The Australian species of Archidendron

Nine species of Archidendron are enumerated for Australia. Two species, A. hir–sutum and A. whitei are described as new. Four new combinations A. grandiflorum (Soland. ex Benth.) Nielsen, A. hendersonü (F. v. Muell.) Nielsen, A. muelleranum (Maid. & R. T. Baker) Nielsen and/4, lovelliae (F. M. Bailey) Nielsen are proposed.     

The genus Archidendron (Leguminosae – Mimosoideae)

An account is given of the morphology and the taxonomy of the Asian, Australian and Pacific genus Archidendron (Leguminosae – Mimosoideae). A new infrageneric classification based on morphological data is presented, the genus being subdivided in 8 series. The phylogeny of the genus is discussed, the base of discussion being all available morphological, palynological and wood–anatomical characters. The presence/absence of stipules, the length of the staminal tube compared with that of the corolla–tube, the sessile/stipitate ovary(–ies), the morphology of the pods and the wood–anatomy have been particularly useful in determining the evolutionary trends within the genus. Analyses of the geographical range of selected character states are presented. The data suggest a Central – W. Malesian origin of the genus. The series endemic to the E. Malesian – Australian area have probably evolved more recently. The pluricarpellate condition of the flowers in several species endemic to the E. Malesian and Australian area is considered to be a derived character state. The following new taxa are proposed: Ser. Calycinae Nielsen, ser. Ptenopae Nielsen, ser. Bellae Nielsen, Archidendron falcatum Nielsen, A. cockburnii Nielsen, A. sabahense Nielsen, A. fagifolium (Bl. ex Miq.) Nielsen var. borneense Nielsen, A. kunsrteri (Prain) Nielsen subsp. ashtonii Nielsen, A. ellipticum (Bl.) Nielsen subsp. cordifoliolatum Nielsen. New combinations are proposed in the Malesian species formerly referred to Abarema, Zygia and Morolobium by Kostermans. Keys to and an enumeration of the species are presented.     

Regional patterns of biodiversity in New Guinea plants

Regional patterns of biodiversity in seven recently-studied, speciose groups of New Guinea plants (comprising 200 species, or 1–2% of the flora) are analysed with maps showing numbers of species in 1^o grid cells. Patterns are correlated with the tectonic history of New Guinea. The New Guinea orogen involved rocks of the northern margin of the Australian craton as well as the terranes accreted to the margin, and the current axial range is geologically and biologically composite. The southern Nothofagus has a main massing on the Australian craton portion of the New Guinea mountains. In contrast, four typical genera of Malesian rainforest (Parsonsia, Archidendron, Aglaia, Amyema) have centres of biodiversity on the accreted terranes north of the craton. There are 32 distinct tectono-stratigraphic terranes (some composite) which have been accreted to the craton at different times through the Tertiary and these may have travelled hundreds or even thousands of kilometres before docking. Finally, the 'decaisninoid group' of Loranthaceae and the fern Grammitis have centres of diversity on both the craton and the accreted terranes.     

The genus Archidendron (Leguminosae - Mimosoideae)

An account is given of the morphology and the taxonomy of the Asian, Australian and Pacific genus Archidendron (Leguminosae - Mimosoideae). A new infrageneric classification based on morphological data is presented, the genus being subdivided in 8 series. The phylogeny of the genus is discussed, the base of discussion being all available morphological, palynological and wood-anatomical characters. The presence/absence of stipules, the length of the staminal tube compared with that of the corolla-tube, the sessile/stipitate ovary(-ies), the morphology of the pods and the wood-anatomy have been particularly useful in determining the evolutionary trends within the genus. Analyses of the geographical range of selected character states are presented. The data suggest a Central - W. Malesian origin of the genus. The series endemic to the E. Malesian - Australian area have probably evolved more recently. The pluricarpellate condition of the flowers in several species endemic to the E. Malesian and Australian area is considered to be a derived character state. The following new taxa are proposed: Ser. Calycinae Nielsen, ser. Ptenopae Nielsen, ser. Bellae Nielsen, Archidendron falcatum Nielsen, A. cockburnii Nielsen, A. sabahense Nielsen, A. fagifolium (Bl. ex Miq.) Nielsen var. borneense Nielsen, A. kunstleri (Prain) Nielsen subsp. ashtonii Nielsen, A. ellipticum (Bl.) Nielsen subsp. cordifoliolatum Nielsen. New combinations are proposed in the Malesian species formerly referred to Abarema, Zygia and Morolobium by Kostermans. Keys to and an enumeration of the species are presented.     

