Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one nonrecombinant marker is considered, but there is no satisfying method when multiple genes are to be combined. In this paper, we propose an algorithm that converts a distance matrix of alleles to a distance matrix among organisms. This algorithm allows the incorporation of allelic variation for reconstructing the phylogeny of organisms from one or more genes. The method is applied to reconstruct the phylogeny of the seven native diploid species of Rosa sect. Cinnamomeae in North America. The glyceralgehyde 3-phosphate dehydrogenase (GAPDH), the triose phosphate isomerase (TPI), and the malate synthase (MS) genes were sequenced for 40 individuals from these species. The three genes had little genetic variation, and most species showed incomplete lineage sorting, suggesting these species have a recent origin. Despite these difficulties, the networks (NeighborNet) of organisms reconstructed from the matrix obtained with the algorithm recovered groups that more closely match taxonomic boundaries than did the haplotype trees. The combined network of individuals shows that species west of the Rocky Mountains, Rosa gymnocarpa and R. pisocarpa, form exclusive groups and that together they are distinct from eastern species. In the east, three groups were found to be exclusive: R. nitida-R. palustris, R. foliolosa, and R. blanda-R. woodsii. These groups are congruent with the morphology and the ecology of species. The method is also useful for representing hybrid individuals when the relationships are reconstructed using a phylogenetic network.

中文翻译：

---

结合等位基因变异重建多基因生物的进化史：以北美罗莎为例

个体内部的等位基因变异包含有关生物体关系的信息，预计这对于重建密切相关类群的进化历史尤为重要。然而，很少有人致力于将这些信息用于重建生物体的系统发育。当考虑一个非重组标记时，单倍型树代表了一种解决方案，但当要组合多个基因时，没有令人满意的方法。在本文中，我们提出了一种将等位基因的距离矩阵转换为生物体之间的距离矩阵的算法。该算法允许结合等位基因变异以从一个或多个基因重建生物体的系统发育。该方法用于重建蔷薇科七种天然二倍体物种的系统发育。北美的肉桂科。对来自这些物种的 40 个个体的甘油醛 3-磷酸脱氢酶 (GAPDH)、丙糖磷酸异构酶 (TPI) 和苹果酸合酶 (MS) 基因进行了测序。这三个基因几乎没有遗传变异，大多数物种表现出不完整的谱系排序，表明这些物种起源于最近。尽管存在这些困难，从使用算法获得的矩阵重建的生物体网络 (NeighborNet) 恢复了比单倍型树更匹配分类边界的组。个体的组合网络表明落基山脉以西的物种 Rosa gemnocarpa 和 R. pisocarpa 形成了独特的群体，并且它们一起与东部物种截然不同。在东部，发现三个组别是：R. nitida-R。沼泽，R. foliolosa 和 R. blanda-R。伍德西。这些群体与物种的形态学和生态学是一致的。当使用系统发育网络重建关系时，该方法也可用于表示混合个体。