Fig 2 - uploaded by Mario Mairal
Content may be subject to copyright.
Bayesian majority-rule consensus trees obtained by MrBayes from: (A) the concatenated A. amellus chloroplast data set (atpI-atpH, rps16-trnK, rpl32trnL, psbE-petL and petN-psbM); (B) the A. amellus nuclear ribosomal (ITS) data set. Numbers above branches indicate Bayesian credibility values (PP); numbers below branches indicate maximum-likelihood bootstrap support values. Depending on their cytotype, each individual is marked in blue (diploids) or green (hexaploids). Codes for A. amellus populations correspond to those shown in Supplementary Data Table S1.
Source publication
Background and Aims
The origin of different cytotypes by autopolyploidy may be an important mechanism in plant diversification. Although cryptic autopolyploids probably comprise the largest fraction of overlooked plant diversity, our knowledge of their origin and evolution is still rather limited. Here we study the presumed autopolyploid aggregate...
Contexts in source publication
Context 1
... data are available online at https://academic. oup.com/aob and consist of the following. Table S1: voucher information and GenBank accession numbers for all samples included in this study. Table S2: primers used for PCR amplifi- cation and sequencing. Table S3: evolutionary model selected with Jmodeltest. Table S4: geographical co-ordinates for the diploid and hexaploid individuals used in the ecological niche modelling of Aster amellus. Table S5: results for the analyses implemented in BEAST to test accuracy of dating estimates. Figure S1: Bayesian majority-rule consensus trees for each chloroplast marker individually. Figure S2: Neighbor-Joining tree with microsatellites. Figure S3: Bayesian majority-rule consensus trees obtained by the standard dating analyses of the linked data sets. Figure S4: haplotype nuclear distribution for the 72 populations sampled for Aster amellus in central ...
Context 2
... 'amellus ITS data set' consisted of 103 sequences of 642 nucleotides (102 individuals + A. alpinus), while the 'amellus pDNA data set' consisted of 101 sequences of 3887 nucleotides (100 individuals + A. alpinus) (Table 1). Nuclear and plastid Bayesian phylogenetic reconstructions showed different topolo- gies (Fig. 2). Analyses of each plastid marker separately showed polytomies and some structured subclades with varying levels of support ( Supplementary Data Fig. S1). The concatenated pDNA showed a topology where both cytotypes were intermingled within different clades (Fig. 2A). The nuclear phylogeny clearly separated the hexaploid individuals into one monophyletic clade and the diploid individuals into another monophyletic clade, except for one hexaploid individual (no. 33 in Supplementary Data Table S1) from the Vrutice Sad, Czech Republic popu- lation, which was grouped within the diploid clade. To avoid mistakes, we checked the unusual position of this individual by resequencing it (confirming its position) and by sequencing additional individuals in this populations, which fitted within the clade of hexaploids from other locations. Both cytotypes of the mixed-ploidy population of Strebersdorf were also sepa- rated into these two clades. The cytotype segregation was sup- ported with a moderate clade support in the MrBayes analysis (PP = 88) and a strong support in the BEAST analysis (PP = 1, not included). ML analyses also separated the two cytotypes, though with lower resolution (Fig. 2B) 15_AU_2 16_AU_2 17_AU_2 18_AU_2 19_AU_2 20_AU_2 21_AU_2 22_AU_2 23_SN_2 24_GE_2 25_SW_2 26_SW_2 27_GE_2 28_CZ_2 29_CZ_2 31_CZ_2 32_CZ_2 33_CZ_6 34_FR_2 35_GE_2 36_SW_2 37_IT_2 38_CR_2 40_AU_2 57_GE_2 61_AU_2 64_AU_2 66_AU_2 72_CR_2 73_CR_2 84_SK_2 85_SN_2 86_SN_2 87_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 95_CZ_2 143_AU_2 152_AU_2 02_PL_6 06_AU_6 30_CZ_6 39_AU_6 41_AU_6 42_AU_6 44_AU_6 45_AU_6 46_AU_6 47_SK_6 48_SK_6 49_SK_6 50_SK_6 51_SK_6 52_SK_6 53_CZ_6 54_PO_6 58_AU_6 59_AU_6 60_AU_6 62_AU_6 63_AU_6 65_AU_6 67_AU_6 68_AU_6 69_AU_6 71_AU_6 74_HU_6 75_HU_6 76_HU_6 77_HU_6 78_HU_6 79_SK_6 80_SK_6 81_SK_6 82_SK_6 83_SK_6 89_CZ_6 96_CZ_6 97_CZ_6 98_CZ_6 99_CZ_6 100_CZ_6 106_AU_6 108_AU_6 118_AU_6 144_AU_6 149_AU_6 151_AU_6 07_PL_2 04_SK_2 06_AU_6 07_PL_2 08_PL_2 09_PL_2 10_SK_2 11_SK_2 13_SK_2 18_AU_2 19_AU_2 21_AU_2 24_GE_2 26_SW_2 27_GE_2 29_CZ_2 31_CZ_2 34_FR_2 36_SW_2 38_CR_2 39_AU_6 40_AU_2 41_AU_6 42_AU_6 44_AU_6 45_AU_6 46_AU_6 48_SK_6 49_SK_6 50_SK_6 52_SK_6 53_CZ_6 54_PO_6 58_AU_6 59_AU_6 60_AU_6 61_AU_2 62_AU_6 63_AU_6 64_AU_2 65_AU_6 66_AU_2 68_AU_6 69_AU_6 71_AU_6 72_CR_2 73_CR_2 75_HU_6 77_HU_6 78_HU_6 79_SK_6 80_SK_6 82_SK_6 83_SK_6 84_SK_2 86_SN_2 87_SN_2 89_CZ_6 108_AU_6 118_AU_6 143_AU_2 144_AU_6 149_AU_6 151_AU_6 152_AU_2 106_AU_6 02_PL_6 16_AU_2 17_AU_2 20_AU_2 25_SW_2 28_CZ_2 30_CZ_6 32_CZ_2 33_CZ_6 47_SK_6 57_GE_2 81_SK_6 85_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 96_CZ_6 97_CZ_6 98_CZ_6 99_CZ_6 100_CZ_6 95_CZ_2 01_CR_2 05_AU_2 14_AU_2 15_AU_2 22_AU_2 51_SK_6 12_SK_2 23_SN_2 35_GE_2 Table ...
