Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus <Emphasis Type="Italic">Sinocyclocheilus</Emphasis> (Pisces: Cypriniformes)

The cyprinid fish genus Sinocyclocheilus, as the most cavefish rich genus, includes many species showing striking adaptation to caves and convergent reduction or even loss of eyes and pigmentation. RH1 is responsible for dim vision. In order to explore the evolution of RH1 gene in this genus, we sequenced the complete gene from 28 individuals of 16 representative species of Sinocyclocheilus, with cave and surface species included. Phylogenetic analyses supported the monophyly of Sinocyclocheilus and polyphyly of the cave species. Codon models implemented in PAML were used to infer the evolution of RH1. We found that Sinocyclocheilus had a significantly higher evolutionary rate for amino acids than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of this genus. In contrast to previous hypotheses, both cave and surface lineages exhibited a similar rate of molecular evolution, so the RH1 of cave species may still be functional, although these species were highly adapted to cave environment. Two amino acid substitutions (D83G and E122V) that were not reported before were found, which may be useful for site-directed mutagenesis in the future. Handling editor: Christian Sturmbauer     

The complete mitochondrial genomes of two species from <Emphasis Type="Italic">Sinocyclocheilus</Emphasis> (Cypriniformes: Cyprinidae) and a phylogenetic analysis within Cyprininae

We determined the complete mitochondrial DNA sequences for two species of surface- and cave-dwelling-cyprinid fishes, Sinocyclocheilus grahami and S. altishoulderus. Sequence comparison of 13 protein-coding genes shows that the mutation pattern of each single gene is quite similar to those of other vertebrate animal species. Analysis of the ratios of Ka/Ks at these loci between Sinocyclocheilus and two other cyprinid species (Cyprinus carpio and Procypris rabaudi) show that Ka/Ks ratios are differed, consistent with purifying selection and variation in functional constraint among genes. Bayesian analysis and maximum likelihood analysis of the concatenated mitochondrial protein sequences for 14 cyprinid taxa support the monophyly of the family Cyprininae, and further confirm the monophyly of the genus Sinocyclocheilus. The two Sinocyclocheilus species fall within the Cyprinion-Onychostoma lineage, including Cyprinus, Carassius, and Procypris, rather than among the Barbinae, as previously suggested on morphological grounds.     

<Emphasis Type="Italic">Sinocyclocheilus guilinensis</Emphasis>, a new species from an endemic cavefish group (Cypriniformes: Cyprinidae) in China

The endemic Chinese cavefish genus Sinocyclocheilus possesses very rich species diversity. Specimens of this genus collected from Guilin, Guangxi, China, were originally described in an unpublished document in 1982. Later, they were recognized as Sinocyclocheilus jii. Comparison to the type specimens of S. jii leads to the conclusion that, though similar, they represent two different species. Herein we describe them as a new species, Sinocyclocheilus guilinensis sp. nov. It can be distinguished from all congeners by its possession of soft, unbranched dorsal ray without serrations, 19–20 (11–12) scale rows above (below) the lateral line, 34–36 circumpeduncular scales and 8–9 pre-dorsal vertebrae. Sinocyclocheilus guilinensis sp. nov. is most similar to S. jii. In addition to the scale count differences, a morphometrics-based principal component analysis (PCA) also supports designation of S. guilinensis and S. jii as two distinct species.     

A new species of Barbine genus Sinocyclocheilus (Teleostei: Cyprinidae) from Zuojiang River drainage in Guangxi, China

A new species of the genus Sinocyclocheilus is described based on specimens collected from Zuojiang River drainage, Guangxi, China. The new species, named Sinocyclocheilus jinxiensis, is distinguished from all congeners by its vestigial eyes, short barbels, long pectoral fin, eight to nine branched dorsal-fin rays, last unbranched dorsal-fin ray soft with serrations on posterior edge of its lower part, and 38–41 lateral line scales.     

Length–weight relationships of four cavefish species from China

Length‐weight relationships (LWRs) were estimated for four cavefish species belonging to the genus Sinocyclocheilus (Cypriniformes: Cyprinidae) occurring in the Nanpanjiang River and Hongshuihe River, which constitute the upstream of the species, S. angularis, S. furcodorsalis, S. rhinocerous, and S. tileihornes, were collected from 2011 to 2017. The b values of LWRs of these four species ranged from 2.830 to 3.719 and the correlation coefficient values (R²) were high for all species. This is the first record of LWRs for cavefish species with the horn in FishBase database.     

