Publication

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)