Context 3
... 'amellus ITS data set' consisted of 103 sequences of 642 nucleotides (102 individuals + A. alpinus), while the 'amellus pDNA data set' consisted of 101 sequences of 3887 nucleotides (100 individuals + A. alpinus) (Table 1). Nuclear and plastid Bayesian phylogenetic reconstructions showed different topolo- gies (Fig. 2). Analyses of each plastid marker separately showed polytomies and some structured subclades with varying levels of support ( Supplementary Data Fig. S1). The concatenated pDNA showed a topology where both cytotypes were intermingled within different clades (Fig. 2A). The nuclear phylogeny clearly separated the hexaploid individuals into one monophyletic clade and the diploid individuals into another monophyletic clade, except for one hexaploid individual (no. 33 in Supplementary Data Table S1) from the Vrutice Sad, Czech Republic popu- lation, which was grouped within the diploid clade. To avoid mistakes, we checked the unusual position of this individual by resequencing it (confirming its position) and by sequencing additional individuals in this populations, which fitted within the clade of hexaploids from other locations. Both cytotypes of the mixed-ploidy population of Strebersdorf were also sepa- rated into these two clades. The cytotype segregation was sup- ported with a moderate clade support in the MrBayes analysis (PP = 88) and a strong support in the BEAST analysis (PP = 1, not included). ML analyses also separated the two cytotypes, though with lower resolution (Fig. 2B) 15_AU_2 16_AU_2 17_AU_2 18_AU_2 19_AU_2 20_AU_2 21_AU_2 22_AU_2 23_SN_2 24_GE_2 25_SW_2 26_SW_2 27_GE_2 28_CZ_2 29_CZ_2 31_CZ_2 32_CZ_2 33_CZ_6 34_FR_2 35_GE_2 36_SW_2 37_IT_2 38_CR_2 40_AU_2 57_GE_2 61_AU_2 64_AU_2 66_AU_2 72_CR_2 73_CR_2 84_SK_2 85_SN_2 86_SN_2 87_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 95_CZ_2 143_AU_2 152_AU_2 02_PL_6 06_AU_6 30_CZ_6 39_AU_6 41_AU_6 42_AU_6 44_AU_6 45_AU_6 46_AU_6 47_SK_6 48_SK_6 49_SK_6 50_SK_6 51_SK_6 52_SK_6 53_CZ_6 54_PO_6 58_AU_6 59_AU_6 60_AU_6 62_AU_6 63_AU_6 65_AU_6 67_AU_6 68_AU_6 69_AU_6 71_AU_6 74_HU_6 75_HU_6 76_HU_6 77_HU_6 78_HU_6 79_SK_6 80_SK_6 81_SK_6 82_SK_6 83_SK_6 89_CZ_6 96_CZ_6 97_CZ_6 98_CZ_6 99_CZ_6 100_CZ_6 106_AU_6 108_AU_6 118_AU_6 144_AU_6 149_AU_6 151_AU_6 07_PL_2 04_SK_2 06_AU_6 07_PL_2 08_PL_2 09_PL_2 10_SK_2 11_SK_2 13_SK_2 18_AU_2 19_AU_2 21_AU_2 24_GE_2 26_SW_2 27_GE_2 29_CZ_2 31_CZ_2 34_FR_2 36_SW_2 38_CR_2 39_AU_6 40_AU_2 41_AU_6 42_AU_6 44_AU_6 45_AU_6 46_AU_6 48_SK_6 49_SK_6 50_SK_6 52_SK_6 53_CZ_6 54_PO_6 58_AU_6 59_AU_6 60_AU_6 61_AU_2 62_AU_6 63_AU_6 64_AU_2 65_AU_6 66_AU_2 68_AU_6 69_AU_6 71_AU_6 72_CR_2 73_CR_2 75_HU_6 77_HU_6 78_HU_6 79_SK_6 80_SK_6 82_SK_6 83_SK_6 84_SK_2 86_SN_2 87_SN_2 89_CZ_6 108_AU_6 118_AU_6 143_AU_2 144_AU_6 149_AU_6 151_AU_6 152_AU_2 106_AU_6 02_PL_6 16_AU_2 17_AU_2 20_AU_2 25_SW_2 28_CZ_2 30_CZ_6 32_CZ_2 33_CZ_6 47_SK_6 57_GE_2 81_SK_6 85_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 96_CZ_6 97_CZ_6 98_CZ_6 99_CZ_6 100_CZ_6 95_CZ_2 01_CR_2 05_AU_2 14_AU_2 15_AU_2 22_AU_2 51_SK_6 12_SK_2 23_SN_2 35_GE_2 Table ...