Modelling invasive alien species distributions from digital biodiversity atlases. Model upscaling as a means of reconciling data at different scales

Aim

There is a wealth of information on species occurrences in biodiversity data banks, albeit presence‐only, biased and scarce at fine resolutions. Moreover, fine‐resolution species maps are required in biodiversity conservation. New techniques for dealing with this kind of data have been reported to perform well. These fine‐resolution maps would be more robust if they could explain data at coarser resolutions at which species distributions are well represented. We present a new methodology for testing this hypothesis and apply it to invasive alien species (IAS).

Location

Catalonia, Spain.

Methods

We used species presence records from the Biodiversity data bank of Catalonia to model the distribution of ten IAS which, according to some recent studies, achieve their maximum distribution in the study area. To overcome problems inherent with the data, we prepared different correction treatments: three for dealing with bias and five for autocorrelation. We used the MaxEnt algorithm to generate models at 1‐km resolution for each species and treatment. Acceptable models were upscaled to 10 km and validated against independent 10 km occurrence data.

Results

Of a total of 150 models, 20 gave acceptable results at 1‐km resolution and 12 passed the cross‐scale validation test. No apparent pattern emerged, which could serve as a guide on modelling. Only four species gave models that also explained the distribution at the coarser scale.

Main conclusions

Although some techniques may apparently deliver good distribution maps for species with scarce and biased data, they need to be taken with caution. When good independent data at a coarser scale are available, cross‐scale validation can help to produce more reliable and robust maps. When no independent data are available for validation, however, new data gathering field surveys may be the only option if reliable fine‐scale resolution maps are needed.     

中国鳞伞属(广义)已知种类及其分布

对中国鳞伞属 (PholiotaKummer)真菌进行了整理、修订 ,并对有关分类学问题进行了扼要讨论。我国文献记载该属有 74个名称 ,分布于 2 7个省区。其中 ,有效名称 63种 (新拟中文名称 1种 )和 2变种 ,而主张转移到其他属的有 3种 ,错拼名称有 3种 ,另有存疑种 3种。     

Three new species of Sporidesmiella from southern China

Sporidesmiella rosae sp. nov., S. machili sp. nov., and S. archidendri sp. nov., occurring, respectively, on dead branches of Rosa chinensis, Machilus grijsii, and Archidendron clypearia, were collected from subtropical forests in southern China. They are described, illustrated, and compared with similar taxa. A dichotomous key to Sporidesmiella species is provided.     

An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae

Background

The domestic goat (Capra hircus), an important livestock species, belongs to a clade of Ruminantia, Bovidae, together with cattle, buffalo and sheep. The history of genome evolution and chromosomal rearrangements on a small scale in ruminants remain speculative. Recently completed goat genome sequence was released but is still in a draft stage. The draft sequence used a variety of assembly packages, as well as a radiation hybrid (RH) map of chromosome 1 as part of its validation.

Results

Using an improved RH mapping pipeline, whole-genome dense maps of 45,953 SNP markers were constructed with statistical confidence measures and the saturated maps provided a fine map resolution of approximate 65 kb. Linking RH maps to the goat sequences showed that the assemblies of scaffolds/super-scaffolds were globally accurate. However, we observed certain flaws linked to the process of anchoring chromosome using conserved synteny with cattle. Chromosome assignments, long-range order, and orientation of the scaffolds were reassessed in an updated genome sequence version. We also present new results exploiting the updated goat genome sequence to understand genomic rearrangements and chromosome evolution between mammals during species radiations. The sequence architecture of rearrangement sites between the goat and cattle genomes presented abundant segmental duplication on regions of goat chromosome 9 and 14, as well as new insertions in homologous cattle genome regions. This complex interplay between duplicated sequences and Robertsonian translocations highlights the rearrangement mechanism of centromeric nonallelic homologous recombination (NAHR) in mammals. We observed that species-specific shifts in ANKRD26 gene duplication are coincident with breakpoint reuse in divergent lineages and this gene family may play a role in chromosome stabilization in chromosome evolution.

Conclusions

We generated dense maps of the complete whole goat genome. The chromosomal maps allowed us to anchor and orientate assembled genome scaffolds along the chromosomes, annotate chromosome rearrangements and thereby get a better understanding of the genome evolution of ruminants and other mammals.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-625) contains supplementary material, which is available to authorized users.     

