The history of extant Ilex species (Aquifoliaceae): Evidence of hybridization within a Miocene radiation

Manen, Jean‐François; Barriera, Gabrielle; Loizeau, Pierre-André; Naciri, Yamama

doi:10.1016/j.ympev.2010.09.006

Cited by 74 publications

(158 citation statements)

References 62 publications

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“…Flowers and fruits are fairly uniform but Ilex species differ greatly in leaf characters, including size, texture, and margins. The genus is widespread in mesic habitats but the global diversity centers are in East Asia and South America, with a single species in tropical Africa, two in northern Australia, four in Europe1, and 17 in North America (http://plants.usda.gov/java/nameSearch). The four other families in the Campanulidae order Aquifoliales, Cardiopteridaceae, Stemonuraceae, Helwingiaceae and Phyllonomaceae, are all small23.…”

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confidence: 99%

“…Cuénoud8 used the chloroplast markers atpB-rbcL spacer and rbcL to construct a phylogeny of 116 species, while Manen9 combined plastid ( atpB-rbcL spacer, rbcL and trnL-trnF ) and nuclear (ribosomal internal transcribed spacer and the 5S RNA spacer) markers for 105 species. Manen1 later increased the phylogenetic resolution by using nuclear markers ITS and ncpGS for 108 species, including species from America, Europe, Africa, and islands in the Atlantic and Pacific. However, this study included only 33 species of the 204 known Chinese species, of which 149 are endemic2.…”

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confidence: 99%

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Chloroplast genome structure in Ilex (Aquifoliaceae)

Yao

Tan

Liu

et al. 2016

Sci Rep

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Aquifoliaceae is the largest family in the campanulid order Aquifoliales. It consists of a single genus, Ilex, the hollies, which is the largest woody dioecious genus in the angiosperms. Most species are in East Asia or South America. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. We produced the first complete chloroplast genomes in this family, including seven Ilex species, by Illumina sequencing of long-range PCR products and subsequent reference-guided de novo assembly. These genomes have a typical bicyclic structure with a conserved genome arrangement and moderate divergence. The total length is 157,741 bp and there is one large single-copy region (LSC) with 87,109 bp, one small single-copy with 18,436 bp, and a pair of inverted repeat regions (IR) with 52,196 bp. A total of 144 genes were identified, including 96 protein-coding genes, 40 tRNA and 8 rRNA. Thirty-four repetitive sequences were identified in Ilex pubescens, with lengths >14 bp and identity >90%, and 11 divergence hotspot regions that could be targeted for phylogenetic markers. This study will contribute to improved resolution of deep branches of the Ilex phylogeny and facilitate identification of Ilex species.

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confidence: 99%

mentioning

confidence: 99%

Chloroplast genome structure in Ilex (Aquifoliaceae)

Yao

Tan

Liu

et al. 2016

Sci Rep

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“…The evolutionary history and diversification of the genus Ilex, based on 108 species, are deduced by analyzing two nuclear (ITS and nepGS) and three plastid (rbcL, trnL-F, and atpB-rbcL) sequences (Manen et al, 2010). Nuclear and plastid trees are highly dissimilar, and the nuclear tree is more in agreement with current taxonomic classifications ( Figure 13.5a breeding programs.…”

Section: Chemotaxonomymentioning

confidence: 87%

“…I. latifolia was found to be closer to I. liukiuensis than to I. cornuta (Gottleib et al, 2005). The significant discrepancy between nuclear and chloroplast phylogenies might be due to intraspecific polymorphism, hybridization, and introgressions (Manen et al, 2010). We sequenced 11 chloroplast noncoding regions for five Ilex species (Hao et al, 2012c and unpublished data).…”

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confidence: 99%

“…However, these studies did not include I. kudingcha and I. pentagona. The most recent common ancestor (MRCA) of extant species is dated from the Miocene, while the fossil records suggest that the Ilex stem lineage originated in the Late Cretaceous, implying extensive lineage extinctions between the Cretaceous and Miocene and explaining the difficulties in clarifying the relationships between Ilex and its closest relatives (Manen et al, 2010). I. latifolia, I. kudingcha, I. cornuta, and I. pentagona intermingled in a cluster and cannot discriminate from each other in the chloroplast phylogenetic tree.…”

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confidence: 99%

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Phytochemistry and biology of Ilex pharmaceutical resources

Hao¹,

Gu²,

Xiao³

2015

Medicinal Plants

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Evidence for ecological speciation via a host shift in the holly leaf miner,Phytomyza glabricola(Diptera: Agromyzidae)

Hébert

Scheffer²,

Hawthorne

2016

Ecology and Evolution

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Evolutionary radiations have been well documented in plants and insects, and natural selection may often underly these radiations. If radiations are adaptive, the diversity of species could be due to ecological speciation in these lineages. Agromyzid flies exhibit patterns of repeated host‐associated radiations. We investigated whether host‐associated population divergence and evidence of divergent selection exist in the leaf miner Phytomyza glabricola on its sympatric host plants, the holly species, Ilex coriacea and I. glabra. Using AFLPs and nuclear sequence data, we found substantial genetic divergence between host‐associated populations of these flies throughout their geographic range. Genome scans using the AFLP data identified 13 loci under divergent selection, consistent with processes of ecological speciation. EF‐1α data suggest that I. glabra is the original host of P. glabricola and that I. coriacea is the novel host, but the AFLP data are ambiguous with regard to directionality of the host shift.

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The history of extant Ilex species (Aquifoliaceae): Evidence of hybridization within a Miocene radiation

Cited by 74 publications

References 62 publications

Chloroplast genome structure in Ilex (Aquifoliaceae)

Chloroplast genome structure in Ilex (Aquifoliaceae)

Phytochemistry and biology of Ilex pharmaceutical resources

Evidence for ecological speciation via a host shift in the holly leaf miner,Phytomyza glabricola(Diptera: Agromyzidae)

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