Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae)

Liao, Min; Shepherd, Lara D.; Zhang, Jun‐Yi; Ye, Feng; Mattapha, Sawai; Zhang, Libing; Gao, Xin‐Fen; Xu, Bo

doi:10.1016/j.ympev.2023.107713

Cited by 7 publications

(12 citation statements)

References 63 publications

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“…Cypripedium (Fatihah et al, 2011;Liao et al, 2024;H Liu et al, 2021a), as suggested by SC Chen et al (2013). Moreover, the species composition of the two clades within sect.…”

Section: Historical Biogeographymentioning

confidence: 95%

“…After the publication of J Li et al (2011), several studies included molecular phylogenies with Cypripedium species, five of which investigated the relationships of the infrageneric taxa of Cypripedium in detail (Fatihah et al, 2011;Guo et al, 2012;Liao et al, 2024;H Liu et al, 2021a;Pérez-Escobar et al, 2023;Szlachetko et al, 2021;J-Y Zhang et al, 2022). These studies employed different phylogenetic reconstruction methodologies (i.e., Parsimony, Maximum Likelihood, and Bayesian Inference) with most using up to eight Sanger-sequenced nuclear and chloroplast DNA markers in different combinations, while the most recent study used plastome data and 41 nuclear loci derived from transcriptomes (Liao et al, 2024). The topologies and the monophyly of some subgeneric taxa were congruent among the produced phylogenies (e.g., sect.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Lagou,

Kadereit,

Morales-Briones

2024

Preprint

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Cypripediumis the most widespread and morphologically diverse genus of slipper orchids. Despite several published phylogenies based on Sanger sequencing data, the topology and monophyly of its infrageneric taxa remained uncertain. Here, we aimed to reconstruct a robust section-level phylogeny ofCypripediumand explore its evolutionary history using target capture data for the first time. We used the orchid-specific bait set "Orchidaceae963" to reconstruct the phylogeny ofCypripediumbased on 614 nuclear loci, covering 11 out of 13 sections. Subsequently, we investigated tree discordance, estimated divergence times and ancestral ranges, searched for anomaly zones, polytomies, and diversification rate shifts, and identified gene duplication and hybridization events. All sections were recovered as monophyletic, contrary to the subsections within sect.Cypripedium. Although the two subclades within this section did not correspond to its two subsections, they matched the geographic distribution of their species. Additionally, we discovered high levels of discordance in the short backbone branches of the genus and within sect.Cypripedium, which can be attributed to gene duplication and hybridization events, a potential whole genome duplication, and incomplete lineage sorting caused by rapid radiation. Our biogeographic analysis suggested a Neotropical origin of the genus during the Early Miocene (~20 Ma). The rapid radiations at the backbone likely occurred in Southeast Asia around the Middle Miocene Climatic Transition (~15-13 Ma), followed by several independent dispersals back to the New World. Moreover, the Pliocene-Quaternary glacial cycles may have contributed to further speciation and reticulate evolution, giving rise to a hybrid swarm within sect.Cypripedium. Our study provided novel insights into the evolutionary history ofCypripediumbased on high-throughput molecular data, shedding light on the dynamics of its distribution and diversity patterns from its origin to the present.

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“…Cypripedium (Fatihah et al, 2011;Liao et al, 2024;H Liu et al, 2021a), as suggested by SC Chen et al (2013). Moreover, the species composition of the two clades within sect.…”

Section: Historical Biogeographymentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Lagou,

Kadereit,

Morales-Briones

2024

Preprint

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“…Compared with genomic data, DNA barcodes, such as trnL-F , rbcL , matK , trnK-matK , psbA-trnH , ITS, and ETS, are more readily available and can still be used to solve many taxonomic problems. Among these, ITS and ETS are important nrDNA markers that are widely used in phylogenetic studies ( Kuzmanović et al., 2017 ; Vicent et al., 2017 ; Zhou and Zhang, 2017 ; Carrizo García et al., 2018 ; Asanuma et al., 2019 ; Pirani et al., 2020 ; Tan et al., 2020 ; Hashim et al., 2021 ; Liao et al., 2023 ). ITS and ETS are effective in discriminating closely related species because of their rapid evolutionary rates and higher interspecies variation ( Li et al., 2011 ).…”

Section: Introductionmentioning

confidence: 99%

Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae)

Xu,

Yang

et al. 2024

Front. Plant Sci.