Canine 5S rRNA: nucleotide sequence and chromosomal assignment of its gene cluster in four canid species

The purpose of this study was to determine the nucleotide sequence of canine 5S rRNA and use this information to develop a molecular probe to assign the gene locus to chromosomes of the dog and three other related canid species using fluorescence in situ hybridization. The nucleotide sequence of canine liver 5S rRNA is 120 base pairs long and identical to the 5S rRNA nucleotide sequence of all other mammalian species investigated so far. A single 5S rRNA gene cluster was localized pericentromerically on chromosomes of four canid species: dog 4q1.3, red fox 4q1.3, blue fox 3q1.3 and Chinese raccoon dog 8q1.3. Chromosome arms carrying the 5S rRNA gene cluster showed striking similarities in their QFQ banding patterns, suggesting high conservation of these chromosome arms among the four species studied. The chromosomal assignments of 5S rRNA genes are among the first gene mapping results for the blue fox and the Chinese raccoon dog, and are in accordance with published data on comparative chromosome maps from human, dog, red fox, blue fox and raccoon dogs.     

中国龟鳖物种多样性及濒危现状

本文对1949年以来我国龟鳖动物的新种和新记录、物种多样性和名录变化状况作了述评,分析了中国龟鳖物种多样性的特点及濒危现状。我国现存龟鳖动物1目6科21属41种。     

中国大鲵繁殖生物学研究进展

中国大鲵（Amndrias davidiamus Blanchard）是我国特有濒危的两栖物种,是研究生物进化、生物多样性、性别决定分子机制等的好材料,对于科学研究具有巨大的潜在贡献。近年来人们对它的研究力度不断加大,本文综述厂大鲵的繁殖生物学的近期研究工作,也简要探讨了大鲵繁殖生物学今后研究的主要工作,以期为大鲵繁殖生物学及繁殖技术的进一步的研究提供有价值的参考。     

四膜虫T.S1株rDNA分子的形态以及限制性内切酶图谱分析

用电镜以及Southern杂交技术测得从我国分离的四模膜虫T.S1株的rDNA(rRNA基因)分子为20kb(相当于12.5×10~6道尔顿)的回文二聚体结构。制定了该rDNA分子的四种限制性内切酶图谱,并与已知的四膜虫10个物种的相应的限制酶图谱作了比较分析,发现T.S1株与其中9个物种的图谱显著地不同,但是与T.australis的rDNA的7种限制酶图谱相比较,竟有6种是一致的。两者的BglI图虽有差别,但也只是一个酶切位点之差。     

A New Species of the Genus Bupleurum (Umbelliferae) from China

Chai-Hu is one of the most popular Chinese traditional drugs used ever since the ancient time and is prescribed principally in the treatment of fevers and influenza. In this article, the authors report a new species, Bupleurum luxieuse Y. Li et S. L. Pan which was discovered in Yunnan Province and used as Chinese drug under the name of Chai-Hu. The morphology was analysed and preliminary phytochemical tests of B. luxiense were carried out. The thin layer chromatograms and gas chromatograms of the essential oil and the qualitative analysis of the saikosaponin of this new species are similar to those of Bupleurum chinense DC., a standard material medica of Chai-Hu. Moreover, the roots of B. luxiense is discovered to have saikoside 2 times more than B. chinense. The results suggest that the new species be used as a substitute of high quality for Chai-Hu.     

Coordinated international action to accelerate genome-to-phenome with FAANG,the Functional Annotation of Animal Genomes project

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0622-4) contains supplementary material, which is available to authorized users.     

中国福利祝蛾属研究及新种记述(鳞翅目:祝蛾科)

福利祝蛾属Frisilia在中国已记载2种,本文记述2新种,安宁福利祝蛾F.anningensissp．nov．和条斑福利祝蛾F．siriapunctatasp．nov．及一新纪录种,黄福利祝蛾F．homochloraMeyrick,至此我国的福利祝蛾达5种。文中对属征作了综述,并编制了分种检索表。模式标本保存在中国科学院动物研究所。     

Reinvestigation on species richness and environmental correlates of bryophytes at a regional scale in China

Aims The aim of this article is 4-fold: (i) to update species richness of bryophytes for each of the Chinese provinces based on the most current knowledge on distributions of bryophytes in China, (ii) to provide a set of analyses based on the updated species richness data and the environmental variables used in a recent article on species richness of bryophytes in China, (iii) to expand the analysis presented in the recent article by relating species richness of bryophytes to over 15 additional climatic variables and (iv) to determine the degree to which the relationships between bryophyte species richness and environmental variables that were reported in the recent article might have been biased.Methods Over 180 literatures with national, provincial and local species lists of bryophytes in China were used in this study. Taxonomy and nomenclature of bryophytes in China were standardized according to The Plant List. Correlation and regression analyses were used to examine the relationships between species richness or species density of bryophytes in Chinese provinces and environmental variables.Important findings On average, each Chinese province possesses 700.6 species of bryophytes, which is 112.1 species more than previously reported. With the updated species richness data reported in this study, stronger relationships between species richness of bryophytes and environmental variables have been found, compared with those found in a recently published study for China. When single environmental variables were considered, precipitation-related variables were, on average, more strongly correlated with species richness and species density than were temperature-related variables. Environmental variables were on average correlated more strongly with species density than with species richness of bryophytes at the regional scale in China. Our study showed that measures quantifying the average and variation of environmental conditions within each Chinese province explained 82.7% and 71.1% of the variation in species richness of liverworts and mosses, respectively, and explained 86.5% and 70.7% of the variation in species density of liverworts and mosses, respectively.     

