Gary D. Swergold

Tracing the LINEs of human evolution

The amplification of DNA by LINE-1 (L1) retrotransposons has created a large fraction of the human genome. To better understand their role in human evolution we endeavored to delineate the L1 elements that have amplified since the emergence of the hominid lineage. We used an approach based on shared sequence variants to trace backwards from the currently amplifying Ta subfamily. The newly identified groups of insertions account for much of the molecular evolution of human L1s. We report the identification of a L1 subfamily that amplified both before and after the divergence of humans from our closest extant relatives. Progressively more modern groups of L1s include greater numbers of insertions. Our data are consistent with the hypothesis that the rate of L1 amplification has been increasing during recent human evolution.

Large Differences between LINE-1 Amplification Rates in the Human and Chimpanzee Lineages

The genomic evolution and causes of phenotypic variation among humans and great apes remain largely unknown, although the phylogenetic relationships among them have been extensively explored. Previous studies that focus on differences at the amino acid and nucleotide sequence levels have revealed a high degree of similarity between humans and chimpanzees, suggesting that other types of genomic change may have contributed to the relatively large phenotypic differences between them. For example, the activity of long interspersed element 1 (LINE-1) retrotransposons may impose significant changes on genomic structure and function and, consequently, on phenotype. Here we investigate the relative rates of LINE-1 amplification in the lineages leading to humans, bonobos (Pan paniscus), and chimpanzees (P. troglodytes). Our data indicate that LINE-1 insertions have accumulated at significantly greater rates in bonobos and chimpanzees than in humans, provide insights into the timing of major LINE-1 amplification events during great ape evolution, and identify a Pan-specific LINE-1 subfamily.

Interspersed repeat insertion polymorphisms for studies of human molecular anthropology

The recent insertion of mobile elements, of the Alu and L1 families, in the human genome provides a distinct class of polymorphism in the human genome. Because the insertion of these elements in the genome is so rare and once they are inserted they are stable; they represent a unique group of markers that are identical by descent. This type of marker is among the most informative in ascertaining relationships between individuals and populations. The assays for these markers are extremely robust, easy to perform, and readily adaptable to mass analysis and automation. In addition, as the insertion alleles are all newly arisen, the ancestral allele is always the allele missing the insertion. This information allows estimations of the roots of trees, which are not possible with all types of markers. The greatest potential for these markers is with upcoming developments that will allow the identification of new insertions in many different genomes simultaneously. These procedures will allow investigators to isolate markers that are particularly informative for specific populations and allow development of panels of markers tailored for particular populations.

Moveable Elements in The Human Genome: Status of Research

The first moveable DNA elements to be studied at the molecular level were the transposable elements found in prokaryotes. Although several different types are now known, they all share two properties: first, the DNA within the element encodes a gene or genes that are required for transposition, and, second, specific DNA sequences are repeated in inverted orientation at the two ends of the element and are required for transposition.