The sequential stages culminating in the publication of a morphological cladistic analysis of weevils in the Exophthalmus genus complex (Coleoptera: Curculionidae: Entiminae) are reviewed, with an emphasis on how early- stage homology assessments were gradually evaluated and refined in light of intermittent phylogenetic insights. In all, 60 incremental versions of the evolving character matrix were congealed and analysed, starting with an assembly of 52 taxa and ten traditionally deployed diagnostic characters, and ending with 90 taxa and 143 characters that reflect significantly more narrow assessments of phylogenetic similarity and scope. Standard matrix properties and analytical tree statistics were traced throughout the analytical process, and series of incongruence length indifference tests were used to identify critical points of topology change among succeeding matrix versions. This kind of parsimony-contingent rescoping is generally representative of the inferential process of character individuation within individual and across multiple cladistic analyses. The expected long-term outcome is a maturing observational terminology in which precise inferences of homology are parsimony-contingent, and the notions of homology and parsimony are inextricably linked. This contingent view of cladistic character individuation is contrasted with current approaches to developing phenotype ontologies based on homology-neutral structural equivalence expressions. Recommendations are made to transparently embrace the parsimony-contingent nature of cladistic homology.

1. Anatomy of a Cladistic Analysis
Nico M. Franz
School of Life Sciences, Arizona State University
XXXI Willi Hennig Meeting – UC Riverside
June 26, 2012; Riverside, CA

2. From the abstract:
• "The monophyly of the Neotropical entimine weevil genus Exophthalmus
Schoenherr, 1823 (Curculionidae: Entiminae: Eustylini Lacordaire) is reassessed."
• […] "The present study scrutinizes these traditional perspectives, based on a cladistic
analysis of 143 adult morphological characters and 90 species, representing 30
genera and seven tribes of Neotropical entimine weevils."
• The character matrix yielded eight most-parsimonious cladograms (length = 239
steps; consistency index = 66; retention index = 91), with mixed clade support that
remains particularly wanting for some of the deeper in-group divergences."

3. (A) E. agrestis (Boheman); (B) E. consobrinus (Marshall); (C) E. hieroglyphicus Chevrolat
(D) E. impressus (Fabricius); (E) E. nicaraguensis Bovie; (F) E. quadrivittatus (Olivier)
(G) E. quinquedecimpunctatus (Olivier); (H) E. roseipes (Chevrolat); (I) E. sulcicrus Champion
(J) E. triangulifer Champion; (K) E. verecundus (Chevrolat); (L) E. vittatus (Linnaeus)

4. Fig. 2. Preferred cladogram &
character state optimizations

5. Dissecting the process – motivating themes
"Cladists may use the congruence test to iteratively refine assessments of homology,
and thereby increase the odds of reliable phylogenetic inference under parsimony.
This explanation challenges alternative views which tend to ignore the effects of
parsimony on the process of character individuation in systematics."
Franz. 2005. Outline of an explanatory account of cladistic practice. Biol. Phil. 20: 489–515.

6. Dissecting the process – motivating themes
"Cladists may use the congruence test to iteratively refine assessments of homology,
and thereby increase the odds of reliable phylogenetic inference under parsimony.
This explanation challenges alternative views which tend to ignore the effects of
parsimony on the process of character individuation in systematics."
Franz. 2005. Outline of an explanatory account of cladistic practice. Biol. Phil. 20: 489–515.
"The identification of the valid scope for character statements cannot be a matter
of mere ostension, or rigid designation, but must be a matter of scientific theory
construction. Scope expansion of character statements can result in a situation
where purportedly similar structures, apparently denoted by the same name
(proper name or kind name), are in fact not the same. The nonhomology of such
characters may be revealed through morphological complexity at the comparative
level, by tree topology at the analytical level, or both."
Rieppel. 2007. The performance of morphological characters in broad-scale phylogenetic analyses. Biol. J. Linn. Soc. 92: 297–308.

7. Sneak preview: 60 matrices, 8 stages – tracking the analysis

8. Legacy character assembly

9. Stage 1: legacy character assembly
Champion (1911) – winged
vs. wingless entimine groups
Source: Champion. 1911. Otiorhynchinae Alatae. In: Biologia Centrali-Americana, Vol. 4, Part 3. London.

10. Stage 1: legacy character assembly
Character has a length of 10 steps in a narrowly scoped analysis
(Exophthalmus and closely related genera).

11. Initial characters and states had a reputable pedigree
Lacordaire. 1863. Histoire naturelle des insectes, Vol 6. Paris, Roret.
Champion. 1911. Otiorhynchinae Alatae. Biologia Centrali-Americana, Vol. 4, Part 3. London; pp. 178–317.
van Emden. 1944. A key to the genera of Brachyderinae of the world. Ann. Mag. Nat. Hist. 11: 503–532, 559–586.
Anderson. 2002. Family 131. Curculionidae. In: American B, Vol. 2. Boca Raton, CRC Press; pp. 722–815.
Franz. 2010. Redescriptions of critical type species in the Eustylini Lacordaire (Coleoptera: Curculionidae: Entiminae). J. Nat. Hist. 44: 41-80.

