Franz 2014 ESA Aligning Insect Phylogenies Perelleschus and Other Cases

Aligning insect phylogenies:

Perelleschus and other cases

Nico M. Franz 1,2

Arizona State University

http://taxonbytes.org/

1 Concepts and tools developed jointly with members of the Ludäscher Lab (UC Davis & UIUC):

Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shawn Bowers & Bertram Ludäscher

2 Systematics, Evolution and Biodiversity Section, Ten Minute Papers

Annual Meeting of the Entomological Society of America

November 18, 2014 - Portland, Oregon

On-line @ http://www.slideshare.net/taxonbytes/franz-2014-esa-aligning-insect-phylogenies-perelleschus-and-other-cases-41654235


http://www.slideshare.net/taxonbytes/franz-2014-esa-aligning-insect-phylogenies-perelleschus-and-other-cases-41654235

Research motivation: 1

How can we represent, and reason over,

taxonomic concept provenance,

based on varying input classifications

and differentially sampled phylogenies?

1 This presentation concentrates on the "how?"; though the "why?" is addressed in the References (listed at the end).

Taxonomic concept: 1

The circumscription of a perceived

(or, more accurately, hypothesized)

taxonomic group, as advocated by

a particular author and source.

Definitional preliminaries, 1

1 Not the same as species concepts, which are theories about what species are, and/or how they are recognized.

Provenance: 1

Information describing the origin, derivation,

history, custody, or context of an entity (etc.).

Provenance establishes the authenticity, integrity

and trustworthiness of information about entities.


1 See, e.g.: http://www.w3.org/2005/Incubator/prov/wiki/What_Is_Provenance

http://www.w3.org/2005/Incubator/prov/wiki/What_Is_Provenance

Alignment ("merge"):

A comprehensive, logically consistent, and

(where possible) well-specified reconciliation

of shared and unique Euler regions that result from

integrating two or more taxonomic concept

hierarchies ("trees") with RCC-5 articulations.1


1 RCC-5 = Region Connection Calculus (set theory relationships: congruence, inclusion, overlap, exclusion, etc.).

Input for provenance reasoning: Perelleschus use case, 1936−2013

Perelleschus salpinflexus Cardona-Duque & Franz sec. Franz & Cardona-Duque (2013)

Female

,

habitu

s

Labium Maxill

a

• Habitus, mouthparts


Female

,

habitu

s

Labium Maxill

a

• Habitus, mouthparts One might call this string a Taxonomic Concept Label.


Synapomorphy (genus-level): Spermatheca

with an acute, sclerotized appendix at

insertion of the collum (character 17:1).

Synapomorphy (subclade-level):

Aedeagus with endophallic

sclerites extending in apical

half of aedeagus (character

11:1).

• Male & female terminalia, showing putative synapomorphies

"11"

"17"

Phylogeny: Perelleschus sec. Franz & Cardona-Duque (2013)

Aedeagal synapomorphy

Spermathecal synapomorphy

Perelleschus concept history:

• 6 classifications,

• 54 taxonomic concepts,

• 75 concept2 RCC-5 articulations;

Suitable for provenance reasoning. 1

1 Franz et al. 2014. Reasoning over taxonomic change: Exploring alignments for the Perelleschus use case. PLoS ONE.

1936: 1st species-

level concept.

1954: Genus named,

+ 2 species.

1986: Validation of

generic name.

2001: Revision & phylogeny,

+ 6 / - 1 species.

2006: Exemplar cladistic

analysis; 3 species. 2013: Revision & phylogeny,

+ 2 species.

1986: Validation of

generic name.


+ 6 / - 1 species.



+ 2 species.

Focal alignments (today)

• 1986 versus 2001

• Classification / Phylogeny

• 2001 versus 2006

• Phylogeny / Exemplar Analysis

• 2001 versus 2013 (appended)

• Phylogeny / Extended Phylogeny

2001 /

2013

"A toolkit for consistently aligning

sets of hierarchically arranged entities

under (relaxable) logic constraints,

and using RCC-5 articulations."

Introducing the Euler/X software toolkit (Open Source)

Desktop tool @ https://bitbucket.org/eulerx

Euler server @ http://euler.asu.edu

https://bitbucket.org/eulerx

http://euler.asu.edu

Euler/X toolkit − Please ask me (later) about a live demonstration!

Euler/X uses Answer Set Programming.

The reasoner asks, and solves, the question:

"Which possible worlds can be generated

that satisfy (i.e., are consistent with)

a given set of input constraints?" 1

Euler/X uses Answer Set Programming.

