Huff et al. (2010) analyzed genome variation of two samples, focusing on the SNPs around the mobile element insertion areas. The theory behind this project is that mobile element insertions (Alu and LINE1) are much rarer, so they have deep genealogies (ancient coalescent time).
Their research basically supports this theoretical point. First, TMRCA estimated based on 9,609 SNPs in the 10 kb around insertion was 462 k years old, which is older than the TMRCA estimated from other genomic regions. Second, more interestingly, they estimated significantly larger ancient effective population size than modern effective population size. They used a coalescent-Maximum likelihood based method to estimate three demographic parameters.
Modern effective population = 8,500
Ancient effective population = 18,500 (C.I. 14,500-26,000)
Time of population size change = 1.2 M years
This means that effective population size before 1.2 M years ago was 18,500. The small effective population size of modern human support many previous genetic studies, but it is interesting to see that modern human have genetic evidence that suggests that ancestors of modern human, such as Homo erectus, had much larger effective population size and they were much more genetically diverse than anatomically modern human. Since effective population size of modern humans is much smaller than Chimpanzee, it has been suggested that our ancestors experienced series of bottleneck, but this research data show the significant reduction in the population size occurred after 1.2 M years ago. Jorde actually said in the NIH Genome Center Lecture series that our ancestors almost became extinct.