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Genetic divergence and phylogeographic history of two closely related species (Leucomeris decora and Nouelia insignis) across the 'Tanaka Line' in Southwest China.

Zhao YJ, Gong X - BMC Evol. Biol. (2015)

Bottom Line: The study revealed comprehensive species divergence and phylogeographic histories of N. insignis and L. decora divided by the Tanaka Line.The phylogeographic pattern inferred from cpDNA reflected ancestrally shared polymorphisms without post-divergence gene flow between species.The marked genealogical lineage divergence in nDNA provided some indication of Tanaka Line for its role as a barrier to plant dispersal, and lent support to its importance in promoting strong population structure and allopatric divergence.

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, 650204, China. zyy36920@126.com.

ABSTRACT

Background: Leucomeris decora and Nouelia insignis (Asteraceae) are narrowly and allopatrically distributed species, separated by the important biogeographic boundary Tanaka Line in Southwest China. Previous morphological, cytogenetic and molecular studies suggested that L. decora is sister to N. insignis. However, it is less clear how the two species diverged, whether in full isolation or occurring gene flow across the Tanaka Line. Here, we performed a molecular study at the population level to characterize genetic differentiation and decipher phylogeographic history in two closely related species based on variation examined in plastid and nuclear DNAs using a coalescent-based approach.

Results: These morphologically distinct species share plastid DNA (cpDNA) haplotypes. In contrast, Bayesian analysis of nuclear DNA (nDNA) uncovered two distinct clusters corresponding to L. decora and N. insignis. Based on the IMa analysis, no strong indication of migration was detected based on both cpDNA and nDNA sequences. The molecular data pointed to a major west-east split in nuclear DNA between the two species corresponding with the Tanaka Line. The coalescent time estimate for all cpDNA haplotypes dated to the Mid-Late Pleistocene. The estimated demographic parameters showed that the population size of L. decora was similar to that of N. insignis and both experienced limited demographic fluctuations recently.

Conclusions: The study revealed comprehensive species divergence and phylogeographic histories of N. insignis and L. decora divided by the Tanaka Line. The phylogeographic pattern inferred from cpDNA reflected ancestrally shared polymorphisms without post-divergence gene flow between species. The marked genealogical lineage divergence in nDNA provided some indication of Tanaka Line for its role as a barrier to plant dispersal, and lent support to its importance in promoting strong population structure and allopatric divergence.

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Clustering analysis of nDNA for Leucomeris decora and Nouelia insignis populations using STRUCTURE. Each bar of the plot represents one individual, with estimated likelihood assignment on the y-axis, when K = 2 cluster is assumed
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Fig3: Clustering analysis of nDNA for Leucomeris decora and Nouelia insignis populations using STRUCTURE. Each bar of the plot represents one individual, with estimated likelihood assignment on the y-axis, when K = 2 cluster is assumed

Mentions: The nucleotide diversity (π) and haplotype diversity (Hd) of each population from both markers in the two species was generally low (Additional file 1: Tables S1 and Additional file 2: Table S2). At the species scale, L. decora had relatively higher nucleotide diversity and haplotype diversity than those of N. insignis (Table 2). The AMOVA analyses of cpDNA and nDNA datasets showed significant genetic differences between species as well as among populations (Table 1). For example, the difference between the two species explained 68.4 % of the total nDNA variation and 35.5 % of cpDNA. Based on the cpDNA data, in L. decora 90.7 % was attributed to differences among populations and 9.3 % was attributed to differences among individuals within the population; and in N. insignis, 92.5 % was attributed to differences among populations and 7.5 % was attributed to differences among individuals within the population. In the Bayesian clustering implemented by STRUCTURE, the most likely number of clusters was two when the ΔK statistic of Evanno et al. [50] was applied (Additional file 4: Fig. S2). When K = 2, all individuals of L. decora and N. insignis formed two separate clusters, except for admixed individuals present in several populations, especially one individual (population 26) of N. insignis (Fig. 3). These patterns of individual assignments were consistent with the result of genealogy.Table 2


Genetic divergence and phylogeographic history of two closely related species (Leucomeris decora and Nouelia insignis) across the 'Tanaka Line' in Southwest China.