A new cavefish of Sinocyclocheilus (Teleostei: Cypriniformes: Cyprinidae) from the Nanpanjiang River in Guizhou,China

A new species, Sinocyclocheilus xingyiensis, is described based on specimens collected from a karst cave in Guizhou Province, China. The authors used an integrated taxonomic approach, including morphological and molecular data, to identify the new species as a member of the Sinocyclocheilu angularis group, and it can be distinguished from all other members of this group by a combination of the following features: two pairs of long barbels and long pectoral fins, 42–46 lateral-line scales, 7 (13–14) on outer (inner) side of the first gill arch and 35 (14–15 + 4 + 16 − 17) vertebrae. Phylogenetic analyses based on the cytochrome b (cyt b) gene fragment suggest that S. xingyiensis is a sister lineage to Sinocyclocheilus flexuosdorsalis. The genetic distance (Kimura 2-parameter) between the S. xingyiensis and S. angularis groups of Sinocyclocheilus species based on cyt b gene fragment ranged from 1.2% to 15.4%.     

A new cavefish species, Sinocyclocheilus brevibarbatus (Teleostei: Cypriniformes: Cyprinidae), from Guangxi, China

A new species of the cavefish genus Sinocyclocheilus is described based on six specimens collected from a subterranean river in Du’an County in the Guangxi Zhuang Autonomous Region of southern China. Sinocyclocheilus brevibarbatus sp. nov. can be distinguished from all congeners by the following combination of characteristics: a completely scaled body with well-developed eyes and a strongly-humped back; an almost straight lateral line possessing 49–51 perforated scales; seven soft rays on the dorsal fin; a relatively large eyeball (3.3–5.7% of SL) and short maxillary and rictal barbels (1.7–5.7% and 4.5–7.0% of SL, respectively).     

Phylogenetic analysis of <Emphasis Type="Italic">Kengyilia</Emphasis> species based on nuclear ribosomal DNA internal transcribed spacer sequences

Phylogenetic analysis was conducted based on sequences of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA in 17 species of Kengyilia, together with those of 18 species from Pseudoroegneria, Agropyron, Roegneria and Douglasdeweya by the maximum parsimony, maximum likelihood and neighbor-joining distance methods. The results indicate that species of Kengyilia had close affinities to species of Douglasdeweya and Agropyron. The species in Kengyilia was identified as two subgroups with regard to geographic distribution, indicating that species from the same distribution had a closer phylogenetic relationship. The genus Kengyilia was found as a ligament-group between Roegneria and Agropyron. The ITS sequence is a useful tool for studying the phylogeny of closely related species.     

Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, <Emphasis Type="Italic">Sinocyclocheilus multipunctatus</Emphasis> (Cypriniformes: Cyprinidae)

The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.     

Do Chinese cavefish show intraspecific variability in morphological traits?

Cavefishes represent one of the most bizarre and intriguing life forms inhabiting groundwater environments. One‐third of the known cavefishes worldwide is endemic to China, and almost half of those belongs to a single genus, Sinocyclocheilus (Cypriniformes: Cyprinidae). Analyzing the morphometrics of three Sinocyclocheilus species, we aimed to assess whether variability among conspecific populations exists. We predict that populations inhabiting different subterranean habitats (shallow vs. deep) show divergences in specific morphological traits to better cope with the local ecological conditions. Our results showed that the populations showing bigger eyes and reduced humpback were those occurring close to the cave entrance (habitats with light and high food availability), while specimens with smaller eyes and increased humpback were collected from deeper groundwater areas (habitats laying in darkness with food scarcity). This explorative study paves the way for further researches aiming to collect novel data on Chinese cavefishes and highlights the usefulness of these species in evolutionary studies.     

