Table of Contents

19 January 2011, Volume 49 Issue 1

Cover illustration: Suggested reconstruction of the life history of the basal eutracheophyte Cooksonia paranensis Gerrienne et al. 2001. See GERRIENNE & GONEZ, pp. 1–16 in this issue.

  

Reviews
• Early evolution of life cycles in embryophytes: A focus on the fossil evidence of gametophyte/sporophyte size and morphological complexity

  Philippe GERRIENNE, Paul GONEZ

  J Syst Evol. 2011, 49(1): 1-16.
  https://doi.org/10.1111/j.1759-6831.2010.00096.x

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  Embryophytes (land plants) are distinguished from their green algal ancestors by diplobiontic life cycles, that is, alternation of multicellular gametophytic and sporophytic generations. The bryophyte sporophyte is small and matrotrophic on the dominant gametophyte; extant vascular plants have an independent, dominant sporophyte and a reduced gametophyte. The elaboration of the diplobiontic life cycle in embryophytes has been thoroughly discussed within the context of the Antithetic and the Homologous Theories. The Antithetic Theory proposes a green algal ancestor with a gametophyte-dominant haplobiontic life cycle. The Homologous Theory suggests a green algal ancestor with alternation of isomorphic generations. The shifts that led from haplobiontic to diplobiontic life cycles and from gametophytic to sporophytic dominance are most probably related with terrestrial habitats. Cladistic studies strongly support the Antithetic Theory in repeatedly identifying charophycean green algae as the closest relatives of land plants. In recent years, exceptionally well-preserved axial gametophytes have been described from the Rhynie chert (Lower Devonian, 410 Ma), and the complete life cycle of several Rhynie chert plants has been reconstructed. All show an alternation of more or less isomorphic generations, which is currently accepted as the plesiomorphic condition among all early polysporangiophytes, including basal tracheophytes. Here we review the existing evidence for early embryophyte gametophytes. We also discuss some recently discovered plants preserved as compression fossils and interpreted as gametophytes. All the fossil evidence supports the Antithetic Theory and indicates that the gametophytic generation/sporophytic generation size and complexity ratios show a gradual decrease along the land plant phylogenetic tree.
• Evolutionary and ecological genomics of non-model plants

  Bao-Hua SONG, Thomas MITCHELL-OLDS

  J Syst Evol. 2011, 49(1): 17-24.
  https://doi.org/10.1111/j.1759-6831.2010.00111.x

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  Dissecting evolutionary dynamics of ecologically important traits is a long-term challenge for biologists. Attempts to understand natural variation and molecular mechanisms have motivated a move from laboratory model systems to non-model systems in diverse natural environments. Next generation sequencing methods, along with an expansion of genomic resources and tools, have fostered new links between diverse disciplines, including molecular biology, evolution, ecology, and genomics. Great progress has been made in a few non-model wild plants, such as Arabidopsis relatives, monkey flowers, and wild sunflowers. Until recently, the lack of comprehensive genomic information has limited evolutionary and ecological studies to larger QTL (quantitative trait locus) regions rather than single gene resolution, and has hindered recognition of general patterns of natural variation and local adaptation. Further efforts in accumulating genomic data and developing bioinformatic and biostatistical tools are now poised to move this field forward. Integrative national and international collaborations and research communities are needed to facilitate development in the field of evolutionary and ecological genomics.
Research Articles
• Integrating fossils in a molecular-based phylogeny and testing them as calibration points for divergence time estimates in Menispermaceae

  Frédéric M.B. JACQUES, Wei WANG, Rosa Del C. ORTIZ, Hong-Lei LI, Zhe-Kun ZHOU, Zhi-Duan CHEN

  J Syst Evol. 2011, 49(1): 25-49.
  https://doi.org/10.1111/j.1759-6831.2010.00105.x

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  The phylogeny of extant Menispermaceae (Ranunculales) is reconstructed based on DNA sequences of two chloroplast genes (rbcL and atpB) from 94 species belonging to 56 genera. Fossilized endocarps represent 34 genera. The positions of these are inferred using 30 morphological characters and the molecular phylogeny as a backbone constraint. Nine of the thirteen nodes that are each dated by a fossil are used as calibration points for the estimates of molecular divergence times. BEAST is used to estimate stem age (121.2 Myr) and crown age (105.4 Myr) for Menispermaceae. This method does not require an input tree topology and can also account for rate heterogeneity among lineages. The sensitivity of these estimates to fossil constraints is then evaluated by a cross-validation procedure. The estimated origin for Menispermaceae is dated to the mid-Jurassic if the customary maximum age of 125 Myr for eudicots is not implemented. All constraints when used alone failed to estimate node ages in some parts of the tree. Fossils from the Palaeocene and Eocene impose strict constraints. Likewise, the use of Prototinomiscium as a dating constraint for Menispermaceae appears to be a conservative approach.
• Phylogenetic reconstruction of Chirita and allies (Gesneriaceae) with taxonomic treatments

