Mobile DNA elements in primate and human evolution

Abstract

Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements. The causes and evolutionary consequences of mobile element insertion, which have received considerable attention during the past decade, are reviewed in this article. Because of their unique mutational mechanisms, these elements are highly useful for answering phylogenetic questions. We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the humanchimpanzee-gorilla trichotomy and New World primate phylogeny. Alu and LINE1 element insertion polymorphisms have also been analyzed in human populations to test hypotheses about human evolution and population affinities and to address forensic issues. Finally, these elements have had impacts on the genome itself. We review how they have influenced fundamental ongoing processes like nonhomologous recombination, genomic deletion, and X chromosome inactivation. Yrbk Phys Mobile DNA elements are discrete DNA sequences that have the remarkable ability to transport or duplicate themselves to other regions of the genome. This process has been occurring in virtually all organisms for many millions of years. As a result, mobile elements are a major component of human and nonhuman primate genomes, accounting for 40-50% of their contents (Lander et al., 2001;CSAC, 2005;Gibbs et al., 2007). The properties and applications of these mobile elements have been the subject of increasing interest during the past two decades. In this review, we will focus on several areas in which the study of mobile elements has made significant contributions to physical anthropology.Because of their unique manner of propagating themselves in the genome, mobile elements are highly useful in tracing relationships of individuals, populations, and species. We will demonstrate how these elements have been used to resolve questions about primate systematics. We will then show how they have been useful in addressing questions about human origins, population affinities, and population history. The potential to use mobile elements as forensic tools, both in human and in nonhuman primates, will be discussed next. Finally, the presence of more than one million mobile elements in the primate genome has had a significant impact on processes such as nonhomologous recombination, genomic deletion and duplication, and gene conversion. The nature and consequences of this impact will be the final topic of the review. Before reviewing these applications, we begin with a brief discussion of the basic biology that underlies mobile elements and their behavior in the genome.

Mosaic retroposon insertion patterns in placental mammals

“…In strong contrast to most of the mammalian branches that we and others investigated previously with this method (e.g., Nishihara et al 2005Nishihara et al , 2006Huchon et al 2007;Möller-Krull et al 2007;Xing et al 2007;Warren et al 2008), we found a rare example of virtually equal support for three competing hypotheses ( Fig. 2B; Supplemental Table S1; .…”

New perspectives on anthropoid origins

“…3). Five SINEs support haplorhine monophyly to the exclusion of strepsirrhines and eight are shared among strepsirrhines (4). Thus, the haplorhine-strepsirrhine split may now be regarded as fact and must underlie any phylogenetic reconstruction of fossil primates.…”

“…Four peculiarities of embryonic implantation have been described (19). Extant anthropoids share 27 Alu-SINE markers (4). Most anthropoids have orbits that are relatively small, forward facing, and convergent (20).…”

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

“…These various effects have participated in evolution and speciation. It has been reported that some 8 Mb of primate sequence has been lost in the human lineage merely as the result of target site deletions induced by TE insertions (Xing et al, 2007). Similarly, bursts of pseudogene amplification often coincide with peaks of TE activity during evolution (Ohshima et al, 2003).…”