The lace web spiders (Araneae,Phyxelididae) of Madagascar: phylogeny,biogeography and taxonomy

We briefly review the potential history of Madagascar as either a Darwinian or a Wallacean island, summarize the phylogenetic evidence regarding the biogeography of Madagascar spiders, examine the dispersal history of the Madagascar Phyxelididae, and monograph the family in Madagascar. Molecular phylogenetic analyses for 32 Malagasy phyxelidid exemplars, nine confamilial outgroup taxa, and seven other more distant outgroups are performed for three nuclear markers and one mitochondrial genetic marker (28S, 18S, H3 and COI) utilizing Bayesian, maximum‐likelihood and parsimony methods. These analyses suggest that there are 14 species of Phyxelididae that may be recognized from Madagascar, that these may be divided into three genera, and that the Malagasy phyxelidids form a monophyletic group, probably resulting from a single invasion of the island by an ancestor from Africa. Two new genera, ten new species, and two new combinations are proposed: Manampoka atsimo gen. nov., sp. nov. ; Rahavavy gen. nov. , including R. ida sp. nov. and R. fanivelona (Griswold, 1990) comb. nov. and R. malagasyana (Griswold, 1990) comb. nov. ; and Ambohima andrefana sp. nov. , A. antsinanana sp. nov. , A. avaratra sp. nov. , A. maizina sp. nov. , A. ranohira sp. nov. , A. vato sp. nov. , A. zandry sp. nov. and A. zoky sp. nov. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 728–810.     

Prediction of pathogenicity islands in Enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes

The genome of lethal animal pathogenic bacterium Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is characterized by the presence of multiple pathogenicity islands (PAIs). Computational methods have been developed to identify PAIs based on the distinguishing G + C levels in some PAI versus non-PAI regions. We observed that PAIs can have a very similar G + C level to that of the host chromosome, which may have led to false negative predictions using these methods. We have applied a novel method of genomic barcodes to identify PAIs. Using this technique, we have successfully identified both known and novel PAIs in the genomes of three strains of EHEC O157:H7.     

Dynamic analysis of a genomic island in Magnetospirillum sp. strain AMB-1 reveals how magnetosome synthesis developed

The entire structure of a 98 kb genomic region that abounds in genes related to magnetosome synthesis was first described in the Magnetospirillum sp. strain AMB-1. The deletion of this 98 kb genomic region and the circular form after excision from the chromosome was detected by PCR amplification. This strongly suggests that the region has undergone a lateral gene transfer. The region has the characteristics of a genomic island: low GC content, location between two repetitive sequences, and the presence of an integrase in the flanking region of the first repetitive sequence. This 98 kb genomic region has the potential for transfer by the integrase activity. Comparative genome analysis revealed other regions with a high concentration of orthologs in magnetic bacteria besides the 98 kb region, and magnetosome synthesis seemed to need not only the exogenous 98 kb region, but also other orthologs and individually originating genes.     

Plant-parasitic Nematode Problems in the Pacific Islands

The Pacific islands have a diverse range of food and cash crops with indigenous and introduced nematode problems. The staple food crops have serious nematode pests, such as Meloidogyne spp. on sweet potato, Hirschmanniella miticausa causing corm rot of taro, and Pratylenchus coffeae and Radopholus sp. producing tuber dry rot of yams. Bananas are infested with P. coffeae or R. similis, citrus with Tylenchulus semipenetrans, rice with Aphelenchoides besseyi, and ginger with Meloidogyne spp. and R. similis. Rotylenchulus reniformis, P. zeae, P. brachyurus, and Helicotylenchus spp. are important on all of these and other crops, such as sugarcane, passion fruit, pawpaw, and cassava. Meloidogyne spp. cause serious damage to local and introduced leaf and fruit vegetables and other crops, such as tobacco, sugarcane, pawpaw, black pepper, and pyrethrum. Many other plant-parasitic genera and species, some undescribed, occur in the Pacific, and there are many islands still to be investigated.     