  Yin-Zheng WANG, Ru-Bing MAO, Yan LIU, Jia-Mei LI, Yang DONG, Zhen-Yu LI, James F. SMITH

  J Syst Evol. 2011, 49(1): 50-64.
  https://doi.org/10.1111/j.1759-6831.2010.00113.x

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  Chirita D. Don, a large genus in the subfamily Cyrtandroideae of Gesneriaceae, has been the subject of much debate whether it is a natural group or not. In addition, the highly heterogeneous Chirita has also been very problematic with regard to delimitation and subdivision. Here we used the nrDNA internal transcribed spacer and cpDNA trnL-F for molecular phylogenetic analaysis, combined with morphological data. Our results suggest that Chirita is an artificial, polyphyletic genus. The most important character that defines Chirita, the dorso-ventrally oblique and bilamellar stigma, has evolved convergently in different clades of diandrous Cyrtandroideae. Chirita sensu stricto only includes the species of Chirita sect. Chirita, whereas Chirita sect. Microchirita is an independent clade located at the basal node of the phylogenetic tree. Chirita sect. Liebigia is closely related to Didymocarpus with an entire stigma unlike other species of Chirita. The species of Chirita sect. Gibbosaccus, Chiritopsis, Primulina, and Wentsaiboea form a monophyletic group that is sister to a strongly supported clade comprising four monotypic genera Paralagarosolen, Calcareoboea, Petrocodon, and Tengia. We further analyzed the morphological evolution of Chirita and identified a series of morphological synapomorphies for the monophyletic groups revealed herein, and thereby provide a taxonomic treatment in this study.
• Phylogenetic relationships among Hystrix species and related species based on expressed sequence tag-polymerase chain reaction

  Rui-Wu YANG, Hisashi TSUJIMOTO, Chun-Bang DING, Li ZHANG, Xiao-Li WANG, Yong-Hong ZHOU

  J Syst Evol. 2011, 49(1): 65-71.
  https://doi.org/10.1111/j.1759-6831.2010.00107.x

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  Twelve species, including three Hystrix species, five Leymus species, Hordeum bogdanii, Pseudoroegneria spicata, Psathyrostachys huashanica, and Roegneria ciliaris, were used for expressed sequence tag-polymerase chain reaction (EST-PCR) assay. A total of 125 products were amplified by 72 sets of EST-PCR markers developed in barley, among which 106 (84.8%) products were found to be polymorphic. Each EST-PCR marker produced 0–6 polymorphic bands, with an average of 1.47. The relationship between H. duthiei ssp. duthiei and H. duthiei ssp. longearistata is close, but they are remote to H. patula. Hystrix duthiei ssp. duthiei and H. duthiei ssp. longearistata were clustered with Leymus species and Psathyrostachys huashanica, which suggested that they have close genetic relationships. The results of EST-PCR analysis are basically comparable with those obtained from studies on cytology, which indicated that EST-PCR can be used to assess the genetic relationships among the perennial species in Triticeae.
• Genetic structure and phylogeography of a relict tree fern, Sphaeropteris brunoniana (Cyatheaceae) from China and Laos inferred from cpDNA sequence variations: Implications for conservation

  Zi-Juan WANG, Kai-Yun GUAN

  J Syst Evol. 2011, 49(1): 72-79.
  https://doi.org/10.1111/j.1759-6831.2010.00108.x

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  In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identified from the 10 investigated populations. Moderate haplotype diversity (h= 0.66580) and low nucleotide diversity (π= 0.23 × 10⁻³) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h= 0.60195, π= 0.35 × 10⁻³) than that of Hainan–Laos (h= 0.00000, π= 0.00). A high level of genetic differentiation (94.74%) between the two regions was revealed by amova. Nested clade analysis identified two major clusters of the five haplotypes, one clade in the Yunnan region and the other in Hainan–Laos. The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes. The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations. The Yunnan populations frequently contained an ancestral haplotype, and most of them harbored other descendent haplotypes. Based on the distribution pattern of haplotypes and the nested clade analysis results, the Yunnan region potentially had several refugia of this species during glacial periods, whereas the Hainan populations were probable new colonizations.