Methods of determining cranial
and postcranial character
By Ross Mounce* and Matthew Wills
* [email protected]
3. Partitioned Goodman-Bremer Support
1. Why compare subsets of cladistic
Another method relatively unused in palaeontological
systematics is that of partitioned Goodman6-Bremer7 support
(GBS). Using this method one can assess not just the number of
characters that support each node in a strict consensus
cladogram, but also from which partition those supporting
characters came from. Negative support indicates otherwise
'hidden' character conflict between partitions.
Optimal estimates of phylogenetic inference work on
the basis of Total Evidence1. We do not contest this.
However, using methods of 'data exploration' to
examine subsignals within datasets, can be both a
justified and useful means with which to gain
quantitative support for more detailed evolutionary
Molecular systematists routinely compare and contrast
data sourced from different genes e.g. nuclear,
mitochondrial & plastid markers. We think
morphologists could stand to gain much insight from
similar statistically-explicit comparisons of
Does my soft tissue data agree with my
What influence do dental characters have on the
Ensemble Consistency Index
f(x) = -0.0006274738x + 0.6109492765
R = 0.1635139213
Postcranial elements from UCMP
Skull of D. wetherilli
Fig. 2 Re-analysing data from Ezcurra & Cuny 2007, JVP, to compare support contributed by
cranial & postcranial character partitions (cranial,postcranial, GBS values on each node).
Note in figure 2 (above) the conflict in GBS from cranial
characters to the strongly postcranially-supported node
(indicated by the arrow) the distribution of states in one cranial
character is incongruent with the topology supported by
postcranial characters. Also there is strongly 'lop-sided'
partition support for this cladogram most nodes are only
supported by postcranial characters despite there being 68
cranial characters in this matrix relative to 77 postcranial.
One would not recommend the consistency index3
despite its popular usage, as it is known4 to be a poor
measure of homoplasy affected by number of taxa,
characters, character states of characters, and the rate of
evolution of characters in cladistic matrix.
4. The Incongruence Length Difference Test
The ILD8 test9 is perhaps one of the most routinely used methods for
comparing sequence data in molecular phylogenetics; with at least 2500
citations to the paper describing it, most of which do use the test10. Given
its long history, we feel this test is under-utilised in palaeontology, but see
some recent uses11,12.
Only 3 random reps were as
Summed length of
at least 999 times, and compare with the
ILD you originally got, to get an ILD p-value
Fig. 4 Example randomised
partition replicates, with which
one can use to determine the
significance of the length
difference between the
partitions you are interested in.
Fig. 5 Re-analysing
Ezcurra&Cuny'07 using the ILD
test to compare cranial and
Having performed the ILD test, and others on 63 vertebrate data
matrices, to compare cranial and postcranial partitions, we find many
Number of taxa in dataset
Fig. 1 Data from re-analysis of 163 vertebrate-only cladistic matrices datasets like figure 5, appear to have unexplained significant
published 2000 2011 (Mounce & Damary-Homan, unpublished) further incongruence (figure 6; p-values < 0.005).
details in ESM.
A) The inverse relationship between CI & characters. B) The inverse
We conclude the
relationship between CI & taxa. Admittedly, taxa & character number are
Figure 1 (above) empirically demonstrates some of
the problems of using CI as a comparative statistic.
We agree with Cuthill et al. that multivariate
approaches are needed to adequately control for Fig. 6 A) Group composition of the datasets analysed
covariates such as these in comparative analyses. A
grey=0.011-0.1 (significant or borderline),
better comparative measure of homoplasy may well
blue=0.101-1.0 (not significant)
be Archie's Homoplasy Excess Ratio (HER) which is
more computationally-demanding. However, if there is Supplementary materials inc. code + data + more refs: http://bit.ly/palass
a high proportion of non-randomly distributed missing
Acknowledgements: Many thanks to all the Macroevolution group
data in the matrix it can lead to negative HER values.
References: 1. Grant & Kluge, 2003 Cladistics 2. Kluge, 1989 Syst. Zool. 3. [email protected]
& Farris, 1969 Syst. Zool. 4. Hoyal Cuthill et al, 2010 Cladistics 5. Archie, 1989 Syst. Zool. 6. Grant &
Kluge, 2008 MPE
7. Bremer, 1988 Evol. 8. Mickevich & Farris, 1981 Syst. Zool. 9. Farris et al, 1994 Cladistics 10. Mounce, 2011 http://bit.ly/ILDreview 11. Ketchum & Benson, 2010 Biol. Rev. 12. Smith, N.D.
*Many of the images displayed on
2010 PLoS ONE
noted* this work is licensed under
this poster are not my creative
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