Franz. Anatomy of a Cladistic Analysis

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

• "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."

From the abstract:

(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)

Fig. 2. Preferred cladogram & character state optimizations

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.

"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.

Dissecting the process – motivating themes

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

Legacy character assembly

Source: Champion. 1911. Otiorhynchinae Alatae. In: Biologia Centrali-Americana, Vol. 4, Part 3. London.

Stage 1: legacy character assembly

Champion (1911) – winged vs. wingless entimine groups

Character has a length of 10 steps in a narrowly scoped analysis (Exophthalmus and closely related genera).

Stage 1: legacy character assembly

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.

Early cladistic outcomes (Stage 1)

52 taxa

Early cladistic outcomes (Stage 1)

100 characters

547 steps!(~ 5.5 / char.)

Early cladistic outcomes (Stage 1)

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

initiallyall external

Number of MPTs and nodes collapsed in consensus

3 trees,3 collapsed

Not publication worthy.

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

Rescoping starts…

Matrices 11-17: rescoping phase I – some examples

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

addressingpoorest

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

steadyincrease

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

Still not ready for publication.

> 1200 trees,> 35 collapsed

Focus on detail homology, perform "aggressive scope reduction"

And so…

Contingent rescoping – tricarinate rostrum of Diaprepes spp.

17. "Rostrum tricarinate, …

7 species

17. "Rostrum tricarinate, …

Contingent rescoping – tricarinate rostrum of Diaprepes spp.

Exophthalmus Otiorhynchus

Pachnaeus Phaops Rhinospathe

7 species

Are these rostra also tricarinate (in homology to Diaprepes)?

17. "Rostrum tricarinate, with a characteristic combination of one median carina and two (dorso-) lateral, apically slightly diverging carinae, each carina narrow, moderately sharp."

Contingent rescoping – tricarinate rostrum of Diaprepes spp.

Exophthalmus Otiorhynchus

Pachnaeus Phaops Rhinospathe

7 species

(1) present (0) absent

(0) absent

(–) inapplicable

(–) inapplicable (–) inapplicable

No, not if intermittent phylogenetic insights are transparently included.

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% internalcharacters

Number of MPTs and nodes collapsed in consensus

8 trees,3 collapsed

Ready for publication.

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]

• 52 taxa• 100 characters• 4 MPTs• L = 547 steps• CI = 28• RI = 66• 3 nodes collapsed• Bremer support

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

Matrix 20[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

Matrix 30[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

Matrix 60[topology]

Exophthalmus spp. Nested within Exoph.

• 52 taxa• 100 characters• 4 MPTs• L = 547 steps• CI = 28• RI = 66• 3 nodes collapsed• Diagnoses unwieldy• Synapomorphies rare

Matrix 10[optimization]

Select legacy characters

• 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

Matrix 60[optimization]

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.

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.

"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.

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."

"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."

Mungall et al. 2012. Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13: R5.

Vogt et al. 2010. The linguistic problem of morphology: structure versus homology and the standardization of morphological data. Cladistics 26: 301–325.

Source: Davis. 2011. Delimiting baridine weevil evolution (Coleoptera: Curculionidae: Baridinae). Zool. J. Linn. Soc. 161: 88–156.

So then is this what we have in mind for classes in phenotype ontologies?

• 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.

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.

Conclusions

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"

Source: Lacordaire. 1863. Histoire naturelle des insectes, Vol. 6. Paris: Roret.

Lacordaire (1863) – typically a 1-3 character system for tribes/genera.

Stage 1: legacy character assembly

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.

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.

Initial characters and states had a reputable pedigree

Examples of poorly performing characters ( recode / eliminate)

Matrix 18: Examples of deactivated characters