Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae)

Fortuné, Philippe; Schierenbeck, Kristina A.; Aïnouche, Abdelkader; Jacquemin, Julie; Wendel, Jonathan F.; Aïnouche, Malika L.

doi:10.1016/j.ympev.2006.11.018

Cited by 83 publications

(93 citation statements)

References 73 publications

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“…Baumel et al 4 (2002) initially detected only one copy of the GBSSI gene for most species of the 5 Spartina. A further study with more clones sampled revealed repeated gene duplication 6 followed by deletion or sometimes without deletion (Fortune et al, 2007). In the case of Peru in the GBSSI tree (Dillon et al, 2007).…”

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confidence: 85%

“…(Poaceae) (Fortune et al, 2007). In Solanaceae, initial phylogenetic studies detected 29 only one copy of the GBSSI gene, such as in the diploid Solanum (Levin et al, 2006; 30 Peralta and Spooner, 2001), the Iochrominae group of the tribe Physaleae (Smith and Baum, 2006), Schizanthus (Perez et al, 2006), and Nolana's close 1 relative Lycieae (Levin and Miller, 2005).…”

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confidence: 99%

“…A particularly compelling example of this situation is the studies of 3 GBSSI for Spartina (Poaceae) (Baumel et al, 2002;Fortune et al, 2007). Baumel et al 4 (2002) initially detected only one copy of the GBSSI gene for most species of the 5 Spartina.…”

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confidence: 99%

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Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron

Dillon

Sun

et al. 2008

Molecular Phylogenetics and Evolution

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Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron

Dillon

Sun

et al. 2008

Molecular Phylogenetics and Evolution

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“…Our sampling includes S. ×townsendii, a sterile F1 hybrid of S. alterniflora (the female parent) and S. maritima (the male parent) and the precursor of the amphidiploid S. anglica (reviewed in Saarela, 2012); the parentage of S. ×townsendii was confirmed based on variation in plastid regions (trnT-trnL, rpl16) and molecular fingerprinting (Ferris & al., 1997;Baumel & al., 2002Baumel & al., , 2003. Curiously, neither S. ×townsendii nor S. anglica were sampled in the earlier phylogenetic studies (Baumel & al., 2002;Fortune & al., 2007Fortune & al., , 2008. They are included here, and in our phylogenetic trees, the plastid sequences are identical for all individuals of S. alterniflora, S. anglica and S. ×town-sendii, consistent with S. alterniflora being the female parent of S. ×townsendii, and S. ×townsendii, in turn, being the progenitor of S. anglica.…”

Section: Sporobolus Cryptandrus Cladementioning

confidence: 99%

A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae)

Peterson

Romaschenko

Arrieta³

et al. 2014

TAXON

107

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The grass subtribe Sporobolinae contains six genera: Calamovilfa (5 spp. endemic to North America), Crypsis (10 spp. endemic to Asia and Africa), Psilolemma (1 sp. endemic to Africa), Spartina (17 spp. centered in North America), Sporobolus (186 spp. distributed worldwide), and Thellungia (1 sp. endemic to Australia). Most species in this subtribe have spikelets with a single floret, 1-veined (occasionally 3 or more) lemmas, a ciliate membrane or line of hairs for a ligule, and fruits with free pericarps (modified caryopses). Phylogenetic analyses were conducted on 177 species (281 samples), of which 145 species were in the Sporobolinae, using sequence data from four plastid regions (rpl32-trnL spacer, ndhA intron, rps16-trnK spacer, rps16 intron) and the nuclear ribosomal internal transcribed spacer regions (ITS) to infer evolutionary relationships and provide an evolutionary framework on which to revise the classification. The phylogenetic analysis provides weak to moderate support for a paraphyletic Sporobolus that includes Calamovilfa, Crypsis, Spartina, and Thellungia. In the combined plastid tree, Psilolemma jaegeri is sister to a trichotomy that includes an unsupported Urochondra-Zoysia clade (subtr. Zoysiinae), a strongly supported Sporobolus somalensis lineage, and a weakly supported Sporobolus s.l. lineage. In the ITS tree the Zoysiinae is sister to a highly supported Sporobolinae in which a Psilolemma jaegeri-Sporobolus somalensis clade is sister to the remaining species of Sporobolus s.l. Within Sporobolus s.l. the nuclear and plastid analyses identify the same 16 major clades of which 11 are strongly supported in the ITS tree and 12 are strongly supported in the combined plastid tree. The positions of three of these clades representing proposed sections Crypsis, Fimbriatae, and Triachyrum are discordant in the nuclear and plastid trees, indicating their origins may involve hybridization. Seven species fall outside the major clades in both trees, and the placement of ten species of Sporobolus are discordant in the nuclear and plastid trees. We propose incorporating Calamovilfa, Crypsis, Spartina, Thellungia, and Eragrostis megalosperma within Sporobolus, and make the requisite 35 new combinations or new names. The molecular results support the recognition of 11 sections and 11 subsections within Sporobolus s.l.; four sections are new:

