-parsimony methods, which attempt to find cladograms (undated trees) implying the fewest character changes
• More generally, we refer to evolutionary trees as phylogenies, particularly if they are dated trees
• Taxa closer together on a cladogram share more traits
~0.5 mm
Maletz
and
Zhan
g, 20
03
; C.E. M
itchell
Phylogenies let us Answer Questions
• When do new species or lineages first evolve?
• Which species are ancestors and which are descendants?
• If organisms have similar morphologies, is that similarity due to a shared evolutionary history?
• Or does shared morphology reflect similarities in ecology and function?
These questions are key to understanding the history of life
New Approaches to Phylogenetic Paleobiology
1. Use combined molecular and morphological datasets in living brachiopods to determine which dataset better reflects evolutionary history
2. Reconstructing relationships between direct ancestors and their descendants across the tree of life
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, 20
09
; S.J
. Car
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New Approaches to Phylogenetic Paleobiology
1. Use combined molecular and morphological datasets in living brachiopods to determine which dataset better reflects evolutionary history
2. Reconstructing relationships between direct ancestors and their descendants across the tree of life
Imag
e So
urc
e: G
on
, 20
09
; S.J
. Car
lso
n
Convergence: When Morphological Similarity Misleads Us
Maletz and Zhang, 2003
~0.5 mm
1. Combined Data Phylogenetics in Rhynchonellids
Mitchell, 1991
Silurian
Ordovician
~0.5 mm
1. Combined Data Phylogenetics in Rhynchonellids
Testing Morphological Phylogenetics
• For most fossil groups, we are forced to assume features reflect shared evolutionary history (homology)
• Test the reliability of morphology-based phylogenies by comparing to independent molecular data for extant taxa• Two datasets will infer incongruent phylogenies, if one or both
datasets have poor phylogenetic signal
• A fossil-rich group with extant diversity:• Rhynchonellida: 19 living genera (500+ extinct genera)
• Important to understand morphology to place extinct lineages
1. Combined Data Phylogenetics in Rhynchonellids
Rhynchonellida• Articulated brachiopods with spirolophe lophophores
supported on crura, features of which are considered important to systematics of the group
• 10/19 extant genera live at bathyal or abyssal depths and are difficult to collect
Crura
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1. Combined Data Phylogenetics in Rhynchonellids
Hard to visualize how these differ… let’s look at tanglegrams
Note: All topologies in this section 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
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1. Combined Data Phylogenetics in Rhynchonellids
Morphology(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Morphology(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Scattered Superfamilies
Why Phylogenetic Analyses Disagree
• Differences in character data used (molecular & morphology)
• Differences in taxa included
• Differences in outgroups used for rooting
1. Combined Data Phylogenetics in Rhynchonellids
Outgroups Determine Where We Root Trees
• Phylogenetic analyses need to include more than just the group of interest (the ingroup taxa)
• Need to include ‘outgroup’ taxa that are strongly assumed to outside the ingroup to give directionality (‘rooting’ the tree)
Mitchell et al., 2013
Outgroups
Root
Trees have no directionalitywithout a root
1. Combined Data Phylogenetics in Rhynchonellids
Morphology(56 Characters, Reweighted Parsimony MPT)
Schreiber et al. 2013
18S and 28S rDNA(3435 base pairs, Bayesian)
Cohen & Bitner 2013
• Revise morphological data to include all rhynchonellides that we have rDNA data for
• Use non-rhynchonellide outgroups• Compare molecular and morphological analyses
using a standardize dataset
Bapst, Schreiber & Carlson, in press, Syst. Biol.1. Combined Data Phylogenetics in Rhynchonellids
with Sandy Carlson & Holly Schreiber
Is incongruence due to differences in character data?
18S and 28S rDNA(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Revised Morphological Matrix (66 characters, Bayesian)
This Study
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
InarticulateBrachiopods
Terebratulids
Rhynch.
Morphology-only analyses don’t even distinguish the rhynchonellides and the
terebratulids as separate clades
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
18S and 28S rDNA(3435 base pairs, Bayesian)
Cohen & Bitner 2013
Revised Morphological Matrix (66 characters, Bayesian)
This Study
InarticulateBrachiopods
Rhynch.
Terebratulids
• Which dataset carries the most signal of shared evolutionary history?
• What if the two datasets both have hidden support for a third alternative topology?
• We can answer both by combining our morphological and molecular datasets, and analyzing them simultaneously
Why do the datasets still disagree?