Context 4
... 'amellus ITS data set' consisted of 103 sequences of 642 nucleotides (102 individuals + A. alpinus), while the 'amellus pDNA data set' consisted of 101 sequences of 3887 nucleotides (100 individuals + A. alpinus) (Table 1). Nuclear and plastid Bayesian phylogenetic reconstructions showed different topolo- gies (Fig. 2). Analyses of each plastid marker separately showed polytomies and some structured subclades with varying levels of support ( Supplementary Data Fig. S1). The concatenated pDNA showed a topology where both cytotypes were intermingled within different clades (Fig. 2A). The nuclear phylogeny clearly separated the hexaploid individuals into one monophyletic clade and the diploid individuals into another monophyletic clade, except for one hexaploid individual (no. 33 in Supplementary Data Table S1) from the Vrutice Sad, Czech Republic popu- lation, which was grouped within the diploid clade. To avoid mistakes, we checked the unusual position of this individual by resequencing it (confirming its position) and by sequencing additional individuals in this populations, which fitted within the clade of hexaploids from other locations. Both cytotypes of the mixed-ploidy population of Strebersdorf were also sepa- rated into these two clades. The cytotype segregation was sup- ported with a moderate clade support in the MrBayes analysis (PP = 88) and a strong support in the BEAST analysis (PP = 1, not included). ML analyses also separated the two cytotypes, though with lower resolution (Fig. 2B) 15_AU_2 16_AU_2 17_AU_2 18_AU_2 19_AU_2 20_AU_2 21_AU_2 22_AU_2 23_SN_2 24_GE_2 25_SW_2 26_SW_2 27_GE_2 28_CZ_2 29_CZ_2 31_CZ_2 32_CZ_2 33_CZ_6 34_FR_2 35_GE_2 36_SW_2 37_IT_2 38_CR_2 40_AU_2 57_GE_2 61_AU_2 64_AU_2 66_AU_2 72_CR_2 73_CR_2 84_SK_2 85_SN_2 86_SN_2 87_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 95_CZ_2 143_AU_2 152_AU_2 02_PL_6 06_AU_6 30_CZ_6 39_AU_6 41_AU_6 42_AU_6 44_AU_6 45_AU_6 46_AU_6 47_SK_6 48_SK_6 49_SK_6 50_SK_6 51_SK_6 52_SK_6 53_CZ_6 54_PO_6 58_AU_6 59_AU_6 60_AU_6 62_AU_6 63_AU_6 65_AU_6 67_AU_6 68_AU_6 69_AU_6 71_AU_6 74_HU_6 75_HU_6 76_HU_6 77_HU_6 78_HU_6 79_SK_6 80_SK_6 81_SK_6 82_SK_6 83_SK_6 89_CZ_6 96_CZ_6 97_CZ_6 98_CZ_6 99_CZ_6 100_CZ_6 106_AU_6 108_AU_6 118_AU_6 144_AU_6 149_AU_6 151_AU_6 07_PL_2 04_SK_2 06_AU_6 07_PL_2 08_PL_2 09_PL_2 10_SK_2 11_SK_2 13_SK_2 18_AU_2 19_AU_2 21_AU_2 24_GE_2 26_SW_2 27_GE_2 29_CZ_2 31_CZ_2 34_FR_2 36_SW_2 38_CR_2 39_AU_6 40_AU_2 41_AU_6 42_AU_6 44_AU_6 45_AU_6 46_AU_6 48_SK_6 49_SK_6 50_SK_6 52_SK_6 53_CZ_6 54_PO_6 58_AU_6 59_AU_6 60_AU_6 61_AU_2 62_AU_6 63_AU_6 64_AU_2 65_AU_6 66_AU_2 68_AU_6 69_AU_6 71_AU_6 72_CR_2 73_CR_2 75_HU_6 77_HU_6 78_HU_6 79_SK_6 80_SK_6 82_SK_6 83_SK_6 84_SK_2 86_SN_2 87_SN_2 89_CZ_6 108_AU_6 118_AU_6 143_AU_2 144_AU_6 149_AU_6 151_AU_6 152_AU_2 106_AU_6 02_PL_6 16_AU_2 17_AU_2 20_AU_2 25_SW_2 28_CZ_2 30_CZ_6 32_CZ_2 33_CZ_6 47_SK_6 57_GE_2 81_SK_6 85_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 96_CZ_6 97_CZ_6 98_CZ_6 99_CZ_6 100_CZ_6 95_CZ_2 01_CR_2 05_AU_2 14_AU_2 15_AU_2 22_AU_2 51_SK_6 12_SK_2 23_SN_2 35_GE_2 Table ...
Context 5
... nuclear and plastid trees showed different phylogenetic signals, which may indicate distinct evolutionary histories (Fig. 2). Our resolved ITS phylogeny supported an explicit phy- logenetic hypothesis, separating diploid and hexaploid individ- uals into two different monophyletic clades (Fig. 2B). However, the inferences obtained from the ITS region could be limited due to additional difficulties such as paralogy, concerted evolu- tion or directional bias in the homogenization process ( Buckler et al., 1997;Eidesen et al., 2017). We can discard the possibility of paralogy, because the polymorphism detected when sequenc- ing the ITS did not show shared sequences between cytotypes (Feliner and Rosell?, 2007). The ITS may be subjected to con- certed evolution leading to clear ITS differentiation of the two clades (Fig. 2B). Additionally, the phylogram method based on genetic distances using simple sequence repeats (SSRs) showed low support values, with diploids and hexaploids not clearly sorting into distinct clades (Supplementary Data Fig. S2). This is likely to be because microsatellites are widely distributed in the euchromatin ( Schl?tterer and Harr, 2001), and it is thus very unlikely that a concerted evolution process would have homog- enized all the alleles. Still, we can, however detect separate genetic clusters in the microsatellite data due to assortative mat- ing within cytotypes (M?nzbergov? et al., 2013). Altogether, the results of the ITS and SSRs seem to indicate that the current mating patterns are strongly assortative within cytotypes. Conversely, the different topology shown by the plastid data could arise due to processes such as hybridization, chloroplast capture or deep coalescence. We can discard hybridization since breeding barriers were detected in A. amellus and the inter- mediate forms found previously are inviable ( Mand?kov? and M?nzbergov?, 2006;Castro et al., 2011Castro et al., , 2012. In terms of chloroplast capture, we detected some identical sequences in cytotypes growing sympatrically in the only mixed-ploidy popu- lation detected in nature. Because individuals with intermediate ploidy levels have rarely been found in the populations (but were never fertile), one cannot completely dismiss the possibility of punctual hybridization and backcrossing in sympatric locations, though it seems unlikely. Thus, the discrepancy between the ITS and chloroplast trees seems to be due to shared ancestral relation- ships (deep coalescence events) or incomplete lineage sorting (ILS) among the chlorotypes ( Maddison and Knowles, ...
