Phylogeography suggest the Yili Valley being the glacial refuge of the genus <i>Ixiolirion</i> (Amaryllidaceae) in China

The Pleistocene climatic oscillations had profound effects on the demographic history and genetic diversification of plants in arid north-west China where some glacial refugia have been recognized. The genus Ixiolirion comprises three species, of which two, I. tataricum and I. songaricum (endemic), occur in China. In some locations they are sympatric. We investigated their population structure and population history in response to past climatic change using a sample of 619 individuals in 34 populations with nITS and ptDNA sequences. A significant genetic divergence between the two species was supported by a high level of pairwise genetic differentiation, very low gene flow, and phylogenetic analysis showing that I. songaricum haplotypes were monophyletic, whereas those of I. tataricum were polyphyletic. We found significant differentiation and phylogeographic structure in both species. The split of the two species was dated to the late Miocene (∼7 Ma), but deep divergence occurred in the mid-late Quaternary. A similar haplotype distribution pattern was found in both species: one to two dominant haplotypes across most populations, with unique haplotypes in a few populations or a geographic group. The genetic diversity, haplotype number, and haplotype diversity decreased from the Yili Valley to the central Tianshan and Barluk Mountains. Additionally, ptDNA analysis showed that I. tataricum diversified in the eastern Tianshan and Barluk Mountains, which might be due to physical barriers to long distance seed dispersal such as desert. In conclusion, our results indicated that the Yili Valley was likely a glacial refuge for Ixiolirion in China, with postglacial dispersal from the Yili Valley eastward to the eastern Tianshan Mountains, and northward to the Barluk Mountains. The climatic changes in the Miocene and Pleistocene and geographic barriers are important factors driving species divergence and differentiation of Ixiolirion and other taxa.</p

Variation in soil volumetric water content across soil depth and δ¹⁸O content in UC and OC.

<p>UC is the community under the <i>P. euphratica</i> canopy, whereas the OC is the community outside the <i>P. euphratica</i> canopy. UC and OC have three measuring plots, respectively. The Independent sample <i>t</i>-test is used to analyze the differences of soil volumetric water content between UC and OC. Different capital letters in each row indicate significant differences of soil volumetric water content between UC and OC. The measurement period of soil volumetric water content lasts from 5th to 8th August, 2010. During the time between 2:30 am to 6:30 am, 11∶30 am to 5∶00 pm at each experimental day, the soil volumetric water content recorded manually at intervals of 2 hours, while the time between 6:30 am to 9:30 am, 9:30 pm to 12:30 am, the soil volumetric water content recorded manually once an hour.</p><p>Variation in soil volumetric water content across soil depth and δ¹⁸O content in UC and OC.</p

Difference in δ¹⁸O value with soil depth between UC and OC groups.

<p>UC is the community under the <i>P. euphratica</i> canopy, whereas the OC is the community outside the <i>P. euphratica</i> canopy. The soils were divided into five layers (0 to 10 cm, 10 to 40 cm, 40 to 70 cm, 70 to 100 cm, and 100 to 150 cm) based on <i>P. euphratica</i> roots and underground water level distributions. Each point in the Fig. 1a showing δ¹⁸O for each soil layer sample, which was measured for three times continuously with the third result as the experimental oxygen isotope value. Nine soil samples for each soil layer from three points were mixed to get one composite soil in each group. ¹⁸O contents of river (−11.55‰) and underground water (−10.59‰) are show through vertical dashed and solid lines respectively in Fig. 1a. Fig. 1b shows the mean comparison between UC and OC groups and the data in parenthesis showing the Paired-Sample <i>t</i>-test result. (Mean ± <i>SD</i>) for significance difference between two groups.</p

Difference in richness and abundance along plant growing season between UC and OC.

<p>UC is the community under the <i>P. euphratica</i> canopy, whereas the OC is the community outside the <i>P. euphratica</i> canopy. Blank and grid boxes indicate shrub and herbage, respectively. The Independent sample <i>t</i>-test is used to analyze the differences of richness and abundance between UC and OC. Different capital letters on each blank box indicate significant differences of shrub richness or abundance between UC and OC. Different lowercase letters on each grid box indicate significant differences of herbage richness or abundance between UC and OC. <i>p</i><0.05. Numbers in figure are the results of Independent sample <i>t</i>-test. (Mean ± <i>SD</i>) for significance difference between UC and OC.</p

Differences of species growth dominance index between the UC and the OC.

<p>UC is the community under the <i>P. euphratica</i> canopy, whereas the OC is the community outside the <i>P. euphratica</i> canopy. For UC, <i>P. euphratica</i> is the only tree species (woody plant, height >6 m) while the others are shrub (woody plant, height <6 m) and herbage (herbaceous plants, height <1 m). For OC, all plants are shrubs and herbages. “–” in table indicating no values because of the ephemeral plants life history turnoff and randomly setting samples along June (early growth period of <i>P. euphratica</i>), August (middle growth period of <i>P. euphratica</i>) and October (defoliating period of <i>P. euphratica</i>). The figures in table showing Growth dominance indices of species belonged to UC and OC. All plots are established in 5×5 km area of Ebinur Lake Wetland Nature Reserve in Xinjiang Uygur Autonomous Region of China.</p><p>Differences of species growth dominance index between the UC and the OC.</p

Logarithmic regression of <i>P. euphratica</i> crown areas against species abundance and richness.