Family values

Evolutionary Genetics (2nd edn) by J. Maynard Smith, Oxford University Press, 1998. £50.00 hbk, £19.95 pbk (368 pages) ISBN 0 19 850232 X/0 19 850231 1Selection in Natural Populations by J.B. Mitton, Oxford University Press, 1998. £50.00 hbk (252 pages) ISBN 0 19 506352 XProgress and Prospects in Evolutionary Biology edited by J.R. Powell, Oxford University Press, 1997. £49.50 hbk (576 pages) ISBN 0 19 507691 5Evolution on Islands edited by P.R. Grant, Oxford University Press, 1997. £24.99 pbk (348 pages) ISBN 0 19 850 1714     

When North and South don’t mix: genetic connectivity of a recently endangered oceanic cycad,Cycas micronesica,in Guam using EST‐microsatellites

Subject to environmental changes and recurrent isolation in the last ca. 250 Ma, cycads are often described as relicts of a previously common lineage, with populations characterized by low genetic variation and restricted gene flow. We found that on the island of Guam, the endemic Cycas micronesica has most of the genetic variation of 14 EST‐microsatellites distributed within each of 18 genetic populations, from 24 original sampling sites. There were high levels of genetic variation in terms of total number of alleles and private alleles, and moderate levels of inbreeding. Restricted but ongoing gene flow among populations within Guam reveals a genetic mosaic, probably more typical of cycads than previously assumed. Contiguous cycad populations in the north of Guam had higher self‐recruitment rates compared to fragmented populations in the south, with no substantial connection between them except for one population. Guam’s genetic mosaic may be explained by the influence of forest continuity, seed size, edaphic differences, and human transport of cycads. Also important are the extent of synchrony among flushes of reproductive female seed‐bearing sporophylls and restricted pollen movement by an obligate mutualist and generalist insects. An NADH EST‐locus under positive selection may reflect pressure from edaphic differences across Guam. This and three other loci are ideal candidates for ecological genomic studies. Given this species’ vulnerability due to the recent introduction of the cycad aulacaspis scale, we also identify priority populations for ex situ conservation, and provide a genetic baseline for understanding the effects of invasive species on cycads in the Western Pacific, and islands in general.     

Genomic specification and epigenetic regulation of eukaryotic DNA replication origins

Identification of DNA replication origins (ORIs) at a genome-wide level in eukaryotes has proved to be difficult due to the high degree of degeneracy of their sequences. Recent structural and functional approaches, however, have circumvented this limitation and have provided reliable predictions of their genomic distribution in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, and they have also significantly increased the number of characterized ORIs in animals. This article reviews recent evidence on how ORIs are specified and maintained in these systems and on their regulation and sensitivity to epigenetic signals. It also discusses the possible additional involvement of ORIs in processes other than DNA replication.     

北麂列岛岩相潮间带贻贝类的群落结构

报导了北麂列岛岩相潮问带贻贝类的群落结构。用Shannon-Wiener多样性指数(H’(S))、Pielous种类均匀度(J)、Margalef种类丰度(d)、McNunghton优势度(D)4个测定群落种类多样性指标进行数值分析,结果表明北麂列岛岩相潮间带贻贝类群落结构简单。     

Islands and evolution: theory and opinion in Darwin's earlier years

Islands were not of special interest to evolutionists before Darwin. It was he who first appreciated their importance for demonstrating evolution in miniature. They were not of special interest because: (a) their peculiar products seemed no more peculiar than those of continents; (b) there was no special category of oceanic islands, but a continuum from such groups as the Canaries, Madeiras and Galápagos through New Zealand and Madagascar to Australia, Britain, and true continents; and (c) the concept of adaptive radiation, if known at all, was applied only to the higher levels of classification, and then very feebly.
When Darwin was young, classification at the lower levels hardly recognized convergence, and at the higher levels was subject to great changes, while only slowly separating out the major groups. In consequence, many of the facts of geographical distribution were misinterpreted, and numerous theories of the origination of species, groups, and biogeographical provinces were still plausible. It was largely the need for a historical, not ecological, explanation of the distribution of some mammals and plants, plus what he saw for himself in the Galápagos Islands, that convinced Darwin that evolution had occurred. His was a remarkable achievement in recognizing through all this 'noise' the meaning of adaptive radiation.     

