J Syst Evol

01 January 2020, Volume 58 Issue 1

Cover illustration: Cyrtandromoea and Wightia are two enigmatic genera with their familial placements once unresolved in the order Lamiales. Evidence shows that they should be placed in the LMPO clade (comprising Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae) based on a large-scale phylogenetic reconstruction of Lamiales. Further phylogenetic analyses of the LMPO clade using six chloroplast markers and two nuclear ribosomal regions, respectively, reveal that Cyrtandromoea i [Detail] ...

Issue Information

Issue Information

J Syst Evol. 2020, 58(1): 0-4.
https://doi.org/10.1111/jse.12507

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Research Articles

Phylogenetic relationships of Cyrtandromoea and Wightia revisited: A new tribe in Phrymaceae and a new family in Lamiales

Bing Liu, Yun-Hong Tan, Su Liu, Richard G. Olmstead, Dao-Zhang Min, Zhi-Duan Chen, Nirmal Joshee, Brajesh N. Vaidya, Richard C. K. Chung, and Bo Li

J Syst Evol. 2020, 58(1): 1-17.
https://doi.org/10.1111/jse.12513

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The familial placements of Cyrtandromoea Zoll. and Wightia Wall., two small and enigmatic South‐East Asian genera, have long been controversial in Lamiales. Here we adopt a two‐step approach to resolve their phylogenetic relationships. We initially reconstructed a large‐scale phylogeny of Lamiales using six chloroplast markers (atpB, matK, ndhF, psbBTNH, rbcL, and rps4). The results showed that both Cyrtandromoea and Wightia emerged in the LMPO clade, including Lamiaceae, Mazaceae, Phrymaceae, Paulowniaceae, and Orobanchaceae. Based on the second set of six chloroplast markers (atpB, matK, ndhF, rbcL, rps16, and trnL‐F) and two nuclear ribosomal regions (external transcribed spacer and internal transcribed spacer) for the analyses focusing on the LMPO clade, our results revealed that Cyrtandromoea was consistently nested within Phrymaceae, whereas Wightia was supported as sister to Phrymaceae by the chloroplast DNA dataset or sister to Paulowniaceae by the nuclear ribosomal DNA dataset. Morphological and anatomical evidence fully supports the inclusion of Cyrtandromoea in Phrymaceae, and an updated tribal classification is done for Phrymaceae with five tribes, that is, Cyrtandromoeeae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Diplaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, trib. nov., Leucocarpeae, Mimuleae, and Phrymeae. The conflicting phylogenetic position of Wightia indicated by different genome markers results in difficulty placing the genus in either Phrymaceae or Paulowniaceae. Considering the distinct morphological differences between Wightia and other families in the LMPO clade, we here propose a new family, Wightiaceae Bo Li, Bing Liu, Su Liu & Y. H. Tan, fam. nov., to accommodate it, which is the 26th family recognized in Lamiales.
Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics: A case study from a clade of neotropical lianas

Luiz Henrique M. Fonseca and Lúcia G. Lohmann

J Syst Evol. 2020, 58(1): 18-32.
https://doi.org/10.1111/jse.12533

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Few botanical studies have explored the potential of nuclear ribosomal DNA (nrDNA) and mitochondrial DNA (mtDNA) data obtained through genome skimming for phylogeny reconstruction. Here, we analyzed the phylogenetic information included in the nrDNA and mtDNA of 44 species of the “Adenocalymma‐Neojobertia” clade (Bignoniaceae). To deal with intraindividual polymorphisms within the nrDNA, different coding schemes were explored through the analyses of four datasets: (i) “nrDNA contig,” with base call following the majority rule; (ii) “nrDNA ambiguous,” with ambiguous base calls; (iii) “nrDNA informative,” with ambiguities converted to multistate characters; and, (iv) “mitochondrial,” with 39 mitochondrial genes. Combined analyses using the nrDNA and mtDNA data and previously published “plastid” datasets were also conducted. Trees were obtained using Maximum Likelihood and Bayesian criteria. The congruence among genomes was assessed. The nrDNA datasets were shown to be highly polymorphic within individuals, while the “mitochondrial” dataset was the least informative, with 0.36% of informative bases within the ingroup. The topologies inferred using the nrDNA and mtDNA datasets were broadly congruent with the tree derived from the analyses of the “plastid” dataset. The topological differences recovered were generally poorly supported. The topology that resulted from the analyses of the “combined” dataset largely resembles the “plastid” tree. These results highlight limitations of nuclear ribosomal DNA and mitochondrial genes for phylogeny reconstruction obtained through genome skimming and the need to include more data from both genomes. The different topologies observed among genomes also highlight the importance of exploring data from various genomes in plant phylogenetics.
Floristic composition and endemism pattern of vascular plants in Ethiopia and Eritrea