<p>In regression line (Fig. 3a), each point indicating the richness of all species (no including <i>P. euphratica</i>) under the <i>P. euphratica</i> canopy. In regression line (Fig. 3b), each point indicating the abundance of all species (no including <i>P. euphratica</i>) under the <i>P. euphratica</i> canopy. The crown area of each sample is the sum of <i>P. euphratica</i> individuals.</p

DataSheet_1_Large plants enhance aboveground biomass in arid natural forest and plantation along differential abiotic and biotic conditions.docx

Big-sized trees, species diversity, and stand density affect aboveground biomass in natural tropical and temperate forests. However, these relationships are unclear in arid natural forests and plantations. Here, we hypothesized that large plants (a latent variable of tall-stature and big-crown, which indicated the effect of big-sized trees on ecosystem function and structure) enhance aboveground biomass in both arid natural forests and plantations along the gradients of climate water availability and soil fertility. To prove it, we used structural equation modeling (SEM) to test the influences of large plants located in 20% of the sequence formed by individual size (a synthetical value calculated from tree height and crown) on aboveground biomass in natural forests and plantations while considering the direct and indirect influences of species diversity as well as climatic and soil conditions, using data from 73 natural forest and 30 plantation plots in the northwest arid region of China. The results showed that large plants, species diversity, and stand density all increased aboveground biomass. Soil fertility declined aboveground biomass in natural forest, whereas it increased biomass in plantation. Although climatic water availability had no direct impact on aboveground biomass in both forests, it indirectly controlled the change of aboveground biomass via species diversity, stand density, and large plants. Stand density negatively affects large plants in both natural forests and plantations. Species diversity positively affects large plants on plantations but not in natural forests. Large plants increased slightly with increasing climatic water availability in the natural forest but decreased in plantation, whereas soil fertility inhibited large plants in plantation only. This study highlights the extended generality of the big-sized trees hypothesis, scaling theory, and the global importance of big-sized tree in arid natural forests and plantations.</p

DataSheet_3_Large plants enhance aboveground biomass in arid natural forest and plantation along differential abiotic and biotic conditions.docx

Big-sized trees, species diversity, and stand density affect aboveground biomass in natural tropical and temperate forests. However, these relationships are unclear in arid natural forests and plantations. Here, we hypothesized that large plants (a latent variable of tall-stature and big-crown, which indicated the effect of big-sized trees on ecosystem function and structure) enhance aboveground biomass in both arid natural forests and plantations along the gradients of climate water availability and soil fertility. To prove it, we used structural equation modeling (SEM) to test the influences of large plants located in 20% of the sequence formed by individual size (a synthetical value calculated from tree height and crown) on aboveground biomass in natural forests and plantations while considering the direct and indirect influences of species diversity as well as climatic and soil conditions, using data from 73 natural forest and 30 plantation plots in the northwest arid region of China. The results showed that large plants, species diversity, and stand density all increased aboveground biomass. Soil fertility declined aboveground biomass in natural forest, whereas it increased biomass in plantation. Although climatic water availability had no direct impact on aboveground biomass in both forests, it indirectly controlled the change of aboveground biomass via species diversity, stand density, and large plants. Stand density negatively affects large plants in both natural forests and plantations. Species diversity positively affects large plants on plantations but not in natural forests. Large plants increased slightly with increasing climatic water availability in the natural forest but decreased in plantation, whereas soil fertility inhibited large plants in plantation only. This study highlights the extended generality of the big-sized trees hypothesis, scaling theory, and the global importance of big-sized tree in arid natural forests and plantations.</p

DataSheet_2_Large plants enhance aboveground biomass in arid natural forest and plantation along differential abiotic and biotic conditions.xlsx

Big-sized trees, species diversity, and stand density affect aboveground biomass in natural tropical and temperate forests. However, these relationships are unclear in arid natural forests and plantations. Here, we hypothesized that large plants (a latent variable of tall-stature and big-crown, which indicated the effect of big-sized trees on ecosystem function and structure) enhance aboveground biomass in both arid natural forests and plantations along the gradients of climate water availability and soil fertility. To prove it, we used structural equation modeling (SEM) to test the influences of large plants located in 20% of the sequence formed by individual size (a synthetical value calculated from tree height and crown) on aboveground biomass in natural forests and plantations while considering the direct and indirect influences of species diversity as well as climatic and soil conditions, using data from 73 natural forest and 30 plantation plots in the northwest arid region of China. The results showed that large plants, species diversity, and stand density all increased aboveground biomass. Soil fertility declined aboveground biomass in natural forest, whereas it increased biomass in plantation. Although climatic water availability had no direct impact on aboveground biomass in both forests, it indirectly controlled the change of aboveground biomass via species diversity, stand density, and large plants. Stand density negatively affects large plants in both natural forests and plantations. Species diversity positively affects large plants on plantations but not in natural forests. Large plants increased slightly with increasing climatic water availability in the natural forest but decreased in plantation, whereas soil fertility inhibited large plants in plantation only. This study highlights the extended generality of the big-sized trees hypothesis, scaling theory, and the global importance of big-sized tree in arid natural forests and plantations.</p