Eller E
Human Genetics Center, University of Texas School of Public Health, Houston, TX 77225, USA.
Am J Phys Anthropol. 2001 Sep;116(1):1-12. doi: 10.1002/ajpa.1096.
Previous genetic and craniometric studies have suggested greater genetic diversity and a larger effective size in Africa. Several demographic scenarios can explain a larger African effective size, and anthropological geneticists have attempted to obtain better estimates of relative population sizes among continental regions in the Old World. A least-squares approach of estimating relative population weights was developed by Relethford and Harpending ([1994] Am. J. Phys. Anthropol. 95:249-270), who applied it to craniometric and genetic data sets and concluded that the ratio of African, Asian, and European effective sizes was 3:1:1, respectively; another data set of short tandem repeat (STR) markers yielded a similar estimate of 7:1:2. However, an estimate from restriction site polymorphism (RSP, also known as restriction fragment length polymorphism, or RFLP) data yielded a very different estimate of 1:1:8. Thus, the European and not the African effective size was largest. Simulations showed that this was the result of ascertainment bias in which polymorphic markers were originally identified in a small panel of Caucasians, leading to inflated heterozygosity in the European sample and thus an inflated population weight. This paper extends those computer simulations to incorporate not only ascertainment bias but also interpopulation gene flow and demographic expansion in two types of genetic data, single nucleotide polymorphisms (SNPs, which are similar but not precisely identical to RSPs) and STRs. The effects of these three parameters on SNP and STR relative weight estimates are described. Simulations show that the ascertainment scheme affects SNP data but not STR data. Gene flow has a noticeable effect on the bias and efficiency of the estimates in both types of genetic data. Population expansions have a large effect only in one ascertainment scheme in the simulated SNP data and no effect in STR data. Relative population weight estimates from four published STR data sets are also reported. These estimates are similar to each other: all show a larger African weight and a European weight somewhat larger than the Asian weight. Because the STR simulations show that when gene flow is greater than 0.01 migrants per generation the African population weight is biased upward, it is likely that the African weights in the four STR data sets are inflated. However, the simulations suggest that the African effective size is still largest of the three regions and is probably at least as great as the sum of the Asian and European effective sizes.
以往的遗传学和颅骨测量学研究表明，非洲具有更高的遗传多样性和更大的有效种群规模。几种人口统计学情景可以解释非洲更大的有效种群规模，人类遗传学家试图对旧大陆各大陆区域之间的相对种群规模进行更精确的估计。雷勒福德和哈彭丁（[1994]《美国体质人类学杂志》95:249 - 270）开发了一种估计相对种群权重的最小二乘法，他们将其应用于颅骨测量和遗传数据集，得出非洲、亚洲和欧洲有效种群规模的比例分别为3:1:1；另一个短串联重复序列（STR）标记数据集得出了类似的估计值7:1:2。然而，来自限制性位点多态性（RSP，也称为限制性片段长度多态性，或RFLP）数据的估计值却大不相同，为1:1:8。因此，欧洲而非非洲的有效种群规模最大。模拟结果表明，这是由于鉴定偏差导致的，即多态性标记最初是在一小群白种人中鉴定出来的，这导致欧洲样本中的杂合度虚高，从而使种群权重虚高。本文扩展了这些计算机模拟，不仅纳入了鉴定偏差，还纳入了两种遗传数据（单核苷酸多态性，即SNP，与RSP相似但并不完全相同，以及STR）中的种群间基因流动和人口扩张。描述了这三个参数对SNP和STR相对权重估计的影响。模拟结果表明，鉴定方案会影响SNP数据，但不会影响STR数据。基因流动对两种遗传数据估计的偏差和效率都有显著影响。种群扩张仅在模拟SNP数据的一种鉴定方案中有较大影响，而对STR数据没有影响。还报告了来自四个已发表的STR数据集的相对种群权重估计值。这些估计值彼此相似：都显示非洲权重更大，欧洲权重略大于亚洲权重。由于STR模拟表明，当基因流动大于每代0.01个迁移个体时，非洲种群权重会向上偏倚，所以四个STR数据集中的非洲权重可能被夸大了。然而，模拟结果表明，在这三个区域中，非洲的有效种群规模仍然最大，可能至少与亚洲和欧洲有效种群规模之和一样大。