Sheng-Wei Wang, Biyansa Hirpo Boru, Antony Waigwa Njogu, Anne Christine Ochola, Guang-Wan Hu, Ya-Dong Zhou, and Qing-Feng Wang

J Syst Evol. 2020, 58(1): 33-42.
https://doi.org/10.1111/jse.12527

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Traditional attempts to delineate floristic regions are typically based on the qualitative analysis of species distribution, often ignoring the phylogenetic relationships among their taxa. Ethiopia and Eritrea are in the Horn of Africa, known as one of the world's biodiversity hotspots. We quantitatively classified the flora of Ethiopia and Eritrea into meaningful geographical units by analyzing the taxonomic and phylogenetic β‐diversity at genera, total species, and endemic species levels at a scale of 0.5° × 0.5° grid cells. Hierarchical clustering was used to quantitatively delimitate the flora and analysis of similarities was used to test the significant difference between the derived groups in taxonomic composition and phylogenetic relatedness. In total, two floristic subprovinces, five floristic districts, and 13 floristic subdistricts, as well as three centers of species endemism associated with three floristic subdistricts were identified. Our results also showed that the species diversity, endemism, and turnover of the highlands in Ethiopia and Eritrea were much higher than the lowlands, indicating that the floristic differences are closely related to the topography of the East African Rift. In this study, we provided a scientific framework for the composition and relationships of the floristic units in the Horn of Africa, and similarly provided a scientific basis for better conservation of the diversity in this region.
A reevaluation of the Andean Genus Petroravenia (Brassicaceae: Thelypodieae) based on morphological and molecular data

Diego L. Salariato, Fernando O. Zuloaga, and Ihsan A. Al-Shehbaz

J Syst Evol. 2020, 58(1): 43-58.
https://doi.org/10.1111/jse.12486

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Petroravenia was until recently considered as a genus of three species (P. eseptata, P. friesii, and P. werdermannii) distributed along the Central Andes of Argentina, Bolivia, Chile, and Peru. This genus was included in the tribe Thelypodieae and was morphologically characterized by being tiny rhizomatous perennial herbs with rosulate leaves, dendritic trichomes, capsular silicles, and incumbent cotyledons. However, the phylogeny of Petroravenia, and its tribal placement, was never analyzed using molecular data. The lack of such studies, as well as the paucity of herbarium collections, suggesting that Petroravenia species are vulnerable and/or endangered, prompted us to address the molecular phylogeny of this genus. For this purpose, we generated comprehensive molecular phylogenies using nuclear (ITS) and plastid (trnL‐F and trnH‐psbA) data, and conducted morphological comparisons between these species and their closest related taxa. Results from the phylogenetic analyses showed that Petroravenia represents a polyphyletic group, with P. eseptata included in tribe Halimolobeae, and P. friesii and P. werdermannii placed within tribe Eudemeae and related to the genus Alshehbazia. Based on the results obtained from morphological and molecular data, we decided herein to retain the original circumscription of Petroravenia as monospecific within the tribe Halimolobeae and to transfer P. friesii and P. werdermannii to the genus Alshehbazia within the tribe Eudemeae. Systematic implications of these results are also discussed.
Recruitment of the high elevation cushion plant Arenaria polytrichoides is limited by competition, thus threatened by currently established vegetation

