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. 2021 Jun 15;11(14):9498-9515.
doi: 10.1002/ece3.7769. eCollection 2021 Jul.

EST-SSR-based landscape genetics of Pseudotaxus chienii, a tertiary relict conifer endemic to China

Shufeng Li  1 , Zhen Wang  1 , Yingjuan Su  1   2 , Ting Wang  2   3
Affiliations

EST-SSR-based landscape genetics of Pseudotaxus chienii, a tertiary relict conifer endemic to China

Shufeng Li et al. Ecol Evol. .

Abstract

Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.

Keywords: EST‐SSR; Pseudotaxus chienii; adaptive evolution; genetic differentiation; genetic diversity; landscape genetics.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Sampling locations of 11 Pseudotaxus chienii populations and genetic boundaries (blue lines) identified by Monmonier's algorithm. The width of blue lines represents the “strength” of the boundaries
FIGURE 2
FIGURE 2
(a) Individual and population memberships to genetic clusters for K = 3, 9, and 11 using STRUCTURE. (b) Heatmap of Nei's genetic distance with UPGMA tree between Pseudotaxus chienii populations. (c) Clustering results of Pseudotaxus chienii populations obtained by discriminant analysis of principal components (DAPC, PCs = 40). (d) The relative migration networks among Pseudotaxus chienii populations. Only Nm values over 0.1 are shown in the graph
FIGURE 3
FIGURE 3
(a) The relationship between genetic distance and geographical distance of Pseudotaxus chienii. (b) The relationship between genetic distance and environmental distance of Pseudotaxus chienii
FIGURE 4
FIGURE 4
The fine‐scale spatial autocorrelation analysis of Pseudotaxus chienii
FIGURE 5
FIGURE 5
Potential geographical distribution of Pseudotaxus chienii in China under current climate condition
FIGURE 6
FIGURE 6
Potential geographical distribution of Pseudotaxus chienii in China under future climate condition (a: RCP2.6 to the year 2050; b: RCP2.6 to the year 2070; c: RCP4.5 to the year 2050; d: RCP4.5 to the year 2070; e: RCP6.0 to the year 2050; f: RCP6.0 to the year 2070; g: RCP8.5 to the year 2050; and h: RCP8.5 to the year 2070)
See this image and copyright information in PMC

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