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Paper text:
the genomes of extinct human groups ( archaic hominins ) , such as neanderthals , are now available with high throughput sequencing technology , which can produce millions of short ( 100 base ) sequences called reads from fossil bone or teeth .
an analysis of a neanderthal and a denisovan genome identified many reads that contained sequences of viral origin , similar to known integrations of retroviruses into the germline of modern humans .
such so - called endogenous retroviruses ( or ervs ) are common , making up 5% of our genome . some of the reads spanned the integration site of an erv , called here a locus , and thus were part viral dna and part archaic hominin dna ( figure 1 ) . in some cases , the authors   did not find an erv at the corresponding coordinate in the human genome reference sequence .
instead they found the pre - integration site , which is the sequence that existed before the virus inserted a copy of itself into the chromosome .
all of these loci belonged to one erv lineage ( family ) , called hervk(hml2 ) or hervk , which is the only lineage that has continued to replicate within humans in the last few million years .
they concluded that these retroviruses had infected the germline of the archaic hominins either after their divergence from modern humans ( 400,000 years ago ) or immediately before divergence ( with the integration and pre - integration sites then segregating differently in the lineages ) .
however , while searching many new genome sequences of modern humans for ervs , we have found most of these loci .
for example , of the eight denisovan loci for which agoni et al . 
  were able to give precise genome coordinates , at least seven exist in modern humans .
we have found six in an analysis of 67 cancer patient genomes ( figure 1 ) , and examination of another study of 43 such genomes   shows all seven to be present ( supplemental information ) .
one is k113 ( 19p12b ) , which is well - described and has a frequency of 16% in modern humans .
the four reported denisovan loci lacking coordinates are within repetitive or unassembled regions of the genome , and we can neither confirm nor refute their presence in the modern human population : e.g. two loci are in transposable elements called alu s , of which there are 1,000,000 copies in the human genome ( making up 10% of the human genome sequence ) .
when an erv integrates into another transposable element , finding this erv locus can be a formidable computational challenge because there are many paralogous copies of the integration site .
two additional loci were reported from the neanderthal fossil , and we have found one of these . it is unlikely that these erv loci in the archaic hominins are contaminants from modern human dna .
average coverage of the denisovan genome was only about twofold and the contamination rate among the reads was estimated using several approaches to have been less than 1% .
we believe that the explanation lies in fundamental population genetics . with the exception of co - opted erv loci such as syncytins , which could increase in frequency due to positive selection
, we assume erv loci become common by genetic drift , and the average time for a neutral allele to go to fixation is 4ne generations ( where ne is the effective population size ) . given estimates of long - term human generation time and population size , this is 800,000 years .
the population divergence of modern humans from the denisovan / neanderthal lineage is more recent , between 170,000 and 700,000 years according to a more recent  and much deeper sequencing of the above denisovan fossil , so many loci will have persisted at fluctuating frequencies in all three lineages . as well as showing how differences in loci between one genome and another must be interpreted cautiously , our finding illustrates how single genomes , whether the human reference or one from an archaic hominin fossil , are likely to only contain those erv loci that after almost a million years have drifted to high frequency .
these old loci give us only a limited insight into the processes that created them , e.g. they will have accrued multiple inactivating mutations during this time . in contrast , loci that have integrated recently are more likely to produce proteins and might even be replicating .
such loci are interesting , perhaps most importantly because they are more likely to be pathogenic . the long - running debate over whether or not ervs cause disease in humans has been handicapped by our poor knowledge of erv polymorphism .
characterising individual loci is necessary to test erv involvement in disease , and will aid the potential exploitation of erv proteins as cancer and hiv immunotherapy targets .
when the erv loci in modern humans have been reasonably well - sampled , fossil loci will help us build a robust mathematical model of erv proliferation .
then , because erv loci make easily detectable and irreversible genetic markers ( the common mechanism called 
recombinational deletion leaves a relict structure called a solo - ltr ) , they might help us in the measurement of divergence dates and population sizes for these archaic hominins .
summaryin the june 5th 2012 issue of current biology , agoni et al.[1 ] reported finding 14 endogenous retrovirus ( erv ) loci in the genome sequences of neanderthal and/or denisovan fossils ( both 40,000 years old ) that are not found in the human reference genome sequence . 
 the authors [ 1 ] concluded that these retroviruses were infecting the germline of these archaic hominins at or subsequent to their divergence from modern humans ( 400,000 years ago ) . 
 however , in our search for unfixed ervs in the modern human population , we have found most of these loci . we explain this apparent contradiction using population genetic theory and suggest that it illustrates an important phenomenon for the study of transposable elements such as ervs 
 .