Species delimitation of North American Nyssa species

The development of next-generation sequencing technologies allows researchers to address complex problems in species delimitation, especially for non-model organisms. The taxonomic status of North American Nyssa species has long been debated and remains controversial. To elucidate the genetic structure and phylogenetic relationships of the five currently recognized North American Nyssa species, we conducted whole-genome sequencing of representative individuals and identified genome-wide single-nucleotide polymorphisms (SNPs) by utilizing the recently released chromosome-level assembly of Nyssa sinensis genome. Population genetic and phylogenetic analyses consistently inferred four well-supported genetic clusters from our sampled individuals, that is, N. aquatica, N. ogeche, N. sylvatica, and N. biflora–N. ursina. Although the identification of N. biflora and N. ursina is primarily based on the morphological characteristics of leaves and drupes, the present evidence, including our principal components analysis of leaf morphological traits, strongly supports the taxonomic designation of N. biflora and N. ursina as a single species. In addition, these four genetic clusters were grouped into two major clades, that is, clade 1 (N. aquatica and N. ogeche) and clade 2 (N. sylvatica and N. biflora–N. ursina). Despite the fact that no evidence of widespread gene flow was found between these two major clades, our analyses revealed the possibility of introgression from N. sylvatica into N. biflora, albeit at a relatively low frequency. This study demonstrates the use of whole-genome sequences as a promising avenue for delimiting species boundaries and further advocates for an integrative approach in the assessment of species delimitation.     

Revision of the genus Noculacia Mayer, 1903 (Crustacea: Amphipoda: Caprellidea) with the description of two new species

The genus Noculacia Mayer, 1903 is reviewed. Two new species, N. africana n. sp. and N. australiensis n. sp., are described based on material collected from southeast Africa and western-southern Australia, respectively. Noculacia bullata Mayer, 1903, the type species of the genus, is redescribed. Noculacia bogisa Mayer, 1903 is transferred to the genus Pseudoprotella Mayer, 1890 mainly on the basis of the presence of a well developed molar, the structure of pereopods 3 and 4, and the setal formula of the mandibular palp being 2-x-1. The genus Noculacia is presently composed of three species: N. africana n. sp., N. australiensis n. sp, and N. bullata Mayer, 1903. The genus Pseudoprotella is composed of P. bogisa (Mayer, 1903), P. inermis Chevreux, 1927, and P. phasma (Montagu, 1804).     

锁阳及其寄主白刺内生真菌的生态分布及遗传关系

首次研究了寄生植物锁阳及其寄主白刺内生真菌的分布特征及遗传关系.采用组织块法分离天然白刺、寄生体中锁阳和白刺的内生真菌,利用ITS-rDNA分子序列并结合形态学方法鉴定菌种,研究内生真菌的分离率、定殖率、分离频率、多样性指数、均匀度指数及相似性系数等的差异,以及寄生关系中内生真菌的多样性、遗传关系及分布特征等.结果表明: 本次获得的49株内生真菌隶属于18个分类单元,95.9%为子囊菌,4.1%为担子菌;内生真菌总分离率为15.3%,总定殖率为25.0%;天然白刺中内生真菌Shannon多样性指数最大,为2.13;锁阳花序与锁阳茎的内生真菌相似性系数最大,为0.50;镰孢菌属为白刺的优势菌属,青霉属为锁阳的优势菌属.锁阳与白刺寄生体中真菌类群的差异性分布表明寄生关系对内生真菌群落存在一定影响.     

豹子花属的研究

豹子花属(Nomccharis Franch.)是百合科百合族(Lilieae)中的一个属,分布于青藏高原东南缘。该属作为一个独立的属,虽被普遍承认,但关于属的范围,即其中与百合属(Lilium L.)及贝母属(Fritillaria L.)有密切关系的种的归属问题,则是一直有争议的。本文仅就这一方面以及在地理分布上的一些问题进行简要讨论。     

Interspecific allozyme variation among Morchella spp. and its inferences for systematics within the genus

The genetic variability of 12 enzymes encoded by 12 loci (Fum, Gapdh, Gpi, Idh, Lap, Mpi, Me, Pgk, Pgd, PepGI, Sod and Tpi) was examined by horizontal starch gel electrophoresis and standard histochemical staining in 19 lines of Morchella spp. The lines could be separated into eight genotypic classes based on their multilocus allelic combinations. Several isolates originally recorded as one species based on morphology were classified as another based on electrophoretic banding patterns. This lack of concordance between allozymic and morphological data sets may help to explain the taxonomic difficulties within the genus. In general, two groupings of the six morphologically identified species could be recognized (M. angusticeps, M. conica and M. elata vs M. esculenta, M. crassipes and M. deliciosa).     

