Phylogenetic relationships of the Chinese cyprinid genus <Emphasis Type="Italic">Rhinogobio </Emphasis>Bleeker (Teleostei: Cyprinidae) based on sequences of the mitochondrial DNA control region,with comments on character adaptations

Rhinogobio is a cyprinid genus restricted to the river drainages of China. Sequences of the mitochondrial DNA control region were determined for four Rhinogobio species and one outgroup species, Coreius heterodon, to investigate the phylogenetic relationships within the genus. The control region of the Rhinogobiospecies ranges from 922 to 930 base pairs and comprises 930 base pairs in Coreius. Our phylogenetic analysis indicates two distinct lineages in the genus Rhinogobio. The first includes only R R. ventralis. In the second lineage there are three species, two closely related species R.cylindricus andR.hunanensis, and their sister speciesR. typus. An analysis of character adaptations suggests an evolutionary trend in this genus towards a relatively lower body and caudal peduncle depth, a shorter dorsal fin, and a more anterior anus. In addition, there is a trend towards shorter barbels and relatively larger eyes. Some or all of these traits may be associated with a habitat shift from fast-flowing turbid rivers to slower-flowing clear river habitats.     

The phylogenetic relationships of Cynoglottis (Boraginaceae- Boragineae) inferred from ITS, 5.8S and trnL sequences

A molecular phylogenetic analysis of Cynoglottis was performed to evaluate previous hypotheses based on non-molecular evidence concerning the position of this genus within Boraginaceae tribe Boragineae. ITS-5.8S and trnL_UAA sequences from the nuclear and chloroplast non-coding genomes were obtained for four Cynoglottis taxa and selected members of the related genera Anchusa, Anchusella, Gastrocotyle, Brunnera and Pentaglottis. Cynoglottis is monophyletic, but neither trnL nor ITS support a close relationship with Brunnera, unlike previously supposed on morphological grounds. Brunnera is, instead, related to the southwestern European monotypic genus Pentaglottis, with which it forms a basal clade. ITS-5.8S sequences show that Anchusa thessala, a southeastern European annual species of Anchusa subg. Buglossellum, is sister to Cynoglottis and that the two taxa form a clade which also includes the Balkan endemic Gastrocotyle macedonica. Species of Anchusa subg. Anchusa form a separate lineage with high bootstrap support, suggesting that this heterogeneous genus is paraphyletic with respect to Cynoglottis. ITS sequences also discriminate between the Balkan-Apenninic diploid C. barrelieri and the Anatolian tetraploid C. chetikiana, albeit with low support. The molecular results are discussed in the light of karyological, morphological and chorological aspects.This work has been supported by M.I.U.R. 40% 2003 and the University of Firenze.     

Nothotalisia, a new genus of Picramniaceae from tropical America

A new genus of Picramniaceae from tropical America, Nothotalisia, is described. Of the three species in the genus, N. piranii and N. cancellata, are new to science. The third, N. peruviana, was originally described as Talisia peruviana in the Sapindaceae. The genus and all three species are described, illustrated, and distinguished by means of a key.     

Molecular identification of <Emphasis Type="Italic">Schoenoplectiella</Emphasis> species (Cyperaceae) by use of microsatellite markers

Over the past few decades, use of molecular markers for species delimitation has drastically increased. Schoenoplectiella Lye has been recognized as a taxonomically difficult genus because of its morphological simplicity and frequent interspecific hybridization. The main objective of this study was to clarify the taxonomic identities of eight Schoenoplectiella species by use of molecular markers. We also evaluated the genetic relationships among S. × trapezoidea, known as a natural hybrid, and its close relatives. We used six microsatellite markers for 44 individuals from 31 natural populations of eight Schoenoplectiella species in South Korea. Six microsatellite marker combinations generated 59 amplification-detectable bands, of which 33 were specifically detected in one or more individuals of each species. Cluster analysis revealed that the grouping was consistent with the taxonomically recognized species. Our results do not support the hybrid origin of S. × trapezoidea. Rather, they suggest that this species is more closely related to S. hotarui. The informative microsatellite markers enabled us to clarify the distinctions among Schoenoplectiella species from South Korea and to identify the genetic relationships among these species. The molecular signatures found suitable for accurate identification of Schoenoplectiella species can be reliably used for studies of the phylogeny and evolution of this genus.     

