Table of Contents

12 January 2017, Volume 55 Issue 1

Cover illustration: The diversification of Tolpis on the Canary Islands is one of many examples of the rapid accumulation of insular plant diversity. A small subset of the variety of plants and habitats for this genus are shown. Left to right, top to bottom: Laurel forest on Tenerife Island; F₂ hybrids between T. santosii and T. coronopifolia, flowering capitula; Tolpis proustii, fruit; Tolpis santosii, plant; Tolpis coronopifolia, floral color variant; and Coastline on La Palma Island. Photographs by Jenny Archibald and Mark Mort. See Crawford & Archibald, pp. 1–15 in this issue. [Detail] ...

  

Review
• Island floras as model systems for studies of plant speciation: Prospects and challenges

  Daniel J. Crawford, Jenny K. Archibald

  J Syst Evol. 2017, 55(1): 1-15.
  https://doi.org/10.1111/jse.12234

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  Oceanic islands have long been called natural laboratories for studying evolution because they are geologically young, isolated, dynamic areas with diverse habitats over small spatial scales. Volcanic substrates of different ages permit the study of different stages of divergence and speciation within plant lineages. In addition to divergence, the dynamic island setting is conducive to hybridization. Discussion will focus on the potential of systematic/ecological studies, in combination with genomic data from high throughput sequencing and an ever-increasing array of analytical techniques, for studying evolution in island plants. These studies may include: generation of highly resolved phylogenies to clarify the biogeography of speciation and whether divergence has occurred with or without gene flow; identification of the barriers to gene flow (extrinsic vs. intrinsic) of importance during divergence; documentation of historical and current hybridization events within island lineages; and elucidation of the genomic composition and ecology of hybrid populations in order to infer the evolutionary consequences of hybridization, such as the origin of stabilized homoploid hybrid species.
Research Articles
• DNA barcoding of East Asian Amentotaxus (Taxaceae): Potential new species and implications for conservation

  Lian-Ming Gao, Yan Li, Loc Ke Phan, Li-Jun Yan, Philip Thomas, Long Ke Phan, Michael Möller, De-Zhu Li

  J Syst Evol. 2017, 55(1): 16-24.
  https://doi.org/10.1111/jse.12207

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  DNA barcoding is a useful tool for species identification using standardized genomic DNA fragments. The genus Amentotaxus, consisting of five or six species, is confined to South China, Northeast India, Laos, and Vietnam. All species have been assessed as globally or nationally threatened. However, there is uncertainty about the number of species involved, especially in the border areas of southern China, northern Vietnam, and Laos. We selected five DNA barcodes (rbcL, matK,trnH-psbA, trnL-F, and internal transcribed spacer (ITS)) to evaluate their discrimination ability in this genus, and to investigate the current taxonomy of Amentotaxus. Our results indicate that all the selected barcoding regions showed a high level of universality for PCR and sequencing. When six species are recognized, the nuclear ribosomal DNA region ITS and the chloroplast DNA region trnL-F used on their own provided the highest identification success (60%). Two barcode combinations that included either ITS or trnL-F had the same species discrimination ability. Combinations using additional barcodes did not improve the species identification success. When only five species are recognized, with A. hatuyenensis T. H. Nguyen treated as a synonym of A. yunnanensis H. L. Li, the discrimination rate rises to 100%. Our results also indicate that recent collections from Yunnan province, China, Lao Cai province, Vietnam, and Laos may represent a potential new species. The findings from this study will be very useful for the formulation of appropriate conservation strategies for threatened Amentotaxus species in national and trans-boundary regions.
• Natural hybridization between Torreya jackii and T. grandis (Taxaceae) in southeast China

