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- Integrated phylogenomic analyses unveil reticulate evolution in Parthenocissus (Vitaceae), highlighting speciation dynamics in the Himalayan–Hengduan MountainsPublication . Yu, Jinren; Niu, Yanting; You, Yichen; J. Cox, Cymon; Barrett, Russell L.; Trias‐Blasi, Anna; Guo, Jing; Wen, Jun; Lu, Limin; Chen, ZhiduanHybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus, a genus with its trifoliolate lineage in the Himalayan-Hengduan Mountains (HHM) region showing perplexing phylogenetic relationships, provides an opportunity for investigating speciation dynamics based on integrated evidence.We investigated phylogenetic discordance and reticulate evolution in Parthenocissus based on rigorous analyses of plastome and transcriptome data. We focused on reticulations in the trifoliolate lineage in the HHM region using a population-level genome resequencing dataset, incorporating evidence from morphology, distribution, and elevation.Comprehensive analyses confirmed multiple introgressions within Parthenocissus in a robust temporal-spatial framework. Around the HHM region, at least three hybridization hot spots were identified, one of which showed evidence of ongoing speciation reversal.We present a solid case study using an integrative methodological approach to investigate reticulate evolutionary history and its underlying mechanisms in plants. It demonstrates an example of speciation reversal through frequent hybridizations in the HHM region, which provides new perspectives on speciation dynamics in mountainous areas with strong topographic and environmental heterogeneity.
- Disentangling knots of rapid evolution: origin and diversification of the moss order HypnalesPublication . Huttunen, S.; Bell, N.; Bobrova, V. K.; Buchbender, V.; Buck, W. R.; Cox, C. J.; Goffinet, B.; Hedenäs, Lars; Ho, B. -C.; Ignatov, M. S.; Krug, M.; Kuznetsova, O.; Milyutina, I. A.; Newton, Alice; Olsson, S.; Pokorny, L.; Shaw, J. A.; Stech, M.; Troitsky, A.; Vanderpoorten, A.; Quandt, D.The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear ITS1–5.8S–ITS2, plastid trnL–F and rps4, and mitochondrial nad5, for 122 hypnalean species and 34 species from closely related groups. Tree topologies from both Bayesian and parsimony analyses resolve the order as monophyletic. Although inferences were made from fastevolving genes, and despite strong phylogenetic signal in the nuclear ITS1–5.8S–ITS2 data, monophyly, as well as backbone nodes within the Hypnales, remains rather poorly supported except under Bayesian inferences. Ancestral distribution based on Bayesian dispersal-vicariance analysis supports a Gondwanan origin of the Hypnales and subsequent geographical radiation in the area of the former Laurasian supercontinent. Reconstruction of historical biogeography is congruent with mainly tropical and Gondwanan distributions in the sister groups Hypnodendrales, Ptychomniales, and Hookeriales, and with the dating for the oldest pleurocarp and hypnalean fossils. We contrast groupings in the phylogenetic tree with recent classifications and other phylogenetic inferences based on molecular data, and summarise current knowledge on the evolutionary history of, and relationships among, the Hypnales.
- Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera Ceterach and Phyllitis in Asplenium (Aspleniaceae)Publication . Pinter, I.; Bakker, F.; Barrett, J.; Cox, C. J.; Gibby, M.; Henderson, S.; Morgan-Richards, M.; Rumsey, F.; Russell, S. J.; Trewick, S.; Schneider, H.; Vogel, J. C.Phylogenetic studies using DNA sequences of two chloroplast regions, rbcL and trnL-F, demonstrate that the proposed genus Ceterach is a small clade within the large genus Asplenium, and sister to the Phyllitis clade. The Ceterach clade is characterised by irregular anastomosing veins and often densely scaled leaf blades. Its taxonomic status as a group nested within Asplenium is confirmed, and it is accepted here as a subgenus with seven species. The Ceterach clade comprises four lineages that correspond to disjunct polyploid complexes: the A. aureum clade forming a polyploid complex (4´, 6´, 8´) in Macaronesia, the A. ceterach clade forming a polyploid complex (2´, 4´, 6´) in the Mediterranean Basin, the A. paucivenosum clade (4´, 6´) in central Asia, and the A. dalhousiae clade (2´) with a disjunct distribution in the Himalaya,Yemen and Eritrea, and southwestern North America. Asplenium paucivenosum is sister to all other members of the Ceterach clade, whereas A. dalhousiae is sister to the A. aureum clade that includes tetraploid A. aureum, hexaploid A. lolegnamense, and octoploid A. parvifolium. Asplenium ceterach and its variations – including the hexaploid A. ceterach subsp. mediterraneum subsp. nov. first described below – form a monophyletic unit, sister to a clade consisting of A. aureum and A. dalhousiae. Asplenium cordatum from Africa and A. haugthonii from the isolated atlantic island of St. Helena are not members of the Ceterach clade, which suggests that leaf blades with dense indumenta have evolved at least twice within asplenioid ferns. The allotetraploid species A. hybridum has the chloroplast DNA from A. ceterach, and therefore the latter species is the maternal ancestor of the former. The other parent of this hybrid species is A. sagittatum that is nested within the sister clade of Ceterach, the Phyllitis clade comprising A. sagittatum and A. scolopendrium. The findings suggest that the current distribution of Ceterach is either the result of long-distance dispersal or represents fragmented relicts of a previously more widely distributed species.