Table of Contents

18 September 2014, Volume 52 Issue 5
Cover illustration: Extensive observations were carried out in wild populations and a large number of specimens of Codonopsis, which has long been controversial in circumscription. The authors counted chromosome numbers of Codonopsis subg. Pseudocodonopsis (mitotic metaphase and karyotype shown down right), subg. Obconicicapsula, and Codonopsis purpurea for the first time, and analyzed palynological and molecular data of the genus and its allies (molecular tree shown down middle). [Detail] ...
    Research Articles
  • Qiang WANG, Xin-Tang MA, De-Yuan HONG
    J Syst Evol. 2014, 52(5): 541-550.
    The genus Codonopsis has been controversial in its circumscription. In the strict sense, the genus consists of three subgenera, Codonopsis, Pseudocodonopsis, and Obconicicapsula. Recent molecular and palynological analyses suggest that the latter two subgenera and Cod. purpurea Wall. are separated from restCodonopsis. In the present study, extensive observations were carried out in wild populations and on more than 800 specimens of subg. Pseudocodonopsis, subg.Obconicicapsula, and Cod. purpurea. Their chromosome numbers were counted for the first time. Recent palynological and molecular data were also analyzed and reevaluated. Our integrated phylogenetic analyses revealed that the three groups are distinct from the rest of Codonopsis. Furthermore, they are also distinct from each other, and cannot be circumscribed in a single genus. Therefore, three new genera are here proposed based on molecular phylogenetics, palynology, cytology, and external morphology. New combinations are made in the present article.
  • Wei WANG, Hong-Lei LI, Xiao-Guo XIANG, Zhi-Duan CHEN
    J Syst Evol. 2014, 52(5): 551-565.
    Previous studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ-petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ-petA, and ITS dataset, and the combinedrbcL, trnL-F, matK/trnK, psbJ-petA, and ITS dataset. Based on the tree-based comparisons, blast searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ-petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which BeckwithiaCyrtorhyncha, Kumlienia, andPeltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus-level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.
  • Cui-Ping WANG, Bin LIN, Yue-Qin ZHANG, Yue-Hui LIN, Ai-Hua LIU, Xue-Jun HUA
    J Syst Evol. 2014, 52(5): 566-579.
    Although the regulatory and the functional aspects of proline accumulation in plant stress tolerance have been well-documented since it was discovered more than half a century ago, the evolution of proline metabolic genes in polyploidy species and their diploidy progenitors is not understood so far. Here, we have studied the retention and the expression regulation of Δ1-pyrroline-5-carboxylate synthetase 1 (P5CS1) genes in allotetraploid, Brassica napus, in comparison with its diploids progenitors, B. rapa and B. oleracea under salt stress. Our results indicated that all six P5CS1 genes from two diploid progenitors were retained. Sequence analysis revealed that all Brassica P5CS1 genes had a highly conserved exon–intron structure, similar to P5CS1 in Arabidopsis. In addition, two homeologous genes with different origin, BnaA.P5CS1.a and BnaC.P5CS1.d exhibited biased expression in different organs in B. napus, implying possible sub-functionalization of P5CS1 in B. napus. All six P5CS1 genes were induced in response to salt stress in B. napus, which rendered gene dose advantage for the level of proline accumulation. These results indicate that in B. napus, P5CS1 gene loss has not occurred during polyploidization, which suggest conserved functionality and evolutionary benefit of proline accumulation for plant adaptation to environmental stresses.
  • Masum BURAK, Ali ERGÜL, Kemal KAZAN, Mehmet Emin AKÇAY, Canan YÜKSEL, Melike BAKIR, Filiz MUTAF, A. Emre AKPINAR, A. Semih YASASIN, Hamit AYANOGLU
    J Syst Evol. 2014, 52(5): 580-588.