  Yi-Xuan Kou, Kun Xiao, Xiao-Rong Lai, Yu-Jin Wang, Zhi-Yong Zhang

  J Syst Evol. 2017, 55(1): 25-33.
  https://doi.org/10.1111/jse.12217

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  The recognition of natural hybridization can help to understand the origin and maintenance of biodiversity. Based on intermediate morphology and overlapped distribution, Torreya grandis var. jiulongshanensis Z. Y. Li, Z. C. Tang & N. Kang was regarded as a putative natural hybrid between T. jackii Chun and T. grandis Fort. ex Lindl. in southeast China. This study tested the hybridization origin of T. grandis var. jiulongshanensis using nuclear internal transcribed spacer (ITS) and cytoplasm (chloroplast rbcL and rpl16 and mitochondrial rps3) DNA sequences. The results showed that most heterozygous sites of nuclear ITS sequences in T. grandis var. jiulongshanensis showed additivity between T. jackii and T. grandis. Cloned ITS sequences of T. grandis var. jiulongshanensis separately clustered withT. jackii and T. grandis in the phylogenetic analyses. Meanwhile, all of chloroplast and mitochondrial haplotypes of T. grandis var. jiulongshanensis were identical to those of T. jackii, not T. grandis. On the chloroplast DNA phylogenetic trees, T. grandis var. jiulongshanensis were grouped into the clade of T. jackii. These results suggest that T. grandis var. jiulongshanensis is a natural hybrid between T. jackii (maternal parent) and T. grandis (paternal parent). This study also implies that T. grandis should be cultivated with caution near the sites of T. jackii, because the endangered status of the latter might be deteriorated due to hybridization.
• Phylogenetic position of two endemic Carthamus species in Algeria and their potential as sources of genes for water use efficiency improvement of safflower

  Imane Mihoub, Thierry Robert, Jaleh Ghashghaie, Roser Vilatersana, Françoise Lamy, Reda Benmrid, Marlène Lamothe-Sibold, Fatiha Aid

  J Syst Evol. 2017, 55(1): 34-43.
  https://doi.org/10.1111/jse.12220

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  Despite the high economic value of safflower (Carthamus tinctorius), the potential of several wild related species as genetic resources is still poorly studied, in particular with regards to drought tolerance, a priority in safflower improvement. This situation is partially explained by the numerous and still discussed uncertainties in phylogenetic relationships within the safflower species complex. In this study, we focused on two rare Algerian wild species, Carthamus strictus and Carthamus chouletteanus. We aimed at: (i) clarifying their taxonomic status, and determining their phylogenetic relationships with safflower and other Mediterranean species ofCarthamus sensu lato (s.l.) (Carthamus sensu stricto (s.s.) and Carduncellus genera) by using nucleotide diversity within the internal transcribed spacer region (ITS) and (ii) assessing the water use efficiency (WUE) of these species by determining their carbon isotope composition. Our results support the existence of two well supported different clusters among the safflower species complex: Carthamus s.s. including Eastern annual species and the vast Carduncellus group constituted by Western perennial species, including the two studied Algerian species. Also, significant differences for carbon isotopic composition between Carthamus s.s. andCarduncellus were revealed. Carduncellus species displayed significantly higher δ¹³C values (i.e., higher WUE) than Carthamus s.s. species. Carthamus chouletteanus displayed the highest average value of δ¹³C (highest WUE) among the species studied. Our data encourage for further studies on the possibility of hybridisations between species of the two genera and suggest that Carduncellus should be considered as potentially more interesting genetic resources to improve the WUE of safflower, rather than Carthamus s.s. species.
• Temporal variation in relative frequency of nectariferous and nectarless inflorescences and its effect on subsequent fecundity in an ephemeral plant, Corydalis ambigua (Fumariaceae)