Below-ground carbon and nitrogen accumulation in perennial grasses: A comparison of caespitose and rhizomatous growth forms

An experiment was conducted to compare below-ground soil organic carbon and total nitrogen accumulation between caespitose and rhizomatous perennial grasses in long-term (<25 yrs) grazed and ungrazed sites in semi-arid and mesic communities in the North American Great Plains. Development of greater nutrient pools beneath than between clones occurred at minimal clone basal areas (<60 cm²) for both caespitose species. Caespitose grasses accumulated substantially greater pools of carbon (20–200 fold) and nitrogen (50–500 fold) in soils to a depth of 10 cm beneath clones than rhizomatous grasses accumulated in rhizomes in both communities. Carbon and nitrogen pools in soils beneath caespitose clones exceeded combined (soil + rhizome) pools for rhizomatous grasses for a majority of the clone basal areas (>90 cm²) in the mesic community. In contrast, both pool sizes were smaller beneath the caespitose grass at all clone basal areas than the combined pools for the rhizomatous grass in the semi-arid community. The occurrence of larger soil nutrient pools beneath the rhizomatous species in the semi-arid community was largely a consequence of niche separation for microsites characterized by soils with higher nutrient concentrations, rather than plant-induced increases in nutrient concentrations. Although nutrient islands do not occur beneath rhizomatous grasses, their distribution in the semi-arid community was restricted to microsites characterized by soils with higher SOC and N concentrations. A greater efficiency of nutrient accumulation per unit rhizome mass and the maintenance of rhizome nutrient pools of similar magnitude to those of the rhizomatous grass in the mesic community may also contribute to the distribution of rhizomatous grasses in semi-arid communities. The existence of nutrient islands beneath a wide range of clone sizes in both mesic and semi-arid communities provides circumstantial evidence to suggest that nutrient islands beneath caespitose grasses may contribute to clone fitness in this growth form.     

Palaeo‐islands as refugia and sources of genetic diversity within volcanic archipelagos: the case of the widespread endemic Canarina canariensis (Campanulaceae)

Geographical isolation by oceanic barriers and climatic stability has been postulated as some of the main factors driving diversification within volcanic archipelagos. However, few studies have focused on the effect that catastrophic volcanic events have had on patterns of within‐island differentiation in geological time. This study employed data from the chloroplast (cpDNA haplotypes) and the nuclear (AFLPs) genomes to examine the patterns of genetic variation in Canarina canariensis, an iconic plant species associated with the endemic laurel forest of the Canary Islands. We found a strong geographical population structure, with a first divergence around 0.8 Ma that has Tenerife as its central axis and divides Canarian populations into eastern and western clades. Genetic diversity was greatest in the geologically stable ‘palaeo‐islands’ of Anaga, Teno and Roque del Conde; these areas were also inferred as the ancestral location of migrant alleles towards other disturbed areas within Tenerife or the nearby islands using a Bayesian approach to phylogeographical clustering. Oceanic barriers, in contrast, appear to have played a lesser role in structuring genetic variation, with intra‐island levels of genetic diversity larger than those between‐islands. We argue that volcanic eruptions and landslides after the merging of the palaeo‐islands 3.5 Ma played key roles in generating genetic boundaries within Tenerife, with the palaeo‐islands acting as refugia against extinction, and as cradles and sources of genetic diversity to other areas within the archipelago.     

