Limits...
Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China.

Liu J, Zhou W, Gong X - Front Plant Sci (2015)

Bottom Line: Wang.For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation.In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China ; Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China ; University of Chinese Academy of Sciences Beijing, China.

ABSTRACT
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic analysis and divergent time obtained from cpDNA haplotypes (A), nDNA SmHP haplotypes (B), and nDNA RPB1 haplotypes (C) of the three Cycas species. Number above the line of each note stands for the bootstrap value of Maximum Likelihood/and posterior probability (PP) inferred from Bayesian inference (for PP > 70). Number below the line represents divergent time by BEAST v1.7. MYR: million years.
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Figure 3: Phylogenetic analysis and divergent time obtained from cpDNA haplotypes (A), nDNA SmHP haplotypes (B), and nDNA RPB1 haplotypes (C) of the three Cycas species. Number above the line of each note stands for the bootstrap value of Maximum Likelihood/and posterior probability (PP) inferred from Bayesian inference (for PP > 70). Number below the line represents divergent time by BEAST v1.7. MYR: million years.

Mentions: Maximum likelihood (ML) analysis and Bayesian inference of cpDNA and nDNA haplotypes generated similar cladograms corresponding to the network analysis, whereas differed in the support values located on internal nodes. For cpDNA, all 13 haplotypes appeared as a distinct comb-like structure with three paraphyletic subclades nested inside. Within the cladogram, haplotypes H12, H11, and H3 clustered in the same subclade which was occupied by C. parvula and C. multiovla from the downstream populations YYM and GJD, implying these two adjacent populations should be closely related. For the other subclades, the most widely distributed H2 was clustered with the haplotype H6, which was specific by upstream population HTP. Haplotype H8, H9 as well as H10 which were all peculiar in YJH shared a close relationship to form a subclade, whereas this subclade was nonexclusive with other haplotypes in the large clade (Figure 3A). As the evidence that none of the above lineage inferred from cpDNA data could be separated from all other populations by a branch in the cladogram, nor could they form a contiguous section in the network analysis (Figure 2), we deduced all the lineages (haplotypes) as one phylogenetic species.


Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China.

Liu J, Zhou W, Gong X - Front Plant Sci (2015)

Phylogenetic analysis and divergent time obtained from cpDNA haplotypes (A), nDNA SmHP haplotypes (B), and nDNA RPB1 haplotypes (C) of the three Cycas species. Number above the line of each note stands for the bootstrap value of Maximum Likelihood/and posterior probability (PP) inferred from Bayesian inference (for PP > 70). Number below the line represents divergent time by BEAST v1.7. MYR: million years.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4562272&req=5

Figure 3: Phylogenetic analysis and divergent time obtained from cpDNA haplotypes (A), nDNA SmHP haplotypes (B), and nDNA RPB1 haplotypes (C) of the three Cycas species. Number above the line of each note stands for the bootstrap value of Maximum Likelihood/and posterior probability (PP) inferred from Bayesian inference (for PP > 70). Number below the line represents divergent time by BEAST v1.7. MYR: million years.
Mentions: Maximum likelihood (ML) analysis and Bayesian inference of cpDNA and nDNA haplotypes generated similar cladograms corresponding to the network analysis, whereas differed in the support values located on internal nodes. For cpDNA, all 13 haplotypes appeared as a distinct comb-like structure with three paraphyletic subclades nested inside. Within the cladogram, haplotypes H12, H11, and H3 clustered in the same subclade which was occupied by C. parvula and C. multiovla from the downstream populations YYM and GJD, implying these two adjacent populations should be closely related. For the other subclades, the most widely distributed H2 was clustered with the haplotype H6, which was specific by upstream population HTP. Haplotype H8, H9 as well as H10 which were all peculiar in YJH shared a close relationship to form a subclade, whereas this subclade was nonexclusive with other haplotypes in the large clade (Figure 3A). As the evidence that none of the above lineage inferred from cpDNA data could be separated from all other populations by a branch in the cladogram, nor could they form a contiguous section in the network analysis (Figure 2), we deduced all the lineages (haplotypes) as one phylogenetic species.

Bottom Line: Wang.For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation.In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China ; Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, China ; University of Chinese Academy of Sciences Beijing, China.

ABSTRACT
Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

No MeSH data available.


Related in: MedlinePlus