Bapst, Schreiber & Carlson, accepted with revisions, Syst. Biol.1. Combined Data Phylogenetics in Rhynchonellids
Quantitative Phylogenetic Methods• Maximum Parsimony (PAUP)
• Bayesian (MrBayes)• Model-based phylogenetics, uses likelihood and prior
probability distributions to sample topologies via an MCMC
• Treat different data types as distinct partitions• Same model of sequence change as Cohen & Bitner 2013
• Two morph model configurations: (1) relaxed assumptions, versus (2) strict assumptions, to maximize information content
• Unlike maximum-parsimony which counts character changes, Bayesian phylogenetics depend on likelihood of character data, not directly connected to differences in # of characters
• Applied both to combined datasets, all taxa versus only those taxa with rDNA
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
Quantitative Phylogenetic Methods• Maximum Parsimony (PAUP)
• Bayesian (MrBayes)• Model-based phylogenetics, uses likelihood and prior
probability distributions to sample topologies via an MCMC
• Treat different data types as distinct partitions• Same model of sequence change as Cohen & Bitner 2013
• Two morph model configurations: (1) relaxed assumptions, versus (2) strict assumptions, to maximize information content
• Unlike maximum-parsimony which counts character changes, Bayesian phylogenetics depend on likelihood of character data, not directly connected to differences in # of characters
• Applied both to combined datasets, all taxa versus only those taxa with rDNA
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
…adds up to 12 analyses! How to compare?
Summarizing phylogenetic analyses often results in polytomies
• When character data equally support multiple hypotheses of relationships, analyses return multiple trees, which can be very large
• Summary trees collapse those areas of uncertainty as nodes that aren’t fully bifurcating
• Referred to as polytomies, or a loss of phylogenetic resolution
Mit
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al.,
201
3
1. Combined Data Phylogenetics in Rhynchonellids
So We Invented A New Measure…
• A measure to quantify how different two summary trees are
• Most metrics treat polytomiesin summary trees as a difference, even though polytomies reflect uncertainty
• Contradiction difference (CD) simply measures incongruence between two summary trees
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
Pairwise Contradiction Difference
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
• Values at one mean trees have no similarity
• Values at zero mean trees have no disagreement
Pairwise Contradiction Distance
The original molecular and morphological analyses produced completely contradictory trees
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
18S and 28S rDNA(3435 base pairs, Bayesian)
Reanalysis in this Study
Combined DatasetsMrBayes, Maximum Information
Shared Taxa Only
Molecular-Only Agrees With Morphology+Molecular
CD = 0.06
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
Revised Morphological Matrix (66 characters, Bayesian)
Combined DatasetsMrBayes, Maximum Information
CD = 0.31
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
Morphology-Only disagrees with Morphology+Molecular
Poor Phylogenetic Signal of Morphological Data Implies Convergence
• Bayesian morphological+molecular analyses were all congruent with each other and the molecular-only tree
• Morphology-only analyses, across different methods and sets of taxa, disagreed with each other
1. Combined Data Phylogenetics in Rhynchonellids
If the molecular-only and morphological+molecular analyses are right, are there any morphological characters that are good indicators of relatedness?
• Calculate consistency indices for each character
• Characters that vary within the Rhynchonellida all have lots of convergence when mapped on the tree from the molecular-only analysis• Including characters
classically used to distinguish traditional taxonomic groups
Classic diagnostic traits for taxa within Rhynch.
Characters for distinguishing articulate and inarticulate taxa
Remainder
More Informative
Mis
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g D
ata
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
Not the Same Story for Short-Loop Terebratulids
Molecular Only Analysis(2574 Sites, Bayesian)
Morphology Only Analysis(85 Characters, Bayesian)
1. Combined Data Phylogenetics in Rhynchonellids Carlson, Bapst & Schreiber, in prep.
Could fossil data improve Rhynchonellide Relationships?• Code large number of fossil taxa within Rhynchonellida to
more finely reconstruct evolutionary lineages and resolve the appearance of convergence across modern groups
1. Combined Data Phylogenetics in Rhynchonellids Bapst, Schreiber & Carlson, Syst. Biol.
Want to read more?
This just out…
New Approaches to Phylogenetic Paleobiology
1. Use combined molecular and morphological datasets in living brachiopods to determine which dataset better reflects evolutionary history
2. Reconstructing relationships between direct ancestors and their descendants across the tree of life
2. Ancestor-Descendants in the Fossil Record
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The Question of Ancestors in the Fossil Record
?
The problem is, very rarely can we read the fossil record as literally as this
How do we infer the relationships among ancestors & their descendants,
given the incompletenessof the fossil record?
