Genetic Structure and Evolutionary History of a Diploid Hybrid Pine Pinus densata Inferred from the Nucleotide Variation at Seven Gene Loci

Fei, Xiao; Szmidt, Alfred E.; Wang, Xiao Ru

doi:10.1093/molbev/msj100

Cited by 98 publications

(83 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…However, the level of nucleotide diversity revealed in our study was in the same order or slightly higher than those reported for other conifers e.g., Cryptomeria japonica (π sil = 0.0039) over seven loci (Kado et al, 2003), Cathaya argyrophylla (π sil = 0.0024) (Wang and Song, 2006), Pinus tabuliformis, P. yunnanensis and P. densata (π sil = 0.0087 ~ 0.0128 over 7 loci, (Ma et al, 2006). It thus appears that contrary to previous suggestions Larix species have levels of nucleotide diversity comparable to other conifers.…”

Section: Discussionsupporting

confidence: 67%

Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes

et al. 2008

Self Cite

View full text Add to dashboard Cite

Larch (Larix Mill.) is one of the most widely distributed tree genera in Eurasia. To determine population structure and to verify classification of five species and three varieties of the Eurasian Larix species, we investigated levels and patterns of nucleotide variation of two nuclear gene regions: the 4-coumarate coenzyme A ligase (4CL) and the coumarate 3-hydroxylase (C3H). In the 4CL region nucleotide diversity at silent sites (π sil ) varied between 0.0020 in L. gmelinii to 0.0116 in L. gmelinii var. japonica and in the C3H region between 0.0019 in L. kaempferi to 0.0066 in L. gmelinii var. japonica. In both gene regions statistically significant population differentiation (F ST ) was detected among adjacent refugial populations of some species suggesting limited gene flow and/or long time isolation of some refugial populations. On the other hand, populations of L. sukaczewii from northwestern Russia, which was glaciated 20,000 years ago showed no differentiation. This result is consistent with recent postglacial origin of these populations. Haplotype composition of some of the investigated Eurasian Larix species suggested that they are considerably diverged. Some haplotypes were unique to individual species. Our results indicate that more intensive sampling especially from known refugial regions is necessary for inferring correct classification of Eurasian Larix species and inferring their postglacial migration.

show abstract

Section: Discussionsupporting

confidence: 67%

Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes

et al. 2008

Self Cite

View full text Add to dashboard Cite

show abstract

“…This trend could be an indication that these populations were less severely affected by Pleistocene glaciations and the ensuing recolonization process than boreal species. Similarly, in Pinus species from the Tibetan plateau, the history of which has been less affected by glaciations, Tajima's D values tended to be positive (Ma et al, 2006). These different trends support the hypothesis that skews towards negative Tajima's D values in white spruce natural populations are likely resulting from demographic history, not from widespread hitchhiking effects.…”

Section: Ld and Selectionmentioning

confidence: 61%

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Pavy

Gagnon

et al. 2011

Heredity

View full text Add to dashboard Cite

In plants, knowledge about linkage disequilibrium (LD) is relevant for the design of efficient single-nucleotide polymorphism arrays in relation to their use in population and association genomics studies. Previous studies of conifer genes have shown LD to decay rapidly within gene limits, but exceptions have been reported. To evaluate the extent of heterogeneity of LD among conifer genes and its potential causes, we examined LD in 105 genes of white spruce (Picea glauca) by sequencing a panel of 48 haploid megagametophytes from natural populations and further compared it with LD in other conifer species. The average pairwise r 2 value was 0.19 (s.d.¼0.19), and LD dropped quickly with a half-decay being reached at a distance of 65 nucleotides between sites. However, LD was significantly heterogeneous among genes. A first group of 29 genes had stronger LD (mean r 2 ¼0.28), and a second group of 38 genes had weaker LD (mean r 2 ¼0.12). While a strong relationship was found with the recombination rate, there was no obvious relationship between LD and functional classification. The level of nucleotide diversity, which was highly heterogeneous across genes, was also not significantly correlated with LD. A search for selection signatures highlighted significant deviations from the standard neutral model, which could be mostly attributed to recent demographic changes. Little evidence was seen for hitchhiking and clear relationships with LD. When compared among conifer species, on average, levels of LD were similar in genes from white spruce, Norway spruce and Scots pine, whereas loblolly pine and Douglas fir genes exhibited a significantly higher LD.

show abstract

“…The average π s values (0.00059 and 0.00003 in R. apiculata and R. mucronata, respectively) were one or two orders lower than those in other plant species (e.g., Cryptomeria japonica: π s = 0.0038 (Kado et al, 2003); A. thaliana: π s = 0.0083 (Schmid et al, 2005); Pinus tabuliformis, P. densata and P. yunnanensis: π s = 0.0087-0.0128 (Ma et al, 2006). Taking into account that five different nuclear loci totaling more than 5500 bp including more than 2900 bp of introns were investigated, the observed low levels of polymorphism appear to be a general feature of both R. apiculata and R. mucronata.…”

Section: Patterns Of Nucleotide Variationmentioning

confidence: 90%

Levels and patterns of DNA variation in two sympatric mangrove species, Rhizophora apiculata and R. mucronata from Thailand

et al. 2009

Self Cite

View full text Add to dashboard Cite

In mangrove species the past geomorphic changes in coastal regions and reproductive systems are important factors of their distribution and genetic structure of populations. However, very little is known about the levels of genetic variation of Rhiozophora species in Southeast Asia. In this study, we surveyed levels and patterns of genetic variation as well as population structure of two sympatric mangrove species, Rhizophora apiculata and R. mucronata in Thailand, using five nuclear genes and two cpDNA regions. In all investigated DNA regions, nucleotide variation within species was low, while nucleotide divergence between the two species was considerable. The nuclear genes evolved 10 times faster than the cpDNA regions. In both R. apiculata and R. mucronata, significant positive F IS values were found, indicating deviation from Hardy-Weinberg proportions and a deficiency of heterozygotes. In both species, we found significant genetic differentiation between populations. However, the pattern of population differentiation (F ST ) of R. apiculata differed from that of R. mucronata. Our results suggest that the two investigated species have different demographic history, even though they are sympatric and have similar reproductive systems.

show abstract

Genetic Structure and Evolutionary History of a Diploid Hybrid Pine Pinus densata Inferred from the Nucleotide Variation at Seven Gene Loci

Cited by 98 publications

References 63 publications

Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes

Phylogeography of Eurasian Larix species inferred from nucleotide variation in two nuclear genes

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

Levels and patterns of DNA variation in two sympatric mangrove species, Rhizophora apiculata and R. mucronata from Thailand

Contact Info

Product

Resources

About