Aligning multiple

incongruent phylogenies

with the Euler/X toolkit

Please

@taxonbytes

Nico M. Franz1 , Shizhuo Yu2 & Bertram Ludäscher3

1 School of Life Sciences, Arizona State University

2 Computer Science, University of California at Davis

3 iSchool, University of Illinois at Urbana-Champaign

iEvoBio Lightning Talk – Evolution 2016 Meetings

June 21, 2016 - Austin, Texas (#Evol2016, #iEvoBio)

@ http://www.slideshare.net/taxonbytes/franz-et-al-evol-2016-aligning-multiple-incongruent-phylogenies-with-the-eulerx-toolkit

https://github.com/

EulerProject

Read more at doi:10.1093/sysbio/syw023

Euler/X toolkit workflow – goal: consistent RCC–5 alignments

Source: Franz et al. 2015. Reasoning over taxonomic change: the Perelleschus use case. PLoS ONE 10(2): e0118247.

Input constraints:

T1 = Tree 1

T2 = Tree 2

...

A = Articulations

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

C = Other constraints

Articulations provided

by human (expert) users.

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 answer the question: "can we join regions N and M?"

Use case:

Avian phylogenies sec. Prum et al. (2015)

versus Jarvis et al. (2014)

2014: 48 terminals 2015: 198 terminals

doi:10.1126/science.1253451 doi:10.1038/nature15697

Subtree alignment: Columbaves sec. Prum et al. (2015)

Columbimorphae + Otidimorphae sec. Jarvis et al. (2014)

Columbaves sec. Prum et al. (2015)

non-monophyletic

sec. 2014

2014 vs. 2015: Deliberately differential low-level sub-sampling

• Only 2 species-level concept pairs are congruent

• Yet also: no 'true' (intensional) non-congruence at species-to-family level

(We can model this in logic by relaxing the coverage constraint for parents)

2014./2015.Pterocles alignment with locally relaxed coverage

• The coverage constraint in Euler/X specifies that the region of a parent is

fully determined (extensionally) by the entirety of the parent's children.

This is the default setting.

• However, coverage is locally relaxable; allowing us to express parent-to-

parent congruence in spite of their reciprocally non-congruent children.

Euler/X input constraints

parent child 1 no parent coverage

parent child 1 no parent

coverage

Parent-to-parent congruence

2014./2015.Pterocles alignment with locally relaxed coverage

• The coverage constraint in Euler/X specifies that the region of a parent is

fully determined (extensionally) by the entirety of the parent's children.

This is the default setting.

• However, coverage is locally relaxable; allowing us to express parent-to-

parent congruence in spite of their reciprocally non-congruent children.

Euler/X input visualization

Parent-to-parent congruence

2014./2015.Pterocles alignment with locally relaxed coverage

• The coverage constraint in Euler/X specifies that the region of a parent is

fully determined (extensionally) by the entirety of the parent's children.

This is the default setting.

• However, coverage is locally relaxable; allowing us to express parent-to-

parent congruence in spite of their reciprocally non-congruent children.

Euler/X alignment visualization

Parent-to-parent congruence

Scaled up to Columbaves sec. Prum et al. 2015

Euler/X input constraints CLI: "align" & "show" commands

Reasoning & visualization products

Alignment visualization recovers intensional 2014/2015 congruence

• There is only one higher-level, intensionally non-congruent alignment region

Overlapping

clade concepts

• 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).

• Euler/X can provide syntax and semantics for a "phylogenetic knowledge

advancement service". The service satisfies queries such as:

1. "Does this sequence of related phylogenetic inferences

have a stabilizing or destabilizing trend?"

2. "Are two or more phylogenies – each differentially sub-sampled

at lower levels – in congruence or in conflict?"

3. "How can an evolutionary study tied to one (earlier) phylogeny

be "updated" (integrated) with another (later) phylogeny?"

Novel (logic) semiotics for assessing phylogenetic advancement

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.

Acknowledgements & links to products and references

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

• Explorer of Taxon Concepts: Hong Cui, Thomas Rodenhausen.

• 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