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Anatomy of a Cladistic Analysis
Nico M. Franz
School of Life Sciences, Arizona State University

XXXI Willi Hennig Meeting...
From the abstract:
• "The monophyly of the Neotropical entimine weevil genus Exophthalmus
Schoenherr, 1823 (Curculionidae:...
(A) E. agrestis (Boheman); (B) E. consobrinus (Marshall); (C) E. hieroglyphicus Chevrolat

(D) E. impressus (Fabricius); (...
Fig. 2. Preferred cladogram &
character state optimizations
Dissecting the process – motivating themes
"Cladists may use the congruence test to iteratively refine assessments of homo...
Dissecting the process – motivating themes
"Cladists may use the congruence test to iteratively refine assessments of homo...
Sneak preview: 60 matrices, 8 stages – tracking the analysis
Legacy character assembly
Stage 1: legacy character assembly
Champion (1911) – winged
vs. wingless entimine groups

Source: Champion. 1911. Otiorhyn...
Stage 1: legacy character assembly

Character has a length of 10 steps in a narrowly scoped analysis
(Exophthalmus and clo...
Initial characters and states had a reputable pedigree

Lacordaire. 1863. Histoire naturelle des insectes, Vol 6. Paris, R...
Early cladistic outcomes (Stage 1)

52 taxa
Early cladistic outcomes (Stage 1)

100
characters
Early cladistic outcomes (Stage 1)

547 steps!
(~ 5.5 / char.)
Matrix 10

Select legacy characters
Consistency index and retention index

rapid
decline
Character coding – binary, multi-state

~ 40%
multi-state
characters
Character provenance – external, internal

initially
all external
Number of MPTs and nodes collapsed in consensus

Return to initial homology
assessments (chars./states).

3 trees,
3 colla...
Rescoping starts…
Matrices 11-17: rescoping phase I – some examples
Intermediate stages 2-5 – rescoping, taxon/character addition

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

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

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

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

rescoping all in
expanded context
Consistency index and retention index

steady
increase
Character coding – binary, multi-state

> 90% binary
characters

"exploratory"
reductive
coding
Character provenance – external, internal

> 20% internal
characters
Number of MPTs and nodes collapsed in consensus

Focus on detail homology,
perform "aggressive scope
reduction"
Still not ...
And so…
Contingent rescoping – tricarinate rostrum of Diaprepes spp.

7 species

17. "Rostrum tricarinate, …
Contingent rescoping – tricarinate rostrum of Diaprepes spp.
Are these rostra also tricarinate (in homology to Diaprepes)?...
Contingent rescoping – tricarinate rostrum of Diaprepes spp.
No, not if intermittent phylogenetic insights are transparent...
Narrowly scoped, deep-level homologies
Narrowly scoped, deep-level homologies
Narrowly scoped, deep-level homologies
Terminal stages 6-8 – added resolution, robustness

narrowly rescoped
characters, more
stable tree length
Consistency index and retention index

approaching
"maximum" levels
Character coding – binary, multi-state

> 20% characters
with inapplicables
Character provenance – external, internal

~ 40% internal
characters
Number of MPTs and nodes collapsed in consensus

Ready for
publication.
8 trees,
3 collapsed
Review…from matrix 10 to 60
Topology, Optimization, Language
Overview of significant topology changes – matrices 1-60

Transition of matrix 30-31 yielded
earliest "reliable" results.
Matrix 10
[topology]

Exophthalmus spp.
Nested within Exoph.

•
•
•
•
•
•
•
•

52 taxa
100 characters
4 MPTs
L = 547 steps...
Matrix 20
[topology]

Exophthalmus spp.
Nested within Exoph.

•
•
•
•
•
•
•
•

52 taxa (=)
69 characters (– 31)
3 MPTs (– ...
Matrix 30
[topology]

Exophthalmus spp.
Nested within Exoph.

•
•
•
•
•
•
•
•

90 taxa (+ 38)
91 characters (+ 22)
2192 MP...
Matrix 60
[topology]

Exophthalmus spp.
Nested within Exoph.

•
•
•
•
•
•
•
•

90 taxa (=)
143 characters (+ 52)
8 MPTs (–...
Matrix 10
[optimization]

Select legacy characters

•
•
•
•
•
•
•
•
•

52 taxa
100 characters
4 MPTs
L = 547 steps
CI = 28...
Matrix 60
[optimization]

•
•
•
•
•
•
•
•
•

90 taxa (+ 38)
143 characters (+ 43)
8 MPTs (+ 4)
L = 239 steps (– 308)
CI = ...
Matrix 10 [language]

Lacordaire. 1863. Histoire naturelle des insectes, Vol 6. Paris, Roret.
Champion. 1911. Otiorhynchin...
Matrix 60 [language]
Related issue…
Which characters should constitute
phenotype anatomy ontologies?
Related issue – the value of parsimony-contingent homology
Special emphasis on constructing phenotypic anatomy ontologies....
Related issue – the value of parsimony-contingent homology
Special emphasis on constructing phenotypic anatomy ontologies....
So then is this what we have in mind
for classes in phenotype ontologies?

