Table of Contents

10 January 2019, Volume 57 Issue 1
Cover illustration: Upper left: Passiflora serratifolia. Lower left: Phylogenetic distribution of plastome rearrangements. Upper right: P. edulis. Middle right: Whole genome alignment of Passiflora plastomes. Lower right: P. nitida. Photographs by Lawrence E. Gilbert. Designed by Alice Tangerini. See Rabah et al., pp. 1–14 in this issue.
    Research Articles
  • Samar O. Rabah, Bikash Shrestha, Nahid H. Hajrah, Mumdooh J. Sabir, Hesham F. Alharby, Mernan J. Sabir, Alawiah M. Alhebshi, Jamal S. M. Sabir, Lawrence E. Gilbert, Tracey A. Ruhlman, and Robert K. Jansen
    J Syst Evol. 2019, 57(1): 1-14.
    Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.
  • Hyoung Tae Kim, Jung Sung Kim, You Mi Lee, Jeong-Hwan Mun, and Joo-Hwan Kim
    J Syst Evol. 2019, 57(1): 15-22.

    Interspecific and intergeneric relationships of Prunus s.l. are still unclear due to low levels of genetic variation among species, and resulting partially unresolved phylogenetic inferences. Here we sequenced and compared six complete plastomes from two subgenera of Prunus in order to choose molecular markers to increase the amount of genetic variation suitable for inference of Prunus phylogeny. The plastomes range between 157 817 and 158 995 bp in length, and we found different levels of inverted repeat (IR) contraction among the three sampled subgenera of Prunus s.l. Most regions in Prunus plastomes considered individually provide low phylogenetic resolution at the subgenus or species level compared to a tree constructed using all 78 coding regions combined. We compared levels of variation among 206 coding regions and noncoding (intergenic and intron) plastid regions and inferred phylogenies from each region considered individually. We then chose using two regions together for future studies of relationships in Prunus, ycf1 and trnT-L, that display high to moderate levels of variation among coding and intergenic regions, respectively, and that individually permit inference of resolved species-level trees in Prunus with moderate to strong branch support. Considered together, these two regions allow inference of the same topology of Prunus inferred using all coding plastid regions combined, with comparable levels of tree support to the full plastome set. These two loci should therefore be useful as a plastid phylogenetic marker set for further inference of relationships within Prunus s.l.

  • Víctor Lucía, M. Montserrat Martínez-Ortega, Enrique Rico, and Kesara Anamthawat-Jónsson
    J Syst Evol. 2019, 57(1): 23-41.

    In this study, we review the classification of two species, Elymus hispanicus and E. marginatus, which are restricted to highly valuable and sensitive Mediterranean ecosystems. The genomic composition of the two species is analysed by in situ hybridization. In addition, lodicule morphology and foliar anatomy of both species are compared with those of E. caninus, E. repens, E. sibiricus (i.e., the type species of Elymus s.s.) and Pseudoroegneria strigosa (i.e., the type species of Pseudoroegneria). The genomic formula 2n = 8x = 56; HStStSt is proposed for E. hispanicus and 2n = 4x = 28; StSt for E. marginatus. In this latter species, the absence of the ribosomal genes in one of the two St genomes suggests that diploidization may have occurred during the evolution the species. Regarding foliar anatomy, E. hispanicus, E. caninus, E. repens, and E. sibiricus shared several characteristics, but the leaf blades of E. marginatus proved anatomically more similar to those of Ps. strigosa. The data compiled support the contention that: (1) E. hispanicus belongs to Elymus s.s.; (2) E. marginatus should be transferred to Pseudoroegneria; and (3) the morphology of the lodicules should be carefully reconsidered for appropriately describing the boundaries between Elymus s.s. and Pseudoroegneria.  The new combination Ps. marginata is proposed and a detailed iconography of the plant is provided.

  • David Gutiérrez-Larruscain, Santiago Andrés-Sánchez, Enrique Rico, and María Montserrat Martínez-Ortega
    J Syst Evol. 2019, 57(1): 42-54.