    The apple is one of the most important fruit species in the world. Turkey has a diverse and ancient apple germplasm that have played a major role in the domestication of the Malus genus. However, so far locally grown Anatolian apple germplasm has largely been uncharacterized. In this study, 171 local apple (M. domestica Borkh.) accessions originated from eco-geographically diverse regions of Anatolia were studied using 16 SSR (simple sequence repeat) loci, which generated 254 alleles. Of the SSR markers used, the CH04g10 locus showed the highest allele diversity. Relatively high genetic similarities were found between some accessions. The factorial correspondence analysis did not clearly separate different all apple accession groups, suggesting that Anatolian apple accessions are highly intermixed. However, most apple accessions were grouped according to their collection sites in structure analyses. In addition, reflecting the richness of the Anatolian apple germplasm, low numbers of synonymous, and identical accessions were identified among the germplasm. Finally, using the publically available SSR data generated in other studies, we investigated genetic relationships between Anatolian accession groups and European apple accession groups. Our results reported here provide a useful base for future studies aimed at investigating the genetic diversity of wild and cultivated apples from Anatolia and the surrounding regions.
  • Prabodh K. BAJPAI, Ashish R. WARGHAT, Anil KANT, Ravi B. SRIVASTAVA, Tsering STOBDAN
    J Syst Evol. 2014, 52(5): 589-597.
    Genome scan was done with 439 dominant marker loci to identify outlier loci in three populations of Morus alba from the trans-Himalayan region. Employing finite and hierarchical island population genetic models, we detected 30 (6.85%) loci under selection, of which 3.64% were under directional selection and 3.19% under balancing selection. The hierarchical island model was efficient in detecting signatures of natural selection with low occurrence of false positives. Data showed significant spatial genetic structure (SGS), especially in population from Nubra valley with significantly high SGS. Bayesian approach revealed high genetic differentiation and inbreeding in Nubra population. Indus and Suru valleys populations showed comparatively low SGS, genetic differentiation, and inbreeding. The study showed that M. alba falls in the range of mixed mating and outcrossing species. However, the population of Nubra valley showed selfing with high SGS. Significant SGS strengthens the presence of natural selection in M. alba natural populations.
    J Syst Evol. 2014, 52(5): 598-611.
    Rare species of plants are especially vulnerable to extinction when populations are few, have small numbers of individuals, and are fragmented. Such conditions lead to a reduction in gene flow and genetic diversity, and encourage inbreeding depression. We conducted a study of the reproductive biology and population genetics of Penstemon debilis (Plantaginaceae), a Federally Threatened species endemic to a small region of oil shale extraction in western Colorado, USA. Most of the habitat area is privately owned and undergoing natural gas extraction activities. Penstemon debilis reproduces both vegetatively and as an outcrosser that requires a pollen vector. Moderate levels of inbreeding, but no inbreeding depression, were found within populations of P. debilis. Genetic divergence among the extant populations surveyed was moderate (FST values = 0.069–0.231; Nm = 0.831–3.385) with levels of genetic diversity within populations relatively low compared to congeners with similar modes of pollination and reproductive biology. STRUCTURE analysis revealed three population clusters with some admixture among all extant populations. Genetic diversity within and among P. debilis populations is similar to genetic diversity found for other rare and endemic outcrossing plant species. Our results are consistent with a pattern of recent population fragmentation or low levels of pollen-mediated gene flow among populations in close proximity to one another. Conservation of P. debilis will require cooperative management strategies between private landowners, government agencies, and concerned NGOs to preserve habitat for this rare species.
  • Yuan ZHANG, Xin-Yan LUO, Jun ZHU, Chen WANG, Yan HONG, Jie LU, Qian-Qian LIU, Bao-Qin LI, Ming-Li ZHU, Zi-Fan WANG, Ya-Qiong ZHANG, Xue-Bin SONG, Peng-Yan LV, Si-Lan DAI
    J Syst Evol. 2014, 52(5): 612-628.
    The Chinese traditional chrysanthemum cultivar is a marvelous group of Chrysanthemum ×grandiflorum Tzvelv., whose floral characters are rich in variation. However, neither the values of floral characters for the classification of chrysanthemums nor the relevance of different characters are yet known. Moreover, the existing classification systems of chrysanthemums are incomplete and unsystematic. In the present study, we selected 16 floral morphological characters on which to carry out diversity and relativity analyses by seven multivariate statistical analysis methods, and we further studied the cultivar classification. The analyses of nested variance, diversity index, and principle components showed that 10 floral morphological characters were of great value for chrysanthemum classification. Clustering analysis classified these 10 characters into three types, in which the variation of the ray floret factor was the highest. The analysis of partial correlations showed that the petal type was significantly affected by the length of the ray florets, the bending state of the outer-layer ray florets, and the tip shape of the ray florets; besides these three characters, the flower head type was also affected by the angle of the outer-layer ray florets and the length and distribution of the disc florets. The multiple linear regression equations for petal type and flower head type were successfully established. All of the cultivars were classified into four groups and 18 forms by cluster and discriminant analyses. These results provide a reference that can be used for cultivar identification and classification of chrysanthemums.