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The HAP clade, mainly including Helichrysum Mill, Anaphalis DC., and Pseudognaphalium Kirp., is a major component of tribe Gnaphalieae (Asteraceae). In this clade, Anaphalis represents the largest genus of Asian Gnaphalieae. The intergeneric relationships among Anaphalis and its related genera and the infrageneric taxonomy of this genus are complex and remain controversial. However, there are few studies that have focused on these issues. Herein, based on the current most comprehensive sampling of the HAP clade, especially Anaphalis, we conducted phylogenetic analyses using chloroplast (cp) genome and nuclear ribosomal DNA (nrDNA) to evaluate the relationships within HAP clade, test the monophyly of Anaphalis, and examine the infrageneric taxonomy of this genus. Meanwhile, the morphological characters were verified to determine the circumscription and infrageneric taxonomy system of Anaphalis. Additionally, the biogeographical history, diversification processes, and evolution of crucial morphological characters were estimated and inferred. Our phylogenetic analyses suggested that Anaphalis is polyphyletic because it nested with Helichrysum and Pseudognaphalium. Two and four main clades of Anaphalis were identified in cp genome and nrDNA trees, respectively. Compared with nrDNA trees, the cp genome trees were more effective for phylogenetic resolution. After comprehensively analyzing morphological and phylogenetic evidence, it was concluded that the achene surface ornamentation and leaf base showed less homoplasy and supported the two Anaphalis lineages that were inferred from cp genome. Our biogeographical analyses based on cp genome indicated that HAP clade underwent rapid diversification from late Miocene to Pliocene. The two Anaphalis lineages appeared to have originated in Africa, then spread to Western and Southern Asia, and subsequently moved into Southwestern China forming a diversity center. The dispersal patterns of the two Anaphalis lineages were different. One dispersed around the world, except in Africa and South America. The other one dispersed to Eastern and Southeastern Asia from the ancestral origin region.

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“…A taxonomy-based phylogenetic tree serves as the foundation for biodiversity conservation and offers guidelines for mining and utilizing germplasm resources in horticulture and agriculture. Previous plant phylogenetic studies primarily relied on Sanger sequencing, utilizing specific region markers, such as ITS, ETS, rbcL, atpB, matK, and trnL-trnF (Shi et al 2013;Zhao et al 2016;Liao et al 2023;Phang et al 2023). However, these markers have inherent limitations, including short lengths (usually <1000 base pairs (bp)), high homogeneity (e.g., plastid loci), or gene paralogs (e.g., ITS).…”

Section: Introductionmentioning

confidence: 99%

Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

Wang,

Xiong,

Wang

et al. 2024

HORTIC. ADV.

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Sequencing strategies have continually advanced, with high-throughput sequencing (HTS) technologies emerging as pivotal tools in plant phylogenomics. As a standard form of target capture sequencing, hybridization target enrichment sequencing (Hyb-seq) is innovative and flexible, and then HTS strategy is widely adopted in phylogenomics. The universal Angiosperms353 probe sets (Angiosperms353) are instrumental in Hyb-seq and have been witnessed increased application in recent years. This review integrates numerous publications and empirical datasets to comprehensively assess the potential applications of Angiosperms353. Through evaluations using 18-taxa and 343-taxa genomic datasets, this review explores potential factors influencing Angiosperms353 gene capture. The RNA-seq strategy yielded the highest number of Angiosperms353 genes, followed by whole-genome sequencing and genome skimming. Increased sequencing depth enhanced gene capture yields, and no evident bias was observed across all tested angiosperm groups. In the genomics era with extensive HTS data, this review provides comprehensive guidelines for the practical application of Angiosperms353, promoting resource recycling and maximizing genomic data sharing and utilization.

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Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae)

Cited by 7 publications

References 63 publications

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Phylogenomic Analysis of Target Enrichment and Transcriptome Data Uncovers Rapid Radiation and Extensive Hybridization in Slipper Orchid GenusCypripediumL

Phylogeny, biogeography, and character evolution of Anaphalis (Gnaphalieae, Asteraceae)

Integrating genomic sequencing resources: an innovative perspective on recycling with universal Angiosperms353 probe sets

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