12. Early cladistic outcomes (Stage 1)
52 taxa

13. Early cladistic outcomes (Stage 1)
100
characters

14. Early cladistic outcomes (Stage 1)
547 steps!
(~ 5.5 / char.)

15. Matrix 10
Select legacy characters

16. Consistency index and retention index
rapid
decline

17. Character coding – binary, multi-state
~ 40%
multi-state
characters

18. Character provenance – external, internal
initially
all external

19. Number of MPTs and nodes collapsed in consensus
Return to initial homology
assessments (chars./states).
3 trees,
3 collapsed
Not publication worthy.

20. Rescoping starts…

21. Matrices 11-17: rescoping phase I – some examples

22. Intermediate stages 2-5 – rescoping, taxon/character addition
addressing
poorest
characters

23. Intermediate stages 2-5 – rescoping, taxon/character addition
evidence of
large gaps in
sampling

24. Intermediate stages 2-5 – rescoping, taxon/character addition
addition of
out-/ingroup
taxa (52 90)

26. Intermediate stages 2-5 – rescoping, taxon/character addition
new taxa
new (unscoped)
characters

27. Intermediate stages 2-5 – rescoping, taxon/character addition
rescoping all in
expanded context

28. Consistency index and retention index
steady
increase

29. Character coding – binary, multi-state
> 90% binary
characters
"exploratory"
reductive
coding

30. Character provenance – external, internal
> 20% internal
characters

31. Number of MPTs and nodes collapsed in consensus
Focus on detail homology,
perform "aggressive scope
reduction"
Still not ready
for publication.
> 1200 trees,
> 35 collapsed

32. And so…

33. Contingent rescoping – tricarinate rostrum of Diaprepes spp.
7 species
17. "Rostrum tricarinate, …

34. Contingent rescoping – tricarinate rostrum of Diaprepes spp.
Are these rostra also tricarinate (in homology to Diaprepes)?
7 species
Pachnaeus
17. "Rostrum tricarinate, …
Exophthalmus
Phaops
Otiorhynchus
Rhinospathe

35. Contingent rescoping – tricarinate rostrum of Diaprepes spp.
No, not if intermittent phylogenetic insights are transparently included.
(1) present
7 species
(0) absent
Pachnaeus
(0) absent
Exophthalmus
(–) inapplicable
Phaops
(–) inapplicable
Otiorhynchus
(–) inapplicable
Rhinospathe
17. "Rostrum tricarinate, with a characteristic combination of one median carina
and two (dorso-) lateral, apically slightly diverging carinae, each carina narrow,
moderately sharp."

36. Narrowly scoped, deep-level homologies

37. Narrowly scoped, deep-level homologies

38. Narrowly scoped, deep-level homologies

39. Terminal stages 6-8 – added resolution, robustness
narrowly rescoped
characters, more
stable tree length

40. Consistency index and retention index
approaching
"maximum" levels

41. Character coding – binary, multi-state
> 20% characters
with inapplicables

42. Character provenance – external, internal
~ 40% internal
characters

43. Number of MPTs and nodes collapsed in consensus
Ready for
publication.
8 trees,
3 collapsed

44. Review…from matrix 10 to 60
Topology, Optimization, Language

45. Overview of significant topology changes – matrices 1-60
Transition of matrix 30-31 yielded
earliest "reliable" results.

46. Matrix 10
[topology]
Exophthalmus spp.
Nested within Exoph.
•
•
•
•
•
•
•
•
52 taxa
100 characters
4 MPTs
L = 547 steps
CI = 28
RI = 66
3 nodes collapsed
Bremer support

47. Matrix 20
[topology]
Exophthalmus spp.
Nested within Exoph.
•
•
•
•
•
•
•
•
52 taxa (=)
69 characters (– 31)
3 MPTs (– 1)
L = 159 steps (– 388)
CI = 48 (+ 20)
RI = 83 (+ 17)
3 nodes collapsed (=)
Bremer support

48. Matrix 30
[topology]
Exophthalmus spp.
Nested within Exoph.
•
•
•
•
•
•
•
•
90 taxa (+ 38)
91 characters (+ 22)
2192 MPTs (+ 2189)
L = 205 steps (+ 46)
CI = 45 (– 3)
RI = 83 (=)
38 nodes collapsed (+ 35)
Bremer support

49. Matrix 60
[topology]
Exophthalmus spp.
Nested within Exoph.
•
•
•
•
•
•
•
•
90 taxa (=)
143 characters (+ 52)
8 MPTs (– 2184)
L = 239 steps (+ 24)
CI = 66 (+ 21)
RI = 91 (+ 8)
3 nodes collapsed (– 35)
Bremer support

50. Matrix 10
[optimization]
Select legacy characters
•
•
•
•
•
•
•
•
•
52 taxa
100 characters
4 MPTs
L = 547 steps
CI = 28
RI = 66
3 nodes collapsed
Diagnoses unwieldy
Synapomorphies rare