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“…Because of the trouble of using molecular data in phylogenetic analyses of polyploid species (RousseauGueutin et al, 2009), a method recommended to reduce the negative effect of polyploidy on reconstructing evolutionary history is to use the low-copy nuclear genes. Furthermore, phylogenetic analyses of mitochondrial and/or low-copy nuclear genes have shed light on the evolution of polyploids (Brysting et al, 2007;Evans et al, 2004Evans et al, , 2005Fortune et al, 2007;Machordom and Doadrio, 2001;Marhold and Lihová, 2006;Sang, 2002;Tsigenopoulos et al, 2002). The nuclear recombination activating gene 2 (RAG2) encodes components of the recombinase involved in recombination of immunoglobin and T-cell receptor genes and appears as conserved single copy in zebrafish (Willett et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

Wang

Gan

et al. 2016

Sci. China Life Sci.

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Origin and diversification of the Tibetan polyploid cyprinids (schizothoracins) may help us to explore relationships between diversification of the cyprinids and the Tibetan Plateau uplift. Cyprininae phylogeny was analyzed using mitochondrial and nuclear DNA sequences to trace origins of polyploidy and diversifications of schizothoracins. Ancestral states reconstruction for ploidy levels indicated that the Cyprininae was diploid origin and the schizothoracin clades tetraploid origins. There were two diversification rate shifts along with diversification of the cyprinine fishes in response to the Tibetan uplift. The unusual diversification shifts were located to branches subtending the clades of Tibetan polyploid cyprinids. Our analyses suggested that (i) phylogeny of Cyprininae recovered two independent origins of the Tibetan polyploidy schizothoracins; (ii) diversifications of the schizothoracins were closely related to the Neogene uplift of the Tibetan plateau in the following ways: the relatively ancient Late Oligocene-Middle Miocene adaptive radiation may be associated with the uplift of the southern Tibet and Himalaya; the Middle Miocene-Early Pleistocene lineage-specific diversification broadly coincident with major phase of the Neogene Tibetan uplift; and the most recent Pleistocene diversification shift in Schizothorax closely coincident with the successive Kunlun-Huanghe and Gonghe movements of the Tibetan uplift and the glaciation-induced climate oscillations on the plateau.Cyprininae, polyploid, schizothoracins, the Tibetan Plateau, diversifications Citation:Wang, X., Gan, X., Li J., Chen, Y., and He, S. (2016). Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau.

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Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae)

Cited by 83 publications

References 73 publications

Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron

Phylogeny of Nolana (Solanaceae) of the Atacama and Peruvian deserts inferred from sequences of four plastid markers and the nuclear LEAFY second intron

A molecular phylogeny and new subgeneric classification of Sporobolus (Poaceae: Chloridoideae: Sporobolinae)

Cyprininae phylogeny revealed independent origins of the Tibetan Plateau endemic polyploid cyprinids and their diversifications related to the Neogene uplift of the plateau

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