franz et al evol 2016 representing phylogeny as a logically tractable variable

Representing phylogeny asa logically tractable variable

Please

@taxonbytes

Nico M. Franz1 , Guanyang Zhang1, Shizhuo Yu2 & Bertram Ludäscher3

1 School of Life Sciences, Arizona State University2 Computer Science, University of California at Davis 3 iSchool, University of Illinois at Urbana-Champaign

Systematics / Bioinformatics Session – Evolution 2016 MeetingsJune 20, 2016 - Austin, Texas (#Evol2016)

@ http://www.slideshare.net/taxonbytes/franz-et-al-evol-2016-representing-phylogeny-as-a-logically-tractable-variable

https://twitter.com/taxonbytes

http://www.slideshare.net/taxonbytes/franz-et-al-escjam-2015-logic-resolution-taxonomic-variable



Source: Thomas, G.H. 2015. An avian explosion. Nature 526: 516–517. doi:10.1038/nature15638

2015 2014

Phylogenetic inferencescan vary over time.

Querying phylogenetic advancement – premises & questions

• The term "tree of life" characterizes a goal that we strive to reach eventually, more so than where we are now (for many perceived groups).


• Therefore it would be useful to have a "phylogenetic knowledge advancement service". The service satisfies queries such as:




1. "Does this sequence of related phylogenetic inferenceshave a stabilizing or destabilizing trend?"





2. "Are two or more phylogenies – each differentially sub-sampledat lower levels – in congruence or in conflict?"






3. "How can an evolutionary study tied to one (earlier) phylogenybe "updated" (integrated) with another (later) phylogeny?"






3. "How can an evolutionary study tied to one (earlier) phylogenybe "updated" (integrated) with another (later) phylogeny?"


Service We can prioritize research agendas accordingly.

Service Sampling an issue? Or are signals complementary?

Service Effects of "phylogenetic variable" on conclusions can be controlled for.

Research question:

How to build such a service?

Phylogenetic advancement service – design specifications

Example service queries:

1. Do succeeding inferences have stabilizing or destabilizing trends?

2. Are multiple, differentially sub-sampled phylogenies congruent or conflicting?

3. How to control for the "phylogenetic variable" affecting evolutionary inferences?






• The service needs more granular identifiers than "just Linnaean names" to account for study-specific phylogenetic (sub-)tree concepts.







• The service needs identifier-to-identifier relationships that match the query semantics by representing congruence, conflict, and achieving reconciliation across concepts associated with multiple inferences.







• The service needs identifier-to-identifier relationships that match the query semantics by representing congruence, conflict, and achieving reconciliation across concepts associated with multiple inferences.

• Compatibility with both human cognitive constraints1 and computational logic is desirable to balance service quality (allowing expert interactions) with scalability (semi-automated reasoning products).

1 Atran, S. 1998. Folk biology and the anthropology of science: cognitive universals and cultural particulars. Behavioral and Brain Sciences 21: 547–569.

Proposed solution: Euler/X – logically consistent RCC–5 alignments

• Input: multiple taxonomies and/or phylogenies; expert-provided articulations

• Output: logic consistency checking; Maximally Informative Relations (MIR); alignment visualizations

Source: Thau, D.M. 2010. Reasoning about taxonomies. Thesis, UC Davis. http://gradworks.proquest.com/3422778.pdf

Region Connection Calculus (RCC–5) articulations

• Two regions N, M are either:

• congruent (N == M)• properly inclusive (N < M)• inversely properly inclusive (N > M)• overlapping (N >< M)• exclusive of each other (N ! M)

http://gradworks.proquest.com/3422778.pdf



Source: Thau, D.M. 2010. Reasoning about taxonomies. Thesis, UC Davis. http://gradworks.proquest.com/3422778.pdf

Region Connection Calculus (RCC–5) articulations

• Two regions N, M are either:

• congruent (N == M)• properly inclusive (N < M)• inversely properly inclusive (N > M)• overlapping (N >< M)• exclusive of each other (N ! M)

• RCC–5 articulations match the query: "can we join regions N and M?"

