A Comparative Approach Shows Differences in Patterns of Numt Insertion During Hominoid Evolution

Abstract

Nuclear integrations of mitochondrial DNA (numts) are widespread among eukaryotes although their prevalence differs greatly among taxa. Most knowledge of numt evolution comes from analyses of whole genome sequences of single species, or more recently from genomic comparisons across vast phylogenetic distances. Here, we employ a comparative approach using human and chimpanzee genome sequence data to infer differences in the patterns and processes underlying numt integrations. We identified 66 numts that have integrated into the chimpanzee nuclear genome since the human-chimp divergence, which is significantly greater than the 37 observed in humans. By comparing these closely related species, we accurately reconstructed the pre-integration target site sequence, and deduced nucleotide changes associated with numt integration. From over 100 species-specific numts, we quantified the frequency of small insertions, deletions, duplications, and instances of microhomology. Most human and chimpanzee numt integrations were accompanied by microhomology and short indels of the kind typically observed in the nonhomologous end-joining pathway of DNA double-strand break repair. Human-specific numts have integrated into regions with a significant deficit of transposable elements, while the same was not seen in chimpanzees. From a separate dataset, we also found evidence for an apparent increase in the rate of numt insertions in the last common ancestor of humans and the great apes using a PCR-based screen. Lastly, phylogenetic analyses indicate that mitochondrial-numt alignments must be at least 500bp, and preferably greater than 1kb in length, in order to accurately reconstruct hominoid phylogeny and recover the correct point of numt insertion.

The genomic landscape of polymorphic human nuclear mitochondrial insertions

“…Fixed NumtS were previously identified as human-specific (19) and are present in the human reference sequence (hg19) as well as every 1000 Genomes sample assessed (38). Polymorphic sequences were chosen from among the longest insertions that were identified.…”

Polymorphic NumtS trace human population relationships

“…Following this procedure, we were able to identify 53 NumtS which were predicted to be absent in the following primate species: chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus abelii), rhesus macaque (Macaca mulatta), and marmoset (Callithrix jacchus), thus increasing the number of previously listed human-speciWc NumtS by approximately 32% (Jensen-Seaman et al 2009; Hazkani-Covo 2009) ( Table 2). None of these human-speciWc NumtS appeared to originate from segmental duplications.…”

“…As most NumtS are thought to derive from single insertion events, excluding the possibility of similarity due to convergent evolution, NumtS may thus be considered as loci free of molecular homoplasy (Zischler 2000;Hazkani-Covo 2009), a characteristic which makes them very good candidates as reliable phylogenetic markers. Comparison of the presence/ absence of NumtS between human, chimpanzee and other primates' genomes has indeed allowed the reconstruction of an accurate primate phylogeny (Hazkani-Covo and Graur 2007;Jensen-Seaman et al 2009). Lastly, the insertion of novel NumtS into the human genome is also thought to be an ongoing process, as suggested by diseasecausing insertions of mitochondrial fragments into proteincoding genes (Willett-Brozick et al 2001;Turner et al 2003;Goldin et al 2004;Chen et al 2005).…”

Analysis of the complete mitochondrial genome and characterization of diverse NUMTs of Macaca leonina

“…After their insertion into the nucleus, NUMTs are not subjected to mitochondrial selective pressure (Perna and Kocher, 1996;Bensasson et al, 2001) and the mutation rate of NUMTs is on average around one order of magnitude slower than the mitochondrial genome (Brown et al, 1982;Lopez et al, 1997). For this reason, NUMTs are commonly believed to be "fossilized" copies of ancient mitochondrial lineages as they are more similar to the ancestral mitochondrial haplotype than the modern mitochondrial counterpart (Perna and Kocher, 1996;Bensasson et al, 2001;Jensen-Seaman et al, 2009). As a result, NUMTs offer good opportunities for the study of mtDNA evolution, and NUMTs can be used as markers for inferring phylogenies (Hazkani-Covo, 2009).…”