Department of Botany and Biodiversity Research, University of Vienna, Faculty of Life Sciences, Vienna, Austria.
CSIRO Plant Industry, Canberra, ACT, Australia.
Heredity (Edinb). 2017 Dec;119(6):389-401. doi: 10.1038/hdy.2017.51. Epub 2017 Oct 4.
Understanding the patterns of contemporary gene dispersal within and among populations is of critical importance to population genetics and in managing populations for conservation. In contrast to diploids, there are few studies of gene dispersal in autopolyploids, in part due to complex polysomic inheritance and genotype ambiguity. Here we develop a novel approach for population assignment for codominant markers for autotetraploids and autohexaploids. This method accounts for polysomic inheritance, unreduced gametes and unknown allele dosage. It can also utilise information regarding the origin and genotype of one parent for population assignment of maternal or paternal parents. Using simulations, we demonstrate that our approach achieves high levels of accuracy for assignment even when population divergence is low (F~0.06) and with only 12 microsatellite loci. We also show that substantially higher accuracy is achieved when known maternal information is utilised, regardless of whether allele dosage is known. Although this novel method exhibited near identical levels of accuracy to Structure when population divergence was high, it performed substantially better for most parameters at moderate (F=0.06) to low levels of divergence (F=0.03). These methods fill an important gap in the toolset for autopolyploids and pave the way for investigating contemporary gene dispersal in a widespread group of organisms.
了解当代基因在种群内和种群间的扩散模式对群体遗传学和保护种群的管理至关重要。与二倍体相比，同源多倍体中的基因扩散研究较少，部分原因是复杂的多倍体遗传和基因型模糊。在这里，我们为同源四倍体和同源六倍体的共显性标记开发了一种新的种群分配方法。该方法考虑了多倍体遗传、未减数配子和未知等位基因剂量。它还可以利用有关亲本的起源和基因型的信息，对母本或父本的种群进行分配。通过模拟，我们证明即使在种群分化程度较低（F~0.06）且仅使用 12 个微卫星标记的情况下，我们的方法也能实现非常高的分配准确性。我们还表明，无论是否知道等位基因剂量，利用已知的母本信息都能显著提高准确性。尽管这种新方法在种群分化程度较高时与 Structure 具有几乎相同的准确性水平，但在中等（F=0.06）到低水平（F=0.03）的分化时，它在大多数参数上的表现要好得多。这些方法填补了同源多倍体工具集的重要空白，为广泛的生物群体中当代基因扩散的研究铺平了道路。