Jian-Guo Chen, Yang Yang, Song-Wei Wang, Jürg Stöcklin, De-Li Peng, and Hang Sun

J Syst Evol. 2020, 58(1): 59-68.
https://doi.org/10.1111/jse.12481

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Cushion plants have been confirmed to be keystone species of alpine ecosystems. However, the adaptive strategies responsible for their recruitment and persistence remain largely unclear. Also, the effect of competition by species already established in surrounding vegetation is not known. We first assessed population size and the frequency distribution of individuals of different size in communities of the keystone cushion Arenaria polytrichoides Edgew. along an elevational gradient in southwestern China. Furthermore, in controlled experiments the effects of soil quality, light availability, and competition by other species on seedling recruitment and survival was tested. At lower elevation individuals were larger (elder), but population size (density) was lower compared to higher elevation; similarly, adults and old individuals were relatively more frequent at low elevation, whereas juvenile and small individuals were more frequent at higher elevations. Seedling recruitment differed depending on soil origin with seeds sown in soils from low elevation having a higher germination percentage and seedling survival when grown without competition. Competition by other species delayed germination but did not influence the final germination percentage, but it increased seedling mortality and reduced their survival. Full light accelerated the germination process, but did not affect final germination percentage and seedling mortality. Results suggest that the recruitment and persistence of A. polytrichoides is strongly affected by competition, whereas temperature and soil quality are less important. We speculate that when populations of cushion A. polytrichoides are likely to be exposed to higher competition due to environmental changes, this species is in danger of being weeded out.
Molecular diversity of the 5S nuclear ribosomal DNA in Campeiostachys with StHY haplome constitution

Cai-Rong Yang, Bernard R Baum, Douglas A Johnson, Hai-Qin Zhang, and Yong-Hong Zhou

J Syst Evol. 2020, 58(1): 69-76.
https://doi.org/10.1111/jse.12484

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To detect the genomic constitutions and investigate the evolutionary relationships between Campeiostachys Drobov and Elymus L. species, we have cloned and analyzed 271 5S nuclear ribosomal DNA sequences from 27 accessions of these species, mostly of Chinese origin. We identified Long H1, Short S1, and Long Y1 unit classes in nine Campeiostachys or Elymus species. The identification of the three orthologous unit classes was confirmed by the neighbor‐joining tree of each unit class from PAUP and the phylogeny tree of three unit classes from MrBayes. The results suggested that these Elymus species comprise StYH haplomes and should be included in Campeiostachys. The phylogeny tree showed a clear separation between the S1 unit class and Y1 unit class. However, Y1 unit class sequences formed a sister clade to the S1 unit class, implying that although the St and Y haplomes might have some affinity, they are distinct from one another. The phylogeny tree also indicated that the five species in sect. Turczaninovia (C. dahurica var. cylindrica, C. dahurica var. dahurica, C. dahurica var. tangutorum, E. purpuraristatus, and E. dahuricus Turcz. ex Griseb. var. violeus C. P. Wang & H. L. Yang) might share a more recent common ancestor, whereas the four species in sect. Elymus (C. nutans, E. breviaristatus (Keng) Keng ex Keng f., E. sinosubmuticus (Keng) Keng f., and E. atratus (Nevski) Hand.‐Mazz.) share a close relationship. By identifying only one type of unit class for each haplome, we propose that the 5S nuclear ribosomal DNA sequences of species within Campeiostachys might have undergone haplome‐specific concerted evolution.
DNA barcoding evaluation of Vicia (Fabaceae): Comparative efficacy of six universal barcode loci on abundant species

Fei-Fei Wu, Qiu Gao, Fang Liu, Zan Wang, Jian-Li Wang, and Xian-Guo Wang

J Syst Evol. 2020, 58(1): 77-88.
https://doi.org/10.1111/jse.12474

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Vicia L. is an invaluable genus with considerable agricultural and economic importance due to its high value as feed, green manure, and medicine. However, most of this genus is not well known and remains underutilized. Due to the imprecise circumscription and delineation of Vicia species, the taxonomic history of this genus is controversial, which has hindered the identification of species with high economic potential. Therefore, rapid and accurate identification of Vicia species is essential. Simultaneously, species identification through DNA barcoding has become an effective taxonomic classification tool. Here, the species‐discrimination abilities of matK, rbcL, trnH‐psbA, trnL‐trnF, ITS1, and ITS2 were tested in 161 Vicia species with both sequence similarity (nearest neighbor, best match, and best close match) and tree‐based (maximum likelihood tree) methods. Among the single barcode sites, trnH‐psbA had the highest level of polymorphism (52.4% variable sites; nucleotide diversity, 0.1338). Additionally, trnH‐psbA had the highest mean interspecific distance (0.1352) and intraspecific distance (0.0071). The combined barcode matK+trnH‐psbA had the highest correct identification rate by the sequence similarity method. Both trnH‐psbA (75.38%) and matK (70.73%) showed higher species discrimination rates than the other barcodes when using the tree‐based method. Based on overall performance, matK and trnH‐psbA, alone or in combination, were the best barcodes for Vicia. Internal transcribed spacer (ITS1) also showed good performance and provided essential information regarding nuclear DNA, so this site is also recommended as a backup barcode for Vicia. These Vicia barcodes can be used to identify species and to evaluate germplasm resource collections.
Mummified Magnoliaceae woods from the upper Oligocene of South China, with biogeography, paleoecology, and wood trait evolution implications