Source: Davis. 2011. Delimiting baridine weevil...
Conclusions
• Analytical phylogenetic methods not only organize character information, but may
furthermore have the purpos...
Conclusions
• Analytical phylogenetic methods not only organize character information, but may
furthermore have the purpos...
Acknowledgments
WHS XXXI Organizers
Juliana Cardona Duque, Jennifer Girón, Anyimilehidi Mazo Vargas, Quentin Wheeler

NSF-...
Stage 1: legacy character assembly
Lacordaire (1863) – typically a 1-3
character system for tribes/genera.

Source: Lacord...
van Emden (1944)

state-of-the-art for entimine tribes / genera

Source: van Emden. 1944. A key to the genera of Brachyder...
Anderson (2002) – identifies subfamilies, genera; not tribes

Source: Anderson. 2002. Family 131. Curculionidae. In: Arnet...
Initial characters and states had a reputable pedigree
Examples of poorly performing characters (

recode / eliminate)
Matrix 18: Examples of deactivated characters
Franz. Anatomy of a Cladistic Analysis.
Franz. Anatomy of a Cladistic Analysis.
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Franz. Anatomy of a Cladistic Analysis.

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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.

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Transcript of "Franz. Anatomy of a Cladistic Analysis."

  1. 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. 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. 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. 4. Fig. 2. Preferred cladogram & character state optimizations
  5. 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. 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. 7. Sneak preview: 60 matrices, 8 stages – tracking the analysis
  8. 8. Legacy character assembly
  9. 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. 10. Stage 1: legacy character assembly Character has a length of 10 steps in a narrowly scoped analysis (Exophthalmus and closely related genera).
  11. 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. 12. Early cladistic outcomes (Stage 1) 52 taxa
  13. 13. Early cladistic outcomes (Stage 1) 100 characters
  14. 14. Early cladistic outcomes (Stage 1) 547 steps! (~ 5.5 / char.)
  15. 15. Matrix 10 Select legacy characters
  16. 16. Consistency index and retention index rapid decline
  17. 17. Character coding – binary, multi-state ~ 40% multi-state characters
  18. 18. Character provenance – external, internal initially all external
  19. 19. Number of MPTs and nodes collapsed in consensus Return to initial homology assessments (chars./states). 3 trees, 3 collapsed Not publication worthy.
  20. 20. Rescoping starts…
  21. 21. Matrices 11-17: rescoping phase I – some examples
  22. 22. Intermediate stages 2-5 – rescoping, taxon/character addition addressing poorest characters
  23. 23. Intermediate stages 2-5 – rescoping, taxon/character addition evidence of large gaps in sampling
  24. 24. Intermediate stages 2-5 – rescoping, taxon/character addition addition of out-/ingroup taxa (52 90)
  25. 25. Intermediate stages 2-5 – rescoping, taxon/character addition new taxa new (unscoped) characters
  26. 26. Intermediate stages 2-5 – rescoping, taxon/character addition rescoping all in expanded context
  27. 27. Consistency index and retention index steady increase
  28. 28. Character coding – binary, multi-state > 90% binary characters "exploratory" reductive coding
  29. 29. Character provenance – external, internal > 20% internal characters
  30. 30. 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
  31. 31. And so…
  32. 32. Contingent rescoping – tricarinate rostrum of Diaprepes spp. 7 species 17. "Rostrum tricarinate, …
  33. 33. 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
  34. 34. 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."
  35. 35. Narrowly scoped, deep-level homologies
  36. 36. Narrowly scoped, deep-level homologies
  37. 37. Narrowly scoped, deep-level homologies
  38. 38. Terminal stages 6-8 – added resolution, robustness narrowly rescoped characters, more stable tree length
  39. 39. Consistency index and retention index approaching "maximum" levels
  40. 40. Character coding – binary, multi-state > 20% characters with inapplicables
  41. 41. Character provenance – external, internal ~ 40% internal characters
  42. 42. Number of MPTs and nodes collapsed in consensus Ready for publication. 8 trees, 3 collapsed
  43. 43. Review…from matrix 10 to 60 Topology, Optimization, Language
  44. 44. Overview of significant topology changes – matrices 1-60 Transition of matrix 30-31 yielded earliest "reliable" results.
  45. 45. 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
  46. 46. 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
  47. 47. 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
  48. 48. 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
  49. 49. 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
  50. 50. 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
  51. 51. 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.
  52. 52. Matrix 60 [language]
  53. 53. Related issue… Which characters should constitute phenotype anatomy ontologies?
  54. 54. 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.
  55. 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. "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.
  56. 56. 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.
  57. 57. 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.
  58. 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. • 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.
  59. 59. 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"
  60. 60. 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.
  61. 61. 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.
  62. 62. 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.
  63. 63. Initial characters and states had a reputable pedigree
  64. 64. Examples of poorly performing characters ( recode / eliminate)
  65. 65. Matrix 18: Examples of deactivated characters
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