The newest bit of Genographic wisdom is that haplogroup J2 in the Mediterranean is associated not with the Neolithic, Greek, or other population movements, but with the sea-faring Phoenicians. They achieve this feat by (allegedly) comparing areas of Phoenician with those of no (or low) such influence.
I have intentionally limited myself to five major weak points of the study: to cover more would be too time-consuming and unnecessary.
1. The Hellenistic age did not happen
A central assumption of this work is that the conquest and occupation of the Middle East by Alexander the Great does not count as Greek influence, despite centuries of Greek domination that followed, both during Hellenistic, and later in Roman times.
The authors write that their method could be further used to:
include systematic investigations of military expansions, such as the Greek signal, from the time of Alexander the Great in central and south AsiaApparently they didn't think of applying it to West Asia itself, which was also conquered by Alexander the Great, and in which the Greek-speaking element persisted far longer than in "south Asia".
Thus, the population of Phoenicia and its "periphery" is implicitly assumed to be free of Greek influence. That is a bizarre contention, given that Greek was spoken in "Phoenicia" long after the Phoenician language became extinct.
2. Crete was influenced by the Phoenicians
This totally unsupported claim is necessary for the authors' thesis, since Crete has the world maximum of haplogroup J2. I have no doubt that Phoenicians traded with Cretans, just as Cretans traded with Phoenicians. But, that is no excuse to think of Crete as an area of Phoenician influence.
Indeed, settlement of the Levant by Aegean peoples is archaeologically supported, while Phoenician settlement of Crete is not.
But, speaking of Phoenician settlement, the only area of Greece where such settlement is believed to have taken place is in mainland Greece, in Thebes, where Cadmus and his Phoenicians founded Cadmeis. I doubt that this had any substantial effect, but if the authors wanted to be intellectually honest, they would list this as an area of Phoenician influence, rather than Crete.
3. West Asia Minor (or the Pontus) was not colonized by Greeks
The most laughable claim of the authors (see map) is the absence of blue (Greek) dots on West Asia Minor, and the Pontus (Northeast Turkey). Apparently the Greek colonies of the far West (such as Marseilles) count as areas of Greek influence, while the countless Greek cities on the Asian side of the Aegean, or in northeast Turkey do not.
The motivation of this is obvious, since Asia Minor is a J2-heavy area and asserting the Greek influence there would upset the paper's thesis. But, it is absurd to place blue dots in Paphlagonia and Caria and not in Ionia or the Pontus.
4. Modern Lebanese are descendants of Phoenicians
This central assumption of the paper has no actual support, except for a vague geographical congruence. Modern Lebanese are a hybrid people, divided into Christians and Muslims. Both are Arabs, with Muslims being more influenced by the original Arabians, and Christians more influenced by the pre-Arab (Greco-Syrian) and post-Arab (West European) migrations. Perhaps, there is a trace of Phoenician genes in them, but this is really not a self-evident claim.
5. R1b in Greece and Turkey is due to the Celts
R1b in Greece and Turkey belongs primarily into the "eastern" variety, and not the "western" variety. It is in Italy and north of Greece where the two varieties begin to blend with each other. No care to distinguish between these varieties is taken.
Certainly, some R1b in this region may be due to Western Europeans (e.g. from the period of the Frankokratia), but to assign its totality to this factor is nonsensical. Apparently, the geniuses of the Genographic project have decreed that the brief foray of the Celts into Greece introduced massive amounts of R1b, but a thousand years of Greco-Roman domination of the Levant did nothing of the kind.
6 (bonus). Haplogroup J2 is more frequent in East than in West Sicily
Sicily is an island which had well-documented and not insignificant settlements by both Greeks and Phoenicians. Moreover, these settlements were geographically divided: Greeks in the East, Phoenicians in the West. It is in the East that J2 has its highest frequency, and not in the Phoenician West.
Is there anything of value in this paper? Well, it's a good idea to try to correlate Y-chromosome distribution with historical rather than pre-historical events. Too bad the authors botched the job, but their paper can at least serve as a reference point for how not to go about doing it.
UPDATE: Take a look at the "haplotype groups" suggested by the authors as signals of Phoenician and Greek colonization.
Not only are haplotype groups not clades (they do not designate common ancestry), but 7-marker haplotypes don't even designate anything that can be remotely tied to the time period in question, given the huge confidence intervals associated with even larger numbers of markers. Feel free to plug these haplotypes to yhrd or ysearch to find plenty of long-lost "Phoenicians" all over the planet.
UPDATE II: The "evolutionary" mutation rate rears its ugly head
From the paper:
Because there is a significant chance that a haplotype existing 3000 years ago has accumulated a one-step difference in an STR (we expect 0.6 mutations per seven-STR haplotype when a rate of 6.9x10-4 per locus per 25 yr is used), these one-step neighbors have been included in each set, producing what we have labeled STR+s. STR-s can contain both haplotypes deriving from mutations, which should have been included, and independent haplotypes unconnected with the migrations that we are trying to detect.UPDDATE III: What of the Arabs?
The modern Lebanese are Arabs, as are most modern North Africans where Phoenician colonies were founded. The Arabs also affected several Mediterranean islands, as well as Iberia. One would think that the most salient feature of modern Mediterranean populations would be mentioned in a paper which attempted to trace patterns of Y-chromosome variation in the Mediterranean.
Certainly, the Neolithic, Greek, and Phoenician migrations, as well as the Jewish Diaspora moved people around. But the Phoenicians have been extinct for 2,000 years. The Jews had (and have) communities around the Mediterranean, but did not amount to a significant population element anywhere. It is the Arabs who are the elephant in the room, and yet they are ignored. Are similarities between the Levant, North Africa and Spain due to Phoenicians or due to this later Arab movement? By failing to trace the distribution of their "Phoenician colonization signals" among Arabians, the authors have overstated their case.
American Journal of Human Genetics doi: :10.1016/j.ajhg.2008.10.012
Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean
Pierre A. Zalloua et al.
The Phoenicians were the dominant traders in the Mediterranean Sea two thousand to three thousand years ago and expanded from their homeland in the Levant to establish colonies and trading posts throughout the Mediterranean, but then they disappeared from history. We wished to identify their male genetic traces in modern populations. Therefore, we chose Phoenician-influenced sites on the basis of well-documented historical records and collected new Y-chromosomal data from 1330 men from six such sites, as well as comparative data from the literature. We then developed an analytical strategy to distinguish between lineages specifically associated with the Phoenicians and those spread by geographically similar but historically distinct events, such as the Neolithic, Greek, and Jewish expansions. This involved comparing historically documented Phoenician sites with neighboring non-Phoenician sites for the identification of weak but systematic signatures shared by the Phoenician sites that could not readily be explained by chance or by other expansions. From these comparisons, we found that haplogroup J2, in general, and six Y-STR haplotypes, in particular, exhibited a Phoenician signature that contributed > 6% to the modern Phoenician-influenced populations examined. Our methodology can be applied to any historically documented expansion in which contact and noncontact sites can be identified.