The reasoner asks, and solves, the question:

"Which possible worlds can be generated

that satisfy (i.e., are consistent with)

a given set of input constraints?" 1

1 Input constraints:

• T1 − taxonomy 1

• T2 − taxonomy 2

• A − user-asserted articulations

• C − additional 'tree' constraints

Alignment 1 - Perelleschus sec. WOB (1986) versus sec. FOB (2001)

T1: Perelleschus sec. 1986

• Traditional classification

• 1 genus-level concept

• 3 species-level concepts

Alignment 1 - Perelleschus sec. WOB (1986) versus sec. FOB (2001)


• Traditional classification

• 1 genus-level concept



• Phylogenetic revision

• 2 genus-level concepts

• 7 clade-level concepts


Year Source

Parent

conceptChild

concepts

T1

T2 to T1Articulations

(as provided

by the user)

Format for alignment input file (constraints: T1, T2, A, C)

T2

Input visualization

Six1 user-asserted input articulations (pink lines) are sufficient to yield a single,

well-specified alignment.

1 Actually, three (species-level) articulations are sufficient to achieve this for the 2001/1986 alignment.

Alignment (merge) visualization

Reasoner infers 66 additional, logically implied articulations (MIR).1

2001.Perelleschus >< 1986.Perelleschus; provenance of overlapping articulation

is explained in the merge taxonomy.

1 MIR = Maximally Informative Relations (among paired concepts of T1, T2).

Legend


3 congruent 2001/1986 species-level concepts.





Legend



6 species-level concepts unique sec. FOB (2001).





Legend






6 clade-level concepts unique to FOB (2001).





Legend




6 clade-level concepts unique to FOB (2001).

2001.PER & 2001.PHY in overlap with 1986.PER.





Legend


We can 'zoom in' on the overlap

and resolve the resulting subregions

in the "merge concept view".





Legend

Merge concept view (in part)

2001 concepts

"2001.PER and 1986.PER share a region (2001.PER * 1986.PER) constituted (at lower

levels) by 2001/1986.P_rectirostris; this latter region is that which is entailed in

1986.PER and excluded from 2001.PHY. (1986.PER\2001.PHY)."

2001/1986 concepts

Merge concept view (in part)

2001 concepts

"2001.PHYsubcin/1986.Psubcin differentially 'participates' in 2001.PHY and

1986.PER; but not 2001.PER (or any of its children)."

2001/1986 concepts



• 8 ingroup species concepts

• 2 outgroup concepts

• 18 concepts total

Alignment 2 - Perelleschus sec. FOB (2001) versus sec. F (2006)




• 2 outgroup concepts



• Exemplar analysis


• 1 outgroup concept


Alignment 2 - Perelleschus sec. FOB (2001) versus sec. F (2006)

Logic representation challenge:

Perelleschus sec. 2001 & 2006 concepts

have incongruent sets of subordinate members,

yet each concept has congruent synapomorphies.

Ostensive alignment: the congruence among higher-level

concepts is assessed in relation to their entailed members.

Ostension: giving meaning through an act of pointing out.

Definitional preliminaries, 4 1

1 See Bird & Tobin. 2012. Natural Kinds. URL: http://plato.stanford.edu/archives/win2012/entries/natural-kinds/

http://plato.stanford.edu/archives/win2012/entries/natural-kinds/

Ostensive alignment: the congruence among higher-level

concepts is assessed in relation to their entailed members.

Ostension: giving meaning through an act of pointing out.

Intensional alignment: the congruence among higher-

level concepts is assessed in relation to their properties.

Intension: giving meaning through the specification of properties.

Definitional preliminaries, 4 1

1 See Bird & Tobin. 2012. Natural Kinds. URL: http://plato.stanford.edu/archives/win2012/entries/natural-kinds/

http://plato.stanford.edu/archives/win2012/entries/natural-kinds/

Ostensive alignment – members are all that counts

Challenge 1: Ostensive alignmentInput constraints

Ostensive alignment

2001 & 2006


Challenge 1: Ostensive alignment

Solution: 11 ingroup concept articulations

are coded ostensively – either as

<, ><, or | – to represent non-

congruence in the representation

of child concepts

Input constraints

Ostensive alignment

2001 & 2006


Challenge 1: Ostensive alignment

Solution: 11 ingroup concept articulations

are coded ostensively – either as

<, ><, or | – to represent non-

congruence in the representation

of child concepts

Result: 2006.PER < 2001.PER

2006.PER | 2001.[5 species concepts]

etc.