Context 6
... nuclear and plastid trees showed different phylogenetic signals, which may indicate distinct evolutionary histories (Fig. 2). Our resolved ITS phylogeny supported an explicit phy- logenetic hypothesis, separating diploid and hexaploid individ- uals into two different monophyletic clades (Fig. 2B). However, the inferences obtained from the ITS region could be limited due to additional difficulties such as paralogy, concerted evolu- tion or directional bias in the homogenization process ( Buckler et al., 1997;Eidesen et al., 2017). We can discard the possibility of paralogy, because the polymorphism detected when sequenc- ing the ITS did not show shared sequences between cytotypes (Feliner and Rosell?, 2007). The ITS may be subjected to con- certed evolution leading to clear ITS differentiation of the two clades (Fig. 2B). Additionally, the phylogram method based on genetic distances using simple sequence repeats (SSRs) showed low support values, with diploids and hexaploids not clearly sorting into distinct clades (Supplementary Data Fig. S2). This is likely to be because microsatellites are widely distributed in the euchromatin ( Schl?tterer and Harr, 2001), and it is thus very unlikely that a concerted evolution process would have homog- enized all the alleles. Still, we can, however detect separate genetic clusters in the microsatellite data due to assortative mat- ing within cytotypes (M?nzbergov? et al., 2013). Altogether, the results of the ITS and SSRs seem to indicate that the current mating patterns are strongly assortative within cytotypes. Conversely, the different topology shown by the plastid data could arise due to processes such as hybridization, chloroplast capture or deep coalescence. We can discard hybridization since breeding barriers were detected in A. amellus and the inter- mediate forms found previously are inviable ( Mand?kov? and M?nzbergov?, 2006;Castro et al., 2011Castro et al., , 2012. In terms of chloroplast capture, we detected some identical sequences in cytotypes growing sympatrically in the only mixed-ploidy popu- lation detected in nature. Because individuals with intermediate ploidy levels have rarely been found in the populations (but were never fertile), one cannot completely dismiss the possibility of punctual hybridization and backcrossing in sympatric locations, though it seems unlikely. Thus, the discrepancy between the ITS and chloroplast trees seems to be due to shared ancestral relation- ships (deep coalescence events) or incomplete lineage sorting (ILS) among the chlorotypes ( Maddison and Knowles, ...
Context 7
... nuclear and plastid trees showed different phylogenetic signals, which may indicate distinct evolutionary histories (Fig. 2). Our resolved ITS phylogeny supported an explicit phy- logenetic hypothesis, separating diploid and hexaploid individ- uals into two different monophyletic clades (Fig. 2B). However, the inferences obtained from the ITS region could be limited due to additional difficulties such as paralogy, concerted evolu- tion or directional bias in the homogenization process ( Buckler et al., 1997;Eidesen et al., 2017). We can discard the possibility of paralogy, because the polymorphism detected when sequenc- ing the ITS did not show shared sequences between cytotypes (Feliner and Rosell?, 2007). The ITS may be subjected to con- certed evolution leading to clear ITS differentiation of the two clades (Fig. 2B). Additionally, the phylogram method based on genetic distances using simple sequence repeats (SSRs) showed low support values, with diploids and hexaploids not clearly sorting into distinct clades (Supplementary Data Fig. S2). This is likely to be because microsatellites are widely distributed in the euchromatin ( Schl?tterer and Harr, 2001), and it is thus very unlikely that a concerted evolution process would have homog- enized all the alleles. Still, we can, however detect separate genetic clusters in the microsatellite data due to assortative mat- ing within cytotypes (M?nzbergov? et al., 2013). Altogether, the results of the ITS and SSRs seem to indicate that the current mating patterns are strongly assortative within cytotypes. Conversely, the different topology shown by the plastid data could arise due to processes such as hybridization, chloroplast capture or deep coalescence. We can discard hybridization since breeding barriers were detected in A. amellus and the inter- mediate forms found previously are inviable ( Mand?kov? and M?nzbergov?, 2006;Castro et al., 2011Castro et al., , 2012. In terms of chloroplast capture, we detected some identical sequences in cytotypes growing sympatrically in the only mixed-ploidy popu- lation detected in nature. Because individuals with intermediate ploidy levels have rarely been found in the populations (but were never fertile), one cannot completely dismiss the possibility of punctual hybridization and backcrossing in sympatric locations, though it seems unlikely. Thus, the discrepancy between the ITS and chloroplast trees seems to be due to shared ancestral relation- ships (deep coalescence events) or incomplete lineage sorting (ILS) among the chlorotypes ( Maddison and Knowles, ...