Lu-Liang Huang, Jian-Hua Jin, Cheng Quan, and Alexei A. Oskolski

J Syst Evol. 2020, 58(1): 89-100.
https://doi.org/10.1111/jse.12480

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In this paper, we describe a new species Magnolia nanningensis sp. nov., based on exceptionally well‐preserved mummified fossil woods from the late Oligocene of the Nanning Basin, Guangxi, South China. The features of these woods indicate a close affinity to the section Michelia of the subgenus Yulania belonging to the genus Magnolia sensu lato (Magnoliaceae). Magnolia nanningensis is the first fossil record of the section Michelia from China, the modern diversity center of this group. These mummified woods provide fossil evidence supporting molecular dating that estimated an Oligocene age for divergence of the tropical evergreen section Michelia and the temperate deciduous section Yulania. Helical thickenings on vessel walls and a high degree of vessel grouping found in these fossil woods could be adaptive to temporary, possibly seasonal, droughts and, as suggested by other woods from the Nanning Basin, could be indicative of a monsoon‐influenced tropical climate in Guangxi during the late Oligocene. Helical thickenings have not been reported in magnoliaceous fossil woods prior to the Oligocene. The appearance of this trait was presumably a response to abrupt climate cooling near the Eocene–Oligocene boundary, followed by increase in climate seasonality. The associated increase of latitudinal zonation might be a possible trigger for divergence between the tropical evergreen sect. Michelia and the temperate deciduous sect. Yulania.
List of Reviewers

J Syst Evol. 2020, 58(1): 101-102.
https://doi.org/10.1111/jse.12561

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The Journal of Systematics and Evolutionwould like to acknowledge and thank the following reviewers for their contributions in the period January 1–December 31 in 2019:

Abbott, Richard

Abdelaziz, Mohamed

Appelhans, Marc

Aptroot, Andre

Bachelier, Julien

Bai, Wei‐Ning

Balao, Francisco

Barker, Bill

Barkworth, Mary E.

Bauret, Lucie

Berrached, Rachda

Besnard, Guillaume

Bisang, Irene

Blanco, Candela

Bomﬂeur, Benjamin

Boratyński, Adam

Campillo, Luke C.

Capblancq, Thibaut

Castells, Juli Caujape

Cellinese, Nico

Chanderbali, Andre

Charboneau, Joseph

Chen, Wen‐Li

Chen, Zhi‐Duan

Clement, Wendy

Cohen, James

Costion, Craig M.

Cronberg, Nils

Crowl, Andrew A.

Davies, Jonathan

De Franceschi, Dario

de Jong, Hans

Del Rio, Cedric

Dickinson, Timothy A.

Drummond, Chloe

Du, Fang

Duckett, Jeffrey

Düsseldorf, Klaus

Ebersbach, Jana

Ebihara, Atsushi

Elliott, Tammy L.

