title: Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.
abstract: BACKGROUND
  Many metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation.
  
  
  RESULTS
  We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c.
  
  
  CONCLUSIONS
  A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.
authors.affiliation: Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77098, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Lv
authors.forename: Paul
authors.initials: P
authors.lastname: Havlak
authors.forename: Nicholas H
authors.initials: NH
authors.lastname: Putnam
mesh_terms: D000818:Animals; D002875:Chromosomes; D019143:Evolution, Molecular; D008040:Genetic Linkage; D016678:Genome; D006801:Humans; D007448:Invertebrates / Q000235:genetics; D008957:Models, Genetic; D012984:Software; D026801:Synteny