Table of Contents

20 July 2015, Volume 53 Issue 4
Cover illustration: Schematic diagram showing evolution of floral MADS-box genes and the interactions among their proteins before and after the occurrence of angiosperms. Flowers of Amborella trichopoda and Nuphar pumila were photographed by Sangtae Kim and Lin Li, respectively. See Li et al., pp. 285–296 in this issue.
  • Research Articles
  • Lin Li, Xian-Xian Yu, Chun-Ce Guo, Xiao-Shan Duan, Hong-Yan Shan, Rui Zhang, Gui-Xia Xu, Hong-Zhi Kong
    J Syst Evol. 2015, 53(4): 285-296.
    Floral organ identity genes, most of which are MADS-box genes, play key roles in flower development and floral organ identity determination. To specify the identities of different floral organ types, proteins of the floral MADS-box genes need to form dimers and higher-level complexes before they bind to the control regions of downstream genes and regulate their expression. Previous studies have shown that understanding the evolution of the interactions among proteins of the floral MADS-box genes may be an excellent step towards uncovering the underlying mechanisms of the origin of the flower. Yet, due to the lack of such information in early-branching angiosperm lineages, it has been difficult to determine the evolutionary changes of the protein–protein interactions (PPIs) before and after the origin of the flower. In this study, we first isolated counterparts of the floral MADS-box genes from Nuphar pumila (Timm) D.C., a representative of the basalmost angiosperms Nymphaeales, and investigated the interactions among their proteins by carrying out yeast two-hybrid assays. We then estimated the PPIs in the most recent common ancestor of extant angiosperms by using two different methods: ancestral character state reconstruction and ancestral sequence reconstruction followed by yeast two-hybrid assay. Based on these results, we examined the evolutionary transitions of the PPIs before and after the occurrence of extant angiosperms, and discussed their contributions to the origin of the flower. We found that duplication and diversification of floral MADS-box genes, as well as non-random losses of some once-existed PPIs, have been the driving force of the origin of the flower.
  • Xiao-Yan Liu, Qi Gao, Jian-Hua Jin
    J Syst Evol. 2015, 53(4): 297-307.
    A new species of Nageia, Nageia maomingensis sp. nov., is described from the Late Eocene of Maoming Basin, Guangdong Province, South China. According to its cuticular characteristics, the present fossil species is assigned to N. sect. Dammaroideae, showing the most resemblance to the extant species N. motleyi (Parl.) de Laub. At present, this section is mainly distributed in the Pacific islands region from South Asia to New Guinea. The discovery of N. maomingensis demonstrates that plants of this section inhabited South China at least by the Eocene. The distribution and living habitat of extant N. sect. Dammaroideae imply that South China was warmer during the Late Eocene than today, and may represent one of the centers for early diversification of Nageia and its section Dammaroideae during the Eocene. In addition, we postulate that plants of sect. Dammaroideae migrated southward in response to climate cooling after the Eocene.
  • Xue Bai, Xiang-Guang Ma, Yun-Dong Gao, Cai Zhao, Xing-Jin He
    J Syst Evol. 2015, 53(4): 308-320.
    In order to clarify the interspecific relationships of a lineage in Pleurospermum, P. hookeri C. B. Clarke, P. yunnanense Franch., and P. giraldii Diels, and to understand intraspecific divergence of P. hookeri, a phylogeographic study was carried out based on 198 individuals from 24 populations. Three chloroplast DNA regions, ndhF-rpl32, trnL-trnF, and trnQ-rps16, were sequenced in the present study. The genetic relationship between P. hookeri and P. giraldii is not as close as previously assumed. Pleurospermum hookeri and P. giraldii may originate from an unknown ancestor located in the Qinling region. Pleurospermum yunnanensewas found to be the closest relative of P. hookeri in all the species included in the phylogenetic analysis. The two haplotypes identified from P. yunnanense are shared with P. hookeri, which is potentially a result of both incomplete linkage sorting and introgression. Three large divergences within P. hookeri were identified, located at the northeastern edge, southeastern edge, and platform of the Qinghai–Tibet Plateau (QTP), respectively. Long-term history can explain the deep intraspecific divergence of P. hookeri. The uplift of the QTP played a key role in that divergence, and then were the climatic changes in the Quaternary. In addition, we found one refugium at the northeastern edge of the QTP, one at the southeastern edge, and at least one in the Hengduan Mountains region on the platform of the QTP.
  • Luo-Yan Zhang, Zhu Zhu, Ji Yang
    J Syst Evol. 2015, 53(4): 321-329.
    HORMA domain-containing proteins play important roles in cell cycle regulation and DNA repair, acting as adaptors to recruit other proteins. Although containing the conserved HORMA domain in structure, different types of HORMA proteins have diverged significantly in function. The mechanisms underlying the evolution and functional diversification of HORMA proteins remain unclear. Here we conduct an integrative approach, combining sequence, structural, gene coexpression and protein–protein interaction data, to trace the structural and functional evolution of HORMA proteins. Comparative sequence and structure analysis revealed that variations in both amino acid sequence and domain composition contributed to the functional diversification of different HORMA domain-containing proteins. Multiple amino acid substitutions at the C-terminal region promoted the functional divergence between MAD2 and REV7 by facilitating interaction with different partners. The emergence of the HOP1CTD domain contributed to the function of HOP1 as a meiosis-specific structural component of the lateral elements of the synaptonemal complex. Additionally, different types of HORMA proteins were recruited into different functional modules in the genetic network while functioning distinctly.