Oocysts of Neospora caninum, Hammondia heydorni, Toxoplasma gondii and Hammondia hammondi in faeces collected from dogs in Germany

Faecal samples of 24,089 dogs were examined coproscopically in two veterinary laboratories in Germany between March 2001 and October 2004. In 47 dogs, oocysts of 9–14 μm size were found. Their morphology was similar to those of Hammondia heydorni and Neospora caninum. Samples of 28 of these dogs were further examined by inoculation into gerbils: seven isolates induced a specific antibody response against antigens of N. caninum NC-1 tachyzoites. This response suggests that the isolates contained N. caninum. In addition to H. heydorni (12 times isolated), Toxoplasma gondii occysts (twice) and Hammondia hammondi oocysts (twice) were observed in dog faeces. The latter findings suggest that coprophagia with a subsequent intestinal passage by dogs plays a role in the dissemination of coccidian parasites for which cats are definitive hosts. Five of the seven N. caninum (NC-GER2, NC-GER3, NC-GER4, NC-GER5, NC-GER6) and the two T. gondii isolates (TG-dgGER1, TG-dgGER2) were successfully passaged into cell culture and are now available for detailed characterization. In contrast to oocysts of other parasites, N. caninum oocysts were predominantly found between January and April (Fisher exact; P=0.038). In the sera of dogs shedding N. caninum, no reactions against the immunodominant antigens with apparent molecular weights of 19, 29, 30, 33 and 37 kDa of N. caninum tachyzoites were observed 3–5 weeks after shedding. However, the animals recognized a 152-kDa N. caninum antigen. Compared with those identified as H. heydorni, T. gondii or H. hammondi, N. caninum oocyst isolates were significantly smaller in length with the 75th percentiles ≤10.7 μm when measured in concentrated sucrose solution and smaller length–width ratios with the 75th percentiles ≤1.06. It may thus be possible to develop criteria for a preliminary identification of N. caninum in dog faeces based on the oocyst morphology.     

Morphological, cytogenetic and allozymic variation within Cephalofovea (Onychophora: Peripatopsidae) with descriptions of three new species

Variation within and between populations of Cephalofovea (Peripatopsidae) has been examined by allozyme, karyological and morphological analyses. Four groups are recognized on the basis of allozyme electrophoresis. One group includes specimens from the type locality of the only described species of the genus, C. tomahmontis. While karyotypic and morphological character states show considerable inter-group variation, the distributions of these states among groups are not concordant when different characters are compared. However, each group of populations is uniquely defined by the full suite of character states it possesses. The four groups are recognized here as distinct species with three species described as new.     

福建漳州水仙花的染色体数目及命名研究

福建漳州的水仙花分为单瓣水仙及重瓣水仙两类,李时珍早就指出它们乃一物二种^[1]。李懋学等(1980)观察了福建漳州、浙江舟山、江苏崇明岛等地的水仙花的染色体数目,均为2n=30,因此认为这三个地区的水仙花都是中国水仙Narcissus tazetta L.var.chinensis Roem.,并从染色体组型分析,阐明它们全是同源三倍体^[8]。我们分别观察了漳州的单瓣水仙及重瓣水仙染色体数目,与他们观察的结果有所不同。说明漳州水仙花的染色体数目及其分类问题,有进一步研究之必要。     

Population genetic structure among populations of three predaceous nabid species: Nabis alternatus Parshley, Nabis roseipennis Reuter and Nabis americoferous Carayon (Hemiptera: Nabidae)

