Plastome sequencing of a 167-year-old herbarium specimen and classical morphology resolve the systematics of two potentially extinct grass species

Hardion, Laurent; Verlaque, Régine; Kaymak, Esra; Vila, Bruno; Haan-Archipoff, Gisèle; Martin, Marion Martinez; Tournay, Frédéric; Migliore, Jérémy

doi:10.1093/botlinnean/boaa065

Cited by 9 publications

(10 citation statements)

References 36 publications

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“…(four species) (Teisher et al, 2017; Hardion et al, 2017). Hardion et al (2021) found close relationships to Crinipes for two potentially extinct monotypic genera, Leptagrostis C.E.Hubb. and Piptophyllum C.E.Hubb., based on plastome and morphological analyses, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…(four species) (Teisher et al, 2017;Hardion et al, 2017). Hardion et al (2021) 2017), but that study noted a similarly long stem for this group and argued for a possible East Asian origin of its three or four genera. In our biogeographical analysis, the stem area is Afrotropical (50%), and the probable crown area is Cosmopolitan (68%).…”

Section: Arundinoideae (Jkt)mentioning

confidence: 91%

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Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

Gallaher

Peterson

Soreng

et al. 2022

J of Sytematics Evolution

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Grasses are widespread on every continent and are found in all terrestrial biomes. The dominance and spread of grasses and grassland ecosystems have led to significant changes in Earth′s climate, geochemistry, and biodiversity. The abundance of DNA sequence data, particularly chloroplast sequences, and advances in placing grass fossils within the family allows for a reappraisal of the family′s origins, timing, and geographic spread and the factors that have promoted diversification. We reconstructed a time‐calibrated grass phylogeny and inferred ancestral areas using chloroplast DNA sequences from nearly 90% of extant grass genera. With a few notable exceptions, the phylogeny is well resolved to the subtribal level. The family began to diversify in the Early–Late Cretaceous (crown age of 98.54 Ma) on West Gondwana before the complete split between Africa and South America. Vicariance from the splitting of Gondwana may be responsible for the initial divergence in the family. However, Africa clearly served as the center of origin for much of the early diversification of the family. With this phylogenetic, temporal, and spatial framework, we review the evolution and biogeography of the family with the aim to facilitate the testing of biogeographical hypotheses about its origins, evolutionary tempo, and diversification. The current classification of the family is discussed with an extensive review of the extant diversity and distribution of species, molecular and morphological evidence supporting the current classification scheme, and the evidence informing our understanding of the biogeographical history of the family.

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Section: Discussionmentioning

confidence: 99%

Section: Arundinoideae (Jkt)mentioning

confidence: 91%

Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

Gallaher

Peterson

Soreng

et al. 2022

J of Sytematics Evolution

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“…Plastome sequences can offer valuable insights into phylogenetic relationships in plants ( Dong et al, 2012 ; Curci et al, 2016 ). They have been increasingly adopted in phylogenetic studies of Poaceae species due to the rapid development of next-generation sequencing technology ( Saarela and Graham, 2010 ; Burke et al, 2016 ; Duvall et al, 2016 , 2020 ; Guo et al, 2019 ; Orton et al, 2019 ; Liu et al, 2020 ; Welker et al, 2020 ; Hardion et al, 2021 ). Plastomes have been used to study phylogenetic relationships within Eragrostis and Triodia of Chloridoideae ( Anderson et al, 2019 ; Somaratne et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

et al. 2021

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Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.

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“…Here, we also analyzed one of the oldest herbarium specimens of Areca collected in Maluku during the Dumont d'Urville's expedition in 1839, andanother collected in Philippines in 1916. This shows how herbarium collections can provide material for phylogenomics studies, and thus facilitate an exhaustive taxa sampling (e.g., Zedane et al 2016;Hardion et al, 2021), especially in remote islands of Wallacea (Strijk et al, 2020).…”

Section: New Genomic Datasets For Investigating Areca Phylogeography ...mentioning

confidence: 95%

Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity

Raimondeau

Manzi

Brucato

et al. 2021

Gene

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Plastome sequencing of a 167-year-old herbarium specimen and classical morphology resolve the systematics of two potentially extinct grass species

Cited by 9 publications

References 36 publications

Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

Grasses through space and time: An overview of the biogeographical and macroevolutionary history of Poaceae

Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity

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