Analysing recombination in nucleotide sequences

Abstract

Throughout the living world, genetic recombination and nucleotide substitution are the primary processes that create the genetic variation upon which natural selection acts. Just as analyses of substitution patterns can reveal a great deal about evolution, so too can analyses of recombination. Evidence of genetic recombination within the genomes of apparently asexual species can equate with evidence of cryptic sexuality. In sexually reproducing species, nonrandom patterns of sequence exchange can provide direct evidence of population subdivisions that prevent certain individuals from mating. Although an interesting topic in its own right, an important reason for analysing recombination is to account for its potentially disruptive influences on various phylogenetic-based molecular evolution analyses. Specifically, the evolutionary histories of recombinant sequences cannot be accurately described by standard bifurcating phylogenetic trees. Taking recombination into account can therefore be pivotal to the success of selection, molecular clock and various other analyses that require adequate modelling of shared ancestry and draw increased power from accurately inferred phylogenetic trees. Here, we review various computational approaches to studying recombination and provide guidelines both on how to gain insights into this important evolutionary process and on how it can be properly accounted for during molecular evolution studies.

Global molecular genetic analysis of porcine circovirus type 2 (PCV2) sequences confirms the presence of four main PCV2 genotypes and reveals a rapid increase of PCV2d

“…The limited numbers of reported IM2-6 strains perhaps indicates a reduced fitness ultimately leading to extinction of these groups, as reported for some RNA viruses (Elena et al, 2000). Some of the IM strains may be relics of intermediate virus strains during PCV2 evolution or represent artificial recombinants, as sequence amplification artefacts during PCR with Taq polymerase have been reported previously (Martin et al, 2011).…”

Impermanence of bacterial clones

“…As might be expected, the power and accuracy of these algorithms are maximized when a donor sequence is included (imparting the source of homology between unrelated lineages) and when the recombinant sequence introduces many polymorphic nucleotides (43,46). Therefore, homoplasiescharacters that are inferred to be shared by, but not present in, the common ancestor of lineages-represent robust signals of recombination and provide a very fine (i.e., per nucleotide site) resolution of recombination maps, as have been performed recently for sequenced strains of Staphylococcus aureus (47).…”

Potential linkage between compound microsatellites and recombination in geminiviruses: Evidence from comparative analysis

“…In the evolution of ssDNA viruses, the rate of recombination and nucleotide substitution are closer to that in RNA viruses (Drake 1993;Martin et al, 2011). Besides rolling circle replication (RCR), geminiviruses also employ recombination dependent replication (RDR) strategy for their multiplication (Jeske et al, 2001;Preiss and Jeske, 2003).…”