Table of Contents

08 September 2016, Volume 54 Issue 5

Cover illustration: Simplified phylogenies of selected groups of eastern Asian-western North American disjunct lineages. Top left: Lysichiton (Araceae). Top right: Paeonia (Paeoniaceae). Lower left: Picea (Pinaceae). Lower right: Cryptogramma (Pteridaceae), illustrating the different phylogenetic patterns in vascular plants. The background shows the polar view of the earth during early Miocene, emphasizing the Beringian biogeographic connection between eastern Asia and western North America. Abbreviations: WNa, Western North America; EAs, Eastern Asia; ENa, Eastern North America; QTP, Qinghai-Tibetan Plateau; SAm, South America. See Wen et al., pp 469–490 in this issue for further explanation. The photograph of Lysichiton americanus was by Gerald and Buff Corsi ©California Academy of Sciences used here with permission. Other photos (Picea glauca, Cryptogramma sitchensis and Paeonia suffruticosa hybrid) were by Stefanie Ickert-Bond. [Detail] ...

  

Review
• Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene

  Jun Wen, Ze-Long Nie, Stefanie M. Ickert-Bond

  J Syst Evol. 2016, 54(5): 469-490.
  https://doi.org/10.1111/jse.12222

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  This review shows a close biogeographic connection between eastern Asia and western North America from the late Cretaceous to the late Neogene in major lineages of vascular plants (flowering plants, gymnosperms, ferns and lycophytes). Of the eastern Asian–North American disjuncts, conifers exhibit a high proportion of disjuncts between eastern Asia and western North America. Several lineages of ferns also show a recent disjunct pattern in the two areas. In flowering plants, the pattern is commonly shown in temperate elements between northeastern Asia and northwestern North America, as well as elements of the relict boreotropical and Neogene mesophytic and coniferous floras. The many cases of intercontinental biogeographic disjunctions between eastern Asia and western North America in plants supported by recent phylogenetic analyses highlight the importance of the Bering land bridge and/or the plant migrations across the Beringian region from the late Cretaceous to the late Neogene, especially during the Miocene. The Beringian region has permitted the filtering and migration of certain plant taxa since the Pliocene after the opening of the Bering Strait, as many conspecific taxa or closely related species occur on both sides of Beringia.
Research Articles
• A genetic delineation of Patchouli (Pogostemon cablin) revealed by specific-locus amplified fragment sequencing

  Hui-Run Huang, Wei Wu, Ji-Xiu Zhang, Ling-Jian Wang, Yong-Ming Yuan, Xue-Jun Ge

  J Syst Evol. 2016, 54(5): 491-501.
  https://doi.org/10.1111/jse.12195

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  Patchouli plant (Pogostemon cablin (Blanco) Benth.) is of important economic value, and it has been grown for medicinal use for more than 1000 years in China and Southeast Asia. There are limited data to underpin the genetic and genomic resource management for Patchouli. Herein, we used specific-locus amplified fragment sequencing to generate a genetic delineation of P. cablin collected from Vietnam, South China, and Indonesia (Sumatra). In total, 15 457 835 reads, 61 334 specific-locus amplified fragments, and 511 reliable single nucleotide polymorphisms were obtained. On the basis of model-based grouping and neighbor-joining trees, we divided the studied accessions into six distinct groups: one Vietnamese group, two Chinese groups, and three Indonesian groups. We also measured the contents of patchouli alcohol and pogostone; all accessions belonged to patchoulol-type except for three accessions from the species' northernmost distribution in China, which have a high content of pogostone. The results from both genetic structure and chemotypes were highly consistent with the possible migration history of Patchouli. Accordingly, ex situ conservation should be immediately established for Patchouli, particularly for the pogostone-type and the germplasm in Vietnam.
• Evolution of the PEBP gene family and selective signature on FT-like clade

  Xiao-Ming Zheng, Fu-Qing Wu, Xin Zhang, Qi-Bing Lin, Jie Wang, Xiu-Ping Guo, Cai-Lin Lei, Zhi-Jun Cheng, Cheng Zou, Jian-Min Wan

