Відмінності між версіями «Ns shared (or are grouped with) I. batatas haplotypes, except for»
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| − | + | batatas, we did not sequence all the 139 varieties for the rpl32-trnL(UAG) marker. Thus, we used cpDNA lineage info from Roullier et al. [29] to finish our dataset. As described in Roullier et al. [29], i) nuclear markers reflect a stronger phylogeographic signal than chloroplast markers but ii) phylogeographic patterns revealed by both sets of data had been globally congruent. Indeed, Southern varieties have been mostly associated to chloroplast lineage 1 and nuclear cluster 1 (39/54 in total). In the Northern region, both signals were also congruent considering that 43/84 sweet potato accessions had been associated to nuclear clusters K2 and K3 and chloroplast lineage 2. Nonetheless, 23 Northern varieties were associated to nuclear clusters K2 and K3, yet carried a chloroplast lineage1 haplotype. Ipomoea sp. [http://www.medchemexpress.com/Fosfluconazole.html Fosfluconazole web] specimens that grouped with all the I. trifida cluster K2 harbored the Northern chloroplast haplotype (or the unclassified rare haplotype 1) and were all positioned inside the Southern region (Ecuador and South Colombia). These in the Northern region carried the Northern chloroplast haplotype and have been grouped with nuclear cluster K3 (Figure 5 and Table two).Interspecific relationships as inferred from SSR markersSSRs could be amplified for all loci and all species, top to a total of 137 alleles. The number of alleles NA, rarefied allelic richness Ar, and expected heterozygosity He, were comparable in I. trifida, I. batatas and Ipomoea sp.Ns shared (or are grouped with) I. batatas haplotypes, except for accession K300-5 (sharing its haplotype with the majority of I. trifida accessions). It should really also be noted that I. batatas haplotypes are distributed on two distinct branches within the tree (Figure 3a and S2).and the genetic distinction involving Southern and Northern genepools is just not clearly identifiable with this representation. For the DAPC clustering evaluation (Figure 4), the acceptable variety of clusters was 5. This grouping also fairly properly reflects species boundaries: I. trifida accessions are represented by cluster K4 and I. triloba accessions by cluster K5. I. batatas accessions were related to 3 distinct clusters, K1, K2 and K3. Some Ipomoea sp. have been attributed to I. trifida cluster (K4) and other people towards the I. batatas cluster (K1 and K3; Figure 4). The majority of the I. batatas accessions in the Southern area (48/56) were grouped in cluster K1 (with one particular Ipomoea sp. from Ecuador and also some I. batatas in the Northern region (5/83)). I. batatas accessions from the Northern region had been subdivided in two clusters, cluster K2 which includes a big part of these Northern accessions (50/83) and cluster K3 such as some accessions in the Northern area (19/83) and a few Ipomoea sp. (23/42). With the model-based clustering analysis (STRUCTURE, Figure S3), the optimal variety of clusters to describe the data was unclear. Consequently, clustering final results had been less informative (taxon boundaries weren't clearly identifiable and many individuals had a mixed genetic constitution; Figure S2). The best Bayesian grouping to be compared with DAPC benefits was obtained for K = six, a clustering option which distinguished cultivated I. batatas accessions from wild relatives, and also separated varieties in the Northern and Southern area (Figure S3).Congruence involving cpDNA haplotype groups and nuclear SSR genetic structureBoth kinds of markers identified diploid I. | |
Версія за 19:27, 7 березня 2018
batatas, we did not sequence all the 139 varieties for the rpl32-trnL(UAG) marker. Thus, we used cpDNA lineage info from Roullier et al. [29] to finish our dataset. As described in Roullier et al. [29], i) nuclear markers reflect a stronger phylogeographic signal than chloroplast markers but ii) phylogeographic patterns revealed by both sets of data had been globally congruent. Indeed, Southern varieties have been mostly associated to chloroplast lineage 1 and nuclear cluster 1 (39/54 in total). In the Northern region, both signals were also congruent considering that 43/84 sweet potato accessions had been associated to nuclear clusters K2 and K3 and chloroplast lineage 2. Nonetheless, 23 Northern varieties were associated to nuclear clusters K2 and K3, yet carried a chloroplast lineage1 haplotype. Ipomoea sp. Fosfluconazole web specimens that grouped with all the I. trifida cluster K2 harbored the Northern chloroplast haplotype (or the unclassified rare haplotype 1) and were all positioned inside the Southern region (Ecuador and South Colombia). These in the Northern region carried the Northern chloroplast haplotype and have been grouped with nuclear cluster K3 (Figure 5 and Table two).Interspecific relationships as inferred from SSR markersSSRs could be amplified for all loci and all species, top to a total of 137 alleles. The number of alleles NA, rarefied allelic richness Ar, and expected heterozygosity He, were comparable in I. trifida, I. batatas and Ipomoea sp.Ns shared (or are grouped with) I. batatas haplotypes, except for accession K300-5 (sharing its haplotype with the majority of I. trifida accessions). It should really also be noted that I. batatas haplotypes are distributed on two distinct branches within the tree (Figure 3a and S2).and the genetic distinction involving Southern and Northern genepools is just not clearly identifiable with this representation. For the DAPC clustering evaluation (Figure 4), the acceptable variety of clusters was 5. This grouping also fairly properly reflects species boundaries: I. trifida accessions are represented by cluster K4 and I. triloba accessions by cluster K5. I. batatas accessions were related to 3 distinct clusters, K1, K2 and K3. Some Ipomoea sp. have been attributed to I. trifida cluster (K4) and other people towards the I. batatas cluster (K1 and K3; Figure 4). The majority of the I. batatas accessions in the Southern area (48/56) were grouped in cluster K1 (with one particular Ipomoea sp. from Ecuador and also some I. batatas in the Northern region (5/83)). I. batatas accessions from the Northern region had been subdivided in two clusters, cluster K2 which includes a big part of these Northern accessions (50/83) and cluster K3 such as some accessions in the Northern area (19/83) and a few Ipomoea sp. (23/42). With the model-based clustering analysis (STRUCTURE, Figure S3), the optimal variety of clusters to describe the data was unclear. Consequently, clustering final results had been less informative (taxon boundaries weren't clearly identifiable and many individuals had a mixed genetic constitution; Figure S2). The best Bayesian grouping to be compared with DAPC benefits was obtained for K = six, a clustering option which distinguished cultivated I. batatas accessions from wild relatives, and also separated varieties in the Northern and Southern area (Figure S3).Congruence involving cpDNA haplotype groups and nuclear SSR genetic structureBoth kinds of markers identified diploid I.