• Phylogenies have multiple RCC–5 alignable components: nodes (parents, children), node-associated traits, even node-anchoring specimens




Overview of RCC–5 alignment use cases

1. Two primate classifications – MSW2 (1993) versus MSW3 (2005)

a. Microcebus + Mirza sec. MSW3 (2005)b. Quantifying name (identifier) reliabilityc. Reasoning achieves scalability (matrix)

2. Lorisiformes sec. MSW3 (2005) versus Springer et al. (2012) phylogeny

a. Phylogeny refines classificationb. Sampling causes non-congruence

3. Avian phylogenies sec. Prum et al. (2015) versus Jarvis et al. (2014)

a. Psittaciformes with & without coverageb. Precise semiotics for the "avian explosion"

Use case 1:

Two primate classifications –

MSW2 (1993) versus MSW3 (2005)

Use case 1.a. Aligning Microcebus + Mirza sec. MSW3 (2005)

"Taxonomic concept labels"identify input concept regions

RCC–5 articulations providedfor each species-level concept

• Input visualization: MSW3 (2005) versus MSW2 (1993)

Source: Franz et al. 2016. Two influential primate classifications logical aligned. Systematic Biology 65: 561–582.

• Alignment visualization: "grey means congruent"


One name &congruent region




Many names &congruent region





One name &non-congruent regions






Many names &non-congruent regions







New names &exclusive regions








• Application of coverage constraint: parent-to-parent articulations (><) are fully defined by alignment signal propagated from their respective children.

Sensible when complete sampling of children is intended.



Use case 1.b.: Quantifying name (identifier) reliability


• Alignment visualization: RCC–5 as an identifier assessment tool [good / not]






• Alignment visualization: RCC–5 as an identifier assessment tool [good / not]





• Query services rendered: (1) MSW3 destabilizes MSW2; (2) non-congruence is not only caused by differential low-level sampling; (3) alignment constitutes a taxonomic meaning integration map to navigate across MSW3 & MSW2.

Use case 1.b.: Quantifying name (identifier) reliability

Source: Franz et al. 2016. Two influential primate classifications logical aligned. Systematic Biology 65: 561–582.

1 in 3 names are unreliable across MSW2/MSW3 classifications

Use case 1.c.: Reasoning achieves scalability (MIR matrix)

Source: Dang et al. 2015. ProvenanceMatrix: a visualization tool for multi-taxonomy alignments. CEUR Workshop Proceedings 1456: 13–24. http://ceur-ws.org/Vol-1456/paper2.pdf

• Input: 402 articulations. Output: 153,111 Maximally Informative Relations

Salmon cells↔ reasoning

http://ceur-ws.org/Vol-1456/paper2.pdf



Use case 2:

Lorisiformes sec. MSW3 versus

Springer et al. (2012) phylogeny

Use case 2.a.: Phylogeny (2012) refines classification (2005)

Springer et al. (2012) @ OpenTree https://tree.opentreeoflife.org/curator/study/view/pg_2656

https://tree.opentreeoflife.org/curator/study/view/pg_2656



Convert OpenTree-supported NeXML files into Euler/X input (credit: Daisie Huang): https://github.com/daisieh/phylogenomics/blob/master/converting/nexml_to_euler.py & https://github.com/daisieh/phylogenomics/blob/master/converting/relabel_euler.py


Euler/X input visualization


https://github.com/daisieh/phylogenomics/blob/master/converting/nexml_to_euler.py



https://github.com/daisieh/phylogenomics/blob/master/converting/relabel_euler.py






Convert OpenTree-supported NeXML files into Euler/X input (credit: Daisie Huang): https://github.com/daisieh/phylogenomics/blob/master/converting/nexml_to_euler.py & https://github.com/daisieh/phylogenomics/blob/master/converting/relabel_euler.py


Euler/X input visualization

MSW3 (2005)











Alignment visualization


• At low-to-mid levels, phylogeny often congruently refines classification.

Congruent refinement



• At low-to-mid levels, phylogeny often congruently refines classification.


Unique species concepts



Use case 2.b.: Sampling alone causes high-level non-congruence

• At low-to-mid levels, phylogeny often congruently refines classification.• However, differential low-level sampling causes 'excessive' non-congruence

at higher levels that may not reflect the authors' intentions.


Unique species concepts

Higher level conflict


Use case 3:

Avian phylogenies sec. Prum et al. (2015)

versus Jarvis et al. (2014)

Source: Thomas, G.H. 2015. An avian explosion. Nature 526: 516–517. doi:10.1038/nature15638

2015 2014

Let's recall..