    Forty-five populations of Pentanema corresponding to seven species included in the Pentanema conyzae clade have been studied using AFLP fingerprinting. The results show that allopolyploidization could have been involved in the diversification of this group, specifically in species P. langeanum and P. maletii. Molecular data confirm the presence of P. britannicum in the Iberian Peninsula and key steps are provided to identify the species that are morphologically the most challenging.

  • Wu-Qin Xu, Jocelyn Losh, Chuan Chen, Pan Li, Rui-Hong Wang, Yun-Peng Zhao, Ying-Xiong Qiu, Cheng-Xin Fu
    J Syst Evol. 2019, 57(1): 55-65.
    The figwort genus Scrophularia L. (Scrophulariaceae) comprises 200–300 species and is widespread throughout the temperate Northern Hemisphere. Due to reticulate evolution resulting from hybridization and polyploidization, the taxonomy and phylogeny of Scrophularia is notoriously challenging. Here we report the complete chloroplast (cp) genome sequences of S. henryi Hemsl. and S. dentata Royle ex Benth. and compare them with those of S. takesimensis Nakai and S. buergeriana Miq. The Scrophularia cp genomes ranged from 152 425 to 153 631 bp in length. Each cp genome contained 113 unigenes, consisting of 78 protein‐coding genes, 31 transfer RNA genes, and 4 ribosomal RNA genes. Gene order, gene content, AT content and IR/SC boundary structure were nearly identical among them. Nine cpDNA markers (trnH‐psbA, rps15, rps18‐rpl20, rpl32‐trnL, trnS‐trnG, ycf15‐trnL, rps4‐trnT, ndhF‐rpl32, and rps16‐trnQ) with more than 2% variable sites were identified. Our phylogenetic analyses including 55 genera from Lamiales strongly supported a sister relationship between ((Bignoniaceae + Verbenaceae) + Pedaliaceae) and (Acanthaceae + Lentibulariaceae). Within Scrophulariaceae, a topology of (S. dentata + (S. takesimensis + (S. buergeriana S. henryi))) was strongly supported. The crown age of Lamiales was estimated to be 85.1 Ma (95% highest posterior density, 70.6–99.8 Ma). The higher core Lamiales originated at 65.6 Ma (95% highest posterior density, 51.4–79.4 Ma), with a subsequent radiation that occurred in the Paleocene (between 55.4 and 62.3 Ma) and gave birth to the diversified families. Our study provides a robust phylogeny and a temporal framework for further investigation of the evolution of Lamiales.
  • Zhe Wang, Min-Jie Fu, Hai-Ge Zhu, Yue Zhu, Xiang-Xiang Zhao, and Bao-Rong Lu
    J Syst Evol. 2019, 57(1): 66-74.

    Weedy rice (WR, Oryza sativa L. f. spontanea) is a noxious agricultural weed, infesting rice fields worldwide and causing tremendous yield losses of cultivated rice. However, little is known about the relationship between genetic diversity and distribution of WR populations across a wide latitudinal gradient, in addition to its reasons for genetic differentiation. To determine the distribution of genetic diversity and differentiation, we analyzed 20 WR populations collected from wide geographic ranges of rice-planting regions across Northeast, Jiangsu and Guangdong provinces of China, and Sri Lanka, based on 20 simple sequence repeat loci. Our results indicated a significant negative correlation (R = 0.84, P < 0.01) between genetic diversity and latitudinal locations of WR populations. The Mantel test (R2 = 0.49, P < 0.01) showed distinct groupings of WR populations from different rice-planting regions, fitting an isolation-by-distance pattern. In addition, the STRUCTURE analysis and principal coordinates (PCoA) analysis indicated considerable genetic differentiation of WR from different rice-planting regions, which was associated with the types of co-occurring rice cultivars. We conclude based on the above results that WR genetic diversity is affected by the latitudes where WR populations are located. The genetic differentiation of WR populations is determined by their spatial distances and co-occurring rice cultivars. Such a pattern of genetic diversity and differentiation across different regions may facilitate the design of effective WR control, in addition to understanding adaptive evolution of this weed.