51. Matrix 60
[optimization]
•
•
•
•
•
•
•
•
•
90 taxa (+ 38)
143 characters (+ 43)
8 MPTs (+ 4)
L = 239 steps (– 308)
CI = 66 (+ 38)
RI = 91 (+ 25)
3 nodes collapsed (=)
Diagnoses concise
Synapomorph. common

52. Matrix 10 [language]
Lacordaire. 1863. Histoire naturelle des insectes, Vol 6. Paris, Roret.
Champion. 1911. Otiorhynchinae Alatae. Biologia Centrali-Americana, Vol. 4, Part 3. London; pp. 178–317.
van Emden. 1944. A key to the genera of Brachyderinae of the world. Ann. Mag. Nat. Hist. 11: 503–532, 559–586.
Anderson. 2002. Family 131. Curculionidae. In: American B, Vol. 2. Boca Raton, CRC Press; pp. 722–815.
Franz. 2010. Redescriptions of critical type species in the Eustylini Lacordaire (Coleoptera: Curculionidae: Entiminae). J. Nat. Hist. 44: 41-80.

53. Matrix 60 [language]

54. Related issue…
Which characters should constitute
phenotype anatomy ontologies?

55. Related issue – the value of parsimony-contingent homology
Special emphasis on constructing phenotypic anatomy ontologies.
"We have taken an integrative approach in the building of Uberon, and in doing so
embrace multiple axes of classification. […] This homology-neutrality of Uberon is a
deliberate design feature of the ontology. We believe that specifying homology
relationships and descent from common ancestral structures is of obvious high value, but
that this need not be tightly coupled to the development of an upper anatomical
ontology."
Mungall et al. 2012. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13: R5.

56. Related issue – the value of parsimony-contingent homology
Special emphasis on constructing phenotypic anatomy ontologies.
"We have taken an integrative approach in the building of Uberon, and in doing so
embrace multiple axes of classification. […] This homology-neutrality of Uberon is a
deliberate design feature of the ontology. We believe that specifying homology
relationships and descent from common ancestral structures is of obvious high value, but
that this need not be tightly coupled to the development of an upper anatomical
ontology."
Mungall et al. 2012. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13: R5.
"Explanatory homology hypotheses should not be mistaken and blended with
morphological descriptions, which in their turn are by nature descriptive and not
explanatory. […] Instead, we differentiate phylogenetic investigations into the step of
producing data and the step of phylogenetic reasoning."
Vogt et al. 2010. The linguistic problem of morphology: structure versus homology and the standardization of morphological data.
Cladistics 26: 301–325.

57. So then is this what we have in mind
for classes in phenotype ontologies?
Source: Davis. 2011. Delimiting baridine weevil evolution (Coleoptera: Curculionidae: Baridinae). Zool. J. Linn. Soc. 161: 88–156.

58. Conclusions
• Analytical phylogenetic methods not only organize character information, but may
furthermore have the purpose of shaping character individuation.
• In the case of the Exophthalmus analysis, I would have been hard pressed to arrive at
the final descriptions of characters and states without benefitting from intermittent
parsimony-driven inferences that led to the reweighting and rescoping of earlier
homology assessments. It is not always conducive to a researcher's reputation to
expose these practices, but they do and must occur frequently.

59. Conclusions
• Analytical phylogenetic methods not only organize character information, but may
furthermore have the purpose of shaping character individuation.
• In the case of the Exophthalmus analysis, I would have been hard pressed to arrive at
the final descriptions of characters and states without benefitting from intermittent
parsimony-driven inferences that led to the reweighting and rescoping of earlier
homology assessments. It is not always conducive to a researcher's reputation to
expose these practices, but they do and must occur frequently.
• Under the cladistic paradigm, the most precise inferences of homology are often
parsimony-influenced and parsimony-contingent, and the two notions are
inextricably linked and entrenched in our maturing observational terminology.
• By integrating expressions of structural equivalence at increasingly greater scales,
phenotype ontologies also run the risk of 'dialing down' the most precise and
phylogenetically scoped assessments of homology that systematics can produce.

60. Acknowledgments
WHS XXXI Organizers
Juliana Cardona Duque, Jennifer Girón, Anyimilehidi Mazo Vargas, Quentin Wheeler
NSF-DEB 1155984:
"Systematics of eustyline and geonemine weevils: Connecting and contrasting Caribbean
and Neotropical mainland radiations"

62. Stage 1: legacy character assembly
Lacordaire (1863) – typically a 1-3
character system for tribes/genera.
Source: Lacordaire. 1863. Histoire naturelle des insectes, Vol. 6. Paris: Roret.

63. van Emden (1944)
state-of-the-art for entimine tribes / genera
Source: van Emden. 1944. A key to the genera of Brachyderinae of the world. Annals and Magazine of Natural History 11: 503-532, 559-586.

64. Anderson (2002) – identifies subfamilies, genera; not tribes
Source: Anderson. 2002. Family 131. Curculionidae. In: Arnett et al. (Eds.): American Beetles, Vol. 2. Boca Raton, CRC Press; pp. 722-815.

65. Initial characters and states had a reputable pedigree

66. Examples of poorly performing characters (
recode / eliminate)

67. Matrix 18: Examples of deactivated characters