Use case 3: Aves sec. Prum et al. (2015) versus Jarvis et al. (2014)

• Sampling is highly differential: 198 versus 48 species-level entities• Only 12 species-level concept pairs are congruent [green cells]

Use case 3.a.: Psittaciformes with & without coverage constraint

• Psittaciformes sec. 2015 – with global coverage constraint

Input visualization Only disjoint articulations

• Psittaciformes sec. 2015 – with global coverage constraint• No low-level congruence ↔ no congruent alignment regions

Input visualization Only disjoint articulations

Alignment visualization 108 MIR; all disjoint


• Psittaciformes sec. 2015 – with coverage locally relaxed

Input visualization


• Psittaciformes sec. 2015 – with coverage locally relaxed• No coverage constraint for 2014/2015.[Psittacidae, Nestor]

Input visualization


• Psittaciformes sec. 2015 – with coverage locally relaxed• No coverage constraint for 2014/2015.[Psittacidae, Nestor]

• Allows for 3 congruent & 7 inclusive RCC–5 articulations

Input visualization


• Psittaciformes sec. 2015 – with coverage locally relaxed• Higher-level congruence despite low-level non-congruence

• 160 MIR: 10 congruent; 65 (inversely) properly inclusive



• Psittaciformes sec. 2015 – with coverage locally relaxed• Higher-level congruence despite low-level non-congruence

• 160 MIR: 10 congruent; 65 (inversely) properly inclusive


Additional 2015 low-level sampling


Use case 3.b.: Precise semiotics for the "avian explosion"

• Aves sec. 2015/2014, down to ordinal level – with coverage locally relaxed


Non-congruence within2015.Paleognathae Non-congruence within

2014.Pelecanimorphae



Non-congruence within2015/2014.Neoaves

(see next slide)


• Neoaves sec. 2015/2014, and 3–4 less inclusive levels

26 overlapping articulations in the sub- Neoavian alignment region cannot be assigned to differential sampling 'Genuine' phylogenetic conflict


Example service queries:1. Do succeeding inferences have stabilizing or destabilizing trends?2. Are multiple, differentially sub-sampled

phylogenies congruent or conflicting?3. How to control for the "phylogenetic variable" affecting evolutionary inferences?

In conclusion:

How to build such a service?

Creating a Phylogenetic Knowledge Advancement Service

• Explicitly represent human theories, and only indirectly taxa (species, clades).

• Identify study-specific phylogenetic (sub-)tree concepts with precision.




• Utilize identifier-to-identifier relationships to represent the multi-component nature of phylogenetic congruence & non-congruence:• RCC–5 for nodes & terminals: w/o coverage ( sampling)• RCC–5 for character concepts & specimen sets (not shown)





• Excel at representing and explaining conflict, as opposed to 'voting' (which is external, a posteriori); enforce multi-theory alignment, not synthesis.





• Excel at representing and explaining conflict, as opposed to 'voting' (which is external, a posteriori); enforce multi-theory alignment, not synthesis.

• Explicitly identify speaker intentions – by modeling phylogenetically localized intentions of semantic precision (and in what specific sense?) versus ambiguity – vis-à-vis their own products, and in relation to those of other author teams. Otherwise, signal interpretation remains unreliable.

Acknowledgements & links to products and references

• Euler/X team: Shawn Bowers, Parisa Kianmajd, Timothy McPhillips.

• ProvenanceMatrix: Tuan Nhon Dang.

• NSF DEB–1155984, DBI–1342595 (PI Franz).• NSF IIS–118088, DBI–1147273 (PI Ludäscher).

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

• Euler/X code @ https://github.com/EulerProject/EulerX

• Franz et al. 2015. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE 10(2): e0118247. Link

• Franz et al. 2016. Two influential primate classifications logically aligned. Systematic Biology 65(4): 561–582. Link

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

https://github.com/EulerProject/EulerX

https://github.com/EulerProject/EulerX

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118247

http://sysbio.oxfordjournals.org/content/65/4/561.abstract

Interested in exploringmulti-phylogeny alignments?

Please contact me.

[email protected]@taxonbytes

https://biokic.asu.edu/