  • Qian-Ru Zhao, Jing Zhou, Hua Peng, and Zhen-Wen Liu
    J Syst Evol. 2019, 57(1): 75-80.
    The monotypic genus Eremotropa Andres (Monotropoideae, Ericaceae) is endemic to central Yunnan. It was first described by Andres in 1953, and was subsequently treated as a synonym of Monotropastrum Andres (1987); however, the phylogenetic placement of this genus has not, to date, been investigated. In this study, phylogenetic analyses were undertaken using DNA sequences from the nuclear internal transcribed spacer from all species of Monotropoideae available in GenBank. Comparative morphological studies on Eremotropa, Monotropastrum, and Monotropa L. were also carried out. The molecular phylogenetic evidence suggests that Eremotropa is sister to a clade formed by Monotropa and the remaining species of Monotropastrum, thus rendering Monotropastrum not monophyletic. Morphologically, Eremotropa differs from Monotropastrum in plant color, inflorescence type, length of the style, and size of the baccate fruit. Consequently, molecular and morphological evidence supports the resurrection of Eremotropa, which contains only one species, E. sciaphila Andres, as distinct from Monotropastrum.
  • Chang-Qiu Liu, Hang Sun
    J Syst Evol. 2019, 57(1): 81-88.
    The geographical distribution of pollinators is an important factor determining the biogeographical pattern of floral evolution and diversification. In Africa, a guild of plant species has converged in a floral syndrome for pollination by long‐tongued hawkmoths (predominantly Agrius convolvuli). It is hypothesized that such floral convergence could track the geographical distribution of long‐tongued hawkmoths, so it may not be confined to Africa. We investigated the pollination biology of Lilium sargentiae E. H. Wilson, which is endemic to China and exhibits traits suggestive of long‐tongued hawkmoth pollination. Lilium sargentiae was visited by A. convolvuli as well as small beetles (Nitidulidae) but pollination was mostly or totally effected by the moth. It was consistent with other hawkmoth‐pollinated plants in terms of floral tube length, nectar traits, tepal reflectance, and scent composition. We present the first experimental evidence for the hypothesis proposed above and for hawkmoth pollination in the widespread and ornamentally and economically important genus Lilium L. in a natural habitat. Our findings imply that long‐tongued hawkmoths (especially the extremely widespread A. convolvuli) as a distinctive pollinator niche may have underlain the evolution of long‐tubed (>8 cm) flowers across different continents.
  • List of Reviewers
  • J Syst Evol. 2019, 57(1): 89-90.

    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 2018:

    Alexander, Jason

    Álvarez Fernández, Inés

    Appelhans, Marc

    Assadi, Mostafa

    Barkman, Todd

    Bauret, Lucie

    Bayer, Randall J

    Bell, Charles

    Bergholz, Kolja

    Bernardello, Gabriel

    Bippus, Alex

    Blackmore, Stephen

    Bocksberger, Gaelle

    Boufford, David E.

    Bruneau, Anne

    Cai, Xing‐Xing

    Cevallos, Sergio

    Chen, Zhi‐Duan

    Clement, Wendy

    Cohen, James

    Comes, Peter

    Crayn, Darren

    Crespo, Manuel B.

    Da Cunha, Maura

    De‐Nova, J.

    Deng, Yun‐Fei

    Dong, Shi‐Yong

    Dong, Wen‐Pan

    Duan, Yuan‐Wen

    Estrada‐Ruiz, Emilio

    Fan, Xing

    Fatoretto, Julio

    Feldberg, Kathrin

    Feliner, Gonzalo

    Fiaschi, Pedro

    Freire, Susana

    Freyman, Will

    Gao, Lian‐Ming

    Garnatje, Teresa

    German, Dmitry A.