Cytology and sexuality of 11 species of Elatostema (Urticaceae) in limestone karsts suggests that apomixis is a recurring phenomenon

Limestone karsts across southern China to southeastern Asia are renowned biodiversity hotspots. The karst are characterized by exposed calcareous rocks, seasonal droughts and thin soils that are deficient in N and P but with high Ca and Mg content. The stressful habitat may result in high biodiversity through mechanisms such as niche differentiation, hybridization, polyploidy and apomixis. The genus Elatostema (Urticaceae) has particularily high species diversity in this area and can be used a model genus to explore the mechanisms of speciation. We conducted cytological studies on 11 species of Elatostema from 12 populations in Guangxi, China. We found five populations to be diploid (2n = 26), and seven triploid populations (2n = 39). We infer x = 13 as the basic chromosome number of Elatostema. The chromosome numbers 2n = 26 and 2n = 39 were both found in populations of E. longistipulum, indicating that this species comprise both diploids and triploids. Both male and female plants of Elatostema were found to be diploid. In contrast, the triploids found were all female plants, and these produce seeds, presumably by apomixis. We found no clear relationship between ploidy level or reproductive pathway and endemism in Elatostema which might be because Elatostema species are wind‐pollinated and independent of biotic pollinators. However, a random sample of 11 karst species revealed that ca 2/3 appeared to be apomictic, suggesting that it is a widespread reproductive strategy of Elatostema in the limestone karsts of Guangxi. Apomixis enables plants to reproduce and disperse from a single individual, allowing ‘hopeful monsters’ adapted to a new habitat to form stable populations.     

Molecular phylogeny of terrestrial holocarpic endoparasitic peronosporomycetes, <Emphasis Type="Italic">Haptoglossa</Emphasis> spp., inferred from 18S rDNA

Phylogenetic relationships of seven isolates of the genus Haptoglossa parasitic on terrestrial nematodes within the Peronosporomycetes were analyzed using 18S rDNA sequence data with 21 peronosporomycetes, 2 marine stramenopilous flagellates, and 2 hyphochytridiomycetes. The marine stramenopilous flagellates and hyphochytridiomycetes were used as the outgroup. All Haptoglossa isolates formed a monophyletic clade and clustered with the marine genus Eurychasma. The clade of Haptoglossa and Eurychasma formed a sister-group to the clade that consisted of all other peronosporomycetes. These results suggest that the genus Haptoglossa and other terrestrial peronosporomycetes included in the two subclasses, the Saprolegniomycetidae and the Peronosporomycetidae, might have originally adapted to the terrestrial environment individually. In the maximum-likelihood (ML) analysis, the Haptoglossa clade was divided into three subclades, one aplanosporic species clade and two zoosporic species clades. Phylogenetic analyses of combined 18S rDNA and cox2 genes among five species of Haptoglossa supported the results of the ML analysis using 18S rDNA and suggested that zoosporic species may be separated into two lineages. This topology of the analysis may suggest that aplanosporic species diverged from zoosporic species.     

A combined morphological and molecular phylogeny of the genus Chironius Fitzinger, 1826 (Serpentes: Colubridae)

Chironius is one of the most speciose genera of the South American colubrid snakes. Although the genus represents a well‐known radiation of diurnal racers, its monophyly, affinities with other Neotropical colubrid genera, and intrageneric relationships are open questions. Here, we present a phylogenetic analysis of Chironius based on a data matrix that combines one nuclear (c‐mos) and two mitochondrial (12S and 16S rRNA) genes with 37 morphological characters derived from scutellation, skull, and hemipenial features. Phylogenetic relationships were inferred using maximum parsimony (MP) and maximum likelihood (ML). Our combined morphological and molecular analyses strongly support the monophyly of the genus Chironius and its sister‐group relationship with a clade formed by the genera Dendrophidion and Drymobius. Phylogenetic relationships within the genus Chironius is still controversial, although five clades are retrieved with medium to strong support. © 2014 The Linnean Society of London     

广西苦苣苔科稀有珍贵植物——弥勒苣苔

首次报道广西苦苣苔科植物一新记录属:弥勒苣苔属.该属接近金盏苣苔属,但不同在于弥勒苣苔属花冠上唇4浅裂,下唇不分裂,2对雄蕊分别着生于花冠中部及其上方,雌蕊具一个柱头.弥勒苣苔属为中国特有的单型属,仅弥勒苣苔一种,分布于云南东南部和广西西部.该种在广西首次记录,凭证标本存放于广西植物标本馆(IBK).     