An electrophoretic survey of 28 presumptive loci distributed among 15 enzyme systems was conducted to determine the genetic structure among local populations of three predaceous nabid species: Nabis alternatus, N. roseipennis and N.americoferous in human-disturbed habitat. For all three species, F_IS values indicated a deficiency of heterozygotes at most loci in most populations. The amount of genetic differentiation based on the standardized variance, F_ST when combined across all poulations was 0.100 for N. alternatus, 0.189 for N. roseipennis, and 0.335 for N. americoferous. When local populations were grouped according to a set of defined geographical limits, based on the naturally occurring spatial arrangement of the sampled localities, some unexpected patterns of genetic variation were revealed. The degree of genetic differentiation detected among local populations of nabids is discussed in light of the frequent disruptions and ecological changes in their ephemeral habitats.     

Characterisation of Pseudomonas aeruginosa isolated from freshwater culture systems

Members of the genus Pseudomonas are important phytopathogens and agents of human infections, while other strains and species exhibit bioremediation and biocontrol activities. Species-specific detection of Pseudomonas species in the environment may help to gain a more complete understanding of the ecological significance of these microorganisms. The objective of present study was comparative analysis of biochemically and PCR based confirmed 10 isolates of Pseudomonas aeruginosa (6 from fish intestine and 4 from pond sediment). PCR-ribotyping and PAGE revealed that there was extensive heterogeneity at the genetic and protein levels. Both genetic and phenotypic heterogeneity were more in the sediment isolates compared to the fish isolates. SDS-PAGE clearly demonstrated the differences between fish and sediment isolates as evident from the higher range of protein profiling. In antibiotic sentivity test no habitat specific antibiogram was obtained. Zinc adversely affected the DNA of all the isolates to be amplified by PCR as DNA banding pattern was different from normal DNA in stressed DNA. Thus stress, particularly, zinc may interfere monitoring of Pseudomonas by PCR.     

Biochemical systematics and evolutionary genetics of the common shiner species group

Electrophoretic analyses were performed on blood proteins of the five members of the Notropiscornutus species group. The protein systems included two plasma esterases, transferrin, a pre-albumin and hemoglobin. Plasma protein polymorphism within and between taxa was common. Hemoglobin appeared to be a more consistent and conservative character for assessing phylogenetic relationships. As deduced by both biochemical and morphological evidence, N. cerasinus is the most primitive member of the species group. Uniqueness for several biochemical characters suggests that the striped shiner should be afforded full species recognition as N. isolepis but additional study is needed concerning its relationship with N. cornutus chrysocephalus. The closest biochemical similarity was between the forms interpreted here as subspecies N. cornutus cornutus and N. c. chrysocephalus. N. albeolus clearly evolved from N. c. cornutus but early hybridization with N. cerasinus resulted in limited introgression from that species.     

Reproductive isolation in snails of the genus Albinaria (Gastropoda: Glausiliidae)

Parapatric, morphologically characterized forms of the Mediterranean snail genus Albinaria have traditionally been regarded as biological species. Recently, this view has been challenged on the basis of small interspecific genetic distances and cross-breeding experiments. In order to test whether traditionally recognized species are reproductively isolated lineages, two cases of syntopy were analysed by means of isozyme electrophoresis. The data suggest that complete reproductive isolation is present. In one of the two cases, ecological differentiation on a small spatial scale was observed.     

Genetic relationship between Salix exigua and other North American willows (Salix L.): Evidence from allozyme variation

Starch gel electrophoresis was used to examine the allozyme variation and the genetic relationship between Salix exigua and other North American willows. A total of 149 clonal collections comprising six willow species were analyzed for 26 putative isozyme loci. Genetic distances between species were estimated and used for distance analysis of species relationships. Individual alleles were used as characters for cladistic analysis of phylogenetic inference. Distance analysis indicates that S. exigua has approximately equal divergence to both subgenus Salix and Vetrix. Results of cladistic analysis suggest that S. exigua may be a separate group isolated from all other willows. Based on evidence of allozyme variation, it is suggested that the taxonomic placement of S. exigua within subgenus Salix need to be revised.     

