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Keenan Amundsen and Scott Warnke

differing topologies ( McBreen and Lockhart, 2006 ). These inconsistencies may arise from reticulation events such as horizontal gene transfer, recombination, and hybridization that are not well represented by bifurcating phylogenetic trees ( Huson and

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Xuelin Shen, Yanmei Zhang, Zhao Lei, Yibo Lin, Minxu Cao, Yueyu Hang, and Xiaoqin Sun

accessions, which could be also inferred from sequence-related amplified polymorphism (SRAP) and simple sequence repeat markers ( Han et al., 2007 ; Ma et al., 2012 ). The other accessions showed little difference in the topology between the phylogenetic

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Xinyi Zhang, Li Liao, Zhiyong Wang, Changjun Bai, and Jianxiu Liu

similarity in topology. Accessions with the same provenance were generally clustered in the same group. Accessions from the same geographical area that were clustered into different groups may reflect gene flow from introduced species or introgression ( Li et

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Xianqin Qiu, Hongying Jian, Qigang Wang, Kaixue Tang, and Manzhu Bao

expression analysis using real-time PCR Methods 50 227 230 Devoto, A. Piffanelli, P. Nilsson, I. Wallin, E. Panstruga, R. Heijne, G. 1999 Topology, subcellular localization, and sequence diversity of the Mlo family in plants J. Biol. Chem. 274 34993 35004

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Qijing Zhang and Dajun Gu

and dry at maturity, whereas the fruit of P. tomentosa is smaller and remains fleshy. However, it is difficult to distinguish the two species without flowers or fruit, and few studies have investigated their phylogenetic relationship. The topology of

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Min Deng, Jianjun Chen, Richard J. Henny, and Qiansheng Li

phylogram showed the genetic relationships of cultivars based on the cluster pattern and genetic distance; the genetic distance was represented by branch length. Because some of the branches were very short, the topology of the tree could not be well

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Giora Ben-Ari, Iris Biton, Yair Mani, Benjamin Avidan, and Shimon Lavee

pairwise D as a distance matrix using an agglomerative method called “ward” ( Odong et al., 2011 ). To reinforce our results of tree topology, a resampling of 1000 times was run on loci to create 1000 SNP sets and 1000 trees. To count the number of

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Enrique I. Sánchez-González, Adriana Gutiérrez-Díez, and Netzahualcóyotl Mayek-Pérez

(≤10) if the number of loci is more than 50, or if the genetic distance is large, and the average heterozygosity of the two species compared is low. Even a single individual may be enough for obtaining the correct topology of a dendrogram if the

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Phillip A. Wadl, Robert N. Trigiano, Dennis J. Werner, Margaret R. Pooler, and Timothy A. Rinehart

. They suggested that more investigation is needed to confirm these results because the bootstrap support for this topology was weak. All of our analyses (SSRs and ITS) are in agreement with the findings of Davis et al. (2002) , Fritsch and Cruz (2012

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Ashish K. Pathak, Sudhir P. Singh, and Rakesh Tuli

produce dendrogram of genetic relationships among cultivars using DARwin software [Version 5.0.158 ( Perrier and Jacquemoud-Collet, 2006 )]. Bootstrapping analysis was carried out for the assessment of the robustness of the dendrogram topology based on