# Predicting the Evolution of Syntenies--An Algorithmic Review
## 1 Introduction  
Genes are the basic units of heredity containing the genetic information responsible for the functioning of a cell. During evolution, they are mutated, duplicated, lost and passed to organisms through speciation, the evolutionary process by which a population evolves to become a distinct species, or Horizontal Gene Transfers (HGT), largely shaping the evolution of bacteria, where genes are passed from one species to another. In addition, their order on the genome is modified through various rearrangement events, such as inversions, transpositions or translocations. See Figure 1(1) for an evolutionary history of gene sequences involving a variety of rearrangement, duplication and loss events, and Figure 1(2) for an evolutionary history of a single gene family also involving a HGT event. Although mutations modifying genomic contents (gene gain and loss) and rearrangements modifying gene orders play a concerted role in shaping gene families, they are usually considered separately: gene gain and loss in the context of inferring the evolution of a given gene family, and rearrangements in the context of understanding genome evolution. In other words, in contrast to rearrangements, gain and loss events are usually considered to be single gene events. For a given gene family \(\Gamma\) with gene copies located in a set \(\Sigma\) of genomes, a gene tree \(T\) for \(\Gamma\) (representing the evolution of the gene sequences through nucleotide or amino acid mutations) and a species tree \(S\) for \(\Sigma\), the reconciliation approach [2] consists of inferring the evolution of \(\Gamma\) by embedding \(T\) into \(S\) and explaining the incongruence between the two trees from duplications, losses or HGT events that would have obscured the speciation scenario. Reconciliation is based on the assumption that each gene family evolves independently. Although this hypothesis holds for genes that are far apart in the genome, it is clearly too restrictive for those grouped into syntenies, i.e., forming a set of _homologous_ chromosomal regions, meaning that they are deriving from a common ancestral interval, with approximately the same gene content and order. Although convergent evolution should not be excluded, such co-linear sequences of genes are more plausibly the result of a concerted evolution from a common ancestral region, rather than of an independent set of gene duplications that would have generated the same gene organization in different genomic regions. The neuropeptide Y-family receptors [3], the Homeobox gene clusters [4; 5; 6], the FGFR fibroblast growth factor receptors [7; 8], the genes of the opioid system [9; 10; 11] or the major histocompatibility complex encoding numerous immunologically vital genes playing an imperative role in controlling the vertebrate adaptive immunity [12], are a few examples of genes organized in syntenies in human, as well as in numerous vertebrate genomes. Many of these gene families, appearing in potentially quadruplicated regions in human and other mammalian genomes, have been considered to be evidence of the \"2R hypothesis\" [13] assessing two rounds of whole genome duplication events in the evolution leading to the contemporary vertebrate genomes. Transposed duplications copying genes or chromosomal segments from an original locus to a new one also play an important role in the evolution of syntenies. Being able to make the difference between the two modes of evolution is also important [14]. Figure 1: **(1)** An evolutionary history of syntenic regions, inspired by Figure 4 in [1], representing the evolution of tRNA repertoires in the _Bacillus_ genus. The tree represents the speciation history of a set of _Bacillus_ species. Each colored arrow represents a block of tRNAs, following the operon subdivision available for _B. cereus_. Two arrows of the same color represents a duplicated block. Gray rectangles indicate the segment affected by an inversion.