Punctuated duplication seeding events during the evolution of human chromosome 2p11

Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within human pericentromeric regions—areas of particularly rapid change in genomic structure. Here, we present a systematic analysis of the evolutionary history of one ∼700-kb region of 2p11, including the first autosomal transition from pericentromeric sequence to higher-order α-satellite DNA. We show that this region is composed of segmental duplications corresponding to 14 ancestral segments ranging in size from 4 kb to ∼115 kb. These duplicons show 94%–98.5% sequence identity to their ancestral loci. Comparative FISH and phylogenetic analysis indicate that these duplicons are differentially distributed in human, chimpanzee, and gorilla genomes, whereas baboon has a single putative ancestral locus for all but one of the duplications. Our analysis supports a model where duplicative transposition events occurred during a narrow window of evolution after the separation of the human/ape lineage from the Old World monkeys (10–20 million years ago). Although dramatic secondary dispersal events occurred during the radiation of the human, chimpanzee, and gorilla lineages, duplicative transposition seeding events of new material to this particular pericentromeric region abruptly ceased after this time period. The multiplicity of initial duplicative transpositions prior to the separation of humans and great-apes suggests a punctuated model for the formation of highly duplicated pericentromeric regions within the human genome. The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions

LTR Variation

<p>A total of 101 loci that contained full-length PTERV1 elements were examined for the number of mismatches between left and right LTR flanks (295 bp). Different distributions were obtained for Old World monkeys (baboon, mean = 1.6 ± 1.4; macaque, mean = 1.6 ± 1.5) and great ape species (chimpanzee, mean = 3.4 ± 2.2; gorilla, mean = 2.9 ± 2.3).</p

Identification and Sequence Analysis of PTERV1

<div><p>(A) A graphical alignment of chimpanzee genomic sequence (AC097267) and an orthologous segment from human Chromosome 16 (Build 34) depicting an example of a PTERV1 (approximately 10 kb) insertion. Aligned sequences are shown in blue (miropeats) [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#plbi-03-04-02-b47" target="_blank">47</a>].</p> <p>(B) The typical retroviral structure of the insert (<i>gag, pol, env,</i> and LTR) is compared to a baboon <i>(Papio cynocephalus)</i> endogenous retrovirus (PcEV). Regions of nucleotide homology are designated by black blocks and inter-sequence connecting lines. The location of probes (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st001" target="_blank">Table S1</a>) used in genomic library hybridizations, Southern blot analyses, and neighbor-joining tree analyses are shown (red).</p></div

PTERV1 Insertion Sites

<p>Large-insert genomic clones that contained full-length endogenous retrovirus were identified by hybridization from four species: chimpanzee (PTR), gorilla (GGO), baboon (PAN), and rhesus macaque (MMU). End sequencing of large-insert clones (<i>n</i> = 1,467) and alignment against the human genome reference sequence identified 287 insertion sites (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st002" target="_blank">Table S2</a>). A total of 95.8% of these sites were non-orthologous when compared between species. chr, chromosome.</p

Southern Hybridization of PTERV1 among Primates

<div><p>Species represented include human (HSA), common chimpanzee (PTR), bonobo (PPA), gorilla (GGO), orangutan (PPY), siamang (HSY), white-handed gibbon (HLA), Abyssinian black-and-white colobus monkey (CGU), olive baboon (PHA), rhesus macaque (MMU), and Japanese macaque (MFU). Below each panel, a restriction map (chimpanzee sequence AC097267) is presented in relation to the hybridization probe: PstI (closed circles), PvuII (open circles), and HpaII/MspI (triangles) (see Figures <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#sg001" target="_blank">S1</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#sg002" target="_blank">S2</a> for additional details).</p> <p>(A) The absence of PTERV1 among Asian apes and humans is shown in contrast to a generally accepted catarrhine species phylogeny. Primate DNAs have been digested with PstI restriction enzyme, Southern-transferred to nylon membrane, and hybridized with PTERV1 <i>gag</i> probe number 1.</p> <p>(B) Multiple African great ape species are compared for both the <i>gag</i> probe number 1 and <i>env</i> probe number 3 (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#pbio-0030110-g001" target="_blank">Figure 1</a>). Proximity of probe number 1 to the VNTR, which is variable in length between copies (400 bp to 10 kb), reveals hundreds of insertion sites.</p> <p>(C) Multiple individuals from different subspecies of the olive baboon are compared for both <i>gag</i> probe number 1 and <i>env</i> probe number 3. The pattern of Southern hybridization shows limited intra-specific variation, indicative of either polymorphism in restriction enzyme sites or copy number variation.</p></div

PTERV1 Phylogenetic Tree

<p>Portions of the <i>gag</i> and <i>env</i> genes (about 823 bp) were resequenced from 101 PTERV1 elements from common chimpanzee (<i>n</i> = 42), gorilla (<i>n</i> = 25), rhesus macaque (<i>n</i> = 14), and olive baboon (<i>n</i> = 20). A neighbor-joining phylogenetic tree shows a monophyletic origin for the gorilla and chimpanzee endogenous retroviruses but a polyphyletic origin among the Old World monkey species. Bootstrap support (<i>n</i> = 10,000 replicates) for individual branches are underlined. Although the retroviral insertions have occurred after speciation, retroviral sequences show greater divergence than expected for a non-coding nuclear DNA element (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st004" target="_blank">Table S4</a>). <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st008" target="_blank">Table S8</a> provides a clone key for number designation. Phylogenetic trees showing the <i>gag, env,</i> and LTR segments separately are presented in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#sg006" target="_blank">Figure S6</a>. Sequences 11 and 30 (red) are mapped to one of the 12 ambiguous overlapping loci described in the text (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030110#st003" target="_blank">Table S3</a>). They do not cluster in this phylogenetic tree, which indicates that they are unlikely to be true orthologs.</p