Table of Contents

12 May 2017, Volume 55 Issue 3

Cover illustration: Selected species of the alpine ginger Roscoea in biodiversity hotspots of Asian mountains. Left: R. humeana, from the Hengduan Mountains. Top right: R. cautleoides, from the Hengduan Mountains. Lower right: R. purpurea, from the Himalayas. Photographs by Qing-Jun Li. See Zhao et al., pp. 215–224 in this issue.

  

Research Articles
• Phylogenomic analysis of Picramnia, Alvaradoa, and Leitneria supports the independent Picramniales

  Maria D. Logacheva, Alexey B. Shipunov

  J Syst Evol. 2017, 55(3): 171-176.
  https://doi.org/10.1111/jse.12246

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  Picramniales is a recently established monotypic order that has not yet acquired a stable position on the phylogenetic tree of flowering plants. While Picramnia andAlvaradoa were transferred from Simaroubaceae (Sapindales) into Picramniaceae (Picramniales), Leitneria was transferred from the “hamamelids” into Simaroubaceae. Using next-generation sequencing, we obtained plastome sequences of Picramnia and Alvaradoa (partial) and Leitneria (complete). Protein coding and rRNA genes common for flowering plant plastomes were used for phylogenetic analysis. The resulting phylogenetic trees demonstrate a robust placement of Picramniales among the rosids as a sister group to Sapindales + Brassicales + Malvales. Leitneria is placed as a sister to Citrus. We also found that the plastome ofLeitneria carries ycf68 gene that is absent from most other rosids and infA pseudogene.
• Phylogenetic study of the tribe Potentilleae (Rosaceae), with further insight into the disintegration of Sibbaldia

  Tao Feng, Michael J. Moore, Min-Hui Yan, Yan-Xia Sun, Hua-Jie Zhang, Ai-Ping Meng, Xiao-Dong Li, Shu-Guang Jian, Jian-Qiang Li, Heng-Chang Wang

  J Syst Evol. 2017, 55(3): 177-191.
  https://doi.org/10.1111/jse.12243

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  Potentilleae, one of 10 tribes of the Rosaceae, are mainly distributed in alpine regions of the Northern Hemisphere. The taxonomy of Potentilleae has been challenging due to extensive hybridization, polyploidization, and/or apomixis characterizing several genera of Potentilleae, such as Alchemilla, Argentina, andPotentilla. To help clarify relationships within Potentilleae, a phylogenetic analysis of the tribe with an emphasis on the polyphyletic genus Sibbaldia was carried out using nuclear ribosomal internal and external transcribed spacer regions and the plastid trnL-F and trnS-G spacer regions. In agreement with previous phylogenetic analyses, three major clades were identified in the present study: the subtribe Fragariinae, the genera Argentina, and Potentilla. The 15 species of Sibbaldia were recovered in five distinct clades: three in subtribe Fragariinae, one in Argentina, and the last in Potentilla. The recently established genus Chamaecallis, comprising a single species formerly treated in Sibbaldia that has intermediate floral character states with respect to Fragariinae and Potentilla, was recovered as sister toDrymocallis. Morphological character state reconstruction indicated that a reduction in the number of stamens (≤10) is a derived character state that has arisen multiple times in Potentilleae. Molecular dating analyses agreed with previously published estimates and suggested that crown group Potentilleae arose in the Middle to Late Eocene, with most generic-level divergences occurring in the Oligocene and Miocene.
• Pollen limitation, plasticity in floral traits, and mixed mating system in an alpine plant Pedicularis siphonantha (Orobanchaceae) from different altitudes

  Wen-Kui Dai, Edwin Luguba Kadiori, Qing-Feng Wang, Chun-Feng Yang

  J Syst Evol. 2017, 55(3): 192-199.
  https://doi.org/10.1111/jse.12240

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  Plant mating systems rapidly respond to pollen limitation in changing environments. However, whether and how floral traits are involved in a mating system shift requires further investigation. A widely distributed and bumblebee-pollinated lousewort, Pedicularis siphonantha D. Don was studied. We investigated pollination systems, reproductive success, and floral traits in four large populations growing from 3200 m to 4300 m. Pollinator activity in low altitude populations was lower and these populations had a decreased fruit set and seed number per capsule compared to populations at high altitudes. Supplemental hand pollination with outcross pollen significantly increased seed production per capsule for plants from high altitudes but not for those from lower altitudes. We also found that bumblebees visited more flowers within an inflorescence in a single foraging bout in high altitudes compared with low altitudes, which caused a high possibility of geitonogamous mating. These differences may be pollination-dependent rather than inheritance-based because hand pollination on bagged flowers did not cause a difference in seed production across populations. Compared to plants from low altitudes, high-altitude plants had increased flower longevity, larger floral displays, higher pollen production per flower, and shorter corolla tubes, which were found to be well in accordance with changes in both pollination environment and mating system. Plasticity in floral traits might help plants to adjust their resource allocation strategies in response to their habitat, which might be linked with pollination environment. The variability among these populations might be beneficial for this widely distributed species to cope with environmental changes.
• Identification and characterization of Rubisco activase genes in Oryza punctata