Context 8
... nuclear and plastid trees showed different phylogenetic signals, which may indicate distinct evolutionary histories (Fig. 2). Our resolved ITS phylogeny supported an explicit phy- logenetic hypothesis, separating diploid and hexaploid individ- uals into two different monophyletic clades (Fig. 2B). However, the inferences obtained from the ITS region could be limited due to additional difficulties such as paralogy, concerted evolu- tion or directional bias in the homogenization process ( Buckler et al., 1997;Eidesen et al., 2017). We can discard the possibility of paralogy, because the polymorphism detected when sequenc- ing the ITS did not show shared sequences between cytotypes (Feliner and Rosell?, 2007). The ITS may be subjected to con- certed evolution leading to clear ITS differentiation of the two clades (Fig. 2B). Additionally, the phylogram method based on genetic distances using simple sequence repeats (SSRs) showed low support values, with diploids and hexaploids not clearly sorting into distinct clades (Supplementary Data Fig. S2). This is likely to be because microsatellites are widely distributed in the euchromatin ( Schl?tterer and Harr, 2001), and it is thus very unlikely that a concerted evolution process would have homog- enized all the alleles. Still, we can, however detect separate genetic clusters in the microsatellite data due to assortative mat- ing within cytotypes (M?nzbergov? et al., 2013). Altogether, the results of the ITS and SSRs seem to indicate that the current mating patterns are strongly assortative within cytotypes. Conversely, the different topology shown by the plastid data could arise due to processes such as hybridization, chloroplast capture or deep coalescence. We can discard hybridization since breeding barriers were detected in A. amellus and the inter- mediate forms found previously are inviable ( Mand?kov? and M?nzbergov?, 2006;Castro et al., 2011Castro et al., , 2012. In terms of chloroplast capture, we detected some identical sequences in cytotypes growing sympatrically in the only mixed-ploidy popu- lation detected in nature. Because individuals with intermediate ploidy levels have rarely been found in the populations (but were never fertile), one cannot completely dismiss the possibility of punctual hybridization and backcrossing in sympatric locations, though it seems unlikely. Thus, the discrepancy between the ITS and chloroplast trees seems to be due to shared ancestral relation- ships (deep coalescence events) or incomplete lineage sorting (ILS) among the chlorotypes ( Maddison and Knowles, ...
Context 9
... vs. single-origin model A previous study of A. amellus using microsatellites (M?nzbergov? et al., 2013) postulated that A. amellus cytotypes probably had a single origin. However, our new evidence shows the need to include chloroplast markers to unravel the origin of cytotypes. The ancient divergences and topological relation- ships reflected by the pDNA suggest that the hexaploid cytotype arose and was established several times from the diploid cytotype (Figs 2A and 3B). On the other hand, the parapatric mosaic of A. amellus cytotypes makes it difficult to interpret the geographical patterns clearly, and a single-origin model could also be expected if the secondary contact occurred after Pleistocence range expan- sion ( Mand?kov? and M?nzbergov?, 2006). Differentiation between these alternatives requires an accurate temporal frame- work, which is not a straightforward task due to the difficulties that exist when dating polyploids (Doyle and Egan, 2010). However, it is remarkable that our different dating approaches were con- gruent and resulted in very similar age estimates (Supplementary Data Table S5). We need, however, to emphasize that our dating identified the point at which gene trees coalescent, which does not necessarily coincide with the polyploidization event (Doyle and Egan, 2010). Overall, dating estimates agree well with an ancient origin of the genetic diversification in A. amellus, suggesting a multiple-origin model for the hexaploid cytotypes. This is further supported by the large number of undetected mutation events separating the chlorotypes (gaps in Fig. 4A), which probably corresponds to extinct ancestral haplotypes (Mairal et al., 2015b), showing older relationships in this ...
Context 10
... based on ITS was partly supported by the Neighbor- Joining tree constructed using previously obtained microsatel- lite data. It showed lower genetic distances within diploids and within hexaploids, although the clades did not precisely sort into diploids and hexaploids ( Supplementary Data Fig. ...
Context 11
... 'amellus ITS data set' consisted of 103 sequences of 642 nucleotides (102 individuals + A. alpinus), while the 'amellus pDNA data set' consisted of 101 sequences of 3887 nucleotides (100 individuals + A. alpinus) (Table 1). Nuclear and plastid Bayesian phylogenetic reconstructions showed different topolo- gies (Fig. 2). Analyses of each plastid marker separately showed polytomies and some structured subclades with varying levels of support ( Supplementary Data Fig. S1). The concatenated pDNA showed a topology where both cytotypes were intermingled within different clades (Fig. 2A). The nuclear phylogeny clearly separated the hexaploid individuals ...
Context 12
... and plastid Bayesian phylogenetic reconstructions showed different topolo- gies (Fig. 2). Analyses of each plastid marker separately showed polytomies and some structured subclades with varying levels of support ( Supplementary Data Fig. S1). The concatenated pDNA showed a topology where both cytotypes were intermingled within different clades (Fig. 2A). The nuclear phylogeny clearly separated the hexaploid individuals into one monophyletic clade and the diploid individuals into another monophyletic clade, except for one hexaploid individual (no. 33 in Supplementary Data Table S1) from the Vrutice Sad, Czech Republic popu- lation, which was grouped within the diploid clade. To avoid ...