  Xing-Nan Zhao, Ji-Min Zhao, Ji-Xun Guo, Yan-Wen Zhang

  J Syst Evol. 2017, 55(1): 44-53.
  https://doi.org/10.1111/jse.12210

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  The occurrence of nectarlessness flowers in nectar-producing plants is a common and stable phenomenon in many species, but their occurrence is still not well understood. The aim of this study is to examine a question from both the plant and pollinator perspectives: why do nectar-producing species produce some nectarless flowers within a plant? We investigate the distribution patterns of nectarless flowers in natural populations and their variation among the populations and years in a spring-flowering self-incompatible perennial herb plant, Corydalis ambigua Chem. & Schlecht (Fumariaceae), we observed the foraging behavior of bumblebees to nectariferous and nectarless inflorescences. We also examined the differences in reproductive success between inflorescence types and the effect of nectar production on flower production of the next flowering season. The results indicated that the frequencies of nectarless flowers varied among inflorescences, individuals, and populations and between years. Plants can revise or keep their inflorescence types or change nectar production status in the next growing season. Bumblebees visited both types with equal frequency but different foraging behavior, which resulted in lower seed production in nectarless inflorescences. However, nectarless inflorescences may save more energy and result in larger bulbs, which produce more flowers in the next flowering season. We found that although nectarless flowers resulted in lower seed set in nectarless inflorescence or individuals, they could affect bumblebees’ foraging behavior and further promote the effective output of pollen. In addition, the resource savings could enhance plant reproductive success in the next flowering season.
• Ribosomal DNA ITS1, 5.8S and ITS2 secondary structure, nuclear DNA content and phytochemical analyses reveal distinctive characteristics of four subclades of Protasparagus

  Partha Sarathi Saha, Mainak Sengupta, Sumita Jha

  J Syst Evol. 2017, 55(1): 54-70.
  https://doi.org/10.1111/jse.12221

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  The use of ribosomal DNA (rDNA) internal transcribed spacer (ITS) primary sequence based phylogeny is a conventional practice to estimate the evolutionary interspecies relationship. However, analysis of the functional folding patterns and higher order secondary structures of ITS regions can provide additional important information regarding species relatedness and interspecies variations. In the present study, we provide the first detailed information on the rDNA ITS secondary structure diversity in the four subclades of the subgenus Protasparagus. Several angiospermic conserved motifs were identified in each of the ITS1, 5.8S and ITS2 secondary structures of the studied taxon. Topological comparison of the ITS1 secondary structures showed variations in the helix- IV regions. Moreover, presence of unique sequence motifs and differences in the internal loop structures were found to be subclade specific. The present study suggests that comprehensive analysis of the ITS1, 5.8S and ITS2 structural elements including helices, loops and bulges can be used as an important tool for species delimitation. The present study investigated the evolution of the secondary structure of ITS marker (its phylogenetic utility), genome size, base chromosome number and phytochemicals, and identified a putative polyploid event shared by a number of Protasparagus species. The phytochemical analysis of two important active compounds, i.e., shatavarin-IV and sarsasapogenin, also reveals their presence in all the studied taxa constitutively even at the subclade level.
• Comparative genomics revealed the origin and evolution of autophagy pathway

  Jian Yang, Xiao-Qiang Chai, Xian-Xian Zhao, Xiao Li

  J Syst Evol. 2017, 55(1): 71-82.
  https://doi.org/10.1111/jse.12212

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  Autophagy is prevalent in eukaryotic organisms. Massive research efforts have focused on the mechanism and functionality of autophagy in eukaryotes, for example, their role in human diseases. However, little is known about how this fundamental pathway evolved; in particular, there is an absence of research in prokaryotes. Here, we carried out a comparative genomics analysis among 84 species ranging from eukaryotes to eubacteria and archaebacteria. We found that most of the core proteins in the autophagy pathway were ubiquitous in eukaryotes, whereas the distribution of proteins involved in selective autophagy were limited. In prokaryotes, distant homologs of autophagy-related proteins were also found. Species in Cyanobacteria and Euryarchaeota possess relatively more of these homologs compared to other prokaryotes, which indicated the prokaryotic origin of some autophagy-related proteins. Phylogenic tree analysis and the distribution of homologs suggested that the presence of proteins involved in autophagosome formation should be an important sign of autophagy. Furthermore, we found that distribution of mitochondrial protein importing-related proteins was quite similar to that of autophagy-related proteins in eukaryotes and that their phylogenic profile was closer to that of several core autophagy proteins compared with 16S/18S ribosomal RNAs, suggesting the engulfment of mitochondria may be the driving force for the evolution of autophagy. Autophagy may have evolved as a quality control system for mitochondria at the very beginning of evolution of eukaryotes. This research shed light on the prokaryotic origin of autophagy and provided a new perspective that mitochondria and autophagy may interplay during the course of eukaryotic evolution.
• List of Reviewers