Morphological variation inLolium (Poaceae) as a measure of species relationships

Analysis of morphological and phenological data for determining the genetic variation within sevenLolium species led to the recognition of two groups within this genus. One group, containing the two inbreeding speciesL. temulentum andL. persicum, was clearly distinct from all other species. Strong morphological and phenological intergradation was found between both species. The cross-breeding species,L. perenne, L. rigidum, andL. multiflorum, formed another group. Little differentiation was found between these species, though they were distinct. Two inbreeding species,L. loliaceum andL. remotum, were clearly distinct from each other and the two groups.L. loliaceum had an isolated position and was most related toL. rigidum. L. remotum had an intermediate position between the cross-breeding and inbreeding species, and was almost equally distant from all three cross-breeding species.Genetic variation inLolium spp. I.     

Phylogenetic relationships among species and genera of Lycoperdaceae based on ITS and LSU sequence data from north European taxa

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses. Morphological characters of species within and among identified clades are discussed.     

Phenetic studies in Nuphar Sm. (Nymphaeaceae):variation in sect. Nuphar

Previous taxonomic assessments of the hydrophytic genus Nuphar Sm. (Nymphaeaceae) have inadequately considered the range of morphological variation existing in the genus. A comprehensive statistical analysis of morphological features among the recognized taxa of Nuphar is presented here, first using 10 fruit characters to delimit the separation of two infrageneric groups of taxa, and secondly using 31 characters to quantify the morphological variation found within sect. Nuphar. Results from combined phenetic analyses provided empirical support for recognition of two infrageneric groups of species in the genus (largely by fruit, stigmatic disk margin, neck, and stigmatic disk size) and for separation of taxa within sect. Nuphar (by leaf size, and fruit disk and neck size). Statistical analyses demonstrate that extensive variation in ranges of character states exists among sect. Nuphar taxa. However, a suite of qualitative and quantitative characters can be used to recognize five species and three subspecies within this predominantly Old World assemblage.     

Molecular phylogeny of animal pathogen Lacazia loboi inferred from rDNA and DNA coding sequences

Lacazia loboi is a geographically restricted, uncultivated fungal pathogen of humans and dolphins. Previous investigations using 18S small unit rDNA, chitin synthase 2 and gp43 DNA sequences positioned L. loboi as a close relative of Paracoccidioides brasiliensis. However, given the few individuals of L. loboi studied and the high degree of genetic variation observed in P. brasiliensis, the existence of L. loboi as an independent species has been questioned. To investigate the phylogenetic position of this species, we conducted a phylogenetic analysis using 20 L. loboi collections (L. loboi was obtained from proven cases of lacaziosis and 14 collections were maintained in mice, the others were analyzed from DNA taken directly from infected human tissue.). L. loboi DNA sequence was compared to that from 17 P. brasiliensis strains that represented the known variation in this species, and outgroup taxa in the Onygenales (Ajellomyces and Coccidioides species). Our analyses used DNA sequence from ITS rRNA, and partial coding sequences of chitin synthase 4, ADP-ribosylation factor, and gp43. Nucleotide variation among strains of L. loboi was minor but numerous nucleotide mismatches and multiple gaps were found for these gene regions among members in the Ajellomycetaceae, including P. brasiliensis. Phylogenies inferred using neighbor-joining, maximum parsimony and Bayesian analyses showed no significant conflict and depicted L. loboi as a well-supported, monophyletic group that was sister to the Paracoccidioides clade. These results argue for maintaining L. loboi as a taxon independent from Paracoccidioides within the Ajellomycetaceae.     

Pollen morphology in <Emphasis Type="Italic">Lysipomia</Emphasis> (Campanulaceae: Lobelioideae) and interpretation of shape artifacts

The pollen of 32 species of Lysipomia was examined by light, scanning, and transmission electron microscopy. Two pollen types occur in the genus: 3-colporate and 6-colporate. The 3-colporate condition occurs in only two species, L. laciniata and L. pumila. The remaining 30 species are 6-colporate, a condition known from only one other genus in the Campanulaceae. Surface sculpturing among the species is uniformly striate. Pollen shape was highly variable within a single individual in comparisons of pollen gathered from herbarium specimens, FAA preserved material collected in the field, and fresh pollen from cultivated individuals grown from seed. Shape may change from oblate spheroidal to subprolate as a result of drying time and temperature, and should not be used as a morphological character in systematic studies if infraspecific variation is seen. When fresh or preserved pollen is not available, rehydrated pollen should be compared to reduce the possibility of inadvertent artifact production confounding the analysis of morphological data.     