  Si Xu, Zong-Yan Qin, Pi-Chang Gong, Qian-Li Dong, Ying Bao

  J Syst Evol. 2017, 55(3): 200-207.
  https://doi.org/10.1111/jse.12242

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  Rubisco activase (Rca), a specific chaperone, catalyzes the in vivo activation of Rubisco, and thus plays a major role in plant photosynthesis. Although the genes encoding Rubisco activase have been studied in many model or economic plants, few studies have analyzed their homologs in plants of closely related crop species. In this study, an Rca gene was identified and characterized in a wild relative of rice, Oryza punctata Kotschy ex Steud. The gene was 2747 bp long and possessed six exons and five introns with 47% GC content. Furthermore, cDNA sequencing produced two transcripts, RcaL and RcaS, that differed in the sequence by an inclusion of 99 bp at the carboxy terminus of RcaL. Sequence comparison between the two transcripts and the genomic DNA showed that there was a 20-bp alternative splicing event that occurred at the fifth intron of the gene leading to the synthesis of a short polypeptide. The leaf transcriptome analysis showed that RcaS had a higher expression level than that of RcaL in a normal growth environment. In addition, the yeast two-hybrid assays showed the small isoform of Rubisco activase in close contact with the large subunit of the Rubisco in this species, supporting the side-on binding model of interaction between two proteins. This study broadens our understanding of the molecular characteristics of some essential genes in photosynthesis.
• Interspecific and intraspecific variation in corolla tube length in Pedicularis species achieved by both cell anisotropy and division

  Xiang-Ping Wang, Shuang-Quan Huang

  J Syst Evol. 2017, 55(3): 208-214.
  https://doi.org/10.1111/jse.12239

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  The association between plants with long corolla tubes and pollinators with long tongues has evolved repeatedly in diverse pollination systems. However, the morphogenesis of long corolla tubes involved in diverse plant groups remains largely unexplored, limiting our understanding of the evolution and maintenance of long corolla tubes. Corolla tubes of Himalayan Pedicularis species exhibit striking length diversity, ranging from less than 10 mm to more than 120 mm. We investigated the role of cell division and cell expansion in determining the corolla tube morphology in eight Pedicularis species and in an experimental population ofP. siphonantha Don in which corolla tubes were elongated under shading and watering treatments. Among species, the corolla tube length was positively correlated with both cell number and cell length but not cell width. Our analyses of intraspecific variation in corolla tube length indicated that it was positively correlated with cell length in all eight species but with cell number in only four of the species, indicating that corolla tube development in Pedicularis generally involves anisotropic cell expansion. The elongation of corolla tubes in P. siphonantha under experimental conditions was caused by the anisotropic elongation of cells; cell number of tube-elongated flowers was not significantly increased. Our results showed that intraspecific variation in corolla tube length in Pedicularis species was largely attributable to changes in cell anisotropy, but the evolutionary innovation underlying the rapid radiation of Pedicularis corolla tubes was attributable to both cell division and cell expansion.
• A preliminary species-level phylogeny of the alpine ginger Roscoea: Implications for speciation

  Jian-Li Zhao, Jinshun Zhong, Yong-Li Fan, Yong-Mei Xia, Qing-Jun Li

  J Syst Evol. 2017, 55(3): 215-224.
  https://doi.org/10.1111/jse.12247

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  Speciation, the evolutionary process forming new species, is a key mode generating biodiversity on the Earth. In this study, we produced a species-level phylogeny ofRoscoea using one nuclear ribosomal and two chloroplast DNA fragments based on Bayesian inference and maximum likelihood. We then explored the possible speciation processes using the species-level phylogeny and the heterozygous sites in the nuclear DNA. The incongruence between nuclear and chloroplast phylogenies, and several heterozygous sites in the nuclear DNA, suggested that R. auriculata might have a hybrid origin with R. purpurea and R. alpina being two possible parental progenitors; however, one alternative possibility through incomplete lineage sorting cannot be ruled out. In addition, R. kunmingensis likely originated from R. tibetica Batalin through the process of “budding speciation”. These results provided a valuable framework to draw testable hypotheses for future in-depth comparative studies to further our understanding of the underpinning speciation and adaptation mechanisms that contribute to ultrahigh biodiversity in the Himalayas and the Hengduan Mountains.
Letter to the Editor
• Patterns of character evolution in phylogenies

  Leandro C. S. Assis

  J Syst Evol. 2017, 55(3): 225-230.
  https://doi.org/10.1111/jse.12241

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• What is the main mechanism of the origin of phosphorylation sites? Still an open question

  Yu-Yu Wang, Zhi-Xi Su, Xun Gu

  J Syst Evol. 2017, 55(3): 231-234.
  https://doi.org/10.1111/jse.12244

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  In spite of high-throughput phosphoproteomics for protein kinase–phosphorylation site interactions, the evolutionary mechanism for the origin of protein phosphorylation remains a mystery. Pearlman and his colleagues proposed that some phosphorylation sites may have evolved from acidic amino acids, because those negatively charged amino acids (Asp/Glu) can mimic the phosphorylated state of a protein. Moreover, phosphorylation has the potential to conditionally restore the salt bridge that was originally constitutively formed by Asp/Glu. Although this insightful mimic hypothesis has been supported by several examples, we point out that the replacements from Asp/Glu to serine/threonine require at least two non-synonymous nucleotide substitutions, casting some doubt about whether it is the major mechanism for the origin of phosphorylation. As the intermediate amino acid types, such as Ala/Asn/Gly, are not observed frequently, we have to invoke the hypothesis of double-mutation driven by natural selection; that is, the very strong positive selection for the second mutation has overcome the deleterious effect caused by the first mutation. Furthermore, we propose an alternative evolutionary scenario that phosphorylation was primarily evolved to introduce negative charges to the protein surface, thus reducing spurious protein–protein interactions in vivo by electrostatic repulsion. The specific protein–protein interaction could be regulated when corresponding signals change surface charges by means of dephosphorylation and other recognition mechanisms. Probably this is a more universal mechanism that provided the first step toward the emergence of more accurate cell signaling and regulation. Further study is needed to distinguish between these hypotheses.