Phylogenetic placement of <Emphasis Type="Italic">Marasmiellus juniperinus</Emphasis>

Recent collections and the type specimen of Marasmiellus juniperinus, the type species of the genus, were examined. Phylogenetic placement, based on ribosomal large subunit (LSU) and internally transcribed spacer (ITS) sequences, is within the lentinuloid clade, nested among Gymnopus taxa. This placement dictates genus name usage and phylogenetic position of other putative species of Marasmiellus. The mating system is tetrapolar.     

Three new species of deep‐sea Gromia (Protista,Rhizaria) from the bathyal and abyssal Weddell Sea,Antarctica

We describe three new species of the genus Gromia from bathyal and abyssal depths in the Weddell Sea. The new species are characterized by a combination of morphological and molecular criteria. All three species possess a distinct oral capsule and a layer of ‘honeycomb membranes’, which form the inner part of the organic test wall. Both these features are typical of gromiids. Their identification as gromiids is confirmed by analyses of partial small subunit ribosomal DNA (SSU rDNA) gene sequences. Gromia marmorea sp. nov. is a rounded species with a prominent oral capsule and a characteristically mottled appearance. In Gromia melinus sp. nov. , the test surface exhibits a polygonal pattern of ridges, with a layer of clay particles coating the surface between the ridges. Gromia winnetoui sp. nov. represents an elongate morphotype in which the organic test is enclosed within an agglutinated case, a feature previously unknown in gromiids. Phylogenetic analysis using the maximum‐likelihood method revealed that all three species form distinct clades, reflecting the morphological differences among Weddell Sea species, as well as between deep‐water Southern Ocean Gromia and previously described gromiids. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 157 , 451–469.     

广西被子植物二新记录属

在第四次中药资源普查中采集了大量标本,经过对这些标本进行仔细鉴定并查阅相关资料,确定其中两号标本为香茜属(Carlemannia Benth.)和粘腺果属(Commicarpus Standl.)植物。这两属植物在广西尚无报道,为首次记录。香茜属植物叶对生,子房下位,无托叶,雄蕊仅有2枚,这和茜草科相似但又不同,系统位置较混乱,以前曾放于茜草科( Rubiaceae)和忍冬科( Caprifoliaceae)中,最近该属和蜘蛛花属独立成香茜科( Car-lemanniaceae)。该属植物共有3种,沿喜马拉雅山脉向东一直分布到缅甸、越南北部。我国西藏东南、云南南部、广西西北部分布一种即香茜( Carlenannia chinenesis Hook. f.)。粘腺果属是紫茉莉科( Nyctaginaceae)主产热带地区的1个属,全世界约25种分布于热带非洲和阿拉伯半岛南部,在南亚、东南亚和墨西哥至热带美洲也有少量分布。中国产2种,其中广西产1种即中华粘腺果[ Commiaicarpus chinensis ( L.) Heim.]。该种植物分布广泛,从南亚次大陆向东至中南半岛、马来半岛,向北到我国西沙群岛、海南岛以及广州附近,在广西首次记录,产凤山县和凌云县。     

Historical biogeography and speciation in the Neotropical highlands: Molecular phylogenetics of the jay genus Cyanolyca

Phylogenetic relationships were studied in the genus Cyanolyca, an assemblage of jays distributed from Mexico south to Bolivia. Given its fragmented distribution along the humid forests of the Neotropics, the genus Cyanolyca is a model group for exploring hypotheses on biogeography and speciation. Phylogenetic analyses were based on two mitochondrial and three nuclear loci; taxon sampling includes all species in the genus and most subspecies. Maximum parsimony, maximum likelihood, and Bayesian analyses produced trees that were congruent and highly robust at both terminal and deep nodes of the phylogeny. Cyanolyca comprises two major clades: one contains the Mesoamerican “dwarf” jays, and the other consists of two main groups—C. cucullata + C. pulchra and the “core” South American species. Prior hypotheses of relationships were explored statistically using Maximum Likelihood and Bayesian approaches. Dispersal-Vicariance analysis revealed the importance of the Northern Andes as a major center for biological diversification, and the effects of dispersal across the Panamanian Land Bridge in the composition of South American and Mesoamerican avifaunas. Phylogenetic patterns are highly congruent with an allopatric mode of speciation. Implications of these results are discussed in the context of the biogeography of Neotropical montane forests.