Context 13
... cytotypes of the mixed-ploidy population of Strebersdorf were also sepa- rated into these two clades. The cytotype segregation was sup- ported with a moderate clade support in the MrBayes analysis (PP = 88) and a strong support in the BEAST analysis (PP = 1, not included). ML analyses also separated the two cytotypes, though with lower resolution (Fig. 2B) 15_AU_2 16_AU_2 17_AU_2 18_AU_2 19_AU_2 20_AU_2 21_AU_2 22_AU_2 23_SN_2 24_GE_2 25_SW_2 26_SW_2 27_GE_2 28_CZ_2 29_CZ_2 31_CZ_2 32_CZ_2 33_CZ_6 34_FR_2 35_GE_2 36_SW_2 37_IT_2 38_CR_2 40_AU_2 57_GE_2 61_AU_2 64_AU_2 66_AU_2 72_CR_2 73_CR_2 84_SK_2 85_SN_2 86_SN_2 87_SN_2 91_CZ_2 92_CZ_2 93_CZ_2 94_CZ_2 95_CZ_2 143_AU_2 152_AU_2 02_PL_6 ...
Context 14
... based on ITS was partly supported by the Neighbor- Joining tree constructed using previously obtained microsatel- lite data. It showed lower genetic distances within diploids and within hexaploids, although the clades did not precisely sort into diploids and hexaploids ( Supplementary Data Fig. ...
Context 15
... nuclear and plastid trees showed different phylogenetic signals, which may indicate distinct evolutionary histories (Fig. 2). Our resolved ITS phylogeny supported an explicit phy- logenetic hypothesis, separating diploid and hexaploid individ- uals into two different monophyletic clades (Fig. 2B). However, the inferences obtained from the ITS region could be limited due to additional difficulties such as paralogy, concerted evolu- tion or directional bias in ...
Context 16
... nuclear and plastid trees showed different phylogenetic signals, which may indicate distinct evolutionary histories (Fig. 2). Our resolved ITS phylogeny supported an explicit phy- logenetic hypothesis, separating diploid and hexaploid individ- uals into two different monophyletic clades (Fig. 2B). However, the inferences obtained from the ITS region could be limited due to additional difficulties such as paralogy, concerted evolu- tion or directional bias in the homogenization process ( Buckler et al., 1997;Eidesen et al., 2017). We can discard the possibility of paralogy, because the polymorphism detected when sequenc- ing the ...
Context 17
... process ( Buckler et al., 1997;Eidesen et al., 2017). We can discard the possibility of paralogy, because the polymorphism detected when sequenc- ing the ITS did not show shared sequences between cytotypes (Feliner and Roselló, 2007). The ITS may be subjected to con- certed evolution leading to clear ITS differentiation of the two clades (Fig. 2B). Additionally, the phylogram method based on genetic distances using simple sequence repeats (SSRs) showed low support values, with diploids and hexaploids not clearly sorting into distinct clades (Supplementary Data Fig. S2). This is likely to be because microsatellites are widely distributed in the euchromatin ( Schlötterer and Harr, ...
Context 18
... (Feliner and Roselló, 2007). The ITS may be subjected to con- certed evolution leading to clear ITS differentiation of the two clades (Fig. 2B). Additionally, the phylogram method based on genetic distances using simple sequence repeats (SSRs) showed low support values, with diploids and hexaploids not clearly sorting into distinct clades (Supplementary Data Fig. S2). This is likely to be because microsatellites are widely distributed in the euchromatin ( Schlötterer and Harr, 2001), and it is thus very unlikely that a concerted evolution process would have homog- enized all the alleles. Still, we can, however detect separate genetic clusters in the microsatellite data due to assortative mat- ing ...
Context 19
... our new evidence shows the need to include chloroplast markers to unravel the origin of cytotypes. The ancient divergences and topological relation- ships reflected by the pDNA suggest that the hexaploid cytotype arose and was established several times from the diploid cytotype (Figs 2A and 3B). On the other hand, the parapatric mosaic of A. amellus cytotypes makes it difficult to interpret the geographical patterns clearly, and a single-origin model could also be expected if the secondary contact occurred after Pleistocence range expan- sion ( Mandáková and Münzbergová, 2006). ...
Citations
... (Linaceae) (Afonso et al., 2021). Another way involves (i) the use of organellar DNA (chloroplast or nuclear regions) as molecular markers as it was described for phylogenetic analysis of the genus Isoëtes (Pereira et al., 2019) or the diploid and autohexaploid cytotypes of Aster amellus (Mairal et al., 2018); or (ii) OMICS-data tools as RAD-Seq (restriction site-associated DNA sequencing) as described in the evolutionary processes of apomictic polyploid complexes on the model system Ranunculus (Karbstein et al., 2022). Thus, the various approaches used in this study, combining morphological and cytogenetic analyses, in situ hybridization and interspecific crosses, could constitute a first step towards phylogenetic studies of species belonging to poorly understood complexes for which there are few genomic resources. ...
... Polyploidy (i.e., the whole-genome duplication) including both auto-and allopolyploidy is one of the major processes involved in the diversification and speciation of plants [2][3][4][5][6]. Autopolyploidy has received relatively little attention due to high levels of morphological similarity between autopolyploids and their parental diploid taxa [7][8][9]. In contrast, allopolyploids have been studied extensively in several plant groups with focus on changes of genome sizes and karyotypes compared to their parental taxa (e.g., Brassica L. [10]; Melampodium L. [11,12]; Nicotiana L. [13]; Prospero Salisb. ...
Background
Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.
Results
The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.
Conclusions
This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.
... Under an adaptive evolutionary scenario such changes can result in organisms taking advantage of new ecological opportunities or facing new environmental challenges (Fawcett et al., 2013;Ohno, 1970;Schranz et al., 2012). Several studies have shown that in species with different ploidy, the cytotypes may have different ecological requirements (Mairal et al., 2018;Rojas-Andrés et al., 2020;Solís Neffa et al., 2022). However, other studies have not detected any habitat differentiation between the cytotypes (Castro et al., , 2019Glennon et al., 2014;Marchant et al., 2016;Via do Pico et al., 2019;Visser and Molofsky, 2015). ...
