Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads

Wu, Ching‐Yi; Chaw, Shu‐Miaw; Huang, Ya‐Yi

doi:10.1093/gbe/evt001

Cited by 58 publications

(59 citation statements)

References 68 publications

(89 reference statements)

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“…Analysis of molecular variance showed that 24 and 76% genetic variation existed within and among the populations of G. biloba, respectively. The Ginkgo genus represents an ancient evolutionary lineage within the gymnosperms (Wu et al, 2013), as demonstrated by extensive fossil findings from the Jurassic to the Tertiary periods in both the Northern and the Southern hemispheres (Zhou and Zheng, 2003;Zhou, 2009;Zhou et al, 2012). The novel polymorphic and monomorphic cpSSR markers developed in this study are useful for genetic studies of G. biloba, but they may also be important for determining the origin and evolutionary history of Ginkgo.…”

Section: Resultsmentioning

confidence: 78%

Development of novel chloroplast microsatellite markers for Ginkgo biloba

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Ginkgo biloba is considered to be a living fossil that can be used to understand the ancient evolutionary history of gymnosperms, but little attention has been given to the study of its population genetics, molecular phylogeography, and genetic resources assessment. Chloroplast simple sequence repeat (cpSSR) markers are powerful tools for genetic studies of plants. In this study, a total of 30 perfect cpSSRs of Ginkgo were identified and characterized, including di-, tri, tetra-, penta-, and hexanucleotide repeats. Fifteen of 21 designed primer pairs were successfully amplified to yield specific polymerase chain reaction products from 16 Ginkgo cultivars. Polymorphic cpSSRs were further applied to determine the genetic variation of 116 individuals in 5 populations of G. biloba. The results showed that 24 and 76% genetic variation existed within and among populations of this species, respectively. These polymorphic and monomorphic cpSSR markers can be used to trace the origin and evolutionary history of Ginkgo.

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Section: Resultsmentioning

confidence: 78%

Development of novel chloroplast microsatellite markers for Ginkgo biloba

et al. 2015

Genet. Mol. Res.

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“…Cycadales and Ginkgoales clearly share various other archaic traits, such as motile sperm and asaccate sulcate pollen 12 . However, it is noteworthy that a Cycadales and Ginkgoales clade has been recovered repeatedly in some recent phylogenetic analyses of seed plants using nuclear 18S ribosomal (r)RNA sequences 41 , chloroplast genes 42 , amino acids 43 and in transcriptome analyses of land plants 44 .…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships

et al. 2017

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Gene sequences form the primary basis for understanding the relationships among extant plant groups, but genetic data are unavailable from fossils to evaluate the affinities of extinct taxa. Here we show that geothermally resistant fossil cuticles of seed-bearing plants, analysed with Fourier transform infrared (FTIR) spectroscopy and hierarchical cluster analysis (HCA), retain biomolecular suites that consistently distinguish major taxa even after experiencing different diagenetic histories. Our results reveal that similarities between the cuticular biochemical signatures of major plant groups (extant and fossil) are mostly consistent with recent phylogenetic hypotheses based on molecular and morphological data. Our novel chemotaxonomic data also support the hypothesis that the extinct Nilssoniales and Bennettitales are closely allied, but only distantly related to Cycadales. The chemical signature of the cuticle of Czekanowskia (Leptostrobales) is strongly similar to that of Ginkgo leaves and supports a close evolutionary relationship between these groups. Finally, our results also reveal that the extinct putative araucariacean, Allocladus, when analysed through HCA, is grouped closer to Ginkgoales than to conifers. Thus, in the absence of modern relatives yielding molecular information, FTIR spectroscopy provides valuable proxy biochemical data complementing morphological characters to distinguish fossil taxa and to help elucidate extinct plant relationships.

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“…Phylogenetic relationships among cpDNA haplotypes were reconstructed using Bayesian inference implemented in MrBayes 3.1.2 (Ronquist and Huelsenbeck 2003) with Cycas taitungensis as the outgroup (Wu et al 2013; Gen-Bank accession No. NC_009618).…”

Section: Plastid Dna Sequence Analysesmentioning

confidence: 99%

Incongruent range dynamics between co‐occurring Asian temperate tree species facilitated by life history traits

Zhao

Yan

Muir

et al. 2016

Ecology and Evolution

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Postglacial expansion to former range limits varies substantially among species of temperate deciduous forests in eastern Asia. Isolation hypotheses (with or without gene flow) have been proposed to explain this variance, but they ignore detailed population dynamics spanning geological time and neglect the role of life history traits. Using population genetics to uncover these dynamics across their Asian range, we infer processes that formed the disjunct distributions of Ginkgo biloba and the co‐occurring Cercidiphyllum japonicum (published data). Phylogenetic, coalescent, and comparative data suggest that Ginkgo population structure is regional, dichotomous (to west–east refugia), and formed ˜51 kya, resulting from random genetic drift during the last glaciation. This split is far younger than the north–south population structure of Cercidiphyllum (~1.89 Mya). Significant (recent) unidirectional gene flow has not homogenized the two Ginkgo refugia, despite 2Nm > 1. Prior to this split, gene flow was potentially higher, resulting in conflicting support for a priori hypotheses that view isolation as an explanation for the variation in postglacial range limits. Isolation hypotheses (with or without gene flow) are thus not necessarily mutually exclusive due to temporal variation of gene flow and genetic drift. In comparison with Cercidiphyllum, the restricted range of Ginkgo has been facilitated by uncompetitive life history traits associated with seed ecology, highlighting the importance of both demography and lifetime reproductive success when interpreting range shifts.

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Chloroplast Phylogenomics Indicates that Ginkgo biloba Is Sister to Cycads

Cited by 58 publications

References 68 publications

Development of novel chloroplast microsatellite markers for Ginkgo biloba

Development of novel chloroplast microsatellite markers for Ginkgo biloba

Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships

Incongruent range dynamics between co‐occurring Asian temperate tree species facilitated by life history traits

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