Generic boundaries in subtribe Saussureinae (Compositae-Cardueae): insights from Hyb-Seq data

Herrando-Moraira, Sonia

doi:10.17632/hrmyfhpb5c.2

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“…For Compositae, Mandel et al (2014) developed a probe set of exons of 1,061 orthologous loci, available as myBaits COS Compositae 1Kv1. This “conserved ortholog set” (COS) for Compositae has been further explored by Mandel et al (2017) ; Jones et al (2019) , and Siniscalchi et al (2021) , and successfully applied to provide a well-resolved family backbone ( Mandel et al, 2019 ), as well as resolving phylogenetic relationships in several difficult groups at different evolutionary levels ( Herrando-Moraira et al, 2018 , 2019 , 2020 ; Siniscalchi et al, 2019 ; Lichter-Marck et al, 2020 ; Thapa et al, 2020 ; Watson et al, 2020 ; Xu and Chen, 2021 ).…”

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New Insights Into the Relationships Within Subtribe Scorzonerinae (Cichorieae, Asteraceae) Using Hybrid Capture Phylogenomics (Hyb-Seq)

2022

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Subtribe Scorzonerinae (Cichorieae, Asteraceae) contains 12 main lineages and approximately 300 species. Relationships within the subtribe, either at inter- or intrageneric levels, were largely unresolved in phylogenetic studies to date, due to the lack of phylogenetic signal provided by traditional Sanger sequencing markers. In this study, we employed a phylogenomics approach (Hyb-Seq) that targets 1,061 nuclear-conserved ortholog loci designed for Asteraceae and obtained chloroplast coding regions as a by-product of off-target reads. Our objectives were to evaluate the potential of the Hyb-Seq approach in resolving the phylogenetic relationships across the subtribe at deep and shallow nodes, investigate the relationships of major lineages at inter- and intrageneric levels, and examine the impact of the different datasets and approaches on the robustness of phylogenetic inferences. We analyzed three nuclear datasets: exon only, excluding all potentially paralogous loci; exon only, including loci that were only potentially paralogous in 1–3 samples; exon plus intron regions (supercontigs); and the plastome CDS region. Phylogenetic relationships were reconstructed using both multispecies coalescent and concatenation (Maximum Likelihood and Bayesian analyses) approaches. Overall, our phylogenetic reconstructions recovered the same monophyletic major lineages found in previous studies and were successful in fully resolving the backbone phylogeny of the subtribe, while the internal resolution of the lineages was comparatively poor. The backbone topologies were largely congruent among all inferences, but some incongruent relationships were recovered between nuclear and plastome datasets, which are discussed and assumed to represent cases of cytonuclear discordance. Considering the newly resolved phylogenies, a new infrageneric classification of Scorzonera in its revised circumscription is proposed.

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