Allozyme diversity and introgression in the Galapagos Islands endemic Gossypium darwinii and its relationship to continental G. barbadense

Gossypium darwiniiWatt is a tetraploid cotton endemic to the Galapagos Islands. Opinion has been divided as to whether or not it deserves recognition at the specific rank, with some considering it a variety of its presumed progenitor, the widely distributed South American species G. barbadense L. A previous hypothesis states that much of the perceived intergradation between the two taxa arose as a consequence of introgression from G. barbadense following its introduction to the archipelago during the past several hundred years. We performed allozyme analysis on 58 accessions of G. darwinii from six islands, using 17 enzymes collectively encoded by 59 loci. Levels of variation were high for an island endemic, with a mean number of alleles per locus of 1.34 and an average panmictic heterozygosity of 0.062. Principal component analysis revealed clustering of accessions according to their island of origin, and a spatial pattern of island-clusters that approximates geographical relationships among islands. Genetic relationships of G. darwinii with G. barbadense and G. hirsutum L. were studied using previously generated allozyme data. Significant introgression of G. hirsutum alleles was detected; however morphological considerations support the hypothesis that much of G. darwinii's diversity stems from interspecific gene flow from G. barbadense, Evidence is presented suggesting that the occurrence of G. hirsutum alleles in G. darwinii derives not from direct hybridization, but from a mediated transfer through introduced, G. hirsutum-introgressed; G. barbadense. Gossypium darwinii and G. barbadense are nearly fixed for different alleles at four loci and each contains a large number of unique alleles. Notwithstanding the high interspecific Nei's genetic identity (0.949), the allozyme data support geographical and morphological evidence in suggesting that a specific rank for G. darwinii is warranted.     

The population genetic structure of Ctenomys porteousi (Rodentia: Octodontidae)

Several aspects of the population biology and the population genetic structure of Ctenomys porteousi were studied. Chromosomal and allozyme polymorphisms in two local populations separated by 10 km were used to infer genetic structure. Heterochromatic addition/deletion rearrangements for six autosomal pairs were employed as genetic markers. Allozyme variants were analysed by the study of thirty-one presumptive loci. Thirteen loci (43%) were polymorphic, average observed heterozygosity per locus was 10%, and mean number of alleles per locus was 1.57. Chromosomal and allozyme frequencies were homogeneous across populations. The estimated F_st values were very low, 0.009 and 0.022 for chromosomal and allozyme data respectively. Gene flow was indirectly estimated by the method of Wright, Nm values (mean number of migrants per generation per deme) was very high (27.2 and 11.3 for chromosomal and allozyme data respectively). The F_is values suggest a significant defect of heterozygotes that could be explained by the Wahlund effect. The ecological data indicate the occurrence of sharp changes in density and in distribution pattern in short time. The genetic and ecological data suggest that the population structure of C. porteousi differs from that found in other species of Ctenomys affected by chromosomal mechanisms of speciation.     

Maternal nutritional condition and genetic differentiation affect brood size and offspring body size in Nicrophorus

In most animal species, brood size and body size exhibit some variation within and between populations. This is also true for burying beetles (genus Nicrophorus), a group in which the body size of offspring depends critically on the number of offspring competing for food due to the discrete nature of resource used for larval nutrition (vertebrate carcasses). In one species, brood size and body size are correlated with population density, and appear to be phenotypically plastic. We investigated potential proximate causes of between-population variation in brood size and body size in two species, Nicrophorus vespilloides and Nicrophorus defodiens. Our first experiment supported the notion that brood size is phenotypically plastic, because it was affected by environmental variation in adult nutritional condition. We found that the pre-breeding nutritional status of female N. vespilloides affected the number of eggs they laid, the number of surviving larvae in their broods, and the body size of their offspring. We do not know whether this plasticity is adaptive because greater offspring body size confers an advantage in contests over breeding resources, or whether starved females are constrained to produce smaller clutches because they cannot fully compensate for their poor pre-breeding nutritional status by feeding from the carcass. Our second experiment documents that brood size, specifically the infanticidal brood-size adjustment behavior, has undergone genetic differentiation between two populations of N. defodiens. Even under identical breeding conditions with identical numbers of first-instar larvae, females descended from the two populations produced broods of different size with corresponding differences in offspring body size.     