Input constraints

Ostensive alignment

2001 & 20065 x |

2 x ><

Intensional alignment – representation of congruent synapomorphies

Input constraints

Intensional alignment

2001 & 2006

Challenge 2: Intensional alignment

"17"

"11"


Input constraints


2001 & 2006


Solution: An Implied Child (_IC) concept is

added to the undersampled (2006)

clade concept; and the (5) "missing"

species-level concepts are included

within this Implied Child

"17"

"11"


Input constraints


2001 & 2006


Solution: An Implied Child (_IC) concept is

added to the undersampled (2006)

clade concept; and the (5) "missing"

species-level concepts are included

within this Implied Child

11 ingroup concept articulations are

coded intensionally – as == or > –

to reflect congruent synapomorphies

(chars. 11, 17) of 2001 & 2006

"17"

"11"


Input constraints


2001 & 2006


Result: The genus- and ingroup clade-level

concepts are inferred as congruent:

2006. PER == 2001.PER

2006.PcarPeve == 2001.PcarPsul

etc.

Review – representing ostensive versus intensional alignments

Ostensive alignment

2001.PER includes more

species-level concepts

than 2006.PER [>].

Review – representing ostensive versus intensional alignments

Ostensive alignment

2001.PER includes more

species-level concepts

than 2006.PER [>].


2006.PER reconfirms the

synapomorphies inferred

in 2001.PER [==].

Is this approach scalable?

Quite possibly yes.

Use case: Alternative phylogenetic schemes of higher-level weevils

T1: Curculionoidea sec. Kuschel (1995)

• Cladistic analysis

• 41 concepts

Use case: Alternative phylogenetic schemes of higher-level weevils

T1: Curculionoidea sec. Kuschel (1995)


• 41 concepts

T2: Curculionoidea sec. Marvaldi &

Morrone (2000)


• 25 concepts

Alignment: Curculionoidea sec. K (1995) versus sec. MM (2000)

Initial visual impression: Lots of green rectangles, yellow octagons, and overlap (><).

Much taxonomic concept incongruence.

Use case: Dwarf lemurs sec. 1993 & 2005 1

Chirogaleus furcifer sec. Mühel (1890) – Brehms Tierleben.

Public Domain: http://books.google.com/books?id=sDgQAQAAMAAJ

1 Franz et al. 2014. Taxonomic provenance: Two influential primate classifications logically aligned. (in preparation)

http://books.google.com/books?id=sDgQAQAAMAAJ

The 2nd & 3rd Editions of the Mammal Species of the World

Primates sec. Groves (1993)

317 taxonomic concepts,

233 at the species level.

Primates sec. Groves (2005)

483 taxonomic concepts,

376 at the species level.

1993 2005

Δ = 143

species-

level

concepts

Alignment of Primates sec. Groves 1993 / 2005

Primates: 800 concepts

402

articulations

153,111 MIR

~ 380x information gain!

Strepsirrhini sec. MSW3

Haplorrhini sec. MSW3

Catarrhini sec. MSW3

Taxonomic provenance quantify name/meaning dissociation

"Reliable names" "Unreliable names"

'Dissociation' means that either un-identical names are paired with congruent concepts,

or that identical names are paired with incongruent concepts.

So, given an input set of [T1, T2, A, C], one gains:

(1) Logical consistency in the alignment;

(2) Intended degree of alignment resolution;

(3) Additional, logically implied articulations;

(4) Visualizations of taxonomic provenance;

(5) Quantifications of name/meaning relations.

In summary (1) − What this approach can provide:

• Compatibility with contemporary Linnaean nomenclature (and PhyloCode too);

• Integration of many-to-many name/circumscription relationships across taxonomies;

• Reconciliation of traditional classifications with fully bifurcated phylogenies;

• Representation of monotypic concept lineages with congruent taxonomic extensions;

In summary (2) − Representation and reasoning abilities





• Accounting for insufficiently specified higher-level entities:

• Undersampled outgroup entities;

• Differentially sampled ingroup entities;

• Resolution of taxonomically overlapping entities and merge concepts;

• Differentiation of ostensive versus intensional readings of concept articulations;

• Representation of topologically localized resolution versus ambiguity in alignments.






• Accounting for insufficiently specified higher-level entities:

• Undersampled outgroup entities;

• Differentially sampled ingroup entities;

• Resolution of taxonomically overlapping entities and merge concepts;

• Differentiation of ostensive versus intensional readings of concept articulations;

• Representation of topologically localized resolution versus ambiguity in alignments.

• Next critical step(s): accessible, scalable, usable, integrated web instance of Euler/X


In summary (3) − Take-home message

We can explain (much of)

taxonomy's legacy to computers (e.g.)

for superior name/meaning resolution.

Well, then, should we?

And at what cost?

And, in the near future..?