荨麻科三新种

该文描述了荨麻科三新种:(1)自中国重庆市发现的荨麻科荨麻属一新种,城口荨麻。此种与异株荨麻有亲缘关系,区别特征为此种的茎被少数刺毛,叶片多为心形,雄、雌花序均不分枝,瘦果在中央稍凹陷。(2)自中国广西发现的荨麻科赤车属一新种,来宾赤车。此种与特产云南东南部的富宁赤车相近缘,与后者的区别在于本种茎的毛开展或向上弯曲,叶片长椭圆形,基部斜楔形,雌花具3~4枚花被片,其中1~2枚较大花被片在背面顶端具一长筒状突起。(3)自缅甸北部发现的荨麻科楼梯草属一新种,克钦楼梯草。此种在体态上与骤尖楼梯草甚为相似,与后者的区别在于本种的每一茎节具正常叶和一退化叶,托叶狭披针状条形和无脉,雌总苞苞片无角状突起,雌小苞片较大,呈楔状长圆形,雌花具一小花被片,以及雌蕊具一宽倒卵球形柱头。     

Phylogenetic characterization of the purple sulfur bacterium Thiocapsa sp. BBS by analysis of the 16S rRNA, cbbL, and nifH genes and its description as Thiocapsa bogorovii sp. nov., a new species

Strain BBS, the purple sulfur bacterium assigned initially to the species Thiocapsa roseopersicina, is the best studied representative of this species. However, no molecular phylogenetic analysis has been performed to confirm its systematic position. Based on the results of analysis of the sequences of 16S rRNA, cbbL, and nifH genes, DNA-DNA hybridization with the T. roseopersicina type strain, and comparative analysis of the phenotypic characteristics of various species belonging to the genus Thiocapsa, we suggest that strain BBS should be assigned to a new species of the genus Thiocapsa, Thiocapsa bogorovii sp. nov. Original Russian Text ? T.P. Tourova, O.I. Keppen, O.L. Kovaleva, N.V. Slobodova, I.A. Berg, R.N. Ivanovsky, 2009, published in Mikrobiologiya, 2009, Vol. 78, No. 3, pp. 381–392.     

Highly repeated DNA analysis and systematics of the Lemuridae,a family of Malagasy prosimians

Hybridization of highly repeated DNA sequences ofEulemur fulvus mayottensis, Lemur catta, andVarecia has been performed on blots of different species of Lemuridae (L. catta, Hapalemur griseus, Varecia variegata variegata, V. v. rubra, E. macaco macaco, E. coronatus, E. mongoz, andE. rubriventer). The probe ofE. fulvus only hybridized with the differentEulemur species, whereas that ofVarecia hybridized with the two subspecies ofVarecia and that ofL. catta with bothL. catta andHapalemur. These results were used to confirm the classification ofVarecia in a separate genus and to review the separation of theL. catta/Hapalemur group from the other species ofEulemur. Comparison of the migration patterns from DNA fragments of these different species has been used to propose a cladogram of the differentEulemur species.     

Phylogeny of Laniarius: molecular data reveal L. liberatus synonymous with L. erlangeri and "plumage coloration" as unreliable morphological characters for defining species and species groups

Laniarius is one of the larger genera within the avian bush-shrike radiation, the family Malaconotidae. Fairly homogenous by size and shape but highly variable by colours, these have been classified mainly on basis of plumage colours. In the present study, which is the first taxon-dense analysis of the genus Laniarius based on molecular sequence data (nuclear BRM15 intron-15, and mitochondrial ND2 and ATPase6 genes), we investigate interrelationships between 16 species and 34 subspecies of Laniarius. Altogether 2094 bp were aligned and subjected to maximum likelihood and Bayesian inference analyses. Results strongly support the monophyly of Laniarius, and place it close to Chlorophoneus, but without outlining a precise sister-group. In a generally well-resolved phylogeny of Laniarius, L. leucorhynchus and L. atrococcineus constitute deep branches and the remaining species form five clades which are not concordant with previously defined superspecies. The black and white boubous belong to two different clades. L. aethiopicus appears polyphyletic and our results support the resurrection of Laniarius major, Laniarius erlangeri and Laniarius sublacteus. We also find that L. liberatus, described in 1991 based on the only known live individual, is identified as an unusual colour morph from L. erlangeri. The black boubous are not monophyletic; L. funebris and L. leucorhynchus appear as isolated species whereas L. poensis and L. fuelleborni are sister-taxa. We recovered the polyphyly of crimson boubous and new hypotheses on their relationships have been generated. Overall, the variation in pigments and patterns does not follow phylogenetic lineages. The plumage coloration could be thoroughly subject to modification and it could not reflect exactly colour plumages of the parents. From then on, the plumage coloration appears as an unreliable morphological character for defining species and species groups.     

