Phylogeny of Anthospermeae of the Coffee Family Inferred Using Clock and Nonclock Models

Thureborn, Olle; Razafimandimbison, Sylvain G.; Wikström, Niklas; Khodabandeh, Anbar; Rydin, Catarina

doi:10.1086/703353

Cited by 9 publications

(34 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the Spermacoceae alliance our results support the position of the Danaideae-Knoxieae-Spermacoceae clade as sister taxon to the remaining members of the alliance. Several previous studies have shown results congruent with this, including a study based on mitochondrial data Rydin et al (2017) , the plastome-based phylogenomic analyses in Wikström et al (2020) , and analyses of a few selected plastid markers alone or in combination with nuclear ribosomal ITS (nrITS, e.g., Rydin et al, 2009a ; Krüger, 2014 ; Wikström et al, 2015 ; Thureborn et al, 2019 ). Other analyses based on a few selected plastid markers, alone or in combination with nuclear ribosomal ITS, have not produced results congruent with ours, but have often found Danaideae as sole sister to the remaining members of the alliance (e.g., Bremer and Manen, 2000 ; Bremer and Eriksson, 2009 ; Rydin et al, 2009b ; Yang et al, 2016 ).…”

Section: Discussionsupporting

confidence: 55%

“…This result is congruent with Ginter et al (2015) who, based on combined plastid and nuclear (nrETS and nrITS) data, found that those two tribes formed a clade that also included yet another recently described monogeneric tribe, the Foonchewieae from China ( Wen and Wang, 2012 ). Thureborn et al (2019) included representation from all these three tribes and found, based on plastid data, that they form a clade together with Argostemmateae (appendix B in Thureborn et al, 2019 ). Recent studies addressing major relationships in Rubiaceae have otherwise typically only included representation from one of these three tribes [for example, Antonelli et al (2021) included Cyanoneuroneae and Rydin et al (2017) and Wikström et al (2020) included Dunnieae], but the close relationship between Foonchewieae and Dunnieae has been confirmed in several studies based on analyses of plastid data ( Wikström et al, 2015 ; Yang et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

“…We included representatives from 11 of the 12 genera of the Anthospermeae; only Nenax was not sampled since a recent study showed that species of Nenax are intermixed with those of Anthospermum in an Anthospermum-Nenax clade ( Thureborn et al, 2019 ). Our results support the position of the South African genus Carpacoce as sister to a clade that unites an African clade and a Pacific clade, which is entirely congruent with results in Thureborn et al (2019) .…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

Self Cite

View full text Add to dashboard Cite

Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.

show abstract

Section: Discussionsupporting

confidence: 55%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…The hybridization experiments between H. yingeri and other Korean Hosta species resulted in less than 60% of pollen viability ( Zonneveld and Van Iren, 2001 ), supporting its reproductive isolation along with its unique floral morphological features. Reproductive isolation is commonly found in island species (reviewed in Crawford and Archibald, 2017 ), which often exhibit incongruence between nuclear and plastome markers ( French et al, 2016 ; Hughes et al, 2018 ; Waselkov et al, 2018 ; Thureborn et al, 2019 ). In addition, its genome size is much more similar to that of H. capitata and H. clausa , when compared to H .…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

et al. 2021

View full text Add to dashboard Cite

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

show abstract

“…Extraction of total genomic DNA was performed according to the cetyltrimethylammonium bromide (CTAB) method [ 87 , 88 ], and purified using a QIAquick PCR Purification Kit (Qiagen, Sweden). PCR reactions were conducted using standard procedures outlined elsewhere [e.g., 89 ], and optimized for the here utilized primers and extractions. Sequencing was performed by the Macrogen Sequencing Service (Amsterdam).…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of Merlin’s grass (Isoetaceae): revealing an “Amborella syndrome” and the importance of geographic distribution for understanding current and historical diversity

et al. 2022

Self Cite

View full text Add to dashboard Cite

Background Merlin’s grass (Isoetes, Isoetaceae, Lycopsida), is the extant remnant of the isoetalean wood-producing lycopsids that originated during the Paleozoic, possibly in aquatic or boggy habitats. Modern day species are aquatic, semi-aquatic or terrestrial and occur almost worldwide. They display little morphological variation; the lobed corm has helically arranged leaves with internal air channels and basal sporangia. Genetic variation has also proven limited, which has hampered phylogenetic inference. We investigate evolutionary relationships in Isoetes, using molecular data and an extended sample of species compared to previous work, adding species that have never before been included in a phylogenetic study. Results Our results reveal an unexpected discovery of an “Amborella syndrome” in Isoetaceae: a single poorly known species is sister to the remaining family. The species, Isoetes wormaldii, is a rare endemic to the Eastern Cape of South Africa. Its leaves are flattened with a rounded point, which sharply contrasts with the awl-shaped leaves of most other species of Isoetes. The remaining species of Isoetes are resolved in five major clades, also indicated in previous work. While the phylogeny shows geographic structure, the patterns are complex. For example, tropical-southern African species occur in at least five clades, and Indian, Australian and Mediterranean species in at least three clades each. Conclusion The evolutionary and biogeographical history of Isoetes is not easily explained, and may conceivably include ample extinction and a mixture of ancient and more recent processes. Previously shown difficulties with node age estimation increase the problem. The here demonstrated sister-relationship between the phylogenetically, morphologically and genetically distinct Isoetes wormaldii and the remaining family appears to bridge the morphological gap between Isoetes and its extinct relatives, although further studies are needed. Moreover, it shortens the branch length to its living sister genus Selaginella, and may enhance node age estimation in future studies. Isoetes wormaldii is critically endangered, known only from one (to a few) minor populations. Immediate actions need to be taken if we want to prevent this unique species from going extinct.

show abstract

Phylogeny of Anthospermeae of the Coffee Family Inferred Using Clock and Nonclock Models

Cited by 9 publications

References 82 publications

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

Phylogeny of Merlin’s grass (Isoetaceae): revealing an “Amborella syndrome” and the importance of geographic distribution for understanding current and historical diversity

Contact Info

Product

Resources

About