Zhao YJ, Gong X - BMC Evol. Biol. (2015)

Clustering analysis of nDNA for Leucomeris decora and Nouelia insignis populations using STRUCTURE. Each bar of the plot represents one individual, with estimated likelihood assignment on the y-axis, when K = 2 cluster is assumed
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4495643&req=5

Fig3: Clustering analysis of nDNA for Leucomeris decora and Nouelia insignis populations using STRUCTURE. Each bar of the plot represents one individual, with estimated likelihood assignment on the y-axis, when K = 2 cluster is assumed
Mentions: The nucleotide diversity (π) and haplotype diversity (Hd) of each population from both markers in the two species was generally low (Additional file 1: Tables S1 and Additional file 2: Table S2). At the species scale, L. decora had relatively higher nucleotide diversity and haplotype diversity than those of N. insignis (Table 2). The AMOVA analyses of cpDNA and nDNA datasets showed significant genetic differences between species as well as among populations (Table 1). For example, the difference between the two species explained 68.4 % of the total nDNA variation and 35.5 % of cpDNA. Based on the cpDNA data, in L. decora 90.7 % was attributed to differences among populations and 9.3 % was attributed to differences among individuals within the population; and in N. insignis, 92.5 % was attributed to differences among populations and 7.5 % was attributed to differences among individuals within the population. In the Bayesian clustering implemented by STRUCTURE, the most likely number of clusters was two when the ΔK statistic of Evanno et al. [50] was applied (Additional file 4: Fig. S2). When K = 2, all individuals of L. decora and N. insignis formed two separate clusters, except for admixed individuals present in several populations, especially one individual (population 26) of N. insignis (Fig. 3). These patterns of individual assignments were consistent with the result of genealogy.Table 2

Bottom Line: The study revealed comprehensive species divergence and phylogeographic histories of N. insignis and L. decora divided by the Tanaka Line.The phylogeographic pattern inferred from cpDNA reflected ancestrally shared polymorphisms without post-divergence gene flow between species.The marked genealogical lineage divergence in nDNA provided some indication of Tanaka Line for its role as a barrier to plant dispersal, and lent support to its importance in promoting strong population structure and allopatric divergence.

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, 650204, China. zyy36920@126.com.

ABSTRACT

Background: Leucomeris decora and Nouelia insignis (Asteraceae) are narrowly and allopatrically distributed species, separated by the important biogeographic boundary Tanaka Line in Southwest China. Previous morphological, cytogenetic and molecular studies suggested that L. decora is sister to N. insignis. However, it is less clear how the two species diverged, whether in full isolation or occurring gene flow across the Tanaka Line. Here, we performed a molecular study at the population level to characterize genetic differentiation and decipher phylogeographic history in two closely related species based on variation examined in plastid and nuclear DNAs using a coalescent-based approach.

Results: These morphologically distinct species share plastid DNA (cpDNA) haplotypes. In contrast, Bayesian analysis of nuclear DNA (nDNA) uncovered two distinct clusters corresponding to L. decora and N. insignis. Based on the IMa analysis, no strong indication of migration was detected based on both cpDNA and nDNA sequences. The molecular data pointed to a major west-east split in nuclear DNA between the two species corresponding with the Tanaka Line. The coalescent time estimate for all cpDNA haplotypes dated to the Mid-Late Pleistocene. The estimated demographic parameters showed that the population size of L. decora was similar to that of N. insignis and both experienced limited demographic fluctuations recently.

Conclusions: The study revealed comprehensive species divergence and phylogeographic histories of N. insignis and L. decora divided by the Tanaka Line. The phylogeographic pattern inferred from cpDNA reflected ancestrally shared polymorphisms without post-divergence gene flow between species. The marked genealogical lineage divergence in nDNA provided some indication of Tanaka Line for its role as a barrier to plant dispersal, and lent support to its importance in promoting strong population structure and allopatric divergence.

Show MeSH
Related in: MedlinePlus