Endress, Peter

Escudero, Marcial

Fan, Xing

Favre, Adrien

Feldberg, Kathrin

Feliner, Gonzalo

Fior, Simone

Frajman, Bozo

Fu, Chao‐Nan

Fujiwara, Tao

Fuse, Shizuka

Gao, Lian‐Ming

Gao, Yong

Gasson, Pete

Ge, Xue‐Jun

Giussani, Liliana

Granados‐Mendoza, Carolina

Gueidan, Cecile

Guo, Chun‐Ce

Guo, Wen‐Wu

Guo, Ya‐Long

Guo, Yan‐Ping

Hao, Gang

Hassel, Kristian

Hassler, Michael

Haufler, Christopher

Hawksworth, David

Herrera, Fabiany

Hervías, Sandra

Ho, Boon Chuan

Hojsgaard, Diego

Hovenkamp, Peter

Huang, Shuang‐Quan

Ickert‐Bond, Stefanie

Ignatov, Michael

Iles, Will

Jia, Gui‐Xia

Jiang, Xiao‐Long

Jin, Jian‐Hua

Kang, Ji‐Chuan

Knoop, Volker

Kowlski, Rafal

Krak, Karol

Krämer, Ute

Kvaček, Jiří

Lakusic, Dmitar

Larhammar, Dan

Lashermes, Philippe

Lazaro, Amparo

Li, Jianhua

Li, Lin‐Feng

Li, Ling

Li, Min‐Jie

Li, Rong

Li, Ying‐Hui

Li, Zheng

Li, Zhong‐Hu

Lim, Jun Ying

Lin, Zhenguo

Liu, Jie

Liu, Zhong‐Jian

López‐Pujol, Jordi

Luo, Zhong‐Lai

Ma, Jian‐Chao

Ma, Xiao

Ma, Yong‐Peng

Magallon, Susana

Mairal Pisa, Mario

Manchester, Steven

Mao, Jian‐Feng

Mao, Kang‐Shan

McDonnell, Angela

McPartland, John

Meza‐Torres, Esteban

Montserrat Martí, Josep M.

Morgan, David

Moyle, Robert G.

Murrell, Zack

Nauheimer, Lars

Nelson, C. Dana

Ni, Zhong‐Fu

Nie, Ze‐Long

Noshiro, Shuichi

Ollerton, Jeff

Olmstead, Richard

Olsson, Sanna

Pannell, Caroline

Paule, Juraj

Pederneiras, Leandro

Percy, Diana

Peruzzi, Lorenzo

Picco, Anna Maria

Pigg, Kathleen

Pirani, Atefeh

Plunkett, Greg

Potter, Daniel

Qian, Hong

Qiu, Ying‐Xiong

Rao, Guang‐Yuan

Reeves, Patrick

Regalado, Ledis

Reginato, Marcelo

Reisch, Christoph

Ren, Zong‐Xin

Riess, Kai

Roedelsperger, Christian

Roeser, Martin

Rojas‐Andrés, Blanca

Rong, Jun

Ronse De Craene, Louis

Roux, Claude

Rubin, Matthew J.

Sakai, Hiroaki

Santos, Carmen

Sauquet, Hervé

Schinnerl, Johann

Sengupta, Aniket

Simpson, Michael

Singliarová, Barbora

Smedmark, Jenny

Smith, James

Snow, Neil

Sochting, Ulrik

Sønstebø, Jørn Henrik

Spalink, Daniel

Stark, Lloyd

Stevens, Peter

Su, Tao

Sun, Feng‐Jie

Sun, Hang

Sun, Yong‐Shuai

Sundue, Michael

Surget‐Groba, Yann

Tate, Jennifer A.

Tembrock, Luke

Testo, Weston

Tu, Tie‐Yao

Uemura, Kazuhiko

Ulrich, Werner

Vanderpoorten, Alain

Vera, Ezequiel

Verstraete, Brecht

Vigueira, Cynthia

Vit, Petr

Walker, Joseph F.

Wallander, Eva

Wang, Heng‐Chang

Wang, Jing

Wang, Wei

Wang, Ying‐Qiang

Wang, Yu‐Fei

Webb, Campbell

Wedger, Marshall

Wen, Jun

Weng, Ensheng

Wester, Petra

Westerberg, Lars

Wilf, Peter

Williams, David

Wu, Zhi‐Qiang

Xia, Hui

Xiao, Guang‐Hui

Xu, Feng‐Xia

Xu, Qiang

Xu, Xiao‐Ting

Yang, Jun

Yang, Qin‐Er

Yang, Ze‐Feng

Yi, Ting‐Shuang

Yu, Yan

Yu, Ying

Zarre, Shahin

Zhai, Wei‐Wei

Zhang, Fa‐Qi

Zhang, Jian‐Wen

Zhang, Liang‐Sheng

Zhang, Wen‐Heng

Zhang, Yong

Zhang, Ze‐Huang

Zhang, Zhi‐Yong

Zhong, Bo‐Jian

Zhou, Tao

Zhou, Yong‐Feng

Zhu, Hai

Zuntini, Alexandre