Detection of Differential Gene Flow from Patterns of Quantitative Variation

Division of Epidemiology, New York State Department of Health, Albany 12237.
Human Biology (Impact Factor: 0.85). 03/1990; 62(1):5-25.
Source: PubMed


A major goal in anthropological genetics is the assessment of the effects of different microevolutionary forces. Harpending and Ward (1982) developed a model that aids in this effort by comparing observed and expected heterozygosity within populations in a local region. The expected heterozygosity within a population is a function of the total heterozygosity of the entire region and the distance of the population from the regional mean centroid of allele frequencies. Greater than average gene flow from an external source will result in a population having greater heterozygosity than expected. Less than average gene flow from an external source will result in a population having less heterozygosity than expected. We extend the Harpending-Ward model to quantitative traits using an equal and additive effects model of inheritance. Here the additive genetic variance within a population is directly proportional to heterozygosity, and its expectation is directly proportional to the genetic distance from the centroid. Under certain assumptions the expectations for phenotypic variances are similar. Observed and expected genetic or phenotypic variance can then be compared to assess the effects of differential external gene flow. When the additive genetic covariance matrix or heritabilities are not known, the phenotypic covariance matrix can be used to provide a conservative application of the model. In addition, we develop new methods for estimation of the genetic relationship matrix (R) from quantitative traits. We apply these models to two data sets: (1) six principal components derived from twenty dermatoglyphic ridge count measures for nine villages in Nepal and (2) ten anthropometric measurements for seven isolated populations in western Ireland. In both cases both the univariate and multivariate analyses provide results that can be directly interpreted in terms of historically known patterns of gene flow.

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    • "Therefore, following standard procedure w is equal across all samples (Relethford, 1994). Trait heritability can also be included, where r ii , r ij , and F st all decrease when h 2 increases (Relethford and Blangero, 1990; Relethford, 1994; Relethford et al., 1997). When heritability is unknown, h 2 5 1 is the default used to calculate minimum F st ; when known, estimated F st may be calculated (Relethford, 1994). "
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    ABSTRACT: Objectives: For bioarchaeological biodistance analyses it is common to "assume" that skeletal samples are representative of the populations to which they are attributed. Here, alternatively, samples with "known" attribution in the Raymond A. Dart Collection are assessed regarding their suitability for use in such analyses. Prior curation issues may call their ascribed identities into question. Materials and methods: These 20th century samples ostensibly derive from South African Ndebele, Sotho, Swazi, Tswana, Venda, Xosa, and Zulu populations. First, the mean measure of divergence (MMD) is used to obtain among-sample dental phenetic distances for comparison with documented population relationships. Second, the Mantel test evaluates fit of the isolation-by-distance model between MMD and geographic distances, i.e., among the historic homelands. Third, R-matrices and minimum and estimated Fst from MMD distances give an indication of genetic micro-differentiation. Results: Output from these model-free and model-bound analyses suggest that five and perhaps six samples are representative of their attributed populations-presenting differences along population lines and evidence of more ancient ancestry. Discussion: Other than the Swazi and perhaps Nedebele, the among-sample variation: 1) mirrors documented population history, 2) reveals a moderately positive correlation between phenetic and geographic distances, and 3) although evidencing much homogeneity, provides measures of genetic distance in support of the phenetic distances. Therefore, with the two noted exceptions-perhaps from collection issues, swamping of past genetic structure, or both, most samples appear suitable for bioarchaeological analyses. On this basis, results are offered to supplement published findings concerning the biological relationships of these peoples. Am J Phys Anthropol, 2015. © 2015 Wiley Periodicals, Inc.
    No preview · Article · Dec 2015 · American Journal of Physical Anthropology
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    • "Fst values between Paleamericans and American series were compared to Fst estimates for all modern series in our sample (as a reference of the magnitude of betweengroup variance that is observed among modern human groups represented in our sample). Fst estimates were computed on PC scores using RMET 5.0 software (Relethford and Blangero, 1990) assuming mean heritability values of 0.55. Finally, all the comparisons were computed on the Full Shape Space (the whole configuration of landmarks), the Facial Shape Space, and the Neurocranium Shape Space. "
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    ABSTRACT: During its expansion across the globe, Homo sapiens successfully survived to major adaptive challenges as a species, inviting scientific research to plunge into the particularities of continental settlement dynamics. A recurrent paleoanthropological concern is about the understanding of the great deal of craniofacial diversity that evolved into the Americas, which includes a vector of continuum variation between a generalized morphology observed among humans groups leading the Out-of-Africa dispersion, and a derived set of craniofacial traits classically labeled as "mongoloid" and that would have arise in Asia during the Holocene. Here, we use geometric morphometric techniques and multivariate statistics along with quantitative genetic approaches to look more closely into the human craniofacial evolutionary history during the Late Pleistocene-Early Holocene from Asia and the New World. We detected significant signals of deviation of the neutral evolutionary expectations, suggesting an important action of non-stochastic evolution (e.g. natural selection, phenotypic plasticity) in the Americas. We also found further support to the Recurrent Gene Flow model that refers to an ancestral, founder population experiencing a standstill in Beringia, and exhibiting high within-group craniofacial variation. This original, internally variable stock would have been the ancestral source of variation that fuelled the subsequent local micro evolution of other derived phenotypic patterns, giving origin to the craniofacial diversity observed among Holocene Native American samples.
    Full-text · Article · Nov 2015 · Quaternary International
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    • "Additionally, those individuals who were missing observations for more than 25% of the remaining traits were eliminated from analyses. This study estimates levels of genetic diversity (F ST ; Relethford 1996, 2003; Relethford and Blangero 1990; Relethford, Crawford, and Blangero 1997; Williams-Blangero 1989a, 1989b; "
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    ABSTRACT: Population structure analyses and biodistance comparisons for Middle Moche (AD 550 - 700), Late Moche (AD 700 - 850), and Transitional (AD 850 - 950) period skeletal samples from San José de Moro with a previously reported Middle Moche period sample from Pacatnamú, a nearby Jequetepeque Valley site, and eight samples from Huaca de la Luna and Cerro Oreja, two sites in the Moche Valley, suggest that substantial levels of extra-local gene flow into the Jequetepeque Valley from the adjacent highlands to the east occurred during the collapse of the Moche polity there, strongly corresponding to evidence for a temporal increase in exotic grave offerings at San José de Moro during the Late Moche and subsequent Transitional periods. The broader implications of these results for our understanding of the collapse of the Moche are discussed.
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