Reticulate evolution in Thuja inferred from multiple gene sequences: Implications for the study of biogeographical disjunction between eastern Asia and North America

Peng, Dan; Wang, Xiaoquan

doi:10.1016/j.ympev.2008.02.001

Cited by 65 publications

(78 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A number of plant groups have shown ‘cytonuclear discordance’ and reticulation in their phylogenetic networks, which is evidence of reticulate evolution3940. Reticulate evolution has been shown to be a driving force for species diversification via hybridization events41.…”

Section: Discussionmentioning

confidence: 99%

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

Hou

Luo

Zhang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

The genus Dendrobium was used as a case study to elucidate the evolutionary history of Orchidaceae in the Sino-Japanese Floristic Region (SJFR) and Southeast Asia region. These evolutionary histories remain largely unknown, including the temporal and spatial distribution of the evolutionary events. The present study used nuclear and plastid DNA to determine the phylogeography of Dendrobium officinale and four closely related taxa. Plastid DNA haplotype and nuclear data were shown to be discordant, suggesting reticulate evolution drove the species’ diversification. Rapid radiation and genetic drift appeared to drive the evolution of D. tosaense and D. flexicaule, whereas introgression or hybridization might have been involved in the evolution of D. scoriarum and D. shixingense. The phylogeographical structure of D. officinale revealed that core natural distribution regions might have served as its glacial refuges. In recent years, human disturbances caused its artificial migration and population extinction. The five taxa may have originated from the Nanling Mountains and the Yungui Plateau and then migrated northward or eastward. After the initial iteration expansion, D. officinale populations appeared to experience the regional evolutionary patterns in different regions and follow the sequential or rapid decline in gene exchange.

show abstract

Section: Discussionmentioning

confidence: 99%

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

Hou

Luo

Zhang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Although the NLY sequence obtained from the parasitic Parasitaxus usta represents a pseudogene, its exon region shares a high similarity (over 90%) with that of other Podocarpaceae species, and thus still could be used in phylogenetic analysis. Actually, the LFY gene has been successfully utilized in phylogenetic and biogeographic studies of several gymnosperm groups, including Gnetum [88], Thuja [89], and Pseudotsuga [90]. In particular, the intergeneric relationships of Cupressaceae s.l.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes

et al. 2014

Self Cite

View full text Add to dashboard Cite

Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can improve the resolution in Podocarpaceae but not in cycads, although divergence times of the cycad genera are similar to or longer than those of the Podocarpaceae genera. Our study strongly supports cycads as the basal-most lineage of gymnosperms rather than sister to Ginkgoaceae, and a sister relationship between Podocarpaceae and Araucariaceae and between Cephalotaxaceae-Taxaceae and Cupressaceae. In addition, intergeneric relationships of some families that were controversial, and the relationships between Taxaceae and Cephalotaxaceae and between conifers and Gnetales are discussed based on the nuclear gene evidence. The molecular dating analysis suggests that drastic extinctions occurred in the early evolution of gymnosperms, and extant coniferous genera in the Northern Hemisphere are older than those in the Southern Hemisphere on average. This study provides an evolutionary framework for future studies on gymnosperms.

show abstract

“…It is well known that hybridization and lineage sorting of ancestral polymorphisms have occurred much more frequently in nature than previously envisioned [17,18]. The issue of combining cpDNA and nrDNA data sets is not new, but it is of greater practical concern today, with the vast amount of molecular data now available, especially as an increasing number of low-copy nuclear genes are used in plant phylogenetics [13,14,19,20]. Careful analysis of cpDNA and nrDNA data and assessment of their combinability is a vital step toward accurate reconstruction of phylogenetic relationships in a plant group.…”

mentioning

confidence: 99%

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

Wang

Chen

2014

Sci. China Life Sci.

View full text Add to dashboard Cite

Correct combination of plastid (cp) and nuclear (nr) DNA data for plant phylogenetic reconstructions is not a new issue, but with an increasing number of nrDNA loci being used, it is of ever greater practical concern. For accurately reconstructing the phylogeny and evolutionary history of plant groups, correct treatment of phylogenetic incongruence is a vital step in the proper analysis of cpDNA and nrDNA data. We first evaluated the current status of analyzing cpDNA and nrDNA data by searching all articles published in the journal Systematic Botany between 2005 and 2011. Many studies combining cpDNA and nrDNA data did not rigorously assess the combinability of the data sets, or did not address in detail possible reasons for incongruence between the two data sets. By reviewing various methods, we outline a procedure to more accurately analyze and/or combine cpDNA and nrDNA data, which includes four steps: identifying significant incongruence, determining conflicting taxa, providing possible interpretations for incongruence, and reconstructing the phylogeny after treating incongruence. Particular attention is given to explanation of the cause of incongruence. We hope that our procedure will help raise awareness of the importance of rigorous analysis and help identify the cause of incongruence before combining cpDNA and nrDNA data. combined analysis, plastid DNA, incongruence, nuclear DNA, phylogenetics Citation:Wang W, Li HL, Chen ZD. Analysis of plastid and nuclear DNA data in plant phylogenetics-evaluation and improvement.

show abstract

Reticulate evolution in Thuja inferred from multiple gene sequences: Implications for the study of biogeographical disjunction between eastern Asia and North America

Cited by 65 publications

References 84 publications

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

Iteration expansion and regional evolution: phylogeography of Dendrobium officinale and four related taxa in southern China

Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes

Analysis of plastid and nuclear DNA data in plant phylogenetics—evaluation and improvement

Contact Info

Product

Resources

About