Friday, July 25, 2008

Cranio-morphological Variation

Cranio-facial variation is perhaps the most overrated phenotypic aspect of human body in societies, aside from skin tone. Not surprising, considering that it is the most regularly exposed part of the body that noticeably sports considerable variation, and goes without saying, forms a biological basis around which an individual's unique identity is established. Socio-ethnic identification is secondary to individual identity in society. Such is the obviousness of cranio-facial variation that images of certain archetypes or "idealized" types have been implanted or socially conditioned in the minds of folks, as socio-ethnic identifiers; this took a particularly notorious turn from ca. 19th century within European bio-anthropological circles, wherein human populations were grouped into narrow rigid "idealized" types, which were usually also identified with major geographical locations. These were presented as non-overlapping types, as though the so-grouped human populations didn't sport intra-group and intra-population variation, and by extension, variation manifestation that is shared with groups outside a reference point group. Howells types rely on such typological groups, and which Forensic science has embraced via Fordisc 2.0. Recent studies have shown that such approach is considerably limited in its ability to account for intra-group variation, and hence, fails the test of classifying individuals of a given population to the correct population of origin, because an 'unknown' or a 'known' specimen may well cluster with individuals in not one but multiple populations. A study on Spanish cranial series ended up having the said specimens cluster all over the map, with individuals in the series clustering with a multitude of groups spanning continents.

"Variation in racial classification represents the lack of a Spanish sample within the FORDISC 2.0 database as well as the human variation inherent within them. Individual crania were classified according to the best fit with the existing samples of the database, but the samples clearly were inadequate to elucidate the specific geographical origin of the overall Spanish sample…some crania were classified into groups with no clear geographic or ancestral relationship with the Spanish sample…

The authors also agree that additional and more complete samples from different geographical regions and groups are needed to augment the existing databases

"race classification of all individuals in this sample using the Forensic Data Bank option. Of the 95 individuals, 42 (44 percent) were classified as white, 35 percent as black, 9 percent as Hispanic, 4 percent as Japanese, 4 percent as American Indian, and the remaining three individuals as Chinese and Vietnamese" - Ubelaker et al., Application of Forensic Discriminant Functions to a Spanish Cranial Sample, 2002.

Williams et al. 2005 provided another example of this, when their examination of Meroitic cranial series showed that the series couldn't be classified into a single homogeneous entity, but rather, produced clusters with multiple series from distinct geographical regions. They say:

The Howells series. Fordisc 2.0 could not effectively classify ten of the crania, and of the remainder, eight were identified as Late Period Dynastic Egyptian, six as Zalavar, four as Easter Islander, three as Lake Alexandrina Tribes, and three as Norse (Medieval Norway). Eight were not significantly different from eight separate populations: Teita, Andaman Islands, Zulu, Arikara, Santa Cruz Island, Ainu, Hokkaido, and Atayal.

"The Howells series. Fordisc 2.0 could not effectively classify ten of the crania, and of the remainder, eight were identified as Late Period Dynastic Egyptian, six as Zalavar, four as Easter Islander, three as Lake Alexandrina Tribes, and three as Norse (Medieval Norway). Eight were not significantly different from eight separate populations: Teita, Andaman Islands, Zulu, Arikara, Santa Cruz Island, Ainu, Hokkaido, and Atayal."

“Fordisc 2.0 classified the Nubian crania with populations over an enormous geopraphic range, including North and Central Europe, Easter Island, the Andaman Islands, Japan, Taiwan, South Africa, Australia, and North America. “

“If Fordisc 2.0 is revealing genetic admixture of Late Period Dynastic Egypt and Meroitic Nubia, then one must also consider these ancient Meroitic Nubians to be part of Hungarian, part Easter Islander, part Norse, and part Australian Aborigine, with smaller contributions from the Ainu, Teita, Zulu, Santa Cruz, Andaman Islands, Arikara, Ayatal, and Hokkaido populations. In fact, all human groups are essentially heterogeneous, including samples within Fordisc 2.0. Using Fst heritability tests, Relethford (1994) demonstrated that Howells’s cranial samples exhibit far more variation within than between skeletal series. There is no reason to assume that the heterogeneity of the Late Period Dynastic Egyptian population exceeds that characterizing our Nubian sample. This heterogeneity may also characterize the populations in the Forensic Data Bank; Fordisc 2.0 classified the Meroitic Nubians not as either all black or all white but as black, white, Hispanic, Chinese, Japanese, and Native American.”

“We suggest that skeletal specimens or samples cannot be accurately classified by geography or by racial affinity because of (1) the wide variation in crania of the known series that crosscuts geographic populations (polymorphism), (2) the clinal pattern of human variation, and (3) cultural and environmental factors. Even a presumably homogeneous population such as the Meroitic Nubians shows extensive variation that preclude its classification as a geographic group.”