  J Syst Evol. 2017, 55(1): 83-83.
  https://doi.org/10.1111/jse.12237

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  The Journal of Systematics and Evolution would like to acknowledge and thank the following reviewers for their contributions in the period January 1‐December 31 in 2016:

  Allen, Geraldine	Hotta, Kohji	Sigel, Erin
  Anderson, Gregory	Huang, Lu‐Qi	Sinn, Brandon
  Archer, Robert	Huang, Shuang‐Quan	Soejima, Akiko
  Barrington, David	Huang, Yong‐Jiang	Soltis, Pamela S.
  Bogunić, Faruk	Jin, Xiao‐Hua	Song, Zhi‐Ping
  Cao, Jun	Jurczyk, Barbara	Sonnante, Gabriella
  Cardoso, Domingos	Kallersjo, Mari	Spalik, Krzysztof
  Chen, Kangming	Kano, Rui	Srivastava, Alok
  Chen, Li‐Juan	Knapp, Sandra	Stevens, Peter
  Chen, Zhi‐Duan	Kong, Hong‐Zhi	Stuessy, Tod
  Cires, Eduardo	Lashermes, Philippe	Sun, Miao
  Crespi, Antonio	Li, Jie	Sun, Yong‐Shuai
  Das, Sudripta	Liao, Wan‐Jin	Tarkhnishvili, David
  de Groot, Arjen	Lin, Zhenguo	Testo, Weston
  Dobeš, Christoph	Liu, Hong‐Mei	Thiv, Mike
  Dubuisson, Jean‐Yves	Liu, Jian‐Quan	Tippery, Nicholas
  Ebihara, Atushi	Liu, Ping‐Li	Van der Meer, Sascha
  Edger, Patrick	Lu, Bao‐Rong	Vidal‐Russell, Romina
  Ekrt, Libor	Ma, Hui	Wang, Heng‐Chang
  Elster, Josef	Ma, Jian‐Chao	Wang, Hong
  Endress, Peter	Mehltreter, Klaus	Wang, Hong‐Wei
  Ercisli, Sezai	Milstein, Daniela	Wanke, Stefan
  Esser, Hans‐Joachim	Murakami, Noriaki	Watkins, James
  Francisco‐Ortega, Javier	Nie, Ze‐Long	Xiang, Qiu‐Yun (Jenny)
  Gao, Lian‐Ming	Oh, Sang‐Hun	Xu, Feng‐Xia
  Ge, Xue‐Jun	Paule, Juraj	Yang, Ze‐Feng
  Gibby, Mary	Potter, Dan	Yin, Zhi‐Tong
  Gong, Xun	Qi, Xinshuai	Zhang, Dian‐Xiang
  Gu, Hong‐Ya	Qiang, Sheng	Zhang, Li‐Bing
  Guo, Jie	Qiu, Ying‐Xiong	Zhang, Ming‐Li
  Guo, Ya‐Long	Regalado, Ledis	Zhang, Ning
  Guo, You‐Hao	Rimington, William R.	Zhang, Ti‐Cao
  Hadadinejad, Mahdi	Salino, Alexandre	Zhang, Xian‐Chun
  Harris, AJ	Salmaki, Yasamin	Zhao, Yun‐Peng
  Hauenschild, Frank	Schmidt‐Lebuhn, Alexander N.	Zhong, Bo‐Jian
  He, Chao‐Ying	Schneider, Harald	Zhou, Ren‐Chao
  Herendeen, Patrick	Schori, Melanie	Zimmer, Elizabeth
  	Shan, Hong‐Yan	Zou, Xin‐Hui