Recent advances on phylogenomics of gymnosperms and a new classification

Yang, Yong; Ferguson, David K.; Liu, Bing; Mao, Kangshan; Gao, Lian‐Ming; Zhang, Shouzhou; Wan, Tao; Rushforth, Keith; Zhang, Zhixiang

doi:10.1016/j.pld.2022.05.003

Cited by 35 publications

(8 citation statements)

References 57 publications

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“…High-level classification for fungi, gymnosperms, angiosperms and pteridophytes follows Tedersoo et al 2018, Yang et al 2022, APG IV (APG IV 2016, and PPG I (PPG I 2016), respectively. For algae, we used specific classification systems for each division (Cavalier-Smith and Chao 1996, Cavalier-Smith 1998, Lewis and McCourt 2004, Cavalier-Smith 2016, Kamiya et al 2017, Garcia-Pichel et al 2019 following Algaebase (Guiry and Guiry 2015).…”

Section: Methodsmentioning

confidence: 99%

12,500+ and counting: biodiversity of the Brazilian Pampa

Andrade¹,

Dröse²,

Aguiar³

et al. 2023

Frontiers of Biogeography

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Knowledge on biodiversity is fundamental for conservation strategies. The Brazilian Pampa region, located in subtropical southern Brazil, is neglected in terms of conservation, and knowledge of its biodiversity is fragmented. We aim to answer the question: how many, and which, species occur in the Brazilian Pampa? In a collaborative effort, we built species lists for plants, animals, bacteria, and fungi that occur in the Brazilian Pampa. We included information on distribution patterns, main habitat types, and conservation status. Our study resulted in referenced lists totaling 12,503 species (12,854 taxa, when considering infraspecific taxonomic categories [or units]). Vascular plants amount to 3,642 species (including 165 Pteridophytes), while algae have 2,046 species (2,378 taxa) and bryophytes 316 species (318 taxa). Fungi (incl. lichenized fungi) contains 1,141 species (1,144 taxa). Animals total 5,358 species (5,372 taxa). Among the latter, vertebrates comprise 1,136 species, while invertebrates are represented by 4,222 species. Our data indicate that, according to current knowledge, the Pampa holds approximately 9% of the Brazilian biodiversity in an area of little more than 2% of Brazil's total land. The proportion of species restricted to the Brazilian Pampa is low (with few groups as exceptions), as it is part of a larger grassland ecoregion and in a transitional climatic setting. Our study yielded considerably higher species numbers than previously known for many species groups; for some, it provides the first published compilation. Further efforts are needed to increase knowledge in the Pampa and other regions of Brazil. Considering the strategic importance of biodiversity and its conservation, appropriate government policies are needed to fund studies on biodiversity, create accessible and constantly updated biodiversity databases, and consider biodiversity in school curricula and other outreach activities.

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Section: Methodsmentioning

confidence: 99%

12,500+ and counting: biodiversity of the Brazilian Pampa

Andrade¹,

Dröse²,

Aguiar³

et al. 2023

Frontiers of Biogeography

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“…Some authors included the genus in the Taxaceae (e.g., Christenhusz et al, 2011); some treated it as a separate family, viz. Cephalotaxaceae, either in the suborder Taxineae (Keng, 1975), in the order Taxales (Pulle, 1937), or in the order Coniferae/Coniferales (Pilger, 1926; Takhtajan, 1953), or in the order Cupressales (Yang et al, 2022), or as a separate order Cephalotaxales (e.g., Cheng & Fu, 1978). Multiple disciplinary studies were conducted in the last century, but no comprehensive study of the genus has been undertaken.…”

Section: Introductionmentioning

confidence: 99%

An integrative view on the systematic position of the cupressophyte Cephalotaxus

Yang,

Ferguson

et al. 2023

Ecology and Evolution

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We made an in‐depth review of historical studies of the cupressophyte conifer genus Cephalotaxus Siebold & Zucc. with an emphasis on its systematic position. We suggest that the systematic position of the genus is better understood using an integrative approach, so the evolution of phenetic characters is discussed within the context of recent phylogenomics. We propose that the genus should be classified as a separate family Cephalotaxaceae belonging to the clade consisting of Cupressaceae, Cephalotaxaceae, and Taxaceae; the family Cephalotaxaceae is sister to the Taxaceae but not nested within the Taxaceae and is characterized by a unique set of characters including morphology, anatomy, embryology, and chemistry. The family Cephalotaxaceae shows transitional characters between the Cupressaceae and the Taxaceae; the family possesses female cones with a primary cone axis bearing 5–8 pairs of decussate bracts, which is similar to the typical female cones of the Cupressaceae, on the one hand, and may have given rise to the reduced female cone of the Taxaceae with one terminal ovule partially or completely enclosed in a fleshy aril. In parallel, the compound male cone of the Cephalotaxaceae evolved into the seemingly “simple” male cones of the Taxaceae by means of reduction, elimination, and fusion.

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“…C. lanceolata belongs to Cupressaceae, with a common name as Chinese fir, and is a fast-growing coniferous tree with great forestation value [ 24 ]. It is naturally widespread from the central to the southeastern zones of China, and has been indicated for cultivation in many countries around the world, such as Vietnam, Brazil, New Zealand, Australia and Canada [ 25 , 26 , 27 ].…”

Section: Introductionmentioning

confidence: 99%

Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View

Huang

Zeng

Deng

et al. 2022

Genes

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Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is a fast-growing conifer with great forestation value and prefers outcrossing with high inbreeding depression effect. Previously, we captured a special Chinese fir parent clone named as ‘cx569’ that lacks early inbreeding depression. In view of the fact that very little has been published about the rare self-fertilizing event in Chinese fir from a genetic view, herein, we conduct an SSR-based study on the variation of open- and self-pollinated offspring of this parent to gain a view of the rare self-fertilizing event. The results indicated that genetic diversity of self-pollinated offspring was significantly reduced by half (Ho: 0.302, vs. 0.595, p = 0.001; He: 0.274 vs. 0.512, p = 0.002) when compared to an open-pollinated set. Self-pollinated offspring also had significantly positive FIS values (FIS = 0.057, p = 0.034) with a much higher proportion of common allele (20.59% vs. 0), reflecting their heterozygote deficiency. Clustering analysis further indicated a separation of the self- and opened- pollinated groups, implying a natural preference of outcrossing for cx569. However, the cx569 still had 6% acceptance for selfing. When accepted 100% for its own pollen, the cx569 led to a genetically unique selfing group. Additionally, this selfing group seemed to be consistently homozygous at seven particular loci. These findings gave us more genetic clues to gain insight into the rare self-fertilizing event in conifer (Chinese fir).

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Recent advances on phylogenomics of gymnosperms and a new classification

Cited by 35 publications

References 57 publications

12,500+ and counting: biodiversity of the Brazilian Pampa

12,500+ and counting: biodiversity of the Brazilian Pampa

An integrative view on the systematic position of the cupressophyte Cephalotaxus

Inbreeding in Chinese Fir: Insight into the Rare Self-Fertilizing Event from a Genetic View

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