Phylogenetic Congruence between Cranial and

Postcranial Charactersin Archosaur Systematics

Ross Mounce and Matthew Wills

rcpm20@bath.ac.uk @rmounce #SVP2011

Introduction

Total Evidence sensu Carnap (1950)

The strongest test of a phylogenetic hypothesis is

provided by the comparison of multiple lines of

independent evidence

Example Data Partitions

Molecular data

+

Morphological data

Example Data Partitions

Molecular data[nuclear genes]

[mitochondrial genes][coding and non-coding]

+

Morphological data

Motivation

“It is commonly believed that there are differences in the evolutionary lability of the crania, dentition, and postcrania of mammals”

(Sanchez-Villagra & Williams, 1998)

“...postcranial characters either from the vertebral column or fins are considerably less used in phylogenetic analyses of lower actinopterygians”

(Arratia, Acta Zoologica 2009)

Generally, there are more cranial characters in real data matrices

> 60% of vertebrate characters are cranial*

* Based upon a stratified sample of 120 datasets across all Vertebrata, published between 2001-2011, excluding matrices that were either 100% cranial or postcranial

But there are some groups that significantly differ from this overall trend e.g. studies of:

Aves, and Sauropods

Alcober 2010 DinosauriaAllain 2008 SauropodsBrusatte 2010 TyrannosaursBurns 2011 AnkylosaursButler 2008 OrnithischiaButler 2011 OrnithischiaCarballido 2010 SauropodsCarrano 2008 CeratosaursCarr 2010 TyrannosaursChoiniere 2010 Theropods Chure 2010 SauropodsCruzado-Caballero 2010 HadrosaursEddy 2011 AllosauroidsEzcurra 2007 CoelophysoidsEzcurra 2010 AbelisauroidsGallina 2011 SauropodsGates 2007 HadrosaursGodefroit 2008 HadrosaursLongrich 2010 CeratopsidsLu 2009 PterosaursLu 2010 Sauropods (basal)Makovicky 2010 OrnithomimosaursMannion (Wilson) 2011 SauropodsMartinez 2009 SauropodomorphsMartinez 2011 DinosauriaMcDonald 2010 IguanodontsMo 2010 Sauropods

Nesbitt 2011 ArchosaursOrtega 2010 TheropodsOsi 2009 AnkylosaursPol 2011 SauropodomorphsPrieto-Marquez 2010 HadrosaursRauhut 2010 TheropodsRiga 2009 SauropodsRowe (Wilson) 2011 SauropodsRowe (Yates) 2011 SauropodsSampson 2010 ChasmosaursSereno 2008 TheropodsSmith 2007 SauropodomorphsSues 2009 HadrosaursSuteethorn 2010 SauropodsTaylor 2009 SauropodsTaylor 2011 SauropodsWhitlock 2011 DiplodocoidsWilson 2002 SauropodsWilson (Wilson) 2009 SauropodsXu 2010 CeratopsidsXu 2011 OrnithomimosaursYates 2007 SauropodsYates 2010 SauropodsYates 2011 SauropodsZaher 2011 SauropodsZanno 2009 CoelurosaursZanno 2011 Troodontids

First Author, Year of Publication, Scope First Author, Year of Publication, Scope

Which is set is most homoplasious?

There is a difference, but it is NOT statistically significant

Furthermore, this 'test' is unsound, as number of characters (as a variable) has a known negative effect on CI

[Klassen et al, 1991]

CI is not an appropriate statistic to compare between datasetsArchie's (1989b) Homoplasy Excess Ratio (HER) is better,

BUT it has problems associated with high levels of missing data

Cranial Postcranialor

Mean CI = 0.587 Mean CI = 0.563for

N = 50

0 50 100 150 200 250 300 350 400 450

0.000

0.100

0.200

0.300

0.400

0.500

0.600

0.700

0.800

0.900

1.000

f(x) = -0.0006274738x + 0.6109492765R² = 0.1635139213

The Consistency Index is not a good statistic for use in comparative cladistic studies

Co

nsiste

ncy In

dex (C

I)

1.0

0

0 Number of Characters in the (Whole) dataset 450

N (datasets) = 163

Incongruence Length Difference

Out 000000000 000000000A 001110011 000000011B 001110000 000001100C 001100011 000111111D 110000000 001111100E 110001101 111111101F 110001100 111111100

Out 000000000 A 001110011 B 001110000 C 001100011 D 110000000 E 110001101 F 110001100

Out 000000000A 000000011B 000001100C 000111111D 001111100E 111111101F 111111100

L=25L=11

L=12ILDvalue = 25 – (11 + 12) = 2

Combined - Separate

(Mickevich & Farris, 1981)

Determining the significance of ILD

Out 000000000 000000000A 001110011 000000011B 001110000 000001100C 001100011 000111111D 110000000 001111100E 110001101 111111101F 110001100 111111100

