Phylogeny and species differentiation of four wild almond species of subgen. Amygdalus in China

doi:10.17521/cjpe.2020.0366

Abstract

Abstract:

Aims Based on the ITS sequences, we aimed to analyze the spatial genetic structure, genealogy relationship, and species differentiation of the Amygdalus ledebouriana, A. mongolica, A. pedunculata, A. tangutica in China, and provide data for the future studies on the four species' genetics and evolution.

Methods The median-joining network and principal coordinate analysis (PCoA) were used to reveal haplotype clustering. The maximum likelihood method and Bayesian method were used to analyze the phylogenetic relationships of haplotypes. The “ecospat” package in R 4.0.2 was used to analyze the ecological niche divergence of four almond species and their environmental drivers.

Important findings The total length of the ITS1-ITS4 fragment after corrected alignment was 634 bp, 27 nucleotide variants detected, and a total of 28 haplotypes were identified. The minimum genetic distance among the four almond species is greater than the maximum genetic distance within species, and there are significant genetic differentiations among species. The haplotypes of the four almond species clustered into two branches: A. ledebouriana, A. mongolicaand A. tanguticafor one clade, and A. pedunculatafor the other. The revealed dendrogram relationship of haplotype network and PCoA analysis is consistent with the phylogenetic tree. The significant niche divergence was observed between A. tangutica and A. mongolica, as well as between A. tangutica and A. pedunculata, with annual mean temperature, max temperature of warmest month, min temperature of coldest month and precipitation of warmest quarter as key drivers of niche divergence.

Key words: wild almond species, ITS sequences, phylogeny, species differentiation, niche divergence

WANG Chun-Cheng, ZHANG Yun-Ling, MA Song-Mei, HUANG Gang, ZHANG Dan, YAN Han. Phylogeny and species differentiation of four wild almond species of subgen. Amygdalus in China[J]. Chin J Plant Ecol, 2021, 45(9): 987-995.

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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2020.0366

https://www.plant-ecology.com/EN/Y2021/V45/I9/987

Figures/Tables 6

Fig. 1 Field sampling points of four subgen. Amygdalus wild plants. BEC, Buerjin County; BTE, Group 2 in Daqing Mountain; BTQ, Group 1 in Daqing Mountain; DBL, Group 1 in Têwo County; DBZ, Group 2 in Têwo County; DMB, Group 3 in Damao Banner; DMD, Group 1 in Damao Banner; DMN, Group 2 in Damao Banner; GQD, Group 1 in Guyang County; GQX, Group 3 in Guyang County; GX, Group 2 in Guyang County; HBK, Habahe County; MZS, Mazong Mountain; SPQ, Songpan County; TBB, Group 2 Tacheng City; TBT, Group 1 Tacheng City; TLB1, Group 1 in Toli County; TLB2, Group 2 in Toli County; WD, Wula Mountain; WG, Ugai Sumu Township; WLB, Dam Mouth; WLJ, Wujiahe Town; WSH, Suhaitu; WSM, Damaili Furrow; YCQ, Longshou Mountain; YLD1, Group 1 in Yulin City; YLD2, Group 2 in Yulin City; YMB1, Group 1 in Yumin County; YMB2, Group 2 in Yumin County; YMF, Group 2 in Yinshan Mountains; YMM, Group 1 in Yinshan Mountains; ZQK, Tukemu Gazha; ZQL, Helan Mountain; ZQX, Zhugqu County; ZTL, Temowula Gazha; ZTM, Su Litu Gazha; ZYS, Qilianshan Mountain.

Fig. 2 Geographical distribution and the haplotype network of 28 haplotypes (R1-R28) of four subgen. Amygdalus wild plants. The population field sampling point codes in the figure are consistent with the ones in Fig. 1. Pie graphs indicate the frequency of each haplotype of these populations. A, In the median-joining haplotypes network, the sizes of the circles in the network are proportional to the haplotype frequencies. Branch lengths are roughly proportional to the number of mutation steps between haplotypes and nodes; the true number of steps is shown near the corresponding branch sections. Padus racemosa and Amygdalus davidiana was used as outgroup.

Fig. 3 Genetic distance among four subgen. Amygdalus wild plants based on ITS sequences.

Fig. 4 Plots of the first three coordinates of the principal coordinates analysis (PCoA) at the population level for four subgen. Amygdalus wild plants.

Fig. 5 Haplotype phylogenetic trees of four subgen. Amygdalus wild plants based on ITS sequences. A, Maximum likelihood (ML) tree. Bootstrap values equal to or greater than 70 are shown above the corresponding branching points. B, Bayesian tree. The values on the right of the branching points represent the posterior probability greater than 0.70; the brackets on the right of the two phylogenetic trees indicate the corresponding subclades of the four species.

Fig. 6 Ecological niche differentiation and the contribution of driving factors of four subgen. Amygdalus plants. A-F, Visualization of ecological niches. The green colour depicts the niche space of the first species, red of the second species and the overlapping range is shown in blue. D is the ecological niche overlap score. G, Driver factors principal component analysis. The arrow depicts the direction of correlation (same direction indicates a high correlation). Bio1, annual mean temperature; Bio4, temperature seasonality (standard deviation × 100); Bio5, max temperature of warmest month; Bio6, min temperature of coldest month; Bio15, precipitation seasonality (coefficient of variation); Bio17, precipitation of driest quarter; Bio18, precipitation of warmest quarter. The numbers in brackets after the environmental factors are the contribution rankings.

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