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ŠUMARSKI LIST 5-6/2018 str. 36     <-- 36 -->        PDF

number of Parsimony informative sites – Pi, number of haplotypes – h, and nucleotide diversity - π) using Arlequin v. (Excoffier and Lischer, 2010). The phylogenetic analyses were performed separately on the combined plastid DNA dataset (trnK-matK + trnH-psbA sequences) and on the nuclear dataset (5.8S + ITS2). We first constructed a plastid haplotype and a nuclear ribotype networks, based on the median-joining network algorithm (Bandelt et. al., 1999) as implemented in the PopArt software (Leigh and Bryant, 2015). Next, to assess the phylogenetic relationships among the studied oak taxa based on the nuclear sequence dataset, we constructed a phylogenetic tree using a maximum parsimony (MP) method with bootstrap analyses of 1000 replicates to test for the branch support. The analysis was carried out using the MEGA v. 7.0.26 and Seaview v4.6.2 software (Gouy et. al., 2010; Tamura et al. 2016) with default parameters (gaps were treated as unknown states). Finally, because the position of hybrid species in a classic phylogenetic tree is often doubtful, we also computed a rooted consensus cluster network based on nuclear sequences to identify putative hybridization events leading to the formation of the “green oak”. This network was based on a set of 1000 original trees obtained with a MP analysis and with a 20 % threshold (minimum support) for a cluster to be included in the procedure using Dendroscope v. 3.5.9 (Huson and Scornavacca, 2012)
Our dataset included 16 sequences of both plastid and nuclear regions for nine oak taxa. Alignment of the trnH-psbA region had 538 characters (bp) in length, 22 variable sites and 7 parsimony informative sites. Alignment of the trnK-matK region displayed 694 characters, 14 variable sites and 12 parsimony informative sites, while the alignment of the combined plastid DNA dataset resulted in a total length of 1232 sites, 36 of which were variable and 19 parsimony informative (Table 2). The alignment of the nuclear dataset resulted in the total length of 371 sites of which 21 were variable and 13 parsimony informative (Table 2).
In total, five haplotypes were identified based on the combined plastid sequences with a low nucleotide diversity π = 0.0073 (Table 2). The plastid DNA haplotype network showed that one haplotype was shared among 11 studied individuals representative of four oak taxa, namely Q.