The Effects of UnsampledLineages In the Fossil Record
• Incompleteness of the rock record means we don’t observe all taxa during all intervals
• Limits our ability to reconstruct precisely when lineages originated, and what the relationships are between morphotaxa
• Are some morphotaxa ancestral to other morphotaxa?
2. Ancestor-Descendants in the Fossil Record
Maletz & Mitchell (1996)
Qualitative Reconstructions of Ancestor-Descendant
Relationships
Kennett and Srinivasan (1983) from Pearson (1998)
2. Ancestor-Descendants in the Fossil Record
Inferring Ancestors in Stratocladistics
Bloch et al., 2001
2. Ancestor-Descendants in the Fossil Record
• Stratocladistic methods treat implied gaps in the fossil record as interchangeable with morphological changes under maximum parsimony (Fisher, 1991; 1994)
• Need formal model of diversification and incompleteness in the fossil record to calculate likelihood of stratigraphic gap of a given duration
Three-Rate Calibrated Time-Scaling (cal3)• Takes an existing undated cladogram, sample potential
divergence dates for nodes under a likelihood function of diversification and incompleteness of the fossil record
• Treats taxa as persistent morphotaxa, allowing for different types of ancestor-descendant relationships based on the overlap of their stratigraphic durations
• Created and implemented in paleotree for R (Bapst, 2012)
cal3
2. Ancestor-Descendants in the Fossil Record Bapst, 2012; Bapst, 2013; Bapst, 2014
‘Budding’ Cladogenesis
Anagenesis
Modes of Differentiation
2. Ancestor-Descendants in the Fossil Record
Notice that budding can look like anagenesis (but not vice versa)
in an incomplete record
Anagenesis
2. Ancestor-Descendants in the Fossil Record
‘Budding’
Ancestor-Descendant (AD) Relationships in Cambrian pterocephaliid trilobites
• Hopkins (2011) reviewed qualitative ancestor-descendant pairs previously suggested for this group
• Does cal3 find support for those pairs, and does it match the mode inferred by earlier studies?
• Apply cal3 to the cladistic analysis from Hopkins (2011)• Obtain 100 dated phylogenies, quantify support for a given
AD pair as the proportion of trees on which that pair is inferred
Bapst & Hopkins, 2017, Paleobio.
with Melanie Hopkins
2. Ancestor-Descendants in the Fossil Record
• Each pair is a stacked barplot
• Dots indicate putative pairs
• Support for alla priori AD pairs, & a few extra
• cal3 finds very little support for anagenesis
• Support for budding suggests globally instantaneous origins of new morphotaxa
Bapst & Hopkins, 2017, Paleobio.2. Ancestor-Descendants in the Fossil Record
Bayesian sampled-ancestor tip-dating• Infer dated phylogenies from character and stratigraphic
data simultaneously in a Bayesian MCMC, under likelihood models for morphological change and the fossilized-birth-death model (Heath et al., 2014)
• Taxa are instantaneous points but can be placed as sampled-ancestors (Gavryushkina et al., 2014)
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2. Ancestor-Descendants in the Fossil Record
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
withApril Wright Graeme LloydNick Matzke
• 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
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 itssister taxon / possible synonym Wellnhoferia
Bapst, Wright, Matzke & Lloyd, 2016
Individual Occurrences as Operational Taxon Units
Hunt, 2007
20 Poseidonomicus species
Time (Mya)
Tip-Dating Ostracod Occurrences
3 previously defined morphospecies are paraphyletic (budding!)
12 sampled ancestors
Outgroups
MCCT
Tip-Dating with FADs and LADs• Ancestors among
Devonian TerebratulideBrachiopods?
• 9 paraphyletic genera among 72 in-group taxa
• 21 sampled ancestors (FADs ancestral to LADs)
FAD = First Appearance DatumLAD = Last Appearance Datum
A New Era of Paleo-Phylogenetics
Thanks for listening! Questions?
• The rapid development and deployment of new methods allows us to leverage phylogenies to better understand evolution in deep time
• Bayesian phylogenetics allows us to model the potential complexities of morphological evolution
• Methods like cal3 and tip-dating take into account what we know about incompleteness of the rock record, and likely existence of ancestral taxa to create dated phylogenies from the fossil record
This research was funded by NSF grant EAR-1147537.
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?
BergstromgraptusMiddle Darrwillian
SinoretiograptusLatest Katian
Branching Times from Time-Scaled Phylogenies
Lloyd, Bapst, Friedman& Davis, 2016 Biol. Lett.
cal3 and a non-parametic dating method agree: accounting for incompleteness of their records, dinosaurs likely diverged millions of years earlier than suggested by the fossil record
2. Ancestor-Descendants in the Fossil Record