  J Syst Evol. 2016, 54(5): 502-510.
  https://doi.org/10.1111/jse.12199

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  The PEBP family of proteins, which encode a phosphatidyl ethanolamine-binding protein (PEBP) domain, serve as a hub in the network of integrating environmental and developmental signals to regulate flowering in all angiosperms. To understand how PEBP duplication genes arose and evolved during plant evolution, we identified 259 genes involved in the PEBP domain from 25 species, including angiosperms, gymnosperms, and embryophytes. We found that plant PEBP genes could be divided into three monophyletic groups, including FT-like, TFL-like and MFT-like subgroups. Based on the phylogeny, FT-like and TFL-like subgroups split before the angiosperm divergence. The likelihood ratio test indicates that the FT-like clade is significantly different in K_a/K_s with TFL-like and MFT-like clades. We found this shift in mutation might be attributed to the positive selection imposed on the fourth exon of recent FT duplications. Divergent expression patterns of FTparalogs indicated that they had undergone subfunctionalization after duplication. In addition, some of the FT-like genes have been targets of selection during domestication in rice and maize, for which the flowering time is an important agronomic trait. These results imply potential recent positive selection on FT-like genes with potential to increase the prevalence of novel functional alleles leading to extensive plant flowering time diversity and adaptation to environmental changes.
• Divergent homoeolog evolution of the anthocyanin regulatory gene R in Oryza allopolyploids

  Ying Bao, Xiao-Lin Zhu, Xiang Jing, Mei Liu

  J Syst Evol. 2016, 54(5): 511-518.
  https://doi.org/10.1111/jse.12200

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  Polyploidization is an important evolutionary force in plant speciation and diversification. Retention and elimination of homoeologs derived by polyploidization are prevalent, whereas the evolutionary details of some duplicated genes in closely related natural polyploids are largely unknown. In the present study, we used an important regulatory gene (R) that encodes a bHLH protein in the anthocyanin metabolism pathway to demonstrate divergent evolutionary fates of homoeologs among four related Oryza allotetraploids. The BBCC genome species O. punctata Kotschy ex Steud. maintained both of its homoeologs, whereas three CCDD genome species (O. alta Swallen, O. grandiglumis (Döll) Prod., and O. latifolia Desv.) lost their C subgenome homoeologous copies. In addition, the evolutionary rates of the homoeologs in the polyploids were equivalent to their corresponding homologs in diploids. We also found a slightly higher level of nucleotide diversity inR for the C subgenome homoeolog than for the B subgenome counterpart in O. punctata. After comparing the two types of polyploids, we conclude that inconsistent evolutionary patterns of R in these polyploids are probably associated with different evolutionary time, asymmetrical subgenome evolutionary dynamics, and unique demographical characteristics of these species.
• A new species of Scytonema isolated from Bilaspur, Chhattisgarh, India

  Prashant Singh, Robin Anigo Minz, Kikku Kunui, Zaid Muneef Shaikh, Archana Suradkar, Yogesh S Shouche, Arun Kumar Mishra, Satya Shila Singh

  J Syst Evol. 2016, 54(5): 519-527.
  https://doi.org/10.1111/jse.12202

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  Filamentous cyanobacterium (strain 10C-PS) isolated from a fresh water body of Bilaspur, Chhattisgarh, India is being described as new species of the polyphyletic genus Scytonema. Phenotypic, molecular and phylogenetic characterization was performed and the combined results validated the strain as a new species. Careful observations of the filaments, presence of a distinctly textured sheath throughout the length of the trichome, differences in the shape and dimensions of the vegetative cells, and heterocytes provided reliable morphological signals that the strain differed from rest of the closely related species. Sequencing of the 16S rRNA gene showed 96.89% sequence similarity with Scytonema hofmanni PCC 7110 while rbcl and psbA sequencing showed 95% and 92% similarities with Scytonema hofmanni PCC 7110 and Nostoc sp. PCC 7524 respectively while the nifD gene sequence similarity was found to be 96% with Scytonema hofmanni PCC 7110. The PC-IGS region was sequenced and concatenated cpcB, IGS and cpcA regions indicated 97% closest similarity with Scytonema sp. PCC 7110 and Scytonema bohnerii Ind24. Subsequent phylogenetic analyses gave a strong pattern of distinct clustering in case of all the molecular markers. The phenotypic, genetic and phylogenetic observations prove conclusively that the strain 10C-PS is a new species in the genus Scytonema with the name proposed being Scytonema bilaspurensis.
• Likely allopatric origins of Adiantum × meishanianum (Pteridaceae) through multiple hybridizations

  Hui Shang, Ying Wang, Xiao-Feng Zhu, Guo-Hua Zhao, Fan-Hong Wang, Jin-Mei Lu, Yue-Hong Yan