结直肠癌中DNA甲基化研究进展

CpG岛是人类基因组中富含CpG二核苷酸的DNA序列,主要位于基因启动子区,大小约为100-1000bp,与约60％编码基因相关。DNA中CpG岛甲基化可导致抑癌基因的表观遗传学转录失活,直接参与肿瘤的发生机制。近年来,甲基化已成为表观遗传学研究的焦点。我们简要综述了DNA甲基化在结直肠癌中的研究进展。     

Diversity of vascular plants on Ssese islands in Lake Victoria, central Uganda

Diversity and distribution of trees [≥5 cm diameter at breast height (dbh)], shrubs and herbs was assessed in thirty 0.05‐ha (10 × 50 m) plots of a tropical high forest in the Ssese islands of Lake Victoria, central Uganda. The aim was to determine the floristic richness and composition of the forests. We recorded 179 species belonging to 70 families and 146 genera. Of these, nine families had five species or more. Rubiaceae was the richest with fourteen species followed by Euphorbiaceae (thirteen), Apocynaceae (ten) and Moraceae (nine). The majority of the families (35) were represented by one species each. Fifty‐eight herbaceous species, 39 lianas, ten shrubs and 72 species of trees were recorded. The commonest species recorded in the forest included: Uapaca guineensis Mull. Arg., Tabernaemontana pachysiphon Stapf., and Aframomum luteoalbum (K Schum.) K. Schum. Among the rare species encountered were Ficus densistipulata De Willd., Englerophytum oblanceolatum (S. Moore) Pennington, and Afromomum zambeziacum (Bak.) K. Schum. The present study has shown that the Ssese islands are floristically rich in species and compare well with other mainland forests. Species richness, rarity and uniqueness of habitats can be considered as approaches in the prioritization of conservation sites within the fragmented forests of Ssese islands.     

Shifts in litterfall and dominant nitrogen sources after expansion of shrub thickets

Woody encroachment into herbaceous ecosystems is emerging as an important ecological response to global change. A primary concern is alterations in C and N cycling and associated variations across a variety of ecosystems. We quantified seasonal variation in litterfall and litter N concentration in Morella cerifera shrub thickets to assess changes in litterfall and associated N input after shrub expansion on an Atlantic coast barrier island. We also used the natural abundance of ¹⁵N to estimate the proportion of litterfall N originating from symbiotic N fixation. Litterfall for shrub thickets ranged from 8,991 ± 247 to 3,810 ± 399 kg ha⁻¹ year⁻¹ and generally declined with increasing thicket age. Litterfall in three of the four thickets exceeded previous estimates of aboveground annual net primary production in adjacent grasslands by 300–400%. Leaf N concentration was also higher after shrub expansion and, coupled with low N resorption efficiency and high litterfall, resulted in a return of as much as 169 kg N ha⁻¹ year⁻¹ to the soil. We estimated that ∼70% of N returned to the soil was from symbiotic N fixation resulting in an ecosystem input of between 37 and 118 kg ha⁻¹ year⁻¹ of atmospheric N depending on site. Considering the extensive cover of shrub thickets on Virginia barrier islands, N fixation by shrubs is likely the largest single source of N to the system. The shift from grassland to shrub thicket on barrier islands results in a substantial increase in litterfall and foliar N concentration that will likely have a major impact on the size and cycling of ecosystem C and N pools. Increasing C and N availability in these nutrient-poor soils is likely to permanently reduce cover of native grasses and alter community structure by favoring species with greater N requirements.     

EGID: an ensemble algorithm for improved genomic island detection in genomic sequences

Genomic islands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID.     

GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences

Genomic Islands (GIs) are genomic regions that are originally from other organisms, through a process known as Horizontal Gene Transfer (HGT). Detection of GIs plays a significant role in biomedical research since such align genomic regions usually contain important features, such as pathogenic genes. We have developed a use friendly graphic user interface, Genomic Island Suite of Tools (GIST), which is a platform for scientific users to predict GIs. This software package includes five commonly used tools, AlienHunter, IslandPath, Colombo SIGI-HMM, INDeGenIUS and Pai-Ida. It also includes an optimization program EGID that ensembles the result of existing tools for more accurate prediction. The tools in GIST can be used either separately or sequentially. GIST also includes a downloadable feature that facilitates collecting the input genomes automatically from the FTP server of the National Center for Biotechnology Information (NCBI). GIST was implemented in Java, and was compiled and executed on Linux/Unix operating systems. AVAILABILITY: The database is available for free at http://www5.esu.edu/cpsc/bioinfo/software/GIST.