MOESM1 of Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

Additional file 1. Proportion of total bacterial (A) and fungal (B) reads assigned to taxonomic ranks

MOESM2 of Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

Additional file 2. Core microbiomes in different compartments of C. panzhihuaensis revealed by 16S rRNA gene and ITS sequences, and their significant levels

DataSheet_1_Phylogeography of Himalrandia lichiangensis from the dry-hot valleys in Southwest China.zip

Both changing tectonics and climate may shape the phylogeographic patterns of plant species. The dry-hot valleys in southwestern China harbor a high number of endemic plants. In this study, we investigated the evolutionary history and potential distribution of an endemic shrub Himalrandia lichiangensis (Rubiaceae), to evaluate the effects of tectonic and climatic processes on this thermophilic plant species from the dry-hot valleys. By sequencing DNA from four plastid non-coding regions (psbM-trnD, trnD-trnT, atpB-rbcL and accD-psaI) and the CAMX1F-CAMX2R region and ITS for 423 individuals from 23 populations, we investigated the genetic diversity, phylogeographical pattern and population dynamics of H. lichiangensis. We found a high degree of differentiation in H. lichiangensis during the middle Miocene (15-13 Myr), possibly triggered by the rapid tectonic uplift event in this period area. accompanied by frequent orogeneses in this period. This hypothesis is also supported by the association between genetic differentiation and altitudinal gradients among populations. The middle reach of the Jinsha River, which harbors the greatest genetic diversity, is most likely to have been a refugia for H. lichiangensis during Quaternary. We also detected a strong barrier effect between the Nanpan River and Jinsha River, suggesting the river system may play a role in geographical isolation between clades on both sides of the barrier. The Maximum Entropy Model (MaxEnt) results showed that future climate warming will lead to the niche expansion in some areas for H. lichiangensis but will also cause a scattered and fragmented distribution. Given the high among-population differentiation and no recent expansion detected in H. lichiangensis, its current phylogeographical pattern is possibly due to a long-term geographical barrier caused by uplifting mountains since the Miocene, as well as Quaternary climate refugia isolated also by high mountains. This study illustrated tectonic and climatic processes may have a continuous effect on plant phylogeography and offers insights into the origin of biodiversity and endemism in the dry-hot valleys of southwestern China.</p

Natural Hybridization and Introgression between <i>Ligularia cymbulifera</i> and <i>L. tongolensis</i> (Asteraceae, Senecioneae) in Four Different Locations

<div><p>Natural hybridization has been considered to represent an important factor influencing the high diversity of the genus <i>Ligularia</i> Cass. in the Hengduan Mountains, China. Natural hybridization has been confirmed to occur frequently in <i>Ligularia</i>. To date, however, it has been demonstrated only within a single population. In this paper, we present evidence of natural hybridization in <i>Ligularia</i> from four different locations. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and three chloroplast intergenic spacers (<i>trn</i>K-<i>rps</i>16, <i>trn</i>L-<i>rpl</i>32 and <i>trn</i>Q-5'<i>rps</i>16) of 149 accessions of putative hybrids and their putative parents (<i>L. cymbulifera</i> and <i>L. tongolensis</i>) were analyzed for evidence of hybridization. The ITS data clearly distinguished two putative parental species and sympatric <i>L. vellerea</i> and supported the hypothesis that those morphological intermediates were products of natural hybridization between <i>L. cymbulifera</i> and <i>L. tongolensis</i>. Moreover, several identified morphological parents were actual introgressed products. Because of hybridization and introgression, chloroplast DNA sequences generated a poorly resolved network. The present results indicate that varying degrees of hybridization and introgression occur differently depending on the habitat context. We conclude that gene flow caused by natural hybridization in <i>Ligularia</i> indeed plays an important role in the species diversity.</p></div

TCS haplotype networks based on plastid non-coding regions.

<p>Rectangular areas represent plastid haplotypes, and circle areas represent haplotypes not detected. Blue and red characters represent sequences of individuals in reference populations. (a) Population locality, <b>J</b>, Jiajinshan; <b>cd</b>, Reference Daocheng; <b>D</b>, Desha; <b>P</b>, Pachahai; <b>X</b>, Xiaoxueshan; <b>L</b>, Jiawa; (b) taxa: <b>v</b>, <i>L. vellerea</i>; <b>t</b>, <i>L. tongolensis</i>; c, <i>L. cymbulifera</i>; h, putative hybrids. Numbers following taxon initials are sample numbers.</p

TCS networks based on nuclear ribosomal internal transcribed spacer (nrITS) sequences.

<p>Rectangular areas in the nrITS network represent nrITS haplotypes and circle areas represent haplotypes not detected. Blue and red characters represent sequences of pure individuals in reference and sympatric populations. Purple characters represent sequences of individuals possess introgressed sequences. (a) Population locality, <b>J</b>, Jiajinshan; <b>Cd</b>, Reference Daocheng; <b>D</b>, Desha; <b>P</b>, Pachahai; <b>X</b>, Xiaoxueshan; <b>L</b>, Jiawa; (b) taxa: <b>v</b>, <i>L. vellerea</i>; <b>t</b>, <i>L. tongolensis</i>; c, <i>L. cymbulifera</i>; h, putative hybrids. Numbers following taxon initials are sample numbers and clone numbers (if any). (TIFF)</p

Phylogenetic relationships of the nrITS4-5 haplotypes of <i>L. cymbulifera</i>, <i>L. tongolensis</i>, their putative hybrids and sympatric <i>L. vellerea</i> from south-western China (H1–H15) generated by PAUP.