... The authors concluded that if genome size and/or chromosome counts might be useful tools for identifying polyploid complex L. suffruticosum s.l., further studies were necessary to identify origin of the not easy disentangle polyploid complex. Another way but more expensive approach to phylogenetic studies involves (i) the use of organellar DNA (chloroplast or nuclear regions) as molecular markers as it was described for phylogenetic analysis of the genus Isoëtes (Pereira et al., 2019) or the diploid and autohexaploid cytotypes of Aster amellus (Mairal et al., 2018); or (ii) OMICS-data tools as RAD-Seq (restriction site-(which was not certified by peer review) is the author/funder. All rights reserved. ...
The genus Ludwigia L. section Jussiaea is composed of a polyploid species complex with 2x, 4x, 6x and 10x ploidy levels, suggesting possible hybrid origins. The aim of the present study is to understand the genomic relationships among diploid and polyploid species in the section Jussiaea. Morphological and cytogenetic observations, controlled crosses, genomic in situ hybridization (GISH), and flow cytometry were used to characterize species, ploidy levels, ploidy patterns, and genomic composition across taxa. Genome sizes obtained were in agreement with the diploid, tetraploid, hexaploid, and decaploid ploidy levels. Results of GISH showed that progenitors of Ludwigia stolonifera (4x) were Ludwigia peploides subsp. montevidensis (2x) and Ludwigia helminthorrhiza (2x), which also participated for one part (2x) to the Ludwigia ascendens genome (4x). Ludwigia grandiflora subsp. hexapetala (10x) resulted from the hybridization between L. stolonifera (4x) and Ludwigia grandiflora subsp. grandiflora (6x). One progenitor of L. grandiflora subsp. grandiflora was identified as L. peploides (2x). Our results suggest the existence of several processes of hybridization, leading to polyploidy, and possibly allopolyploidy, in the section Jussiaea due to the diversity of ploidy levels. The success of GISH opens up the potential for future studies to identify other missing progenitors in Ludwigia L. as well as other taxa.
... When polyploid complexes do not show further genetic substructure (Mairal et al., 2018;Münzbergová et al., 2013), global niche comparison between cytotypes is relevant. But unfortunately, the intraspecific genetic structure of polyploid complexes is often unknown due to limitations associated with challenges surrounding population genetic data analysis of polyploids (Rojas-Andrés et al., 2020;Rothfels, 2021), and if known, it is rarely taken into account when evaluating polyploid niche evolution (see López-Jurado et al., 2019 as an exception). ...
Aim
Although whole-genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.
Location
Europe.
Taxon
Arabidopsis arenosa (Brassicaceae).
Methods
Leveraging a total of 352 cytotyped populations of diploid-autotetraploid A. arenosa, we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested whether there was an effect of additional interploidy introgression from other sympatric but ancestrally divergent diploid lineages of A. arenosa on climatic niches of tetraploids.
Results
Ecological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of the tetraploid ruderal lineage of A. arenosa.
Main conclusions
The niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post-WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD—which usually remain undetected by studies neglecting evolutionary history of polyploids—may play a key role in the adaptation of polyploids to challenging environments.
... Genomic patterns in the sub-Antarctic and Antarctic flora have been studied in a few areas (Bennett et al. 1982;González et al. 2016), but it is unknown if there are general trends that reflect those observed in the northern polar region (but see Rice et al. 2019). Additionally, many polyploids correspond to cryptic species that are morphologically similar to their diploid predecessors (Soltis et al. 2007;Husband et al. 2013), especially in autopolyploids (Soltis et al. 2007;Mairal et al. 2018). Thus, the possible presence of cryptic lineages makes the estimation of genome size and ploidy level especially relevant for unraveling evolutionary processes in sub-Antarctic ecosystems. ...
The flora of sub-Antarctic Marion Island forms part of the unique South Indian Ocean Biogeographic Province, and is under threat from climate change and invasive species. Current information on the flora is necessary to rapidly identify and manage future changes. We conducted a literature search on the taxonomy of indigenous vascular plant species on Marion Island and found nomenclatural changes following taxonomic revisions for Austroblechnum penna-marina (Poir.) Gasper & V.A.O.Dittrich, Carex dikei (Nelmes) K.L.Wilson, Leptinella plumosa Hook.f., Notogrammitis crassior (Kirk) Parris, Phlegmariurus saururus (Lam.) B.Øllg., and Polypogon magellanicus (Lam.) Finot. Additionally, Ranunculus moseleyi Hook.f. was removed from our species checklist due to its long absence in floristic surveys, leaving 21 species in the indigenous vascular plant flora present on Marion Island. We also amplified and sequenced the universal plant barcoding loci rbcL and matK for 19 and 13 species, respectively, and found that ample interspecific genetic distance and minimal intraspecific genetic distance allowed for easy discrimination between species. Lastly, we obtained genome size estimates using flow cytometry for 12 species. Mean 2C genome size for species on Marion Island ranged from 0.44 to 21.44 pg, which is on the lower end of the known range for vascular plant species. We detected two distinct cytotypes in Poa cookii (Hook.f.) Hook.f. and one cytotype in all other species measured.
... Recurrent autopolyploidization events have been inferred in many other plant species showing similar combinations of phylogeographical and cytogeographical patterns (e.g. Segraves et al., 1999;Yamane, Yasui & Ohnishi, 2003;Mairal et al., 2018). Specifically, multiple origins of autopolyploids have also been reported in Artemisia tridentata Nutt. ...
Artemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and North-West Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids.