Apparently multiple variables go into shaping variations in human crano-facial development. Williams et al. put this simply, when they say:

“Finally, the assumption that cranial form is an immutable “racial” character is very likely to be false, given the diversity of studies of immigrants and the known effects of food preparation and masticatory stress upon cranial form. Cranial form, like other aspects of the body, is a phenotype partly determined by heredity but also strongly influenced by the conditions of life.”

As far as the "conditions of life" is concerned, "acclimatization" is one notable factor. Michael A. Little and Jere D. Haas summarize it, when they say:

“there is a recognition of the importance of the process of acclimatization. Acclimatization is defined as a biological response to repeated exposure to a climatic stressor (Prosser 1964). It is an expression of the genetic plasticity of the population, and with acclimatization, it is assumed that an adaptive response can occur without genetic change. Three forms of physiological acclimatization have been recognized: (1) simple, reversible acclimatization-a physiological response to a stressful environment that gradually disappears at the cessation of the stress; (2)irreversible acclimatization—acquired as a result of climatic stress but remaining after the stress is removed; and (3) developmental acclimatizationmuch like irreversible acclimatization except that the exposure must occur at a particular time during the growth process. Until the process of acclimatization was appreciated and its varieties identified much inter-operation variation was attributed to genetic difference. Attempting to define the limits of acclimatization has become as important as defining the underlying genetic basis of adaptation. Indeed it is only after acclimatization is accounted for that genetic adaptations can be identified.

A third manner by which contemporary studies of climatic adaptation differ from earlier efforts is through an appreciation of the role of culture (Baker 1960). Anthropologists since the time of Darwin have played lip service to cultural factors using such generalities as “sexual selection” and “cultural selection.” But it is only with recent empirical studies that cultural mechanisms are being identified and quantified. These have shown that culture is a buffer that modifies rather than eliminates climatic exposure (Wulson 1949, Planalp 1971, Little and Hanna 1978).” - Courtesy of Michael A. Little and Jere D. Haas—Human Population Biology: A Transdisciplinary Science, 1989.

From the genetic standpoint, it is generally known that when only a small segment of a larger population diverges and then locates elsewhere to assume the role as a founder group, the likelihood of loss of diversity is a strong possibility that goes along with it. Hence, pronounced reduction of diversity characterizing the newly-divergent offshoot group allows the distribution of certain traits to figure more prominently than the case would be in the parent population, and alternatively, other traits die out more dramatically. The result of such development, has been invoked in marked departure of offshoot founder groups from their ancestral population. As Little & Haas note, cultural behavior patterns chime in to "modify" these variations. Hence, putting acclimatization effects aside [not to leave out natural selection in the complex mix of factors], on one hand, certain variations brought upon by genetic mutation can be quite dramatic secondary to random genetic drift, wherein certain variations are magnified while others not so much; on another hand, cultural behavior patterns, which can be exemplified in "sexual selection" tendencies, factor in and contribute further to the sustenance and prevalence of certain elements of the overall variation over other elements, and hence, lending hand in certain intra-population morphological tendencies.

*Subject to modification upon new information without notice.

Ubelaker et al., Application of Forensic Discriminant Functions to a Spanish Cranial Sample, 2002

Williams et al. 2005, Forensic Misclassification of Ancient Nubian Crania: Implications for Assumptions about Human Variation.

—Michael A. Little and Jere D. Haas—Human Population Biology: A Transdisciplinary Science, 1989.

—Discussion link: Nile Valley discussion board.

Monday, July 7, 2008

U6: A standalone clade?

It is a lineage that spans west and east Africa, and spilling over to portions of southern Europe and "southwest Asia".

In looking at the following diagram...

For those with inadequate screen size, view the above image in full with: here is apparent that at the least, U5 and U6 diverge into respective branches independent from that of the rest of U macro-haplogroup. Similar observation has been made about U1, which too, seems to have an independent branch from the rest of the U haplogroup. In other words, these three—either U1, U5 or U6—don't appear to have an ancestral clade within the main haplogroup U branch which is defined by the nucleotide transition at 1811 or vice versa. This is how it goes, courtesy of Maca-Meyer et al. 2003:

U6 is defined by two motifs represented by positions in the coding and HVR respectively: 3348 and 16172.

U5 is defined by the transitions at: 3197, 9477, 13617 and 16270.

And the rest of the U haplgroup [sans U1], defined by the mutation designated by position: 1811.

Maca-Meyer et al. add that:

U presents the following mutations with respect to rCRS: 73, 263, 311i, 750, 1438, 2706, 4769, 7028, 8860, 11467, 11719, 12308, 12372, 14766 and 15326.
- Maca-Meyer et al. 2003

N macrohaplogroup is removed from the root of L3 by about 5 mutations, we are told. This is relevant, in that U haplogroup is often posited as having split from R, which derives from Haplogroup N. Speaking of haplogroup U splitting from R, we are told that this is the case via three mutations represented by: 11467, 12308 and 12372

Hence, the family association has been made between U6 [as is for U1 & U5] and the rest of the U haplogroup, primarily thanks to sharing of the above mentioned transition trio; if it weren't for these basic transitions, U6 would have likely just been considered as just another separate sub-branch of haplogroup R. Perhaps, if a clade was located—sharing the same transition trio but devoid of any known downstream coding or HVR mutations in either U6, U1 or U5 and the rest of haplogroup U, it could provide us with a possible candidate as the proto-U ancestor that gave rise to the divergent U branches in question. However, to date, no such lineage has come to light.