A phylogenetic analysis of <Emphasis Type="Italic">Leucothoe</Emphasis> s.l. (Ericaceae; tribe Gaultherieae) based on phenotypic characters

Phylogenetic relationships within the genus Leucothoe s.l. (including all eight species) and related taxa of the Gaultherieae, Andromedeae, and Vaccinieae were investigated by a cladistic analysis based on phenotypic (external morphology, anatomy, chromosome number, and secondary chemistry) characters. The parsimony analysis resulted in two most parsimonious trees, both very similar, which show Leucothoe s.l. to be polyphyletic, with its species distributed among three distinct clades. Our results indicate that L. racemosa and L. recurva form a strongly supported clade, which is sister to Chamaedaphne calyculata, and these three species are probably the sister-group of the wintergreen clade (consisting of Gaultheria and Diplycosia). Leucothoe axillaris, L. fontanesiana, L. davisiae, L. griffithiana, and L. keiskei, consistently form a monophyletic group corresponding to Leucothoe s.s., which is probably sister to the remaining members of the tribe Gaultherieae. Leucothoe grayana, the final species traditionally placed in the genus, belongs to neither of these clades and may be sister to Andromeda. Phenotypic characters provide no support for the monophyly of Leucothoe, instead suggesting that it is polyphyletic, in agreement with preliminary DNA-based analyses. Thus, we redefine the genus Leucothoe, placing its species into three genera: 1) Eubotrys (the E. racemosa + E. recurva clade), 2) Leucothoe s.s. (the L. axillaris + L. fontanesiana + L. davisiae + L. griffithiana + L. keiskei clade), and 3) Eubotryoides (containing only E. grayana).     

Development of microsatellite DNA loci for <Emphasis Type="Italic">Pugionium dolabratum</Emphasis> (Brassicaceae), an endangered psammophyte

Pugionium (Brassicaceae) is a small Central-Asian endemic genus with four tentative species described before. All of them grow in the desert habitat and have been considered as important psammophytes for evolutionary studies and ecological restorations. However, the wild resources of these species have been declined because of overexploitation. In this study, 12 polymorphic microsatellite loci have been developed for P. dolabratum Maxim, and the performance of primer pairs amplifying these loci in related three species has also been tested. The number of alleles in 18 individuals from 13 geographically distant populations ranged from three to seven per locus. The observed and expected heterozygosities varied from 0.17 to 0.30 and from 0.32 to 0.48, respectively. We further performed cross-priming tests in the remaining three species of this genus, P. cornutum, P. calcaratum and P. cristatum. These newly recovered microsatellite loci will be useful for studying the population genetics and adaptive evolution of these endangered psammophytes in the desert.     

Molecular taxonomy and species delimitation in Andean Schistocerca (Orthoptera: Acrididae)

The acridian genus Schistocerca comprises about 50 species which are endemic to the New World, except the Old World locust S. gregaria. Their morphological identification is rendered difficult by phase polyphenism, geographical overlap due to migrations or swarming, the difficulty to easily differentiate genitalia and the occurrence of interspecific hybrids. The three species reported from Peru include the swarming species S. interrita, a pest that can be recognized only by taxonomists. We show that it can be unambiguously identified using a mitochondrial DNA fragment known to have barcoding properties in this genus. We used several methods to delimitate Peruvian species. While S. interrita and S. pallens were well characterized, S. piceifrons peruviana was split into several taxa by a phylogeny-based method, whereas a combination of population genetics methods led one to identify only the three nominal species. A tentative reconstruction of the species history shows that several populations of S. piceifrons peruviana have recently increased in number, while exchanging some migrants, whereas an isolated population at the northern margin of the species range is substantially differentiated while exchanging no migrants with the others. This complex history has resulted in an atypical lineage pattern that appears to have confounded the standard assumptions underlying available species delimitation methods. Because of its behavioral property which tends to keep it panmictic, the identification of the swarming S. interrita remained unaffected.     

利用DNA片段测序方法探究枳属和富民枳的分类地位

富民枳(Poncirus polyandra)属于芸香科(Rutaceae)枳属(Poncirus Raf.).自发表以来,分类地位一直备受争议,其中在Flora of China中认为富民枳为柑橘杂交种(Poncirus polyandra),把枳属归并于柑橘属(Citrus).该研究选取枳属的富民枳、枳(Ponci...     

Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis

Background

The Leishmania (Viannia) braziliensis complex is responsible for most cases of New World tegumentary leishmaniasis. This complex includes two closely related species but with different geographic distribution and disease phenotypes, L. (V.) peruviana and L. (V.) braziliensis. However, the genetic basis of these differences is not well understood and the status of L. (V.) peruviana as distinct species has been questioned by some.Here we sequenced the genomes of two L. (V.) peruviana isolates (LEM1537 and PAB-4377) using Illumina high throughput sequencing and performed comparative analyses against the L. (V.) braziliensis M2904 reference genome. Comparisons were focused on the detection of Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs), aneuploidy and gene copy number variations.

Results

We found 94,070 variants shared by both L. (V.) peruviana isolates (144,079 in PAB-4377 and 136,946 in LEM1537) against the L. (V.) braziliensis M2904 reference genome while only 26,853 variants separated both L. (V.) peruviana genomes.Analysis in coding sequences detected 26,750 SNPs and 1,513 indels shared by both L. (V.) peruviana isolates against L. (V.) braziliensis M2904 and revealed two L. (V.) braziliensis pseudogenes that are likely to have coding potential in L. (V.) peruviana. Chromosomal read density and allele frequency profiling showed a heterogeneous pattern of aneuploidy with an overall disomic tendency in both L. (V.) peruviana isolates, in contrast with a trisomic pattern in the L. (V.) braziliensis M2904 reference.Read depth analysis allowed us to detect more than 368 gene expansions and 14 expanded gene arrays in L. (V.) peruviana, and the likely absence of expanded amastin gene arrays.

Conclusions

The greater numbers of interspecific SNP/indel differences between L. (V.) peruviana and L. (V.) braziliensis and the presence of different gene and chromosome copy number variations support the classification of both organisms as closely related but distinct species.The extensive nucleotide polymorphisms and differences in gene and chromosome copy numbers in L. (V.) peruviana suggests the possibility that these may contribute to some of the unique features of its biology, including a lower pathology and lack of mucosal development.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1928-z) contains supplementary material, which is available to authorized users.     

Phylogeny and comparative seed morphology of epiphytic and terrestrial species of <Emphasis Type="Italic">Liparis</Emphasis> (Orchidaceae) in Japan

To elucidate the evolution of epiphytes in Liparis section Liparis, we examined the phylogenetic relationships of 16 species by using internal transcribed spacer regions of 18S–26S nuclear ribosomal DNA (ITS) and three chloroplast DNA regions (trnS-trnG spacer, trnL with trnL-trnF spacer, and partial matK). Results showed that the epiphytic L. fujisanensis is sister to the terrestrial L. koreana and L. kumokiri, while another epiphyte, L. truncata, is sister to the terrestrial L. krameri. Therefore, the two epiphytic species evolved from terrestrial species independently in section Liparis. Comparative seed morphology revealed that the epiphytes have larger embryos than their closely related terrestrial counterparts. A similar trend toward the increase of embryo size in the two epiphytic species belonging to closely related, but distinct clades suggests that the large embryo may have an advantage in the epiphytic lifestyle. The two epiphytic species share another character state, smaller air spaces in the seed than that of closely related terrestrial species, suggesting possible low dispersibility of the epiphytes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biogeography of Dwarf Lemurs: Genetic Evidence for Unexpected Patterns in Southeastern Madagascar

Seven species of dwarf lemurs (Cheirogaleus spp.) are currently recognized after a recent revision of the genus. During a field study in southeastern Madagascar, we observed 3 distinct morphotypes of Cheirogaleus resembling Cheirogaleus medius, C. major and C. crossleyi. In particular, for Cheirogaleus crossleyi southeastern Madagascar was far away from the known distribution range of the species when referring to the recent revision of the genus. In order to clarify the taxonomic status of the 3 morphotypes, we compared field samples from southeastern Madagascar to museum specimens from several locations in Madagascar and to field samples from Kirindy/CFPF, western Madagascar by genetic analyses using the mitochondrial cytochrome b gene. Genetic data yield strong support for 2 of the 3 morphotypes to represent Cheirogaleus medius and C. major. The third morphotype is genetically closely related to Cheirogaleus crossleyi, albeit more distantly than the other 2 morphotypes to the respective reference samples. The genetic distance is related to a considerable geographic distance between the location of our field study and the origin of the respective reference specimen, because Cheirogaleus crossleyi had been reported only from northern Madagascar. Our field observations indicate an isolated population in southeastern Madagascar. We propose to identify them as Cheirogaleus crossleyi and discuss the population genetic and biogeographic considerations supporting this conclusion.