Cranial | Postcranial

Out 000000000 000000000A 001110011 000000011B 001110000 000001100C 001100011 000111111D 110000000 001111100E 110001101 111111101F 110001100 111111100

Out 000000000 000000000A 001110011 000000011B 001110000 000001100C 001100011 000111111D 110000000 001111100E 110001101 111111101F 110001100 111111100

Out 000000000 000000000A 001110011 000000011B 001110000 000001100C 001100011 000111111D 110000000 001111100E 110001101 111111101F 110001100 111111100

Randomized partition 1

Random. Partition 2 … Random. Partition 999

4 3 2 1 00

50

100

150

200

250

300

350

400

450

ILD

ILD = 2 ILD = 1

ILD = 1 ILD = 3

Cran | Post

(Farris et al, 1995a,b)

Significant ILD p-values

Key:

ILD p-values less than 0.050 are generally

considered to indicate SIGNIFICANT

incongruence between the data partitions

being tested.(Cranial | Postcranial)

* 999 random reps, heuristic search, TBR-swapping, maxtrees 10000, hold 1000, RAS 10

Nesbitt 2011 Archosaurs 0.003Ezcurra 2007 Coelophysoids 0.005Martinez 2011 Dinosauria 0.014Makovicky 2010 Ornithomimosaurs 0.026

Chure 2010 Sauropods 0.001Allain 2008 Sauropods 0.005Wilson 2002 Sauropods 0.007Wilson 2009 Sauropods 0.014Mannion 2011 Sauropods 0.016Zaher 2011 Sauropods 0.023Carballido 2010 Sauropods 0.024Taylor 2011 Sauropods 0.034Suteethorn 2010 Sauropods 0.035Taylor 2009 Sauropods 0.036Mo 2010 Sauropods 0.067

Incongruence Relationship Difference

To cut what would otherwise be a long story short... it's like the ILD test

…but instead of measuring difference in length (steps)

Topological difference (between cladograms) is measured quantitatively using tree-2-tree distances and

compared to the distance between cladograms from randomly generated partitions (of the same size).

e.g. Symmetric Difference (Robinson-Foulds distance) Agreement Subtrees (AgD1, Goddard, 1994)

Subtree Prune and Regraft distance (e.g. Wu, 2008)

(a new randomization-based method, Mounce & Wills, in prep.)

The IRD test results: complicated

IRD(RF) significance p-values

ILD significance p-values

The IRD(RF,majrule) results appear to show even more sig. incongruence

An example, using data from Chure et al, Naturwissenschaften, 2010

Tanglegram visualization produced using Dendroscope 3, Huson & Scornavacca (2011)

14 MPTs104 MPTs

Visualising Taxonomic Overlap

Created using http://namesonnodes.org/ by T. Michael Keesey

Wilson02 1 0 0 0 0 0 1Harris06 0 0 1 1 1 0 0You08 0 0 1 1 1 0 0Taylor09 0 1 1 1 1 0 0Mo10 0 1 1 1 1 1 0Suteethorn10 1 0 0 0 0 0 1Taylor11 0 1 1 1 1 0 0Mannion11 1 0 0 0 0 0 1

Using presence/absence of taxa as 'characters' to optimize

Neuquensaurus

Xenoposeidon

Neuquensaurus

Limaysaurus

Rayososaurus

Suuwassea

Liubangosaurus

Losillasaurus

Recap & Conclusions

'Apparent' significant incongruence of phylogenetic signal between cranial and postcranial data partitions is not uncommon, however one choses to measure it (ILD or IRD)

Particularly incongruent in Sauropod datasets

There can only be 3 possible explanations:

1.) Coding error (impossible, many expert authors agree on the characters and how they are coded, differences are relatively few)

2.) An error of the method (unlikely, the ILD test is resilient to missing data)

3.) Modularity of evolutionand/or a difference in the rate of evolution (possible?)

AcknowledgementsFunding Computational Resources

Help and Guidance

Matthew WillsSylvain Gerber

Biodiversity Lab 1.07Ward Wheeler

Data

…and all authors who kindly provided me their data, knowingly or otherwise

www.graemetlloyd.com/data

Mounce, A. Butler, K. Davis, Dunhill, Garwood, Lamsdell, Legg, Lloyd, Pittman, Warnock, Wolfe+ ~150 signatories inc Benton, Ruta, Rannala, Wagner, Upchurch, Sutton, Farke, Dunlop...

A brighter future for digitalised paleontology?

“To promote the preservation of and future access to data, the Journal of Vertebrate Paleontology is considering following other key journals in instituting a policy requiring that data supporting the results presented in a publication be archived in a public repository.”

Fairbairn, D. J. (2011) The advent of mandatory data archiving. Evolution 65, 1-2

http://dx.doi.org/10.1111/j.1558-5646.2010.01182.x

Berta, A. & Barrett, P. M. (2011) Editorial. Journal of Vertebrate Paleontology 31, 1