  • Dong-Rui KONG, Melanie SCHORI, Shu-Gang LU, Lu LI, Hua PENG
    J Syst Evol. 2014, 52(5): 629-642.
    Cardiopteris is unique in the expanded Cardiopteridaceae for several distinctive features, including its gynoecial structure and ovular morphology. We studied the floral development of Cardiopteris to clarify floral morphology and document floral development. Cardiopteris has three carpel primordia, which are separate at their tips but congenitally fused at their bases. The synascidiate zone (the fused proximal part) develops into the unilocular ovary; the three discrete carpel apices diverge in development: the apex of the adaxial carpel differentiates into a style and stigma, while the apices of the two lateral-abaxial carpels elongate and develop into a fleshy appendage only after fertilization. The ovules are attached to the lateral-abaxial carpels. At anthesis, the ovules are ategmic and orthotropous without funicles (morphologically undifferentiated). Functional differentiation occurs in the three carpels of Cardiopteris: the adaxial one is the site of pollination, while the lateral-abaxial two produce ovules. The ategmic orthotropous ovule is unusual in Cardiopteridaceae and is an apomorphy of Cardiopteris.
    J Syst Evol. 2014, 52(5): 643-650.
    Our molecular phylogenetic analyses shed some light on the evolutionary relationships within the Hamelieae tribe. Phylogenetic reconstructions based on Internal Transcribed Spacer and trnL-F sequence data revealed the presence of three distinct evolutionary lineages. The first clade includes Hamelia and Syringantha, the second clade includes Deppea s.l. (including Bellizinca, Csapodya, and Edithea), and the third clade includes Pinarophyllon, Deppeopsis, Hoffmannia,Pseudomiltemia, Plocaniophyllon, Omiltemia, and Renistipula. The phylogenetic analysis re-evaluated some taxonomical combinations. The transfer of Deppeopsistaxa from Deppea s.l. is supported, but however, the monophyly of the genus is not. The transfer of Renistipula from Rondeletieae is also highly supported. BothCsapodya and Edithea species form a well-defined group among Deppea s.l. with high posterior probabilities, allowing to reconsider the exclusion or integration of these taxa to Deppea.
  • Rui-Dong JIA, Chun-Ce GUO, Gui-Xia XU, Hong-Yan SHAN, Hong-Zhi KONG
    J Syst Evol. 2014, 52(5): 651-659.
    Cyclins are key regulators of cell cycle progression. Previous studies have shown that cyclin genes in plants can be divided into 10 groups. However, because those studies only focused on genes from two well-known model plants (i.e., Arabidopsis thaliana (L.) Heynh. and Oryza sativa L.), it remains unclear whether the 10 groups are reasonably defined. In this study, by analyzing the genomes of 10 representative plants (Chlamydomonas reinhardtii P. A. Dang, Physcomitrella patens(Hedw.) Bruch & Schimp., Selaginella moellendorffii Hieron., Picea abies (L.) H. Karst., Amborella trichopoda Baill., A. thaliana, Populus trichocarpa Torr. & A. Gray ex Hook., Vitis vinifera L., O. sativa, and Sorghum bicolor (L.) Moench), we estimated the phylogenetic relationships of plant cyclins and investigated their evolutionary patterns. We confirmed that plant cyclins can be classified into 10 groups, although only eight ancestral genes may have existed in the most recent common ancestor of extant green plants. We also found that, due to the frequent occurrences of gene duplication events, several groups have expanded extensively in seed plants and, particularly, flowering plants, so that multiple genes belonging to different subgroups are present in a species. Reconciliation of the evolutionary histories of these groups and subgroups further led to the identification of evolutionarily highly conserved and rapidly duplicating gene lineages. These results will guide the classification and nomenclature of plant cyclins and help understand the conservativeness and variation in their functions.