We've come a long way together, mutt. When I first encountered you, you said there was no evidence. Now we are talking about the quality of the evidence.<quoted text>
I was surprised that DNA had been extracted from fossils, and very skeptical of the quality of it. It turns out that it is, indeed, very difficult to extract the DNA, and what has been gathered is poor quality. Another concern is modern-human DNA contamination. Even a small amount mixed in with the "Neanderthal's" will skew the results.
Look at this govt website, and in particular, the section about "Authenticity".
And you linked to a good article, form a good journal. Well done!
I read all of the "Authenticity" section, and here's what I came away with: this is a difficult problem, and even the most careful scientist can be done in by contamination of samples. Instead of giving up in the face of this difficult challenge, science presses on, and tries to fix the technical problems.
"These observations have spurred the development of several quality control steps in Neanderthal DNA handling and sequencing, including ligating adapters to Neanderthal DNA immediately after extraction to provide molecular barcodes that will distinguish it from modern DNA potentially introduced in downstream applications (Green et al. 2009)."
The best way to understand an article like this is to start with the abstract, a short summary which precedes the article. Here's the essence of this project, from the abstract:
"Here, I will discuss efforts to obtain genomic sequence from Neanderthal, the closest known relative of modern humans. Recent studies in this nascent field have focused on developing methods to recover nuclear DNA from Neanderthal remains. The success of these early studies has inspired a Neanderthal genome project, which promises to produce a reference Neanderthal genome sequence in the near future. Technical issues, such as the level of Neanderthal sequence coverage that can realistically be obtained from a single specimen and the presence of modern human contaminating sequences, reduce the detection of authentic human–Neanderthal sequence differences but may be remedied by methodological improvements. "
Of course, you could also just jump in at the beginning of the article:
"We are a young species. The most recent genetic and fossil evidence suggests that modern humans emerged in East Africa ∼200,000 yr ago, a fraction of the estimated 6 million yr since the divergence of the human and chimpanzee lineages (Cavalli-Sforza and Feldman 2003; McDougall et al. 2005). In this brief time, modern humans have spread across the globe, far surpassing all other primate and archaic human species in sheer numbers, geographic range, technological sophistication, and impact on the environment. Our success is due in part to complex biological features, including increased brain size, bipedalism, and modifications in craniofacial and limb morphology, which began to emerge on the human lineage well before the rise of modern humans. These adaptations facilitated the evolution of uniquely human behavioral traits such as language and are ultimately due to DNA sequence changes arising on the human lineage since the human–chimpanzee split. Identifying these changes has become a major focus of human genetics and genomics."