Leaf epidermal features of Quercus subgenus Cyclobalanopsis (Fagaceae) and their systematic significance

Leaf epidermal features are important taxonomic features in Quercus. We studied leaf epidermal features of 91 species and one forma of Quercus subgenus Cyclobalanopsis using light and scanning electron microscopy. Trichome terminology in oaks was assessed and clarified, aiming to score the epidermal features accurately for genus‐wide comparison. Nine trichome types, anomocytic and cyclocytic stomatal apparatus, smooth layer and platelet epicuticular wax flakes, and two trichome base types were found in subgenus Cyclobalanopsis. The epidermal features revealed three main groups in subgenus Cyclobalanopsis. The epidermal features of Quercus s.l. were uniform, supporting recognition of Cyclobalanopsis as a subgenus of Quercus rather than as a separate genus. Most leaf epidermal features show a mosaic pattern, although their numerous variations offered valuable resources for species identification. The leaf epidermal features that can be used for identification of Quercus leaves are also discussed and summarized. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 224–260.     

Two-year cycles of synchronous acorn and leaf production in biennial-fruiting evergreen oaks of subgenus Cyclobalanopsis (Quercus, Fagaceae)

Many masting species switch resources between vegetative growth and reproduction in mast and non-mast years. Although masting of oak species is well known, there have been few investigations of the relationship between vegetative growth and reproduction based on long-term monitoring data, especially in evergreen oaks of subgenus Cyclobalanopsis. We investigated annual variations over 13?years in acorn and leaf production of three evergreen oak species in subgenus Cyclobalanopsis, genus Quercus (Fagaceae)??Q. acuta, Q. salicina and Q. sessilifolia??in western Japan. In these species, the maturation of acorns occurs in the second autumn after flowering, which is known as a biennial-fruiting habit. We found a pattern of acorn production and masting in alternate years that was synchronized in all three species. Masting was not correlated with temperature and precipitation. Annual leaf-fall also showed 2-year cycle in the three oak species; peak years were synchronized between species and peak leaf-fall alternated with acorn production in all three species. Furthermore, there was a significant negative correlation between acorn and leaf production in all three species. Data showing 2-year cycles of acorn and leaf production and the negative correlation between them supports the hypothesis of resource switching between vegetative growth and reproduction. The 2-year cycle might be the basic, intrinsic rhythm of resource allocation in biennial-fruiting Cyclobalanopsis species.     

Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar

Phylogeographic analysis of the Coffea subgenus Coffea was performed using data on plastid DNA sequences and interpreted in relation to biogeographic data on African rain forest flora. Parsimony and Bayesian analyses of trnL-F, trnT-L and atpB-rbcL intergenic spacers from 24 African species revealed two main clades in the Coffea subgenus Coffea whose distribution overlaps in west equatorial Africa. Comparison of trnL-F sequences obtained from GenBank for 45 Coffea species from Cameroon, Madagascar, Grande Comore and the Mascarenes revealed low divergence between African and Madagascan species, suggesting a rapid and radial mode of speciation. A chronological history of the dispersal of the Coffea subgenus Coffea from its centre of origin in Lower Guinea is proposed. No relation was found between phylogenetic topology and the age of emergence of the volcanic islands that Coffea species have colonised in the Indian Ocean, suggesting dispersal from mainland Africa after the emergence of the youngest island, Grande Comore, 500,000 years ago. Additional sequences were obtained from GenBank for 24 species of other Rubiaceae genera, including the Rubia genus whose origin has been dated from the Upper Miocene. Estimates of substitution rates suggested that diversification in Coffea subgenus Coffea occurred about 460,000 years ago or as recently as the last 100,000 years, depending on the cpDNA region considered and calibration. The phylogenetic relationships based on plastid sequences confirmed biogeographic differentiation of coffee species, but they were not congruent with morphological and biochemical classifications, or with the capacity to grow in specific environments. Examples of convergent evolution in the main clades are given using characters of leaf size, caffeine content and reproductive mode.     

