The expansion of premodern humans into western and eastern Europe approximately 40,000 years before the present led to the eventual replacement of the Neanderthals by modern humans approximately 28,000 years ago. Here we report the second mitochondrial DNA (mtDNA) analysis of a Neanderthal, and the first such analysis on clearly dated Neanderthal remains. The specimen is from one of the eastern-most Neanderthal populations, recovered from Mezmaiskaya Cave in the northern Caucasus. Radiocarbon dating estimated the specimen to be approximately 29,000 years old and therefore from one of the latest living Neanderthals. The sequence shows 3.48% divergence from the Feldhofer Neanderthal. Phylogenetic analysis places the two Neanderthals from the Caucasus and western Germany together in a clade that is distinct from modern humans, suggesting that their mtDNA types have not contributed to the modern human mtDNA pool. Comparison with modern populations provides no evidence for the multiregional hypothesis of modern human evolution.
LINE-1 (L1) elements play an important creative role in genomic evolution by distributing both L1 and non-L1 DNA in a process called retrotransposition. A large percentage of the human genome consists of DNA that has been dispersed by the L1 transposition machinery. L1 elements are not randomly distributed in genomic DNA but are concentrated in regions with lower GC content. In an effort to understand the consequences of L1 insertions, we have begun an investigation of their genomic characteristics and the changes that occur to them over time. We compare human L1 insertions that were created either during recent human evolution or during the primate radiation. We report that L1 insertions are an important source for the creation of new microsatellites. We provide evidence that L1 first strand cDNA synthesis can occur from an internal priming event. We note that in contrast to older L1 insertions, recent L1s are distributed randomly in genomic DNA, and the shift in the L1 genomic distribution occurs relatively rapidly. Taken together, our data indicate that strong forces act on newly inserted L1 retrotransposons to alter their structure and distribution.
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.T he genomes of all sexually reproducing multicellular eukaryotes harbor type I (non-long terminal repeat) retrotransposons (1). These elements, which first arose over 600 million years ago (2), have amplified to very high copy numbers and constitute a major fraction of the genomic DNA of many organisms. Their activity has exerted a powerful influence on the evolution of eukaryotic species and their genomes. In humans, LINE-1 (L1; long interspersed element) sequences are by far the predominant elements of this type (3). Although more than 500,000 L1s are present in human DNA, most are ancient and predate the mammalian radiation (4, 5). Only a relatively small number are capable of undergoing transposition (6). This situation, which appears to be a characteristic of all mammalian genomes, allows L1s to be grouped into subfamilies that amplified during different periods of evolution (7-9). A complete picture of the activity of L1s and their influence on the evolution of the human genome can be derived only once the identities and sizes of all of the L1 subfamilies that amplified during human evolution have been ascertained.Many criteria can be used to assign relative ages to L1 subfamilies. Subfamilies with members that are present in several related species are usually older than those whose members are restricted to only one of the species. A second criterion is the degree to which the members of a subfamily have become fixed in the genome of a single species. When a new L1 transposition occurs, a genomic dimorphism-i.e., the presence or absence of the insertion-is created. Over evolutionary time, the occupied allele can either be lost or become fixed in the population. Consequently, younger subfamilies have higher fractions of dimorphic elements than do older subfamilies. Also, older insertions have had time to accumulate more random mutations, therefore older subfamilies have greater average sequence divergences than younger ones (7, 10, 11). L1 subfamilies possess shared sequence variants (SSVs) that evolve in a stepwise fashion. These too can be used to ascertain the relative evolutionary order of the subfamilies.A general classification scheme for human L1s has been proposed. In this scheme...
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