  • Zhuo-Jun Song, Zhe Wang, Yang Feng, Nan Yao, Ji Yang, Bao-Rong Lu
    J Syst Evol. 2015, 53(4): 330-338.
    Weedy rice, the same biological species of cultivated rice, is a noxious weed that infests rice fields worldwide. To determine the genetic diversity, structure, and relationships of weedy rice in China, we applied insertion/deletion (InDel) molecular fingerprints to analyze weedy rice populations from northeastern to southern rice planting regions, using japonica and indica rice cultivars as references. The InDel fingerprints indicated relatively high overall genetic diversity (He = 0.42) for the 240 samples from 14 weedy rice populations. However, much lower within-population diversity was detected, particularly for populations from northeastern and southern China, with the He value ranging from 0.006 to 0.06. Jiangsu populations showed much higher within-population genetic diversity (He = 0.12–0.31) than those from other regions. Analysis of molecular variance and Fst showed ∼88% genetic variation among weedy rice populations. Principal component and structure analyses indicated substantial japonica–indica genetic differentiation of weedy rice populations. Weedy rice from Jiangsu province was undergoing indica–japonicadifferentiation even within populations, which was likely due to the replacement of indica by japonica rice varieties in this region. In conclusion, significant genetic divergence has taken place among weedy rice populations in China, which is associated with their geographic locations and coexisting rice varieties. Introgression from cultivated rice has a critical role in shaping the genetic diversity and structure of weedy rice populations in agro-ecosystems influenced by humans.
  • De Ma, Hua-Tao Liu, Ya-Jie Ji, Cheng-Min Shi, Yu-Hui Yang, De-Xing Zhang
    J Syst Evol. 2015, 53(4): 339-350.
    The black-spotted pond frog Pelophylax nigromaculatus is a typical temperate-adapted amphibian species, largely endemic to East Asia. It occurs from central, east, and northeast China, to the Russian Far East, the Korean Peninsula, and part of Japan. So far, little is known about this frog from the Loess Plateau, a region that has experienced profound changes in climate and environment since the late Miocene. Particularly, between the Loess Plateau and the North China Plain, stand the Lüliang and Taihang mountain ranges, which form an important geographical divide in East China. Therefore, frogs from the Loess Plateau are indispensable for understanding the biogeography and evolution of this species. In this study, a total of 933 specimens of P. nigromaculatus collected range-wide were sequenced for the mitochondrial Cyt b gene, with 345 of them being genotyped at 10 nuclear microsatellite loci. Both mitochondrial and microsatellite data resolved four major frog clades: (i) Loess Plateau clade, containing only frogs from the Loess Plateau; (ii) East China clade, containing frogs from the rest of China except those from the Liaodong Peninsula; (iii) Peninsulas clade, comprising frogs from the Korean Peninsula and Liaodong Peninsula; and (iv) Japan clade. Frogs from the Loess Plateau have deeply diverged from frogs in the remaining regions, with 11.5%–13.1% sequence divergence, which is comparable to distances between congeneric ranid species. Ecological niche modeling analysis showed that the potential distribution ranges of the Loess Plateau frogs and the non-Loess Plateau frogs are rather different; niche identity testing indicated that the environmental niches of frogs from the Loess Plateau and other regions are not equivalent. Our data thus suggest that the Loess Plateau frogs represent a cryptic species. The uplift of the Lüliang Mountains was the most plausible trigger of this cryptic diversification.
  • Paul M Peterson, Konstantin Romaschenko, Yolanda Herrera Arrieta
    J Syst Evol. 2015, 53(4): 351-366.
    Bouteloua (Poaceae: Chloridoideae: Cynodonteae; Boutelouiane) is an important genus of forage grasses containing 60 species found primarily in the Americas with a center of diversity in northern Mexico. A modern subgeneric classification is lacking. The goals of our study were to reconstruct the evolutionary history among the species of Bouteloua using molecular data with increased species sampling compared to previous studies. A phylogenetic analysis was conducted on 209 samples, of which 59 species (206 individuals) were in Bouteloua, using two plastid (rpl32-trnL spacer and rps16-trnK spacer) and nuclear ITS 1&2 (ribosomal internal transcribed spacer) sequences to infer evolutionary relationships and produce a subgeneric classification. Overall, ITS and plastid phylogenies rendered similar patterns. However, the ITS phylogeny lacked backbone structure, recovering only four internal clades out of nine found in the plastid phylogeny. The ITS network shows a radiative evolutionary pattern and indicates a number of incompatible splits, suggesting past hybridization between species of different sections. The maximum-likelihood tree from the combined plastid and ITS regions is well resolved and depicts a strongly supported monophyletic Bouteloua that includes ten strongly supported clades and one moderately supported clade. The molecular results support the recognition of 10 sections and two subsections within Boutelouas.l.; three sections are new: Barbata, Hirsuta, and Trifida; four sections are new combinations: Buchloe, Cyclostachya, Opizia, and Triplathera; and two subsections are new: Eriopoda and Hirsuta. Based on our molecular results and the possession of unique morphological characters we describe a new species from Nuevo León, Bouteloua herrera-arrietae.
  • Book Review