A molecular investigation of the genus Ecklonia (Phaeophyceae,Laminariales) with special focus on the Southern Hemisphere

Brown algae of the order Laminariales, commonly referred to as kelps, are the largest and most productive primary producers in the coastal inshore environment. The genus Ecklonia (Lessoniaceae, Phaeophyceae) consists of seven species with four species in the Northern Hemisphere and three in the Southern Hemisphere. It was recently transferred to the family Lessoniaceae based on phylogenetic analyses of nuclear and chloroplastic markers, though the type of the genus was not included and its relationship with allied genera Eckloniopsis and Eisenia remained unresolved. The present study is the first to produce a phylogeny focussed on the genus Ecklonia. It included sequences from nuclear, mitochondrial, and chloroplastic DNA, for most of the distribution range of the three current Southern Hemisphere species (Ecklonia radiata, Ecklonia maxima, and a sample of a putative Ecklonia brevipes specimen), sequences for East Asiatic species (Ecklonia cava, Ecklonia kurome, and Ecklonia stolonifera), as well as the closely related genera Eckloniopsis and Eisenia. Results confirmed E. radiata and E. maxima as two distinct species in South Africa, E. radiata as a single species throughout the Southern Hemisphere (in South Africa, Australia, and New Zealand) and East Asiatic species as a distinct lineage from the Southern Hemisphere clade. Results further pointed out a close sister relationship between Eckloniopsis radicosa and two Eisenia species (including the type species: Eisenia arborea) to the genus Ecklonia suggesting that the genera Eckloniopsis and Eisenia are superfluous.     

Significance of pre-Quaternary climate change for montane species diversity: Insights from Asian salamanders (Salamandridae: Pachytriton)

Despite extensive focus on the genetic legacy of Pleistocene glaciation, impacts of earlier climatic change on biodiversity are poorly understood. Because amphibians are highly sensitive to variations in precipitation and temperature, we use a genus of Chinese montane salamanders (Salamandridae: Pachytriton) to study paleoclimatic change in East Asia, which experienced intensification of its monsoon circulation in the late Miocene associated with subsequent Pliocene warming. Using both nuclear and mitochondrial DNA sequences, we reconstruct the species tree under a coalescent model and demonstrate that all major lineages originated before the Quaternary. Initial speciation within the genus occurred after the summer monsoon entered a stage of substantial intensification. Heavy summer precipitation established temporary water connectivity through overflows between adjacent stream systems, which may facilitate geographic range expansion by aquatic species such as Pachytriton. Species were formed in allopatry likely through vicariant isolation during or after range expansion. To evaluate the influence of Pliocene warming on these cold-adapted salamanders, we construct a novel temperature buffer-zone model, which suggests widespread physiological stress or even extinction during the warming period. A significant deceleration of species accumulation rate is consistent with Pliocene range contraction, which affected P. granulosus and P. archospotus the most because they lack large temperature buffer zones. In contrast, demographic growth occurred in species for which refugia persist. The buffer-zone model reveals the Huangshan Mountain as a potential climatic refugium, which is similar to that found for other East Asian organisms. Our approach can incorporate future climatic data to evaluate the potential impact of ongoing global warming on montane species (particularly amphibians) and to predict possible population declines.     

Divergence in size,but not in shape: variation in skull size and shape within Ommatotriton newts

Using a geometric morphometric approach, we explored the variation in skull size and skull shape in banded newts (genus Ommatotriton). The genus Ommatotriton is represented by two allopatric, genetically well‐defined species: Ommatotriton ophryticus and O. vittatus. Within each species, two subspecies have been recognised. The samples used in this study cover the geographical and genetic variation within each species. We found statistically significant variation in skull size between species and among populations within species. When corrected for size, there was no significant variation in shape between species. Our results indicate that the variation in skull shape within the genus Ommatotriton is almost entirely due to size‐dependent, allometric shape changes. The exception is the shape of the ventral skull in males. Males of O. ophryticus and O. vittatus significantly diverge in the shape of the ventral cranium. The ventral skull, more precisely the upper jaw and palate, is directly functionally related to feeding. In general, our results indicate that allometry is a significant factor in the morphological variation of banded newts. However, the divergence in the ventral skull shape of males indicates that sexual selection and niche partitioning may have influenced the evolution of skull shape in these newts.     

