The phylogenetic history of New World monkey β globin reveals a platyrrhine β to δ gene conversion in the atelid ancestry

Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting

“…The reciprocal painting results, in general, support the molecular genomic assemblage of Cebidae [36-38,40,41]. We demonstrated that the five chromosome associations, which phylogenetically link tamarins and marmosets are homologous and derive from shared chromosome rearrangements in a common ancestor (table 1).…”

Repeated Evolution of Chimeric Fusion Genes in the β-Globin Gene Family of Laurasiatherian Mammals

“…In contrast, functionally intact copies of the reciprocal HBD / HBB fusion gene appear to be completely absent. Second, contrary to conventional wisdom that the HBD gene is a vestigial relict that is always either inactivated or expressed at negligible levels (Martin et al 1983; Hardies et al 1984; Hardison 1984; Hardison and Margot 1984; Koop et al 1989; Prychitko et al 2005), we identified a surprisingly large number of laurasiatherian taxa in which the β-type subunits of adult-expressed Hb contain HBD -like primary structures. Taken together, our results confirm that the retention and ascendancy of genes with HBD -like coding sequence require the retention of HBB -like promoter sequence via unequal crossing-over or the secondary acquisition of HBB -like promoter sequence via gene conversion.…”

“…The rationale for conducting phylogenetic analyses on each of these different data partitions is that interparalog gene conversion between tandemly duplicated globin genes is typically restricted to coding sequence, so noncoding flanking sequence typically records the most accurate history of gene duplication and species divergence (Hardison and Gelinas 1986; Hoffmann and Storz 2007; Storz et al 2007, 2008, 2009, 2010, 2012; Hoffmann et al 2008a, 2008b; Opazo et al 2008a, 2008b, 2009; Runck et al 2009, 2010). In the case of mammalian HBD , ectopic recombinational exchanges are typically restricted to the 5′-end of the gene as HBB → HBD conversion events typically overwrite exon 1, intron 1, and exon 2 of the HBD recipient sequence (Hardies et al 1984; Hardison 1984; Hardison and Margot 1984; Prychtiko et al 2005; Hoffmann et al 2008a; Opazo et al 2008b, 2009). Thus, sequence variation in intron 2 and the 3′-flanking region is best suited to the task of assigning orthology, and comparisons of 5′- and 3′-flanking regions can reveal whether chimeric fusion genes were created via unequal crossing-over or gene conversion (Hoffmann et al 2008b; Opazo et al 2009).…”

“…1), and these exchanges appear to be highly asymmetric, as the coding region of HBD has been converted by the downstream HBB gene in multiple lineages, particularly in the 5′-coding region (Jeffreys et al 1982; Martin et al 1983; Goodman et al 1984; Hardies et al 1984; Hardison 1984; Hardison and Margot 1984; Koop et al 1989; Tagle et al 1991; Prychitko et al 2005; Hoffmann et al 2008a; Opazo et al 2008a). However, these events typically result in HBD coding sequence that is fused to HBB -like upstream sequence that does not extend to the HBB CCAAT promoter element (Hardies et al 1984; Koop et al 1989), so that expression levels of the resultant fusion gene are not altered.…”

Molecular Phylogeny and Evolution in Primates

“…Recent studies using nuclear DNA data also suggested the same topology ( Fig. 16.5b ), although the support for the position of the Pitheciidae was not as strong and depends on the methods used in the analyses (von Dornum and Ruvolo 1999 ;Steiper and Ruvolo 2003 ;Prychitko et al 2005 ;Opazo et al 2006 ) . Furthermore, Ray et al ( 2005 ) provided robust support for the latter topology, which has a sister relationship between the Atelidae and Cebidae, by SINE analyses.…”