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Molecular phylogeography and population evolution analysis of Citrus ichangensis (Rutaceae)

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Abstract

Ichang papeda (Citrus ichangensis), a wild and endemic perennial plant in Rutaceae, is characterized by the existence of wild and natural populations in southwestern and middle-west China. We analyzed a total of 231 individuals across 16 natural populations using chloroplast SSR markers, nuclear SSR markers, and single-copy nuclear genes. Standard population genetic analyses as well as Bayesian and maximum likelihood models were used to clarify the genetic diversity, population differentiation, barriers to gene flow, bottleneck events, isolation by distance, history migration, demographic history among populations, and phylogeny evolution. The chloroplast and nuclear genome analyses revealed a low level of genetic diversity in C. ichangensis. Clear signals of recent bottlenecks and strong patterns of isolation by distance were detected among different subpopulations, indicating a low extent of historical gene flow for this species and that genetic drift would occur after population differentiation. Bayesian clustering analyses revealed a clear pattern of genetic structure, with one cluster spanning the potential refugia in Wuling Mountains and Ta-pa Mountains, and other two clusters covering a more limited distribution range. The demographic history also supported the scenario that two isolated clusters originated in parallel from the genetic diversity center. Taxonomically, Ichang papeda may be a member of subgenus Citrus. Owing to the complicated topography, the mountainous regions and the Yangtze River have provided long-term stable habitats for C. ichangensis and acted as main barriers for its expansion, which might facilitate the process of speciation. Statistical population models and genetic data indicated strong genetic structure in C. ichangensis, which might result from the restricted gene flow, genetic drift, and population bottlenecks.

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Acknowledgements

This work was funded by the National Natural Science Foundation of China (31521092, 31630065) and the Ministry of Agriculture (CARS-27). We are grateful to Mr. Zuoxiong Liu from the College of Foreign Languages, Huazhong Agriculture University, China, for discussion and modification of the English of this manuscript. We also acknowledge members in our lab for their collaboration in the field investigation and sample collection.

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  1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei, 430070, People’s Republic of China

    Xiaoming Yang, Hang Li, Huiwen Yu, Lijun Chai, Qiang Xu & Xiuxin Deng

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  1. Xiaoming Yang
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  2. Hang Li
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  3. Huiwen Yu
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Correspondence to Xiuxin Deng.

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Communicated by W.-W. Guo

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Supplementary Data Figure S1

F st values of 85 microsatellite loci vs heterozygosity in populations of C. ichangensis. Red area represents positive selection, gray area represents neutral selection, and yellow area represents balancing selection. Ten loci were subjected to balancing selection and eleven loci were subjected to positive selection. The corresponding primer information could be found in Supplementary Data Table S3. (GIF 310 kb)

High Resolution Image (TIFF 2060 kb)

Supplementary Data Figure S2

Fixation indices obtained with the SAMOVA program as a function of the user-defined number K of groups of populations based on cpSSR datasets. F st, differentiation among populations within a group; F ct, differentiation among groups of populations; F sc, differentiation among populations from different groups. (GIF 274 kb)

High Resolution Image (TIFF 70 kb)

Supplementary Data Figure S3

Plot of Delta K (filled circles, solid line) calculated as the mean of the second-order rate of change in likelihood of K divided by the standard deviation of the likelihood of K, m(|L”(K)|) / sd (L(K)) based on the nSSR datasets. (GIF 29 kb)

High Resolution Image (TIFF 490 kb)

Supplementary Data Figure S4

Isolation by distance analysis using nSSR datasets. F st / (1-F st) is plotted against the natural logarithm of the geographical distances (kilometers) between populations. We obtained Pearson correlation coefficients (r) and P-values (P) for test. (GIF 56 kb)

High Resolution Image (TIFF 3251 kb)

Supplementary Data Figure S5

Network showing the genetic relationships among the observed nuclear DNA haplotypes of C. ichangensis. Each haplotype is represented by a circle, the area of which is proportional to the number of individuals with this haplotype. The length of lines is proportional to mutational change between haplotypes. Missing haplotypes are represented by small unfiled circles. Haplotypes belonging to three different clusters are indicated by different colors (red, cluster I; blue, cluster II; green, cluster III). (GIF 87 kb)

High Resolution Image (TIFF 1930 kb)

Supplementary Data Figure S6

Principal Component Analysis (PCA) in the space of the summary statistics performed on the selected scenario C. The observations are the simulated datasets and the variables are the summary statistics. The yellow dot corresponds to the real dataset of C. ichangensis. Each large blue dot corresponds to a dataset simulated with parameters drawn from the posterior distributions. Each small blue dot corresponds to a dataset simulated with parameters drawn from the prior distributions. 10,000 datasets are randomly shown here for each of the prior and posterior distributions. (GIF 60 kb)

High Resolution Image (TIFF 1169 kb)

Supplementary Data Table S1

(DOCX 19 kb)

Supplementary Data Table S2

(DOCX 41 kb)

Supplementary Data Table S3

(DOCX 27 kb)

Supplementary Data Table S4

(DOCX 17 kb)

Supplementary Data Table S5

(DOCX 16 kb)

Supplementary Data Table S6

(DOCX 15 kb)

Data archiving statement

All nuclear gene sequences will be submitted to GenBank, and accession numbers will be provided once available.

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Yang, X., Li, H., Yu, H. et al. Molecular phylogeography and population evolution analysis of Citrus ichangensis (Rutaceae). Tree Genetics & Genomes 13, 29 (2017). https://doi.org/10.1007/s11295-017-1113-4

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