Teleocichla preta,a new species of cichlid from the Rio Xingu Basin in Brazil (Teleostei: Cichlidae)

Teleocichla preta nov. sp. inhabits the rapids along the Rio Xingu and lower portion of the Rio Iriri. It is the largest species in the genus, reaching 121·3 mm standard length (L_S) while others do not reach more than 87·8 mm L_S. Teleocichla preta is distinguished from all other species of Teleocichla by the unique blackish (in live specimens) or dark brown (preserved specimens) overall colouration of the body, which masks the faint vertical bars or zig‐zag pattern of blotches on the flanks. Teleocichla preta also has a deeper body and a deep laterally compressed caudal peduncle, unlike any other congener, as well as a stout lower pharyngeal tooth plate bearing molariform teeth on its median area.     

Evolutionary history of the complex polymorphic dobsonfly genus Neoneuromus (Megaloptera: Corydalidae)

The dobsonfly genus Neoneuromus van der Weele is endemic to the Oriental region. Species possess highly variable body and wing colouration and markings, not only among species but also among conspecific individuals of certain species. This stark polymorphism hinders accurate species identification, and obscures an undocumented species diversity as well as our understanding of the evolutionary history of this genus. We used multiple methods of molecular identification combined with morphological evidence to delimitate species, circumscribing a total of 13 species in Neoneuromus . Five new species are herein described: Neoneuromus indistinctus Liu, Hayashi & Yang, sp.n. , Neoneuromus maculatus Liu, Hayashi & Yang, sp.n. , Neoneuromus niger Liu, Hayashi & Yang, sp.n. , Neoneuromus similis Liu, Hayashi & Yang, sp.n. and Neoneuromus vanderweelei Liu, Hayashi & Yang, sp.n. The dated phylogeny with reconstructed ancestral areas indicates an initial divergence of Neoneuromus during the mid‐Eocene. A broad area including northeastern India and northern Indochina could be a centre for early divergence of the genus, while complex dispersal and vicariance events dating from the late Eocene to the Pliocene probably shaped the present diversity and distribution of the genus. Our ancestral character state reconstruction suggests that the pale and dark colour forms among different species, or conspecifics, could evolve rapidly and that changes in colouration could be driven by species‐specific mate recognition.     

Combination of local selection pressures drives diversity in aposematic signals

The diversity of aposematic signals is one of the most difficult phenomena for understanding the evolution of such signals because aposematic animals are most effectively protected when they are common. Theoretical and experimental studies predict that a combination of local selection pressures could maintain variation in aposematic signals. However, the application of this hypothesis to large-scale geographic variation in aposematic signals, other than mimicry systems, is yet to be tested empirically. I investigated geographic variation in morphological and behavioural aposematic signals of the newts, Cynops pyrrhogaster, and in predation pressures on them in populations ranging over 800 km of latitude. Field experiments demonstrated that local differences in predation pressures explain well the island-mainland variation in the aposematic colouration and behaviour of newts. Furthermore, I found a latitudinal gradient in aposematic colouration but not in behaviour, independent of predation pressures. The results suggested that island-mainland variation in aposematic signals resulting from local differences in predation pressures might also be shaped by several factors, such as temperature, body size variation, and genetic differences, and such factors might act on each aposematic trait differently.     

Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes

Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous ( approximately 69Ma) or Middle Eocene ( approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea ( approximately 29Ma).     

Hellcotytencnus spp. (Nematoda: Tylenchida) from managed soils in New Zealand

Abstract

Helicotylenchus species collected from managed soils in New Zealand were identified. They were found at 159 sites. H. pseudorobustus was found at 82 of these sites, H. labiatus at 56, H. varicaudatus at 28, and H. canadensis at 4. Only 11 sites had more than one species present and most (7) of these sites had mixtures of H. pseudorobustus and H. labiatus. H. labiatus, reported only twice before, was the most common species found in cotula bowling greens. H. canadensis was restricted to sites south of 45°S. Measurements are given for 15 populations, and H. labiatus is illustrated. Characters separating the four species are given.     

