array(14 items) uid => 725 (integer) title => 'Relative Timing Information and Orthology inEvolutionary Scenarios' (66 chars) abstract => 'Background: Evolutionary scenarios describing the evolution of a family of g
enes within a collection of species comprise the mapping of the vertices of
a gene tree T to vertices and edges of a species tree S. The relative timing
of the last common ancestors of two extant genes (leaves of T) and the last
common ancestors of the two species (leaves of S) in which they reside is i
ndicative of horizontal gene transfers (HGT) and ancient duplications. Ortho
logous gene pairs, on the other hand, require that their last common ancesto
rs coincides with a corresponding speciation event. The relative timing info
rmation of gene and species divergences is captured by three colored graphs
that have the extant genes as vertices and the species in which the genes ar
e found as vertex colors: the equal-divergence-time (EDT) graph, the later-d
ivergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which
together form an edge partition of the complete graph. Results: Here we giv
e a complete characterization in terms of informative and forbidden triples
that can be read off the three graphs and provide a polynomial time algorith
m for constructing an evolutionary scenario that explains the graphs, provid
ed such a scenario exists. While both LDT and PDT graphs are cographs, this
is not true for the EDT graph in general. We show that every EDT graph is pe
rfect. While the information about LDT and PDT graphs is necessary to recogn
ize EDT graphs in polynomial-time for general scenarios, this extra informat
ion can be dropped in the HGT-free case. However, recognition of EDT graphs
without knowledge of putative LDT and PDT graphs is NP-complete for general
scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We
finally connect the EDT graph to the alternative definitions of orthology th
at have been proposed for scenarios with horizontal gene transfer. With one
exception, the corresponding graphs are shown to be colored cographs.' (1969 chars) authors => array(6 items) 0 => array(3 items) last_name => 'Schaller' (8 chars) first_name => 'David' (5 chars) sorting => 1 (integer) 1 => array(3 items) last_name => 'Hartmann' (8 chars) first_name => 'Tom' (3 chars) sorting => 2 (integer) 2 => array(3 items) last_name => 'Lafond' (6 chars) first_name => 'Manül' (6 chars) sorting => 3 (integer) 3 => array(3 items) last_name => 'Stadler' (7 chars) first_name => 'Peter Florian' (13 chars) sorting => 4 (integer) 4 => array(3 items) last_name => 'Wieseke' (7 chars) first_name => 'Nicolas' (7 chars) sorting => 5 (integer) 5 => array(3 items) last_name => 'Hellmuth' (8 chars) first_name => 'Marc' (4 chars) sorting => 6 (integer) type => '0' (1 chars) keywords => '' (0 chars) year => 2023 (integer) affiliation => 0 (integer) link_paper => 'https://www.researchsquare.com/article/rs-2678762/v1' (52 chars) link_supplements => '' (0 chars) file_published => 0 (integer) journal => '' (0 chars) doi => '10.21203/rs.3.rs-2678762/v1' (27 chars) preprint => '-1' (2 chars)
Relative Timing Information and Orthology inEvolutionary Scenarios
2023: David Schaller; Tom Hartmann; Manül Lafond; Peter Florian Stadler; Nicolas Wieseke; Marc HellmuthLink to Publication DOI: 10.21203/rs.3.rs-2678762/v1
Background: Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree T to vertices and edges of a species tree S. The relative timing of the last common ancestors of two extant genes (leaves of T) and the last common ancestors of the two species (leaves of S) in which they reside is indicative of horizontal gene transfers (HGT) and ancient duplications. Orthologous gene pairs, on the other hand, require that their last common ancestors coincides with a corresponding speciation event. The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph. Results: Here we give a complete characterization in terms of informative and forbidden triples that can be read off the three graphs and provide a polynomial time algorithm for constructing an evolutionary scenario that explains the graphs, provided such a scenario exists. While both LDT and PDT graphs are cographs, this is not true for the EDT graph in general. We show that every EDT graph is perfect. While the information about LDT and PDT graphs is necessary to recognize EDT graphs in polynomial-time for general scenarios, this extra information can be dropped in the HGT-free case. However, recognition of EDT graphs without knowledge of putative LDT and PDT graphs is NP-complete for general scenarios. In contrast, PDT graphs can be recognized in polynomial-time. We finally connect the EDT graph to the alternative definitions of orthology that have been proposed for scenarios with horizontal gene transfer. With one exception, the corresponding graphs are shown to be colored cographs.