Detection of differential gene flow patterns of quantitative variation
ABSTRACT 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.
- SourceAvailable from: Katerina Harvati
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- "We developed a matrix of pairwise P st values representing phenotypic differentiation between populations (Table 4). P st follows the quantitative analytical framework of neutral genetic evolutionary theory and is analogous to the fixation index, F st , in population genetics (Relethford and Blangero, 1990; Holsinger and Weir, 2009). It assumes an equal and additive model of inheritance of phenotypic traits, where phenotypic variances are proportional to genetic variances (Harpending and Ward, 1982; Relethford and Harpending, 1994). "
ABSTRACT: The modern human expansion process out of Africa has important implications for understanding the genetic and phenotypic structure of extant populations. While intensely debated, the primary hypotheses focus on either a single dispersal or multiple dispersals out of the continent. Here, we use the human fossil record from Africa and the Levant, as well as an exceptionally large dataset of Holocene human crania sampled from Asia, to model ancestor-descendant relationships along hypothetical dispersal routes. We test the spatial and temporal predictions of competing out-of-Africa models by assessing the correlation of geographical distances between populations and measures of population differentiation derived from quantitative cranial phenotype data. Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.Journal of Human Evolution 07/2015; DOI:10.1016/j.jhevol.2015.06.008 · 3.87 Impact Factor
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- "The Jirels have been the focus of extensive genetic and epidemiological studies for over 25 years (e.g., Blangero, 1988, 1990; Relethford and Blangero, 1990; Williams- Blangero, 1989a,1989b,1990a, 1993, 1998, 1999, 2002; Williams-Blangero and Blangero, 1989c1990b, Williams- Blangero et al., 2002). All subjects in this study were participants in the Jiri Growth Study (Williams et al., 2007, 2012, 2013, 2015), a genetic epidemiological study of growth and development. "
ABSTRACT: We report cross-sectional, objectively measured physical activity data for 399 children and adolescents aged 6 to 18 years. We evaluated physical activity of children and adolescents, considered time spent in each activity intensity category, and explored the impact of growth disruption (stunting and wasting) on physical activity patterns. Participants wore an Actical (Mini-Mitter, Bend, OR) omnidirectional accelerometer for one week as part of their annual visit to the Jiri Growth Study. The percentage of time spent in standard activity intensities were computed using standard metabolic equivalents (METS) cutpoints and compared by chronological age, sex, and school versus non-school days. Primary findings include (1) children are more active on non-school days and adolescents are more active during the school week; (2) Jirel children do not exhibit the reduction in physical activity that most Western populations experience during the transition from childhood to adolescence; and (3) Jirel children and adolescents routinely meet the suggested one hour/day MVPA threshold; (4) Stunting is prevalent and factors leading to this growth disruption may contribute to the amount of time in sedentary or light physical activity. We report child and adolescent physical activity patterns from the Jirel population of eastern Nepal. In this rural context, children and adolescents are more active than populations reported from Western contexts. This key finding has important biomedical implications for the maintenance of healthy body composition, skeletal health, and other health traits. Am. J. Hum. Biol., 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.American Journal of Human Biology 06/2015; in press. DOI:10.1002/ajhb.22762 · 1.93 Impact Factor
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- "where C ii are the diagonal elements of a codivergence matrix C calculated from M and u i is the weighting factor for the relative census population size, which is fixed as 1/g in this study under the assumption of equal population sizes (Relethford and Blangero, 1990). We calculated Q st for each quasi-landmark based on Q RÀB st , using the corresponding three coordinate values x, y, z as different traits. "
ABSTRACT: There has been much debate about why humans throughout the world differ in facial form. Previous studies of human skull morphology found levels of among-population differentiation that were comparable to those of neutral genetic markers, suggesting that genetic drift (neutral processes) played an important role in influencing facial differentiation. However, variation in soft-tissue morphology has not been studied in detail. In this study, we analyzed high-resolution 3D images of soft-tissue facial form in four Eurasian populations: Han Chinese, Tibetans, Uyghur and Europeans. A novel method was used to establish a high-density alignment across all of the faces, allowing facial diversity to be examined at an unprecedented resolution. These data exhibit signatures of population structure and history. However, among-population differentiation was higher for soft-tissue facial form than for genome-wide genetic loci, and high-resolution analyses reveal that the nose, brow area and cheekbones exhibit particularly strong signals of differentiation (Qst estimates: 0.3–0.8) between Europeans and Han Chinese. Our results suggest that local adaptation and/or sexual selection have been important in shaping human soft-tissue facial morphology.Journal of Human Evolution 10/2014; 75. DOI:10.1016/j.jhevol.2014.08.001 · 3.87 Impact Factor