Phylogenetic affiliation of the desert truffles <Emphasis Type="Italic">Picoa juniperi</Emphasis> and <Emphasis Type="Italic">Picoa lefebvrei</Emphasis>

The molecular phylogeny and comparative morphological studies reported here provide evidence for the recognition of the genus Picoa, an hypogeous desert truffle, in the family Pyronemataceae (Ascomycota, Pezizales). Picoa juniperi and Picoa lefebvrei were reassigned to the genus Picoa based on large subunit (LSU) sequence (28S) rDNA and internal transcribed spacer (ITS) rDNA (including the partial 18S, ITS1, ITS2, 5.8S gene, and partial 28S of the nuclear rDNA) data. Morphological studies of spores, asci, perida, and gleba revealed high similarities between P. lefebvrei and P. juniperi, thereby confirming the membership of both species in the genus Picoa. These two species were primarily distinguishable based on ascospore ornamentation.     

Caryology and taxonomy of the Catarrhine monkeys

The number and the morphology of chromosomes are a characteristic of the species. Knowledge of the mechanisms of chromosome breakage and rearrangement offers the possibility of understanding caryotype evolution. On the basis of this knowledge, we can trace the phylogeny and organize the taxonomy of a group of living forms. In the present paper, the available data on the number and morphology of the chromosomes of the Catarrhine monkeys have been analyzed from the standpoint of taxonomy and evolution. According to this karyological revision, the suborder Catarhine might be divided into two groups (superfamilies): Cercopithecoidea and Hominoidea. Within the Cercopithecoidea the following main groups should be further distinguished: 1. a group which includes all the species of the genus Cercopithecus; 2. a group which includes the different species belonging to the genera Papic, Macaca, Theropithecus and Cercocebus; 3. a group which includes the genus Colobus, Presbytis and Hylobates. Within the Hominoidea, the three anthropoid apes (Pan, Pongo, Gorilla) can be distinguished from man by the difference in the number of chromosomes. Moreover, among the anthropoid apes, the Orang-outang can be differentiated from the others by the morphology of the chromosomes.     

Preliminary analysis of numerical taxonomy of the genusSaguinus based on dental measurements

Although several investigations have been made from different viewpoints, the classification or interspecific relationships ofSaguinus still remain uncertain. In the present study, we applied multivariate analysis methods to dental measurements of part ofSaguinus populations of sufficient sample size and obtained the following conclusions.Saguinus can be classified into two main groups: one consists ofS. oedipus andS. leucopus, and the other ofS. fuscicollis, S. nigricollis, S. labiatus, andS. mystax. Concerning the former group, the two subspecies ofS. oedipus, S. o. oedipus, andS. o. geoffroyi, show a close affinity with each other and also a close relationship toS. leucopus, while the latter group consists of two subgroups of species, one includingS. fuscicollis andS. nigricollis, and the other includingS. labiatus andS. mystax. The biological distance betweenS. oedipus oedipus andS. o. geoffroyi is slightly larger than that between the pairs ofS. fuscicollis andS. nigricollis and ofS. labiatus andS. mystax. Factor analysis revealed significant factors which could explain the differences among the seven maleSaguinus populations. Taking all the results into account, it seems necessary to reconsider the phylogenetic relationships within the genusSaguinus.     