Morphophylogenetic study revealed that Erysiphe gracilis (powdery mildew of evergreen oaks,Erysiphales) is a species complex consisting of six different species

Erysiphe gracilis is a powdery mildew species that occurs on evergreen oak species belonging to Quercus subgen. Cyclobalanopsis in East Asia (China and Japan). In a previous report, we found that E. gracilis var. gracilis is divided into four genotypes each of them forming a separate clade with strong bootstrap support. In this study, we further investigated genotype speciation in E. gracilis var. longissima occurring on Q. acuta and Q. sessilifolia, and found that this variety is also divided into two distinct genotypes. These results suggested that E. gracilis represents a species complex consisting of six different species. Based on detailed morphological examinations correlating with results of molecular sequence analyses, we propose to divide E. gracilis into six species, encompassing three new species (E. uncinuloides, E. pseudogracilis, and E. longiappendiculata), one new name (E. longifilamentosa), and two known species (E. gracilis s. str. and E. hiratae). A key to the species concerned is provided.     

Analyses of cpDNA matK sequence data place Tillaea (Crassulaceae) within Crassula

Analysis of cpDNA matK sequences for a total of 43 members of the succulent plant family Crassulaceae, including 24 taxa of Crassula, recovered a well-supported clade comprising Crassula species that is sister to the remainder of the family. The resulting topologies do not support the monophyly of the currently recognized subgenera of Crassula, as one member of subgenus Disporocarpa (C. crenulata) is placed as sister to an otherwise monophyletic subgenus Crassula. The major synapomorphy that has been used to recognize the latter subgenus is a base chromosome number of x = 7 versus a base of x = 8 in the other subgenus. We cannot assess the utility of this feature for defining subgenus Crassula because a chromosome count of C. crenulata has yet to be published. The five accessions of the recently resurrected segregate genus Tillaea (of 24 total Crassula species) included here were placed in four separate, well-supported lineages, one of which is greatly removed from the other four accessions. This suggests that this genus is not valid and should not be recognized. An initial examination of the evolution of habit indicates that a perennial habit is ancestral and that the annual habit is a feature that has been derived at least twice in the genus.     

Two new hosts of anamorphic Erysiphe quercicola: Cinnamomum camphora and Murraya paniculata

Based on collections of powdery mildews (Erysiphales) in Taiwan and combined molecular and morphological analyses, camphor tree (Cinnamomum camphora) and orange jasmine (Murraya paniculata) are recognized as new hosts of the anamorph of the powdery mildew Erysiphe quercicola. The anamorphic powdery mildew on C. camphora has been known as Pseudoidium cinnamomi, but its relationship to a teleomorph was unknown. For M. paniculata as substrate of powdery mildew, only an anamorphic Cystotheca species has been named. Morphological investigation of the fungus on this host shows that the specimens from Taiwan belong to another genus because of the lack of fibrosin bodies. Analysis of internal transcribed spacer sequences indicates that the anamorphic powdery mildews on camphor and orange jasmine belong to a clade representing E. quercicola, with the teleomorph found only on oak species (Quercus, Fagaceae), but with its anamorph reported from a broad host range, particularly in the tropics.     

Correlation between the shoot-cutting behavior of the acorn weevil and the reproductive traits of host fagaceous trees

Many fagaceous species mature acorns during the second autumn after flowering and are called “2-year species.” In 2-year species of subgenus Cyclobalanopsis (genus Quercus), alternate bearing (2-year seed production cycle) is prominent, but this has not been reported for other 2-year species in the genera of Lithocarpus and Castanopsis. We tested the hypothesis that the difference in reproduction of 2-year species is linked to the weevil, Mechoris ursulus. After ovipositing on acorns, this insect cuts the shoots to which the acorns are attached. We examined the host preference of M. ursulus and reproductive traits of fagaceous 2-year species. Percentage infestation was remarkably high in the subgenus Cyclobalanopsis, whereas Lithocarpus and Castanopsis species suffered almost no damage. Furthermore, unlike Lithocarpus and Castanopsis, most of the acorn-producing shoots in subgenus Cyclobalanopsis had no current-year shoots. The clear relationship suggests that alternate bearing in subgenus Cyclobalanopsis is an adaptation to the shoot-cutting behavior of M. ursulus.     