    Gernandt, David

    Gerrath, Jean

    Gillespie, Emily

    Gong, Xun

    Graham, Alan

    Grote, Paul

    Gu, Hong‐Ya

    Gu, Xingyou

    Guo, Yan‐Ping

    Guo, Zhen‐Hua

    Harbert, Robert

    Harris, AJ

    Hartman, Ronald

    Hearn, David

    Herrera, Fabiany

    Hodel, Richard

    Hu, Zhong‐Li

    Huang, Jian

    Huang, Jin‐Ling

    Huang, Shuang‐Quan

    Ickert‐Bond, Stefanie

    Jha, Sumita

    Jimenez, Pedro

    Jin, Jian‐Hua

    Jin, Xiao‐Hua

    John, MacDougal

    Johnson, Leigh

    Jud, Nathan

    Kazempour‐Osaloo, Shahrokh

    Keeley, Sterling

    Keppel, Gunnar

    Kikvidze, Zaal

    Kilian, Norbert

    Kim, Ki‐Joong

    Kong, Hang‐Hui

    Kunzmann, Lutz

    Kwembeya, Ezekiel G.

    Li, Hong‐Tao

    Li, Huang

    Li, Jianhua

    Li, Lin‐Feng

    Li, Rong

    Li, Zhong‐Hu

    Liang, Liang

    Liao, Wan‐Jin

    Liu, Jian‐Quan

    Liu, Jie

    Liu, Xiao‐Yan

    Lombardi, Julio Antonio

    Lu, Li‐Min

    Lu, Zhi‐Qiang

    Ma, Jian‐Chao

    Ma, Xiao

    Ma, Xiao‐Fei

    Manchester, Steven

    Mao, Kang‐Shan

    Marhold, Karol

    Maurin, Olivier

    McAllister, Hugh

    Metzgar, Jordan

    Meyer, Herbert

    Michael, Möller

    Michelangeli, Fabian A.

    Mishler, Brent

    Momohara, Arata

    Morales‐Briones, Diego F.

    Morrone, Juan José

    Nakajima, Jimi

    Nauheimer, Lars

    Nie, Ze‐Long

    Nowak, Michael

    Olsen, Kenneth M.

    Ornelas, Juan Francisco

    Patel, Nikisha

    Paun, Ovidiu

    Peralta, Denilson F.

    Pirie, Michael

    Qi, Zhe‐Chen

    Qiang, Sheng

    Qiu, Ying‐Xiong

    Ran, Jin‐Hua

    Reagon, Micheal

    Reginato, Marcelo

    Rojas‐Andrés, Blanca

    Rong, Jun

    Rubin, Matthew J.

    Salazar‐Mendias, Carlos

    Salino, Alexandre

    Sanchez‐Puerta, Virginia

    Scherson, Rosa

    Schwarz Taylor, Erika

    Sessa, Emily

    Shan, Hong‐Yan

    Shi, Gong‐Le

    Shi, Su‐Hua

    Simpson, Michael

    Soejima, Akiko

    Song, Bao‐Hua

    Spalink, Daniel

    Španiel, Stanislav

    Stevens, Peter

    Stone, Robert

    Strijk, Joeri

    Su, Tao

    Su, Xu

    Sun, Bai‐Nian

    Sun, Hai‐Qin

    Sun, Hang

    Sun, Yan‐Xia

    Tank, David

    Thomas, Daniel

    Tomescu, Alexandru

    Uncu, Ayse

    Vargas, Pablo

    Vatanparast, Mohammad

    Vorontsova, Maria S.

    Wang, Hong‐Fang

    Wang, Jian‐Bo

    Wang, Wei

    Wen, Jun

    Wheeler, Elisabeth

    Wilson, Barbara

    Wilson, Peter

    Wolfe, Andrea

    Xia, Hui

    Xiao, Sha

    Xie, Lei

    Yan, Yue‐Hong

    Yang, Chun‐Feng

    Yang, Shi‐Xiong

    Yang, Yong‐Ping

    Yu, Wen‐Bin

    Yu, Yan

    Yue, Ji‐Pei

    Zarco, Carlos Romero

    Zhang, Jian

    Zhang, Ti‐Cao

    Zhang, Wenheng

    Zhang, Wen‐Ju

    Zhao, Gui‐Fang

    Zhao, Ting‐Ting

    Zhou, Ren‐Chao

    Zhou, Shi‐Liang

    Zhou, Yong‐Hong

    Zhou, Yong‐Feng

    Zhou, Zhe‐Kun

    Zhou, Zhuo

    Zimmer, Elizabeth