Phylogeny and taxonomy of the Prenolepis genus‐group of ants (Hymenoptera: Formicidae)

Abstract. We investigated the phylogeny and taxonomy of the Prenolepis genus‐group, a clade of ants we define within the subfamily Formicinae comprising the genera Euprenolepis, Nylanderia, gen. rev. , Paraparatrechina, gen. rev. & stat. nov. , Paratrechina, Prenolepis and Pseudolasius. We inferred a phylogeny of the Prenolepis genus‐group using DNA sequence data from five genes (CAD, EF1αF1, EF1αF2, wingless and COI) sampled from 50 taxa. Based on the results of this phylogeny the taxonomy of the Prenolepis genus‐group was re‐examined. Paratrechina (broad sense) species segregated into three distinct, robust clades. Paratrechina longicornis represents a distinct lineage, a result consistent with morphological evidence; because this is the type species for the genus, Paratrechina is redefined as a monotypic genus. Two formerly synonymized subgenera, Nylanderia and Paraparatrechina, are raised to generic status in order to provide names for the other two clades. The majority of taxa formerly placed in Paratrechina, 133 species and subspecies, are transferred to Nylanderia, and 28 species and subspecies are transferred to Paraparatrechina. In addition, two species are transferred from Pseudolasius to Paraparatrechina and one species of Pseudolasius is transferred to Nylanderia. A morphological diagnosis for the worker caste of all six genera is provided, with a discussion of the morphological characters used to define each genus. Two genera, Prenolepis and Pseudolasius, were not recovered as monophyletic by the molecular data, and the implications of this result are discussed. A worker‐based key to the genera of the Prenolepis genus‐group is provided.     

Morphological variation versus genetic divergence: a taxonomic implication for Mogannia species (Cicadidae: Cicadinae)

Species showing intraspecific morphological variation tend to be very difficult to identify using morphological characters. One such example is the cicada genus Mogannia where some species show considerable intraspecific variation mainly exhibited by wing pattern and body colouration. Thirty-one variants covering different putative species of Mogannia were recognized and illustrated in the present paper. Molecular data of mitochondrial COI and Cytb sequences were employed to test the level of variation and phylogeny of them. The existence of a ‘barcoding gap’ between intraspecific and interspecific genetic divergences and the reciprocally monophyletic clades indicate that all the closely related variants represent a single species, and that all these variants correspond to six species, respectively. However, the evolutionary relationships of intraspecific variants are not resolved possibly due to insufficient genetic variation among them. Our results indicated that some morphological characters, especially the wing pattern and body colouration, and even the number of apical processes of the aedeagus in a couple of related species, must be used with great caution in delimiting Mogannia species and their relatives. The factors responsible for intraspecific morphological variation and phylogeny of Mogannia spp. are preliminarily discussed.     

Contribution to the cytotaxonomy of Oryzopsis (Poaceae)

Meiotic studies were performed in twelve populations of four Oryzopsis species (O. pubiflora, O. lateralis, O. holciformis var. longiglomis and O. barbellata) to obtain data on the ploidy level and cytological evolution of the genus. The chromosome number 2n=2x=24 was revealed in all the species and populations studied. The present and other studies show the occurrence of two basic chromosome numbers in the genus, i.e. x=11 and x=12. Although Oryzopsis species and populations studied are diploid and are expected to form only bivalents in metaphase of meiosis‐I, quadrivalents were observed in O. pubiflora and O. lateralis, possibly due to the occurrence of heterozygote translocations. B‐chromosomes of 0–2 were observed in all species and populations studied. This is the first report of the occurrence of B‐chromosomes in the genus Oryzopsis. Several meiocytes showed the presence of double chromosome number in O. lateralis, and multipolar cells were observed in populations of O. barbellata, O. lateralis and O. holciformis var. longiglomis. The occurrence of large pollen grains (possibly unreduced) was observed along with smaller (normal) pollen grains in these species. Significant differences observed in chiasma frequency and distribution among studied species may be of use in species delimitation. The Kakan population differed significantly from the other populations of O. lateralis in meiotic characteristics. If such cytological differences are accompanied by morphological variation (under investigation), we may consider this population as a new variety or subspecies.     

