Evolutionary Origins of Three Rare Alpine-Endemic Species of<i>Lomatium</i>(Apiaceae) in the Wallowa and Elkhorn Mountains of Northeastern Oregon

Ottenlips, Michael V.; Feist, Mary Ann; Mansfield, Donald H.; Plunkett, Gregory M.; Buerki, Sven; Smith, James F.

doi:10.1086/709373

Cited by 3 publications

(2 citation statements)

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“…The internal transcribed spacer of nuclear ribosomal DNA (ITS) has been useful in understanding the problematic tribal relationships in Apioideae (summarized by Downie et al, 2010). The majority of molecular phylogenetic studies of Apiaceae relied on plastid loci (e.g., Downie et al, 1996, 2000; Plunkett et al, 1996a; Calviño and Downie, 2007; Nicolas and Plunkett, 2009, 2012, 2014; Magee et al, 2010), ITS (e.g., Downie and Katz‐Downie, 1996; Spalik et al, 2004; Valiejo‐Roman et al, 2006; Spalik and Downie, 2007; Banasiak et al, 2013), or a combination of the two (e.g., Spalik et al, 2009, 2010, 2019; Feist et al, 2012; Banasiak et al, 2016; Calviño et al, 2016; Smith et al, 2018; Ottenlips et al, 2020; Mousavi et al, 2021). More recently, high‐throughput DNA sequencing has been used in Apiaceae to sequence the carrot genome (Iorizzo et al, 2016), whole chloroplasts (Downie and Jansen, 2015; Tan, 2020), and transcriptomes (Wen et al, 2020) and to explore population genetics (Ottenlips et al, 2021), but these were deep rather than broad studies that gathered large quantities of sequence data but within only few taxa.…”

Section: Figurementioning

confidence: 99%

A higher‐level nuclear phylogenomic study of the carrot family (Apiaceae)

Clarkson

Zuntini

Maurin

et al. 2021

American J of Botany

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The carrot family (Apiaceae) comprises 466 genera, which include many wellknown crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap.METHODS: Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. RESULTS:We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. CONCLUSIONS:We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.

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Section: Figurementioning

confidence: 99%

A higher‐level nuclear phylogenomic study of the carrot family (Apiaceae)

Clarkson

Zuntini

Maurin

et al. 2021

American J of Botany

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“…Across Apiaceae lineages, the rpl32-trnL , trnE-trnT , ndhF-rpl32 , rps16-trnQ and trnT-psbD intergenic spacers are among the most fast-evolving loci, while the trnD-trnY-trnE-trnT combined region presents the greatest number of potentially parsimony informative characters [ 25 ]. In which, rps16-trnQ , rpl32-trnL intergenic spacers and rps16 introns have previously been considered useful in resolving low-level relationships of Apiaceae [ 34 – 38 ]. In addition to these loci, we found that a total of nine regions held a relatively higher Pi values for Sium : trnQ , trnG-atpA , rps4-trnT , accD-psbI , rpl16 , ycf1-ndhF , ndhE-ndhG , ycf1a and ycf1b .…”

Section: Discussionmentioning

confidence: 99%

Plastome evolution in the genus Sium (Apiaceae, Oenantheae) inferred from phylogenomic and comparative analyses

Niu¹,

Wang²,

Yue³

et al. 2023

BMC Plant Biol

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Background Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced. Results The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029–155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61–67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported. Conclusions The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

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