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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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Marginal distribution of posterior probabilities for demographic parameters estimated by IM model. The IM analysis was performed for combined cpDNA and nDNA sequences. a. Population sizes of Leucomeris decora, Nouelia insignis and their ancestral population; a. migration rate between Leucomeris decora and Nouelia insignis
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Fig4: Marginal distribution of posterior probabilities for demographic parameters estimated by IM model. The IM analysis was performed for combined cpDNA and nDNA sequences. a. Population sizes of Leucomeris decora, Nouelia insignis and their ancestral population; a. migration rate between Leucomeris decora and Nouelia insignis

Mentions: For three independent runs of IMa, consistent unambiguous marginal posterior probability distributions of most demographic parameters were obtained for the two species (Fig. 4). However, the marginal posterior probability distributions of the parameter t did not drop to zero when sufficient high values were reached. This estimated result was likely due to small data set that may not be enough to achieve convergence [65]. The maximum-likelihood estimates (MLEs) and 90 % highest posterior densities (HPDs) were shown in Additional file 5: Table S3. Effective population sizes of L. decora and for N. insignis were not significantly different and larger than that of the ancestral species, indicating that both L. decora and N. insignis have undergone marked population expansion. The estimates of migration between L. decora and N. insignis were low and asymmetric. The gene flow from N. insignis to L. decora was larger than zero: m2 = 0.228 (90 % HPD interval: 0.008–1.563), while there was almost no evidence for gene flow in the opposite direction: m1 = 0.01 (90 % HPD interval: 0.01–1.41). The population migration rate was 2N2m2 = 0.049 from N. insignis to L. decora and 2N1m1 = 0 from L. decora to N. insignis, respectively.Fig. 4


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)

Marginal distribution of posterior probabilities for demographic parameters estimated by IM model. The IM analysis was performed for combined cpDNA and nDNA sequences. a. Population sizes of Leucomeris decora, Nouelia insignis and their ancestral population; a. migration rate between Leucomeris decora and Nouelia insignis
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Marginal distribution of posterior probabilities for demographic parameters estimated by IM model. The IM analysis was performed for combined cpDNA and nDNA sequences. a. Population sizes of Leucomeris decora, Nouelia insignis and their ancestral population; a. migration rate between Leucomeris decora and Nouelia insignis
Mentions: For three independent runs of IMa, consistent unambiguous marginal posterior probability distributions of most demographic parameters were obtained for the two species (Fig. 4). However, the marginal posterior probability distributions of the parameter t did not drop to zero when sufficient high values were reached. This estimated result was likely due to small data set that may not be enough to achieve convergence [65]. The maximum-likelihood estimates (MLEs) and 90 % highest posterior densities (HPDs) were shown in Additional file 5: Table S3. Effective population sizes of L. decora and for N. insignis were not significantly different and larger than that of the ancestral species, indicating that both L. decora and N. insignis have undergone marked population expansion. The estimates of migration between L. decora and N. insignis were low and asymmetric. The gene flow from N. insignis to L. decora was larger than zero: m2 = 0.228 (90 % HPD interval: 0.008–1.563), while there was almost no evidence for gene flow in the opposite direction: m1 = 0.01 (90 % HPD interval: 0.01–1.41). The population migration rate was 2N2m2 = 0.049 from N. insignis to L. decora and 2N1m1 = 0 from L. decora to N. insignis, respectively.Fig. 4

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