<p>Phylogenetic relationships of the nrITS4-5 haplotypes of <i>L. cymbulifera</i>, <i>L. tongolensis</i>, their putative hybrids and sympatric <i>L. vellerea</i> from south-western China (H1–H15) generated by PAUP.</p

Key morphological differences among <i>Ligularia cymbulifera</i>, <i>L. tongolensis</i> and putative hybrids.

<p>Key morphological differences among <i>Ligularia cymbulifera</i>, <i>L. tongolensis</i> and putative hybrids.</p

Additional file 1 of Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis

Additional file 1: TableS1. Collectioninformation, morphological classification, vouchers, characteristics andplastome NCBI accessions of the Cycas samples used in this study. Allspecimens are identified by the authors of this study (Anders J. Lindstrom,Jian Liu, and Xun Gong). TableS2. Thebest nucleotide substitution model for the whole plastome (WP) and the partitioned protein-codinggenes (PCGs) datasetsused in Bayesian Inference as determined by PartitionFinder2. TableS3. Plastid genes and functional groups included in the analyses. Genesindicated with asterisk are those with estimated nonsynonymous substitutionrates (dN) lower than 0.0003. TableS4. Theestimated substitution rates, nucleotide diversity, aligned length and numberof variable sites (segregates) and percent of variationsof 82 protein-coding genes in 47 Cycas of this study. Order is ranked bypercent of variation. TableS5. Treedistance between concatenated dataset and gene cluster datasets as inferred bydifferent methods (Bayesian and MaximumLikelihood: ML). Genenames of different clusters can be referred in Table 1. FigureS1. Chloroplastgenome graph of Cycas wadei. Genes on the outside of the large circleare transcribed clockwise and those on the inside are transcribedcounterclockwise. The genes are color-coded based on their function. The dashedarea represents the GC composition of the chloroplast genome. IR (a & b):inverted repeat region a & b; LSC: large single-copy region; SSC: smallsingle-copy region. FigureS2. Globalalignment of 11 Cycas genomes and using mVISTA. Alignment was performedusing C. aenigma as a reference. Grey arrows above thealignment indicate the orientation of genes. Purple bars represent exons, blueones represent introns, and pink ones represent non-coding sequences (CNS). Acut-off of 50% identity was used for the plots. The Y-scale axis represents thepercent identity within 50–100%. FigureS3. Comparison of inverted-repeat (IR) andsingle-copy (SC) borders among 11 Cycas chloroplast genomes from sixsections. Gene annotation or portions are represented by colored boxes. JSA:junction between SSC and IRa; JSB: junction between SSC and IRb; JLA: junctionbetween LSC and Ira; JLB: junction between LSC and IRb. FigureS4. Thetype and distribution of SSRs in the 47 Cycas chloroplast genomes. (a) Theproportion of SSR distribution in different species (b) Number of identifiedSSR motifs in different repeat class types. FigureS5. CombinedML topology inferred by ASTRAL (species tree) for Cycas, with summary ofconflicting and concordant genes. For each branch, the top number indicates thenumber of homologs concordant with the species tree at that node, and thebottom number indicates the number of homologs in conflict with that clade in thespecies tree. The pie charts at each node present the proportion of homologsthat support that clade (blue), the proportion that support the mainalternative for that clade (pink), the proportion that support the remainingalternatives (orange), and the proportion that inform (conflict or support)this clade that have no bootstrap support (grey). FigureS6. Principalcoordinate analyses depicting ordinations of rooted tree topologies (Robinson-Foulds)of four species trees versus six gene-cluster trees. (a): Plots for the firsttwo principal coordinates; (b) Plots for the first and third principalcoordinates. In both plots, a total of 10 trees were obtained from different phylogeneticinference methods (ML: maximum likelihood, BY: Bayesian method) based on allprotein-coding genes (Concatenate_ML: inferred ML tree based onconcatenated genes; Concatenate_BY: inferred Bayesian treebased on concatenated genes; Astral_ML: inferred species tree using ASTRAL-IIIbased on ML gene trees, Astral_BY: inferred species tree using ASTRAL-III basedon Bayesian gene trees), and different gene tree clusters (Clusters 1–3) areplotted. The inset dendrograms reflect the tree distances between the speciestree and the cluster trees revealed by TREESPACE. FigureS7. Inferredphylogenies of Cycas using RaxML based on different concatenated plastidgene clusters obtained by Maximum likelihood and Bayesian gene trees (clusters1-3, see Table 1 for the genes grouped by different methods). FigureS8. Principalcoordinate analyses depicting ordinations of rooted tree topologies (Robinson-Foulds)of two species trees (ASTRAL species tree and concatenated gene tree) versus 11gene trees based on different gene functional groups (see Figure 2 and Table S3 for the group information). (a): Plots for the first two principal coordinates;(b) Plots for the first and third principal coordinates. FigureS9. Inferredphylogenies of Cycas using RaxML based on different concatenatedfunctional gene groups (see Figure 2 and Table S3 for the information of 11genes groups). The three indicated groups correspond to the clusters revealedin Fig. S8

Distribution of ITS4-5 haplotypes and three cpDNA haplotypes in 6 locations.

<p>Note:* indicates only three or four individuals for this taxon were found within the population.</p><p>Distribution of ITS4-5 haplotypes and three cpDNA haplotypes in 6 locations.</p