Evolutionary and biogeographic history of the subfamily Neoplecostominae (Siluriformes: Loricariidae)

Freshwater fish evolution has been shaped by changes in the earth's surface involving changes in the courses of rivers and fluctuations in sea level. The main objective of this study is to improve our knowledge of the evolution of loricariids, a numerous and adaptive group of freshwater catfish species, and the role of geological changes in their evolution. We use a number of different phylogenetic methods to test the relationships among 52 representative taxa within the Neoplecostominae using 4676 bps of mitochondrial and nuclear DNA. Our analysis revealed that the subfamily Neoplecostominae is monophyletic, including Pseudotocinclus, with three lineages recognized. The first lineage is composed of part of Pareiorhina rudolphi, P. cf. rudolphi, and Pseudotocinclus; the second is composed of Isbrueckerichthys, Pareiorhaphis, Kronichthys, and the species Neoplecostomus ribeirensis; and the third is composed of Pareiorhina carrancas, P. cf. carrancas, Pareiorhina sp. 1, a new genus, and all the species of the genus Neoplecostomus, except N. ribeirensis. The relaxed molecular clock calibration provides a temporal framework for the evolution of the group, which we use for a likelihood‐based historical biogeographic analysis to test relevant hypotheses on the formation of southeast Brazil. We hypothesize that headwater capture events and marine regressions have shaped the patterns of distribution within the subfamily Neoplecostominae throughout the distinct basins of southeast Brazil.     

Subtractive screen of potential limb regeneration related genes from Pachytriton brevipes

Regeneration capacity varies greatly among different animal species. In vertebrate, amphibian especially the Urodela, has been used as a powerful model system to study the mechanism of tissue regeneration because of the strong ability to regenerate their damaged or lost appendages. Pachytriton brevipes, a species of newt, which is widely distributed in south of China, can completely restore their damaged limbs within several months. In this study, we use modified suppression subtractive hybridization assay and dot-blot screening to identify candidate genes involved in tissue regeneration in P. brevipes. We successfully isolated 81 ESTs from a forward regeneration subtraction library. And we further verified the differential expression of four candidate genes, Rpl11, Cirbp, Ag2 and Trimx, between regenerating blastema and non-regeneration tissues by in situ hybridization. These genes were also be further characterized by phylogenetic and bioinformatic analysis. In general, we provided a comparative experimental approach to study the mechanisms of vertebrate regeneration.     

A study of Sarcocornia A.J. Scott (Chenopodiaceae) from Western Mediterranean Europe

The latest publications on Sarcocornia taxonomy and phylogeny recognize six taxa in this genus on the Iberian Peninsula: S. perennis, S. fruticosa, S. alpini, S. alpini subsp. carinata, S. hispanica, and S. pruinosa. The present study represents a comprehensive revision of the different taxa in the Sarcocornia genus present in Western Mediterranean Europe by means of morphological, micromorphological and phylogenetic internal transcribed spacer (ITS) analysis. Morphological and micromorphological data were studied from Sarcocornia samples from 113 populations in coastal salt marshes and inland salt pans in Portugal, France, Spain and Italy. Sixteen new ITS sequences were obtained from Mediterranean Sarcocornia species and analysed together with previous reported data. Published karyological, ecological and biogeographical data from Western Mediterranean Europe were also reviewed. The results indicate the presence of a new species, S. lagascae, found growing in coastal Mediterranean areas of the Iberian Peninsula. The species S. fruticosa was found to be absent from the Iberian territories.     

Oreonectes guilinensis (Teleostei,Cypriniformes, Nemacheilidae), a new loach species from Guangxi,China

A new loach Oreonectes guilinensis sp. nov. is described from Guangxi Zhuang Autonomous Region, China. It is the second surface-dwelling fish identified in the genus Oreonectes after the type species Oreonectes platycephalus. This new species can be distinguished from other species within the genus by the combination of the following features: a round caudal fin, 13–14 branched rays, an incomplete lateral line with 4–6 pores, a short pelvic fin located some distance from the anus, a scale-covered body, a stout build (body width 14.0%–16.7% of standard length), a posterior chamber of well-developed airbladder and a yellowish-brown body with a lateral dark brown strip. The maximum likelihood phylogenetic analysis based on cytb gene recovered this new species in a well-supported clade with the type species O. platycephalus, sister to the Lefua clade. Morphological comparisons as well as our phylogenetic tree support Oreonectes shuilongensis, Oreonectes daqikongensis, Oreonectes jiarongensis as species of Troglonectes. Based on our results there are 6 valid species in the genus Oreonectes.