Geographical variability of allozyme variation and genetic divergence between Tunisian lizards of the sand-dwelling lacertid genus Acanthodactylus

Acanthodactylus is a widespread lacertid genus including about thirthy species whose systematics remains much debated.The present study is aimed at improving the taxonomic status of the Tunisian species whose geographical distribution and ecological requirements have been studied elsewhere. Allozymic variation at 22 loci was scored in 14 populations for a total of 249 individuals. High genetic variability is confirmed in all samples; it is higher in species displaying a wide bioclimatic habitat range. No reduction of genetic variability was observed in two insular populations.Any interspecific hybrid could be detected from our genetic data, even in sympatric areas arguing in favor of specific status of four taxons in Northern, Central and Southern Tunisia.Phylogenetic relationships are discussed on the basis of UPGMA and Fitch-Margoliash procedures applied to the genetic distances matrix and centered data analysis of allozyme frequencies.     

Morphological and allozyme studies of small terrestrial snails (Opeas sp., Subulina sp. and Huttonella bicolor) collected from Peninsular Malaysia

Shell morphological characters and allozyme electrophoresis were used to study the relationships among six geographical populations of land snails collected from Peninsular Malaysia. Allozyme electrophoresis was used to study the genetic variations to complement the morphological features studied that included shell lengths, numbers of whorls and shell colour. Ten loci coding for six enzymes (MDH, LAP, ALP, PGM, G6PDH and EST) could be reliably scored in samples from the six populations studied. The dendrogram showed two major clusters with one cluster comprising Subulinidae populations from Perak, Selangor, Johor, Terengganu and Pahang while the other cluster included only the Streptaxidae Huttonella bicolor (red) population. The Subulinidae populations were grouped into two subclusters: one subcluster included the Subulina sp. populations from Perak, Selangor an Johor while the other subcluster included the Opeas sp. populations from Terengganu and Pahang. Morphological features can identify the different families and therefore they can complement the allozyme genetic studies on the land snail populations. Like other reports in the literature, our results also underline the importance of a genetic approach in conjunction with a morphological approach, for discriminating land snail species. The present results suggest that small land snails, which were similar in colour but different in sizes, were not of the same family/genus.     

Allozyme differentiation and relationships within Hypostomus Lacépède, 1803 (Osteichthyes: Loricariidae) from the upper Paraguay River basin, Brazil

Nine hypostomine populations from Manso Reservoir (Rio Manso and Rio Cuiabá, upper Paraguay River basin, Brazil) were surveyed using allozyme electrophoresis. Three, sampled at the same sites, were not identified to the species level and were designated as Hypostomus sp. 1, Hypostomus sp. 2 and Hypostomus sp. 3. The survey resulted in 25 loci from 14 scored enzyme systems. Allozyme data allowed diagnostic marker recording for all species analyzed, including the undescribed taxa. Mean expected heterozygosity values were quite variable, ranging from 0.029 to 0.079. Hypotheses to explain this variation are discussed. The allelic frequencies and Nei's genetic identity values showed that Hypostomus sp. 1, Hypostomus sp. 2 and Hypostomus sp. 3 should be considered true biological species, and distinct from the other five Hypostomus species and Pterygoplichthys anisitsi.     

一株南海指海绵共附生真菌多样性及其抗菌活性

本研究通过采用6种不同的培养基对南海指海绵上的共附生真菌进行平板涂布法分离培养,结合ITS-rDNA基因序列特征和形态学特征进行鉴定来研究海绵共附生真菌多样性。共分离培养出55株(21种)真菌菌株,优势菌属为木霉菌属Trichoderma sp.(31株),其中的哈茨木霉Trichoderma harzianum 22株作为优势菌种,占真菌菌株总数的40%。其余真菌则属于枝孢菌属Cladosporium、迈耶氏酵母属Meyerozyma、茎点霉属Phoma、红酵母属Rhodotorula、青霉菌属Penicillium、曲霉属Aspergillus等10个属,还有两株未鉴定到种的子囊菌。选取金黄色葡萄球菌Staphylococcus aureus等7种病原指示菌,采用琼脂扩散法对21种真菌的代表性菌株进行抗菌活性筛选,其中有3种真菌至少对一种指示菌表现出抑菌效果,占菌株种类总数的11%。