  J Syst Evol. 2016, 54(5): 528-534.
  https://doi.org/10.1111/jse.12205

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  Adiantum × meishanianum F. S. Hsu ex Y. C. Liu & W. L. Chiou was regarded as an endemic species in Meishan Village, Kaohsiung, Taiwan, China and a hybrid between A. malesianum Ghatak (the maternal parent) and a sexually reproducing diploid cryptic species of A. philippense L. (the paternal parent), as revealed by chloroplast and nuclear markers. However, morphological research revealed that A. × meishanianum is also disjunctively distributed in Yunnan and that its paternal parent is possibly A. menglianense Y. Y. Qian. Thus, this study aimed to confirm these findings by using two chloroplast regions and a low-copy nuclear marker in DNA barcoding and phylogenetic analyses, spore measurement, and flow cytometry. Our results indicated that A. × meishanianum in Yunnan is triploid and abortive, the same as A. × meishanianum in Taiwan, and they both originated from the hybridization between the maternal parent of A. malesianum and the paternal parent ofA. menglianense, but not A. philippense. In conclusion, A. × meishanianum probably originated from multiple hybridizations in Taiwan and Yunnan.
• Phylogenetic placement of Psilopeganum, a rare monotypic genus of Rutaceae (the citrus family) endemic to China

  Marc S. Appelhans, Sabrina Krohm, Sara Manafzadeh, Jun Wen

  J Syst Evol. 2016, 54(5): 535-544.
  https://doi.org/10.1111/jse.12208

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  Psilopeganum (Rutaceae) is a rare monotypic genus endemic to the vicinity of the Yangtze River valley in Chongqing, Hubei, Sichuan and Guizhou provinces in China. It differs from most Rutaceae taxa by its herbaceous habit and has been treated as a member of the tribe Ruteae. Our study is the first attempt to place Psilopeganumin a phylogenetic context and our results show that the genus belongs to a clade with Boenninghausenia, Ruta and Thamnosma, which are part of Ruteae. Within this group, the position of Psilopeganum remains unclear because the Boenninghausenia-Thamnosma clade, Psilopeganum and Ruta form a trichotomy in most analyses. The ITS dataset placed Psilopeganum as sister to the Mediterranean and Canarian genus Ruta, which is corroborated by morphological similarities. Our studies support that Ruteae is paraphyletic with respect to Aurantioideae and that Dictamnus does not belong to Ruteae. The Indian, Sri Lankan, and Malagasy genusChloroxylon is sister to the Boenninghausenia-Psilopeganum-Ruta-Thamnosma clade, despite its traditional placement in the subfamily Flindersioideae. The placement of Chloroxylon is consistent with an origin of the group of Chloroxylon, Boenninghausenia, Psilopeganum, Ruta and Thamnosma in southern Asia. The rapid uplifts of the Himalayas could account for one or two vicariance events splitting the lineages of the Boenninghausenia-Psilopeganum-Ruta-Thamnosma clade, and may explain the short branch length and low support for the relationships among Psilopeganum, Ruta, and the Boenninghausenia-Thamnosma clade.
• Insufficient resolving power of mitogenome data in deciphering deep phylogeny of Holometabola

  Nan Song, Shi-Heng An, Xin-Ming Yin, Te Zhao, Xin-Yu Wang

  J Syst Evol. 2016, 54(5): 545-559.
  https://doi.org/10.1111/jse.12214

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  The mitochondrial genome (mitogenome) is one of the most widely used markers for phylogenetic analysis. Compared with whole-genome data, mitogenome data are less expensive to obtain and easier to manipulate. However, compositional bias and accelerated evolutionary rate reduce the effectiveness of the mitogenome in determining insect phylogeny. This study shows that mitogenome data are not suitable to reconstruct deep holometabolan evolution, even with a most comprehensive data coding scheme and the more realistic CAT model. For the deep levels of divergence within Holometabola, protein-coding genes only retain weak phylogenetic signals, leading to peculiar interordinal relationships. Consensus relationships in the Holometabola phylogeny, such as the monophyly of Holometabola, the most basal position of Hymenoptera, and the sister group relationship between the Strepsiptera and Coleoptera were rarely resolved in our analyses. The relationships of the holometabolan groups as inferred by mitogenomes are highly vulnerable to gene types, data coding regimes, model choice, and optimality criteria, and no consistent alternative hypothesis of Holometabola's relationships is supported. Thus, we suggest that the slowly evolving nuclear genes or genome-scale approaches may be better options for resolving deep-level phylogeny of Holometabola.