Vibrio zhuhaiensis sp. nov., isolated from a Japanese prawn (Marsupenaeus japonicus)

A Gram-negative, oxidase-positive, facultatively anaerobic bacterium, designated strain E20121, was isolated from the digestive tract of a Japanese prawn (Marsupenaeus japonicus) collected from the coastal sea water area of Zhuhai, Guangdong province, China. The new isolate was determined to be closely related to Vibrio ponticus DSM 16217^T, having 97.6 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on recA, pyrH and rpoA also showed low levels of sequence similarities (72.6–96.6 %) with all species of the genus Vibrio. A multigene phylogenetic tree using concatenated sequences of the four genes (16S rRNA, rpoA, recA and pyrH) clearly showed that the new isolate is different from the currently known Vibrio species. DNA–DNA hybridization experiments revealed similarity values below 70 % with the closest related species V. ponticus DSM 16217^T. Several phenotypic traits enabled the differentiation of strain E20121 from the closest phylogenetic neighbours. The DNA G+C content of strain E20121 was determined to be 47.6 mol % and the major fatty acid components identified were C_16:1ω7c and/or C_16:1ω6c (39.8 %), C_18:1ω7c (13.6 %) and C_16:0 (9.6 %). Based on genotypic, phenotypic, chemotaxonomic, phylogenetic and DNA–DNA hybridization analyses, strain E20121 is proposed to represent a novel species of the genus Vibrio for which the name Vibrio zhuhaiensis sp. nov. is proposed. The type strain is E20121^T(=DSM 25602^T = CCTCC AB 2011174^T).     

An unexpected clade of South American ground beetles (Coleoptera,Carabidae, Bembidion)

Phylogenetic relationships of the Antiperyphanes Complex of the genus Bembidion are inferred using DNA sequences from seven genes (two nuclear ribosomal, four nuclear protein coding, and one mitochondrial protein coding). Redefined subgenera within the complex are each well-supported as monophyletic. Most striking was the discovery that a small set of morphologically and ecologically heterogeneous species formed a clade, here called subgenus Nothonepha. This unexpected result was corroborated by the discovery of deep pits in the lateral body wall (in the mesepisternum) of all Nothonepha, a trait unique within Bembidion. These pits are filled with a waxy substance in ethanol-preserved specimens. In one newly discovered species (Bembidion tetrapholeon sp. n., described here), these pits are so deep that their projections into the body cavity from the two sides touch each other internally. These structures in Bembidion (Nothonepha) are compared to very similar mesepisternal pits which have convergently evolved in two other groups of carabid beetles. The function of these thoracic pits is unknown. Most members of subgenus Nothonepha have in addition similar but smaller pits in the abdomen. A revised classification is proposed for the Antiperyphanes Complex.     

Almost a century of oblivion: Integrative taxonomy allows the resurrection of the longnose skate Zearaja brevicaudata (Marini, 1933) (Rajiformes; Rajidae)

Zearaja chilensis has been reported from Southern Brazil in the Southwest Atlantic (SWA) to northern Chile in the Southeast Pacific (SEP), and it was listed as vulnerable by the IUCN. Recent molecular studies have called into question the conspecificity between specimens from these opposite coasts of South America, which can have implications for the conservation status of the species. To verify the identity of specimens identified as Z. chilensis, 47 individuals from SWA and 22 from SEP were examined. By comparing external morphology, spinulation pattern, clasper, egg cases, and mitochondrial cytochrome c oxidase I (COI) sequence data, differences between groups were found. Adults from SWA presented longer snout length and shorter tail than those from SEP. Dermal denticles were restricted to the rostral area in SWA skates, whereas in SEP skates most of the dorsal surface was covered with denticles. Marked differences in the morphology of several components of clasper were noticeable. Egg cases of SWA skates had thinner lateral keels than those of SEP. Molecular analysis revealed two well-defined cohesive clusters, corresponding to SWA and SEP specimens, respectively. Average K2P distance between groups was 3.4%, higher than expected for intraspecific differences, and sequences were assigned to different BINs. These integrative approaches strongly support that specimens from SWA known as Z. chilensis correspond to a different nominal species than those from SEP. Herein, Z. brevicaudata (Marini 1933) is resurrected from synonymy with Z. chilensis.     

