Continuing my quest into the possible early peopling of America by Neanderthals, I have come across an interesting paper by James Guthrie (2001)  on Human Leukocyte Antigens (HLA).
In a previous post, I wrote the following:
Human leukocyte antigen (HLA) system
HLA are the loci of genes which encode for major histocompatibility complex (MHC) in humans and as such have an important role in the immune system. Ten Neanderthal HLA class I alleles have been found among humans: A*02, A*26, A*66, B*51:01/08, B*07:02/03/06, C*16:02, C*07:02.
Of these, two are found among Native Americans: The paired alleles A*02 and C*07:02. While their average global frequency is approx. 2% , the highest global frequency occurs among the Yucpa of Venezuela (26.9%), followed by Navajo, US (13.1%) and Lisu, Yunan, China (10.4%).
The high frequency in America and China is consonant with the high proportion of Neanderthal admixture in those regions.
Guthrie's paper deals with Native American HLA and mentions one of those "Neanderthal HLA alleles", the A*02 (bold is mine):
Distributions of these ten HLAs in other parts of the world are not what would be expected from the premise that Americans stem mainly from Northeast Asians. Instead, the basic American populations seem most like those of western Asia and of Southeast Asia, paralleling the findings of Steele and Powell (1992) regarding Paleo-Indian skulls. Their multivariate analysis showed craniofacial features closer to those of southern Asians and Europeans than to those of northern Asians. The only HLA prominent in both America and northern Asia is A*2, which CS call ubiquitous and which is also strong throughout Europe, South China, and Japan... 
The A*2 prevalence in Europe and China is evidently due to their closeness to Neanderthals.
The resemblance of Amerindians to Western Asians is also supported by the genome sequenced from a 24 Kya H. sapiens (named MA-1) from Mal’ta in south-central Siberia:
- It suggests that between 14 to 38% of Native American autosomal ancestry originated through a gene flow from this population.
- MA-1 is closer to contemporary Native Americans than to Northeast Asians suggesting that those groups may have originated in secondary wave(s) of immigrants from East Asia , or that back-migrations from America dispersed other lineages in Central and Western Eurasia .
- Ma-1’s estimated shared drift statistic, (f3), places Amerindians closest to Northern Europeans and Northern - Central and Western Siberians, and furthest apart from Eastern Siberians and Asians. Possibly indicating a common Neanderthal background, which could explain the European signature found in pre-Hispanic Amerindians (i.e. Kennewick man).
The Phoenician connection
Guthrie's paper also deals with other HLAs, with interesting inferences:
The A*32 allele seems to indicate a Mediterranean or specifically Aegean impact in the Caribbean region (including on the Cherokee) as well as on Tupians of the lower Amazon (Oyampí and Parakana). It seems to connect this set and the Central Amerind composite with northern India, Sardinia, the Tuareg of Algeria, and with populations around the Adriatic Sea in Greece, Yugoslavia, and Italy. A*32 is absent from other South American samples except the Mapuche.
A*32 levels in the Mapuche, Oyampí, and the Central Amerind composite samples are among the top nine in the CS tabulation (7-9%), and the Tupian Oyampí near the mouth of the Amazon River have the second highest American frequency. If this is not an artifact of sampling [...]
Both A*32 and A*30 are found at significant levels in Greece, Sardinia, and in the Central Amerind composite. They also appear at anomalously high frequencies in Samoan outliers but are not documented elsewhere in Pacific islands. This may reflect limited exploration of the Pacific by Mediterraneans who otherwise left few traces except (controversial) petroglyphs. 
Curiously this may be an indication of Phoenician, Cretan, Mycenean or Carthaginian genes during their sea voyages beyond Gibraltar. (See my many posts on Phoenicians in America).
No Paracas HLA data
Online sources cite Guthrie as having proven that Paracas mummies HLA is European. This is false. Check his only comment on Paracas Mummies below:
European Genes from other Systems
There may be no clear marker for European ancestry among the “classical” genetic variants, although a high frequency of the Rhesus cde (r) allele might qualify. CS [Cavalli-Sforza] also considered immunoglobin f;b, adenylate kinase 1, and ABO type B, when found together, to indicate Caucasoid admixture in eastern North America (p. 337). Occurrences among indigenous Americans of cde or A or B of the ABO system were once attributed to recent admixture and databases were “corrected” accordingly. It is now understood that some of these unexpected alleles arrived in antiquity. Mummies from Paracas, Peru, possessed both A and B antigens (Allison et al. 1976, 1978). 
So he does not mention HLAs, only Blood groups and the fact that Paracas Mummies had A and B antigens. Which does not mean that they were Europeans.
 James L. Guthrie, (2001). Human Lymphocyte Antigens: Apparent Afro-Asiatic, Southern Asian, & European HLAs in Indigenous American Populations
Pre-Columbiana, Volume 2, Number 2 & 3, December 2000 & June 2001 (online at New England Antiquities Research Association
 Raghavan M., Pontus Skoglund P., et al., (2013). Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (02 Jan 2014) doi:10.1038/nature12736
 Dziebel, G., (2013). The Demographic Isolation of Amerindians and Back Migrations to the Old World in the Late Pleistocene/Early Holocene: From the History of Ideas to Contemporary Scientific Realities. Paleoamerican Odyssey Conference in Santa Fe, New Mexico 17 Oct. 2013
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