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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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Geographic distribution and network of cpDNA haplotypes. a. Distribution of 5 chloroplast DNA (cpDNA) haplotypes detected within and among 27 populations of Leucomeris decora and Nouelia insignis. Full names of the abbreviations for the populations are shown in Additional file 1: Table S1 and Additional file 2: Table S2. b. Statistical parsimony network of genealogical relationships between five cpDNA haplotypes. Letters in/around circles represent haplotypes at each locus. The size of the circles corresponds to the frequency of each haplotype and each solid line represents one mutational step
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Fig1: Geographic distribution and network of cpDNA haplotypes. a. Distribution of 5 chloroplast DNA (cpDNA) haplotypes detected within and among 27 populations of Leucomeris decora and Nouelia insignis. Full names of the abbreviations for the populations are shown in Additional file 1: Table S1 and Additional file 2: Table S2. b. Statistical parsimony network of genealogical relationships between five cpDNA haplotypes. Letters in/around circles represent haplotypes at each locus. The size of the circles corresponds to the frequency of each haplotype and each solid line represents one mutational step

Mentions: One indel and three substitutions were detected from the cpDNA region rpl32- trnL(UAG) (894-900 bp excluding the mononucleotide repeats) of L. decora and N. insignis samples, and were recoved 5 chloroplast haplotypes (C1-C5). All haplotype sequences were deposited in GenBank databases under the accession numbers JF915764–JF915768. The most common haplotype C2 (frequency 62.1 %) was shared by the two species, and 37 %, 78 % of the investigated individuals carried this haplotype in L. decora and N. insignis, respectively. C3 (24.7 %) only occurred in L. decora and the other haplotypes (C1, C4, C5) were only found in N. insignis with low frequencies ranging from 1.95 % to 5.98 % (Additional file 1:Table S1 and Additional file 2: Table S2). The distribution and network of cpDNA haplotypes C1–C5 are shown in Fig. 1. The network of chloroplast haplotypes indicated that C2 was possibly ancestor to the others and away from the remaining haplotypes by a single mutation (Fig. 1b). And it was fixed in most of N. insignis populations located in the Jinsha drainage and northwestern populations of L. decora (Fig. 1). All the remaining populations of L. decora in centre/southwest Yunnan were fixed for C3 except one population SP. C1 and C4 were restricted to the Nanpan drainage (CJ, HN and ML) and C5 was only found in population DY and YM. The total cpDNA diversity was slightly higher in L. decora (HT = 0.487) than in N. insignis (HT = 0.422). Between-population differentiation levels estimated by both GST and AMOVA are relatively low within N. insignis (GST = 0.849, FST = 0.896) than in L. decora (GST = 0.862, FST = 0.907) (Tables 1, 2). The Bayesian TMRCA analysis indicated that all sampled cpDNA haplotypes of L. decora and N. insignis coalesce at about 0.54 Ma (95 % confidence interval: 0.01–1.32 Ma) or 0.38 Ma (95 % confidence interval: 0.01–0.93 Ma), assuming minimum and maximum (average) rates of synonymous substitution in cpDNA, respectively. This suggests that the divergence between L. decora and N. insignis falls into the mid-late Pleistocene.Fig. 1


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)

Geographic distribution and network of cpDNA haplotypes. a. Distribution of 5 chloroplast DNA (cpDNA) haplotypes detected within and among 27 populations of Leucomeris decora and Nouelia insignis. Full names of the abbreviations for the populations are shown in Additional file 1: Table S1 and Additional file 2: Table S2. b. Statistical parsimony network of genealogical relationships between five cpDNA haplotypes. Letters in/around circles represent haplotypes at each locus. The size of the circles corresponds to the frequency of each haplotype and each solid line represents one mutational step
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Geographic distribution and network of cpDNA haplotypes. a. Distribution of 5 chloroplast DNA (cpDNA) haplotypes detected within and among 27 populations of Leucomeris decora and Nouelia insignis. Full names of the abbreviations for the populations are shown in Additional file 1: Table S1 and Additional file 2: Table S2. b. Statistical parsimony network of genealogical relationships between five cpDNA haplotypes. Letters in/around circles represent haplotypes at each locus. The size of the circles corresponds to the frequency of each haplotype and each solid line represents one mutational step
Mentions: One indel and three substitutions were detected from the cpDNA region rpl32- trnL(UAG) (894-900 bp excluding the mononucleotide repeats) of L. decora and N. insignis samples, and were recoved 5 chloroplast haplotypes (C1-C5). All haplotype sequences were deposited in GenBank databases under the accession numbers JF915764–JF915768. The most common haplotype C2 (frequency 62.1 %) was shared by the two species, and 37 %, 78 % of the investigated individuals carried this haplotype in L. decora and N. insignis, respectively. C3 (24.7 %) only occurred in L. decora and the other haplotypes (C1, C4, C5) were only found in N. insignis with low frequencies ranging from 1.95 % to 5.98 % (Additional file 1:Table S1 and Additional file 2: Table S2). The distribution and network of cpDNA haplotypes C1–C5 are shown in Fig. 1. The network of chloroplast haplotypes indicated that C2 was possibly ancestor to the others and away from the remaining haplotypes by a single mutation (Fig. 1b). And it was fixed in most of N. insignis populations located in the Jinsha drainage and northwestern populations of L. decora (Fig. 1). All the remaining populations of L. decora in centre/southwest Yunnan were fixed for C3 except one population SP. C1 and C4 were restricted to the Nanpan drainage (CJ, HN and ML) and C5 was only found in population DY and YM. The total cpDNA diversity was slightly higher in L. decora (HT = 0.487) than in N. insignis (HT = 0.422). Between-population differentiation levels estimated by both GST and AMOVA are relatively low within N. insignis (GST = 0.849, FST = 0.896) than in L. decora (GST = 0.862, FST = 0.907) (Tables 1, 2). The Bayesian TMRCA analysis indicated that all sampled cpDNA haplotypes of L. decora and N. insignis coalesce at about 0.54 Ma (95 % confidence interval: 0.01–1.32 Ma) or 0.38 Ma (95 % confidence interval: 0.01–0.93 Ma), assuming minimum and maximum (average) rates of synonymous substitution in cpDNA, respectively. This suggests that the divergence between L. decora and N. insignis falls into the mid-late Pleistocene.Fig. 1

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