... Recurrent autopolyploidization events have been inferred in many other plant species showing similar combinations of phylogeographical and cytogeographical patterns (e.g. Segraves et al., 1999;Yamane, Yasui & Ohnishi, 2003;Mairal et al., 2018). Specifically, multiple origins of autopolyploids have also been reported in Artemisia tridentata Nutt. ...
Artemisia herba-alba is an important component of Mediterranean dry steppe floras, being widely distributed in arid areas of the Iberian Peninsula and NorthWest Africa. In this study, we use genetic, cytogenetic and niche modelling tools to investigate the natural history of the species, focusing particularly on the role played by polyploidization to explain current diversity patterns throughout the main distribution range of the plant. Our sequencing data indicate a complex phylogeographical structure showing similar haplotype diversity patterns on both sides of the Strait of Gibraltar and no clear signals of genetic refugia. According to our cytogeographical results, we inferred multiple polyploidization events, which probably took place on the Iberian Peninsula and in North Africa independently. Environmental niche modelling suggested stable potential distributions of A. herba-alba on both sides of the Mediterranean Sea under present and past Last Glacial Maximum conditions, which could be related to the intricate spatial genetic and cytogenetic patterns shown by the species. Finally, environmental modelling comparison among cytotypes revealed that the niche of tetraploids is narrower and nested in that of diploids, a result that could indicate environmental specialization and could potentially explain recurrent establishment success of tetraploids.
... Climate is a major determinant of the distribution of plant species and is also thought to explain a large part of the spatial separation of lineages with different ploidy levels (Glennon et al., 2014;McAllister et al., 2015;Muñoz-Pajares et al., 2018). Ecological niche modeling (Mairal et al., 2018;Muñoz-Pajares et al., 2018) and multivariate analysis of niche variables allow a quantitative evaluation of the ecological divergences of plant lineages with different ploidy levels and also permit a statistical comparison of the niche overlap of the different taxa (Warren et al., 2008;Broennimann et al., 2012). However, the evidence for climatic or ecological niche differentiation between different cytotypes of a species is still inconclusive. ...
Premise:
Different cytotypes of a species may differ in their morphology, phenology, physiology, and their tolerance of extreme environments. We studied the ecological niches of two subspecies of Saxifraga rosacea with different ploidy levels: the hexaploid Central European endemic subspecies sponhemica and the more widely distributed octoploid subspecies rosacea.
Methods:
For both cytotypes, we recorded local environmental conditions and mean plant trait values in populations across their areas of distribution, analyzed their distributions by niche modeling, studied their performance at two transplant sites with contrasting conditions, and experimentally tested their cold resistance.
Results:
Mean annual temperature was higher in hexaploid than in octoploid populations and experiments indicated that frost tolerance of the hexaploid is lower than that of the octoploid. Reproduction of octoploids from Central Europe was higher than that of hexaploids at a transplant site in subarctic Iceland, whereas the opposite was true in temperate Luxembourg, indicating adaptation of the octoploids to colder conditions. Temperature variables were also most important in niche models predicting the distribution of the two cytotypes. Genetic differences in survival among populations were larger for the octoploids than for the hexaploids in both field gardens, suggesting that greater genetic variability may contribute to the octoploid's larger distributional range.
Conclusions:
Our results support the hypotheses that different cytotypes may have different niches leading to spatial segregation, and that higher ploidy levels can result in a broader ecological niche and greater tolerance of more extreme conditions.
... Thus, genome duplication may allow polyploids to expand to new habitats previously unavailable to their diploid counterparts (Stebbins, 1984(Stebbins, , 1985Thompson and Lumaret, 1992;Maceira et al., 1993;te Beest et al., 2012). Numerous studies that have recently assessed this hypothesis have found ecological differences among ploidy levels (see Ramsey and Ramsey, 2014;Mairal et al., 2018). However, other studies failed to detect habitat differentiation among cytotypes, suggesting that niche differentiation patterns are not universal (Glennon et al., 2014;Visser and Molofsky, 2015;Marchant et al., 2016;Castro et al., 2018Castro et al., , 2019. ...
Background and aims:
The distribution of cytotypes and its potential correlation with environmental variables represent a cornerstone to understanding the origin and maintenance of polyploid lineages. Although many studies have addressed this question in single species at a regional scale, only a few have attempted to decipher this enigma in groups of closely related species at a broad intercontinental geographical scale. Here, we consider ca. 20 species of a diploid-polyploid complex (Veronica subsect. Pentasepalae) of recent and rapid diversification represented in Europe and North Africa to study the frequency and distribution of cytotypes and its relationship with environmental variables.
Methods:
A total of 680 individuals (207 populations) were sampled. Ploidy levels were determined using flow cytometry. Ecological differentiation among cytotypes was tested using climatic and environmental variables related to temperature, precipitation, vegetation and biogeographical region, among others, and by performing univariate and multivariate (constrained PCoA) analyses.
Key results:
Four ploidy levels (2x, 4x, 6x, 8x) were found and genome downsizing was observed to occur within the group. Plants of different ploidy level are ecologically differentiated, with hexaploids and octoploids occurring in wetter and colder habitats with a higher seasonality than diploids. A south-to-north distribution pattern was found, with diploids occupying southern refugial areas and octoploids being more frequent in northern regions of Europe above the permafrost boundary.
Conclusions:
The distribution of cytotypes can be explained by ecological differentiation, the geographical position of refuge areas during the Quaternary climatic oscillations, as well as by ice and permafrost retreat patterns. The Balkan Peninsula constitutes the most important contact zone between cytotypes. This work provides the first comprehensive ploidy screening within V. subsect. Pentasepalae at a broad scale and indicates that polyploidy and genome downsizing might have contributed to the colonization of new habitats in a recently diverged polyploid complex.
