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 Coastl [Detail] ...
  • Daniel J. Crawford, Jenny K. Archibald
    J Syst Evol. 2017, 55(1): 1-15.
    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
  • 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.
    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.
  • Yi-Xuan Kou, Kun Xiao, Xiao-Rong Lai, Yu-Jin Wang, Zhi-Yong Zhang
    J Syst Evol. 2017, 55(1): 25-33.
    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.
  • 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.
    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.
  • Xing-Nan Zhao, Ji-Min Zhao, Ji-Xun Guo, Yan-Wen Zhang
    J Syst Evol. 2017, 55(1): 44-53.
    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.
  • Partha Sarathi Saha, Mainak Sengupta, Sumita Jha
    J Syst Evol. 2017, 55(1): 54-70.
    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.
  • Jian Yang, Xiao-Qiang Chai, Xian-Xian Zhao, Xiao Li
    J Syst Evol. 2017, 55(1): 71-82.
    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.
  • J Syst Evol. 2017, 55(1): 83-83.

    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