First record of Teleogryllus (Brachyteleogryllus) marini Otte & Alexander, 1983 (Orthoptera: Gryllidae) in korea and discussion of its continued misidentification using DNA barcoding

DNA barcoding is useful for identifying species that are difficult to distinguish via morphological analysis. However, if the public DNA barcode database includes misidentified DNA samples, subsequent molecular studies could generate incorrect results. Here, we report a misidentified DNA barcode for the North Coastal Black Field Cricket Teleogryllus (Brachyteleogryllus) marini. T. (B.) marini is routinely misidentified using DNA barcoding; it has been reported as Teleogryllus (Brachyteleogryllus) commodus since its misidentification in various studies of Asian samples. Here, we report the first occurrence of T. (B.) marini in Korea, along with its morphological diagnosis, bioacoustic signals, and DNA barcoding findings. T. (B.) marini is transferred to the subgenus Brachyteleogryllus from the subgenus Teleogryllus, based on the male genitalia morphology and phylogenetic analysis. Genetic distance analyses have shown that cytochrome c oxidase I barcoding is useful for species identification of the genus Teleogryllus, but detailed morphological investigations are essential for DNA barcoding before any molecular study.     

Inonotus taiwanensis sp. nov. (Basidiomycota) from Taiwan

Inonotus taiwanensis (Hymenochaetales) is described as a new species collected from southern Taiwan, and all specimens grew on the trunk of Trema tomentosa. This new species is characterized by having resupinate, effuse-reflexed to pileate basidiocarps, bright yellow context, long setal hyphae in context and trama, setae in hymenium and trama, and fairly small basidiospores. Maximum likelihood and Bayesian inference phylogenies inferred from both sequences of 28S and internal transcribed spacer (ITS) region of rDNA indicated that I. taiwanensis forms a distinct clade within Inonotus, and the species is sister to I. tricolor. The comparison of morphological differences among I. taiwanensis and some closely related Inonotus spp. is presented.     

Evolution of Iris subgenus Xiphium based on chromosome numbers, FISH of nrDNA (5S, 45S) and trnL–trnF sequence analysis

The subgenus Xiphium is one of the six infrageneric divisions of the genus Iris. Chromosome numbers of six of the seven Xiphium species are known. Here the aim was to infer genetic and phylogenetic relationships based on chromosome numbers, chromosome markers and plastid sequences. Chromosomal locations of 5S and 45S rDNA loci were determined in 19 populations of the 7 species by fluorescence in situ hybridization (FISH). Additionally, the trnL–trnF plastid spacer was sequenced and a phylogenetic analysis performed. Based on chromosome markers, subgenus Xiphium species were classified into four groups that differed in the number and locations of both types of nrDNA: (1) I. tingitana (2n = 28), I. filifolia (2n = 30, 34) and I. xiphium (2n = 34), (2) I. juncea (2n = 32) and I. boissieri (2n = 36), (3) I. serotina (2n = 34) and (4) I. latifolia (2n = 42). Although the trnL–trnF phylogeny was not fully resolved, the sequence analysis showed a well-supported subgroup of I. filifolia, I. tingitana and I. xiphium, as well as I. juncea. FISH physical maps of the Iris subgenus Xiphium taxa are species dependent. I. filifolia, I. tingitana and I. xiphium are very closely related species and share cytogenetic characteristics. Disploidy appears to have been central in the evolution of this subgenus, given a series of chromosome numbers (2n = 28, 30, 32, 34, 36, 42) and our phylogenetic results. Clear differences were found among European and African populations of I. filifolia. A different taxonomic treatment of I. filifolia is supported for populations on both sides of the Strait of Gibraltar.     

The Tien Shan vole (Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe

Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine–Bair–Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.     

Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae,subg. Erythrovariae,sect. Variae) and its related sexual species in Japan

Apogamous fern species are often difficult to distinguish from related species because of their continuous morphological variations. To clarify the genetic relationships among the members of the Dryopteris varia complex, we analyzed the nucleotide sequences of the plastid gene rbcL and the nuclear gene PgiC. We also analyzed the diploid sexual species D. caudipinna and D. chinensis, which have not been included in the complex, but were recently shown to be closely related to the complex in a molecular phylogenetic study. The PgiC sequences of the diploid sexual species, D. varia, D. saxifraga, D. sp. ‘protobissetiana’ (undescribed diploid sexual species), D. caudipinna, and D. chinensis, were well differentiated and hence designated A, B, C, D, and E, respectively. Thus, the PgiC constitution of apogamous species in the complex was as follows: D. bissetiana, B + C; D. kobayashii, B + C + E); D. pacifica, A + C, A + B + C, or A + C + D; D. sacrosancta, A + C + E; and D. saxifragivaria, B + C. These results suggest that these apogamous species are formed by hybridizations of species including not only the three diploid sexual species of the D. varia complex (A, B, and C) but also the two diploid sexual species D. caudipinna (D) and D. chinensis (E), which do not belong to the complex.     

Dujardinascaris mormyropsis n. sp. (Nematoda: Anisakidae) from the osteoglossiform fish Mormyrops anguilloides (Linnaeus) (Mormyridae) in Central Africa

A new nematode species, Dujardinascaris mormyropsis n. sp. (Anisakidae), is described from specimens found in the stomach and intestine of the cornish jack Mormyrops anguilloides (Linnaeus) (Osteoglossiformes; Mormyridae) in the Sangha River (Congo River basin) in Dzanga-Sangha Protected Areas, Central African Republic. Based on light and scanning electron microscopical examination, the new species differs from the only other congeneric species parasitising fishes in Africa, D. malapteruri (Baylis, 1923), mainly in the presence of dentigerous ridges on lips, absence of lateral caudal alae in the cloacal region, in the anteriorly curved, non-bifid distal tip of the gubernaculum and larger eggs (60–90 × 52–78 vs 45 × 30 μm); males of D. mormyropsis are characterised by the presence of a ventral precloacal cuticular ornamentation not observed in other Dujardinascaris spp. Dujardinascaris mormyropsis and D. malapteruri also differ in the order of their fish hosts (Osteoglossiformes vs Siluriformes). Specimens previously reported as Dujardinascaris graberi Troncy, 1969, a junior synonym of D. malapteruri, from Mormyrops engystoma Boulenger in Chad belong to the new species D. mormyropsis.     

Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus

Phylogenetic relationships among 108 oak species (genus Quercus L.) were inferred using DNA sequences of six nuclear genes selected from the existing genomic resources of the genus. Previous phylogenetic reconstructions based on traditional molecular markers are inconclusive at the deeper nodes. Overall, weak phylogenetic signals were obtained for each individual gene analysis, but stronger signals were obtained when gene sequences were concatenated. Our data support the recognition of six major intrageneric groups Cyclobalanopsis, Cerris, Ilex, Quercus, Lobatae and Protobalanus. Our analyses provide resolution at deeper nodes but with moderate support and a more robust infrageneric classification within the two major clades, the ‘Old World Oaks’ (Cyclobalanopsis, Cerris, Ilex) and ‘New World Oaks’ (Quercus, Lobatae, Protobalanus). However, depending on outgroup choice, our analysis yielded two alternative placements of the Cyclobalanopsis clade within the genus Quercus. When Castanea Mill. was chosen as outgroup, our data suggested that the genus Quercus comprised two clades corresponding to two subgenera as traditionally recognized by Camus: subgenus Euquercus Hickel and Camus and subgenus Cyclobalanopsis Øersted (Schneider). However, when Notholithocarpus Manos, Cannon and S. Oh was chosen as an outgroup subgenus Cyclobalanopsis clustered with Cerris and Ilex groups to form the Old World clade. To assess the placement of the root, we complemented our dataset with published data of ITS and CRC sequences. Based on the concatenated eight gene sequences, the most likely root position is at the split between the ‘Old World Oaks’ and the ‘New World Oaks’, which is one of the alternative positions suggested by our six gene analysis. Using a dating approach, we inferred an Eocene age for the primary divergences in Quercus and a root age of about 50–55 Ma, which agrees with palaeobotanical evidence. Finally, irrespective of the outgroup choice, our data boost the topology within the New World clade, where (Protobalanus + Quercus) is a sister clade of Lobatae. Inferred divergence ages within this clade and the Cerris–Ilex clade are generally younger than could be expected from the fossil record, indicating that morphological differentiation pre-dates genetic isolation in this clade.