Total geographical ranges (lines) and sampling sites (dots) of <i>Diapensia</i>.

<p>HHM: Himalayan-Hengduan Mountains. Sample IDs refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140175#pone.0140175.t001" target="_blank">Table 1</a>. The ranges of <i>D</i>. <i>lapponica</i> and <i>D</i>. <i>obovata</i> are redrawn after Hultén & Fries [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140175#pone.0140175.ref044" target="_blank">44</a>]. The photo of <i>D</i>. <i>lapponica</i> was attributed by Alinja (<a href="https://commons.wikimedia.org/wiki/File:Diapensia_lapponica_Kilpisj%C3%A4rvi_2012-07.jpg#/media/File:Diapensia_lapponica_Kilpisj%C3%A4rvi_2012-07.jpg" target="_blank">https://commons.wikimedia.org/wiki/File:Diapensia_lapponica_Kilpisj%C3%A4rvi_2012-07.jpg#/media/File:Diapensia_lapponica_Kilpisj%C3%A4rvi_2012-07.jpg</a>)</p

Results after filtering and clustering RAD-seq data from 14 samples of <i>Diapensia</i> and 4 samples of the outgroup using pyRAD.

<p>m4/m14: data matrix clustering RAD-seq reads at 90% similarity threshold and consisting of loci that shared by at least 4 (‘m4’) or 14 (‘m14’) samples.</p><p>^aNumber of reads after quality filtering.</p><p>^bClusters that passed filtering for 2× minimum coverage.</p><p>^cAfter descarding all loci without parsimony informative sites (pis), blast filtering and trimming the last 5 bases from all loci.</p><p>Results after filtering and clustering RAD-seq data from 14 samples of <i>Diapensia</i> and 4 samples of the outgroup using pyRAD.</p

Primary concordance trees inferred at the α of 100 (a) and 0.1 (b) using BUCKy.

<p>The α parameter represents the <i>a priori</i> level of discordance expected among loci, where a high α assumes a high level of discordance among the gene trees and a low α assumes a low level of discordance. 246 loci with at least two parsimony informative sites covering eight <i>Diapensia</i> samples were used in the BUCKy analyses. Sample IDs refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140175#pone.0140175.t001" target="_blank">Table 1</a>. The concordance factors (CFs) and their 95% confidence intervals are shown on the branches; those in bold did not overlap with any conflicting CF, and those in bold and with an asterisk had no conflicting splits.</p

Phylogeny of <i>Diapensia</i> inferred from two RAD-seq data sets (a to d).

<p>(a) and (b) are based on the m4 data set, in which all loci were shared by at least 4 samples; and (c) and (d) are based on the m14 data set, in which all loci were shared by at least 14 samples. Sample IDs refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140175#pone.0140175.t001" target="_blank">Table 1</a>. Maximum likelihood trees were estimated using RAxML; numbers above branches are bootstrap (BS) values generated from 1,000 replicates. Bayesian consensus trees were inferred using MrBayes; numbers above branches are posterior probabilities (PP). Asterisks on branches indicate BS = 100 or PP = 1.</p

Correlation between three important statistics in RAD-seq data sets and clustering similarity thresholds.

<p>Square: number of parsimony informative sites; triangle: total number of loci; and dots: number of loci that contain at least one parsimony informative site.</p

Four-taxon D-statistic test for introgression between <i>Diapensia purpurea</i> and <i>D</i>. <i>himalaica</i>.

<p>P1, P2 and P3: him1: <i>D</i>. <i>himalaica</i> 55962, him2: <i>D</i>. <i>himalaica</i> 55969, him3: <i>D</i>. <i>himalaica</i> 55976, pur1: <i>D</i>. <i>purpurea</i> 56014, pur2: <i>D</i>. <i>purpurea</i> 56025, pur3: <i>D</i>. <i>purpurea</i> 56031 (sample IDs refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140175#pone.0140175.t001" target="_blank">Table 1</a>); O: outgroup ‘A’ consists of all individuals from the two arctic species <i>D</i>. <i>lapponica</i> and <i>D</i>. <i>obovata</i>. D-statistic values (D) and their standard deviation (Std(D)) are given for each test. ABBA, BABA: the number of alleles that support each pattern (the fractions are due to heterozygosity). No. loci: the number of loci analyzed in each test; pdisc: the percentage of discordance.</p><p>*Z-scores that are statistically significant after conversion to a two-tailed P-value and using α = 0.01 as a conservative cutoff for significance.</p><p>Four-taxon D-statistic test for introgression between <i>Diapensia purpurea</i> and <i>D</i>. <i>himalaica</i>.</p

COI sequences

COI sequence

Structure input data (Libyan set)

Structure input data (Libyan set

Sequences from dataset 1 with identification using the Afro-alpine reference library

The unique P6 loop trnL sequences produced by amplification of DNA preserved in sediments from the crater swamp and crater lake on Mt. Gahinga and Mt. Muhavura, respectively, on the Virunga Volcanoes of the Albertine Rift, eastern Africa. Taxonomic identification of sequences was inferred using the Afro-alpine reference library v.1. Further details can be found in the ReadMe file

Sequences from dataset 2 with identification using the Afro-alpine reference library

The unique P6 loop trnL sequences produced by amplification of DNA preserved in sediments from the crater swamp and crater lake on Mt. Gahinga and Mt. Muhavura, respectively, on the Virunga Volcanoes of the Albertine Rift, eastern Africa. Taxonomic identification of sequences was inferred using the Afro-alpine reference library v.1. Further details can be found in the ReadMe file