Correlation study between gastronomy culture and content of selenium towards prevalence of cardiovascular and diabetes in West Java,Indonesia

Background and aimSelenium (Se) is an important element in the human body. Deficiency or excess of Se can cause harm to human health. A previous study showed an association of Se with cardiovascular and diabetes diseases. One of the food sources of Se is vegetables. In West Java, Indonesia, people consume fresh vegetables such as Garlic, Jengkol, and Petai. This research aims to study the correlation between the gastronomy culture of people in West Java, Se content in Garlic (Allium sativum), Jengkol (Archidendron pauciflorum) and Petai (Parkia speciosa) from several Regencys/cities in West Java, and the prevalence cardiovascular and diabetic diseases.MethodA cultural study was conducted based on a literature review. Cluster sampling was chosen for the sampling method. The prevalence of cardiovascular disease and diabetes in these regencies were obtained from the Ministry of Health of Indonesia. The measurement of Se content in a sample was conducted by the fluorometry method, based on the formation of the piazoselenol complex from the reaction between selenite ion and DAN (2,3-diaminonapthalene).ResultsPeople in West Java prefer to consume garlic, jengkol, and petai as a fresh vegetable as part of their culture. The highest content of Se in Allium sativum was found in Tasikmalaya City with a value of 69.20 ng/g. For Archidendron pauciflorum from Subang Regency values were 498 ng/g. Parkia speciosa found in the Bandung Barat Regency had a mean value 257.9 ng/g. There is a positive correlation between Se-concentration in Archidendron pauciflorum and the prevalence of diabetes while negative correlation with the prevalence of cardiovascular disease. In addition, no correlation was observed for Allium sativum and Parkia Specose might be due to a lower Se-concentration in these vegetables that in the Archidendron fauciflorum.ConclusionDifferent areas have varying concentrations of Se in plants that grow in the region. The gastronomy culture and Se content may play a role to increase or decrease cardiovascular and diabetes prevalence in that area.     

Development and applications of a molecular genetic linkage map of the mouse genome

Interspecific mouse backcrosses provide almost limitless genetic variation for gene mapping. We have used interspecific backcrosses to develop the first comprehensive molecular genetic linkage map of the mouse genome. More than 600 loci have been positioned on the map; the current average map resolution is less than 3 cM. Since all loci were mapped using a single backcross panel, gene order can be determined unambiguously. With this level of resolution, it is now possible to position any new locus on the linkage map with virtually 100% certainty. In this article, we review how interspecific linkage maps are constructed, the salient features of our linkage map, and some of the many applications of interspecific linkage maps, in general, for future research.     

Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps

The sequencing of the 12 genomes of members of the genus Drosophila was taken as an opportunity to reevaluate the genetic and physical maps for 11 of the species, in part to aid in the mapping of assembled scaffolds. Here, we present an overview of the importance of cytogenetic maps to Drosophila biology and to the concepts of chromosomal evolution. Physical and genetic markers were used to anchor the genome assembly scaffolds to the polytene chromosomal maps for each species. In addition, a computational approach was used to anchor smaller scaffolds on the basis of the analysis of syntenic blocks. We present the chromosomal map data from each of the 11 sequenced non-Drosophila melanogaster species as a series of sections. Each section reviews the history of the polytene chromosome maps for each species, presents the new polytene chromosome maps, and anchors the genomic scaffolds to the cytological maps using genetic and physical markers. The mapping data agree with Muller's idea that the majority of Drosophila genes are syntenic. Despite the conservation of genes within homologous chromosome arms across species, the karyotypes of these species have changed through the fusion of chromosomal arms followed by subsequent rearrangement events.     

中国粘菌蚊属Sciophila研究（双翅目：菌蚊科）

中国粘菌蚊属Ｓｃｉｏｐｈｉｌａ研究（双翅目：菌蚊科）吴鸿（浙江农业大学植保系,浙江省杭州市３１００２９）粘菌蚊属ＳｃｉｏｐｈｉｌａＭｅｉｇｅｎ,全北区已知７９种,其中古北区３９种,新北区５４种;东洋区已知５种。中国东北曾记载过１种。本研究对中国的粘菌...