A future beyond concept-to-concept alignments

Reasoning over the provenance / identity of:

• Taxonomic concepts;

• Concept-associated traits;

• Vouchered specimens.

Acknowledgments

• Euler/X team: Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shawn Bowers

& Bertram Ludäscher.

• Juliana Cardona-Duque, Charles O'Brien (Perelleschus), Naomi Pier (primates) &

Alan Weakley (Magnolia).

• taxonbytes lab members: Andrew Johnston & Guanyang Zhang.

• NSF DEB–1155984, DBI–1342595 (Franz); IIS–118088, DBI–1147273

(Ludäscher).

• Information @ http://taxonbytes.org/tag/concept-taxonomy/

• Euler/X code @ https://bitbucket.org/eulerx

• Euler server @ http://euler.asu.edu

https://sols.asu.edu/Franz Lab: http://taxonbytes.org/

http://taxonbytes.org/tag/concept-taxonomy/

https://bitbucket.org/eulerx

http://euler.asu.edu

https://sols.asu.edu/


Select references on concept taxonomy and the Euler/X toolkit

• Franz et al. 2008. On the use of taxonomic concepts in support of biodiversity

research and taxonomy. In: The New Taxonomy; pp. 63–86. Link

• Franz & Peet. 2009. Towards a language for mapping relationships among

taxonomic concepts. Systematics and Biodiversity 7: 5–20. Link

• Franz & Thau. 2010. Biological taxonomy and ontology development: Scope and

limitations. Biodiversity Informatics 7: 45–66. Link

• Chen et al. 2014. Euler/X: a toolkit for logic-based taxonomy integration. WFLP

2013 – 22nd International Workshop on Functional and (Constraint) Logic

Programming. Link

• Chen et al. 2014. A hybrid diagnosis approach combining Black-Box and White-

Box reasoning. Lecture Notes in Computer Science 8620: 127–141. Link

• Franz et al. 2014. Names are not good enough: Reasoning over taxonomic change in

the Andropogon complex. Semantic Web – Interoperability, Usability, Applicability –

Special Issue on Semantics for Biodiversity. (in press) Link

• Franz et al. 2014. Reasoning over taxonomic change: Exploring alignments for the

Perelleschus use case. PLoS ONE. (in press) Link

• Franz et al. 2015. Taxonomic provenance: Two influential primate classifications

logically aligned. (in preparation)

http://taxonbytes.org/pdf/FranzEtAl2008-UseTaxonomicConcepts.pdf

http://www.tandfonline.com/doi/abs/10.1017/S147720000800282X#.VBZQ7y5dVVM

http://taxonbytes.org/pdf/FranzThau2010-BiologicalTaxonomyOntologyDevelopment.pdf

http://arxiv.org/abs/1402.1992

http://link.springer.com/chapter/10.1007/978-3-319-09870-8_9

http://www.semantic-web-journal.net/system/files/swj623.pdf

http://arxiv.org/abs/1411.0940

Miscellaneous appended slides

T1 = Taxonomy 1

T2 = Taxonomy 2

A = Input articulations

[==, >, <, ><, |]

C = Taxonomic constraints

User/reasoner interaction: achieving well-specified alignments

Articulations are asserted

by taxonomic experts.

User/reasoner interaction: achieving well-specified alignments

MIR =Maximally Informative Relations

[==, >, <, ><, |]for each concept pair

Yes

Yes

Euler/X toolkit − Desktop version downloadable on Bitbucket

Alan Weakley 2014 (UNC Herbarium) - Magnolia concept evolution

R32 lattice of RCC-5 articulations (lighter color = less certainty)

The other piece in the puzzle: Concept-to-voucher identifications

Source: Baskauf & Webb. 214. Darwin-SW. URL: http://www.semantic-web-journal.net/system/files/swj635.pdf

http://www.semantic-web-journal.net/system/files/swj635.pdf

1986: Validation of

generic name.


+ 6 / - 1 species.



+ 2 species.

Focal alignments (today)

• 1986 versus 2001

• Classification / Phylogeny

• 2001 versus 2006

• Phylogeny / Exemplar Analysis

• 2001 versus 2013

• Phylogeny / Extended Phylogeny

2001 /

2013

Ostensive alignment

10 overlapping articulations

Species-level congruence

'Cascading' clade concepts


Congruent synapomorphies

reconfirmed across sub-

clades; with minor low-

level concept additions

Alignment 3 - Perelleschus sec. FOB (2001) versus sec. FCD (2013)

Franz 2014 ESA Aligning Insect Phylogenies Perelleschus and Other Cases

Science

Transcript of Franz 2014 ESA Aligning Insect Phylogenies Perelleschus and Other Cases