In their publication "The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa" - 2006, Anna Olivieri et al.'s argument, like that of Gonzalez et al., depends on the idea that U6 entered Africa in a parallel dispersal with M1, which the present author has demonstrated elsewhere to be a weak hypothesis [see: Mitochondrial DNA M1 haplogroup: A Response To Ana M. Gonzalez et al. 2007]. M1 basal coding markers emerge from that of an African background, and the "missing-link" lineage of the M Macrohaplogroup was found in a sub-Saharan sample [specifically in a Senegalese sample].

Furthermore, Olivieri et al. 2006 themselves acknowledge:

An ancient arrival of M1 in Africa (or in its close proximity) is supported by the fact that none of the numerous M haplogroups in Asia (20, 21) harbors any of the distinguishing M1 root mutations, and by the lack of Asian-specific clades within M1 (and U6), as might be expected in the case of a more recent arrival. The arrival of M1 and U6 in Africa 40 to 45 ka would temporally overlap with the event(s) that led to the peopling of Europe by modern humans.

Not to mention...

Indeed, M1 and U6 in Africa are mostly restricted to Afro-Asiatic–speaking areas.

Why is that? Where did the Afrisan super language phylum emerge? Answer: East Africa.

And they say...

The hypothesis of a back-migration from Asia to Africa is also strongly supported by the current phylogeography of the Y chromosome variation, because haplogroup K2 and paragroup R1b*, both belonging to the otherwise Asiatic macrohaplogroup K, have been observed at high frequencies only in Africa (15, 16). However, because of the relatively low molecular resolution of the Y chromosome phylogeny as compared to that of the mtDNA, it was impossible to come to a firm conclusion about the precise timing of this dispersal (15, 16).

To which, elsewhere [see: R1*-M173 bearing chromosomes in Cameroon], I commented:

By the way, previous genetic research work made very enthusiastic attempts to correlate the likes of U6 and possible "Eurasian"-tagged mtDNA with R1*-M173, supposedly as an attempt to buttress a possible back-migration into Africa; all but failed, with results showing considerable African mtDNA gene pool instead, for populations bearing these chromosomes.

Not only is there lack of apparent parallelism between R1* paragroup distribution and those markers, as the authors seem to be so desperately yearning for, but also the paragroup is essentially absent in all Afrasan speaking groups but those in the Northeast African corner. The marker is even rarer in so-called Southwest Asia than it is in Africa.

Thus, the re-examination point:

— U6 with respect to U5 , or U6 with respect to U1, and U6 with respect to the rest of haplogroup U, doesn't share defining motifs, outside of the basic transitions, particularly at the aforementioned position trio.

— In relation to the above, U6 doesn't have a common recent ancestor that is a U5 sub-lineage or vice versa, U6 doesn't have a common recent ancestor that is a U1 sub-lineage or vice versa, nor does U6 have a common recent ancestor that is a U*(xU1, U5) sub-lineage or vice versa.

...brings us to the question of:

Could U6 then be a standalone clade, in that, short of the aforementioned basic mutations by which the U-designated lineages diverge from macro-haplogroup R — particularly at 11467, 12308 and 12372, it is essentially mutually-independent of the other U-designated lineages?

Simply put...

The relationship of U6 with other U haplogroups is only inferred from non-U subclade-specific basal markers.

U6 is a branch on its own, independent from other U groups, and proto-U6 has not been located to date.

Time will tell, as to whether much more improved resolution of mtDNA will bear out the possible candidate of the elusive proto-U6 ancestor, but until then, it would appear that the proto-U6 bearing population was quite small in size, such that proto-U6 itself would eventually be overwhelmed and essentially be erased by expansion of descendant U6 carriers and possibly, incursions from other populations. It is uncertain whether a proto-U6 ancestor would have been the very same ancestor that begot U1, U5 and U*(xU6,U1,U5) respectively elsewhere, or whether it would have been a single step or a few steps genetic-neighbor to those which begot the latter U groups, but it appears that the latter respective ancestors too were modestly represented 'population-wise', such that they too would have been overwhelmed by subsequent demographic expansions that gave rise to descendant populations and incoming groups from elsewhere. Whatever may be said about a proto-U6 ancestor's origin, one thing is clear: U6 itself is an autochthonous African marker, which would eventually spill over to parts of Europe, particularly those hugging the Mediterranean sea, and parts of "southwest Asia". It too, like M1 (clickable), has been implicated in the expansion of proto-Afrasan (aka proto-Afro-Asiatic) and/or Afrasan speakers outside of mainland Africa.

— Maca-Meyer et al. 2003, Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography.