Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems

Arising in the context of biodiversity conservation, the Budgeted Nature Reserve Selection (BNRS) problem is to select, subject to budgetary constraints, a set of regions to conserve so that the phylogenetic diversity (PD) of the set of species contained within those regions is maximized. Here PD is measured across either a single rooted tree or a single unrooted tree. Nevertheless, in both settings, this problem is NP-hard. However, it was recently shown that, for each setting, there is a polynomial-time ${(1-\frac{1}{e})}$ -approximation algorithm for it and that this algorithm is tight. In the first part of the paper, we consider two extensions of BNRS. In the rooted setting we additionally allow for the disappearance of features, for varying survival probabilities across species, and for PD to be measured across multiple trees. In the unrooted setting, we extend to arbitrary split systems. We show that, despite these additional allowances, there remains a polynomial-time ${(1-\frac{1}{e})}$ -approximation algorithm for each extension. In the second part of the paper, we resolve a complexity problem on computing PD across an arbitrary split system left open by Spillner et?al.     

The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree

The Gapped Consecutive-Ones Property (C1P) Problem, or the (k, δ)-C1P Problem is: given a binary matrix M and integers k and δ, decide if the columns of M can be ordered such that each row contains at most k blocks of 1's, and no two neighboring blocks of 1's are separated by a gap of more than δ 0's. This problem was introduced by Chauve et al. ( 2009b ). The classical polynomial-time solvable C1P Problem is equivalent to the (1, 0)-C1P problem. It has been shown that, for every unbounded or bounded k ≥ 2 and unbounded or bounded δ ≥ 1, except when (k, δ) = (2, 1), the (k, δ)-C1P Problem is NP-complete (Maňuch et al., 2011 ; Goldberg et al., 1995 ). In this article, we study the Gapped C1P Problem with a third parameter d, namely the bound on the maximum number of 1's in any row of M, or the bound on the maximum degree of M. This is motivated by the reconstruction of ancestral genomes (Ma et al., 2006 ; Chauve and Tannier, 2008 ), where, in binary matrices obtained from the experiments of Chauve and Tannier ( 2008 ), we have observed that the majority of the rows have low degree, while each high degree row contains many rows of low degree. The (d, k, δ)-C1P Problem has been shown to be polynomial-time solvable when all three parameters are fixed (Chauve et al., 2009b ). Since fixing d also fixes k (k ≤ d), the only case left to consider is the case when δ is unbounded, or the (d, k, ∞)-C1P Problem. Here we show that for every d > k ≥ 2, the (d, k, ∞)-C1P Problem is NP-complete.     

广东郁南同乐大山自然保护区种子植物区系研究

通过野外调查与查阅资料,广东郁南同乐大山自然保护区共有野牛种子植物149科542属1 002种.种子植物区系组成丰富,区系地理成分复杂,以南亚热带和热带北缘植物区系地理成分为主.区内珍稀濒危植物多,特有现象较明显,植物区系起源古老.与其它邻近地区植物区系相比较,同乐大山自然保护区种子植物区系与广西龙虎山自然保护区、广东黑石顶自然保护区的相似性较高,与湖南武陵源的相似性较低.     

Xenopus crescent encoding a Frizzled-like domain is expressed in the Spemann organizer and pronephros

The Spemann organizer can be subdivided into head- and trunk-inducing tissues along the anteroposterior axis (Mangold, 1933. Naturwiisenschaften 43, 761-766; Spemann, 1931. Wilhelm Roux Arch. Entwicklungsmech. Org. 123, 389-517). Recent studies have suggested that head formation is brought about by repression of both Wnt and BMP signalling (Glinka et al., 1998. Nature 391, 357-362; Glinka et al., 1997. Nature 389, 517-519). Several Wnt inhibitors secreted from the head organizer region have been identified in Xenopus, such as Cerberus (Bouwmeester et al., 1996. Nature 382, 595-601), Frzb-1 (Leyns et al., 1997. Cell 88, 747-756; Lin et al., 1997. Proc. Natl. Acad. Sci. USA 94, 11196-11200), and Dkk-1 (Glinka et al., 1998. Nature 391, 357-362), supporting this two-inhibitor model. To isolate genes expressed in the head organizer, we screened a prechordal plate cDNA library by sequencing and expression pattern, and isolated the Xenopus ortholog of chick crescent encoding a Frizzled-like domain that is related to Wnt-binding regions of the Frizzled-family proteins. Expression of Xenopus crescent was first detected in the Spemann organizer region at the early gastrula stage and later in prechordal plate cells lining the boundary of mesoderm and ectoderm layers and in the anterior endoderm. At tailbud stages, the expression in the endomesoderm region was diminished, while expression in the pronephros became detectable. In animal cap assays, crescent gene was synergistically upregulated by coexpression of Xlim1, Ldb1, and Siamois, but not by Activin treatment.     

中国伏革菌科二新记录种

I<正>NTRODUCTION Changbaishan Nature Reserve is one of the most important forest reserves in China and it is very rich in wood-rotting fungi (Dai, 1997, 2000, 2003; Dai et al., 2003). Nearly 100 species of the Corticiaceae sensu lato     

广西拉沟自然保护区种子植物区系研究

通过调查统计,广西拉沟自然保护区共有野生种子植物153科594属985种.种子植物区系组成丰富,地理成分复杂,具有中亚热带向南热带过渡性质.在科、属水平上对植物区系特性进行了统计分析,热带性质均强于温带性质,属的成分以泛热带分布、热带亚洲分布为主.与邻近地区植物区系相比较,拉沟自然保护区与广西大瑶山自然保护区相似性较高,与广西花坪自然保护区相似性较低.     

向海自然保护区土地覆盖分类研究

探讨了Fuzzy ARTMAP神经网络在向海自然保护区土地覆盖分类中的应用.全文阐述了Fuzzy ARTMAP网络结构及其采用的算法,提出一种引入遥感图像判读结果的警戒系数自动调整方法,能够解决人为选择警戒参数效率低、难以取得合适数值的问题.结果表明,具有警戒系数调整功能的Fuzzy ARTMAP神经网络能够有效的对向海自然保护区的TM影像进行分类,它与最大似然法和传统的Fuzzy ARTMAP神经网络相比对样本的依赖程度较低,分类精度较高.警戒系数自动调整方法根据遥感影像判读结果自动调整网络参数,提高了网络的运行速度.从分类结果可以看出,向海自然保护区目前开荒现象比较严重,草场有所退化,沼泽有荒漠化迹象,应当采取相应的措施保护向海湿地资源.     

福田自然保护区规划的研究

1 Preface Futain Nature Reserve for mangrove and birds is one part of the Guangdong Neilingding and Futian Nature Reserve,which was set up in October 1984.     

Joint analysis for genome-wide association studies in family-based designs

In family-based data, association information can be partitioned into the between-family information and the within-family information. Based on this observation, Steen et al. (Nature Genetics. 2005, 683-691) proposed an interesting two-stage test for genome-wide association (GWA) studies under family-based designs which performs genomic screening and replication using the same data set. In the first stage, a screening test based on the between-family information is used to select markers. In the second stage, an association test based on the within-family information is used to test association at the selected markers. However, we learn from the results of case-control studies (Skol et al. Nature Genetics. 2006, 209-213) that this two-stage approach may be not optimal. In this article, we propose a novel two-stage joint analysis for GWA studies under family-based designs. For this joint analysis, we first propose a new screening test that is based on the between-family information and is robust to population stratification. This new screening test is used in the first stage to select markers. Then, a joint test that combines the between-family information and within-family information is used in the second stage to test association at the selected markers. By extensive simulation studies, we demonstrate that the joint analysis always results in increased power to detect genetic association and is robust to population stratification.     

云南纳板河保护区蕨类植物区系地理研究

通过多次野外调查及资料整理,对纳板河流域国家级自然保护区蕨类植物的区系组成、地理成分、区系联系、性质及起源等方面进行了分析研究。结果显示:(1)纳板河保护区共有蕨类植物43科90属239种,优势科为水龙骨科、金星蕨科、凤尾蕨科、蹄盖蕨科、三叉蕨科,优势属为凤尾蕨属、鳞盖蕨属、毛蕨属、石韦属。(2)纳板河保护区蕨类植物区系具有明显的热带向亚热带过渡的性质,当属热带亚洲蕨类植物区系,但在一定程度上受到中国-喜马拉雅蕨类植物区系的影响。(3)纳板河保护区在地理亲缘关系上与云南大围山最为密切,与海南岛、哀牢山保护区的关系次之,与苍山、轿子雪山及雕林山保护区的联系较为疏远。     

A note on efficient computation of haplotypes via perfect phylogeny.

The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is partly due to the observation that there are many regions on human genomic DNA where genetic recombination is rare (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. Gusfield's solution based on matroid theory was followed by direct theta(nm2) solutions that use simpler techniques (Bafna et al., 2003; Eskin et al., 2003), and also bound the number of solutions to the PPH problem. In this short note, we address two questions that were left open. First, can the algorithms of Bafna et al. (2003) and Eskin et al. (2003) be sped-up to O(nm + m2) time, which would imply an O(nm) time-bound for the PPH problem? Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes. We give reductions that suggests that the answer to both questions is "no." For the first problem, we show that computing the output of the first step (in either method) is equivalent to Boolean matrix multiplication. Therefore, the best bound we can presently achieve is O(nm(omega-1)), where omega < or = 2.52 is the exponent of matrix multiplication. Thus, any linear time solution to the PPH problem likely requires a different approach. For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979).     

Expression of human interleukin-2 receptor cDNA in E. coli

cDNAs for human interleukin-2 receptor were recently cloned and sequenced (Leonard et al., 1984, Nature 311, 626-631; Nikaido et al., 1984, Nature 311, 631-635; Cosman et al., Nature 312, 768-771). In the studies reported here, we describe the expression of a cDNA clone for the human interleukin-2 receptor in E. coli using an "open reading frame" expression vector pMR100. The inserted cDNA was expressed in E. coli transformants as a tripartite fusion polypeptide fused to the lambda cI protein at its amino terminus and to beta-galactosidase at its carboxy terminus. We demonstrate that the bacterially produced IL-2 receptor protein can bind to IL-2.     

云南药山自然保护区蕨类区系研究

基于馆藏标本,对云南药山自然保护区蕨类进行区系分析.结果表明:该保护区共有蕨类30科、67属、177种及10变种;属的区系地理成分可划分为10个类型11个亚型;种的区系地理成分可划分为9个类型、20个亚型及7个变型;该保护区温带区系成分占优势;与相邻地区区系成分比较发现,蕨类区系与云南药山联系的紧密程度为:轿子雪山>梅里雪山及附近地区>玉龙雪山>黄山.     

Cloning and nucleotide sequence of the structural gene encoding for human tryptophanyl-tRNA synthetase.

A structural gene encoding bovine (b) tryptophanyl-tRNA synthetase (WRS) has recently been cloned and sequenced [Garret et al., Biochemistry 30 (1991) 7809-7817]. Using part of this sequence as a hybridisation probe we have cloned and sequenced a structural gene encoding human polypeptide highly homologous with two mammalian proteins, bWRS [Garret et al., Biochemistry 30 (1991) 7809-7817; EMBL accession No. X52113] and rabbit peptide chain release factor [Lee et al., Proc. Natl. Acad. Sci. USA 87 (1990) 3508-3512]. Identification of the sequence encoding a human WRS is based on (i) the presence of 'HIGH' and 'KMSKS' structural motifs typical for class-I aminoacyl-tRNA synthetases [Eriani et al., Nature 347 (1990) 203-206]; (ii) coincidence of the number of SH groups per subunit estimated experimentally [Muench et al., Science 187 (1975) 1089-1091] and deduced from the cDNA sequence (six in both cases); (iii) close resemblance of two WRS polypeptides sequenced earlier [Muench et al., Science 187 (1975) 1089-1091] and the predicted structure in two different regions.     

Mixture modelling of gene expression data from microarray experiments

MOTIVATION: Hierarchical clustering is one of the major analytical tools for gene expression data from microarray experiments. A major problem in the interpretation of the output from these procedures is assessing the reliability of the clustering results. We address this issue by developing a mixture model-based approach for the analysis of microarray data. Within this framework, we present novel algorithms for clustering genes and samples. One of the byproducts of our method is a probabilistic measure for the number of true clusters in the data. RESULTS: The proposed methods are illustrated by application to microarray datasets from two cancer studies; one in which malignant melanoma is profiled (Bittner et al., Nature, 406, 536-540, 2000), and the other in which prostate cancer is profiled (Dhanasekaran et al., 2001, submitted).     

卧龙自然保护区综合功能评价

保护区是一种特殊的土地利用类型,以保护物种,生态系统或自然遗产为主要目的,但是保护的成败依赖于保护区管理的有效性和可持续性,这是保护区健康发展的根本保障,功能评价就是促进保护区持续有效管理的重要手段,本文以模糊逻辑和问卷调查为基础,对卧龙自然保护区功能进行了综合评价。评价中,将卧龙自然保护区的整体功能划分为五大方面,即自然保护、宣传教育,科学研究,社会发展和经济发展,其中每项功能再进一步划分为3到5个次级指标,从而形成了一个具有3个层次的评价指标体系,评价结果表明,自然保护功能的评价为“好”,其余4项功能均评价为“一般”,因此,作为5方面功能综合的整体功能状况也为“一般”。卧龙自然保护区五大功能的相对良好次序为：自然保护,科学研究,社会发展,宣传教育和经济发展,这就意味着,卧龙自然保护区的功能具有综合整体性,任何方面的功能失调都会影响到保护区整体功能的发挥和保护区自身的健康发展,改善保护区的整体功能,也必须注重各项功能的相互影响,和彼此协调,只有这样才能解决好影响保护区发展的各种矛盾。克服管理和决策中的各种片面性和低效性,促使保护区的管理不断完善,从而保证保护区的可持续发展,进一步分析卧龙自然保护区各项功能的次级指标,对从各方面寻求改善保护区的功能状况很有帮助。     

Habitat Assessment for Giant Pandas in the Qinling Mountain Region of China

ABSTRACT Because habitat loss and fragmentation threaten giant pandas (Ailuropoda melanoleuca), habitat protection and restoration are important conservation measures for this endangered species. However, distribution and value of potential habitat to giant pandas on a regional scale are not fully known. Therefore, we identified and ranked giant panda habitat in Foping Nature Reserve, Guanyinshan Nature Reserve, and adjacent areas in the Qinling Mountains of China. We used Mahalanobis distance and 11 digital habitat layers to develop a multivariate habitat signature associated with 247 surveyed giant panda locations, which we then applied to the study region. We identified approximately 128 km²of giant panda habitat in Foping Nature Reserve (43.6% of the reserve) and 49 km²in Guanyinshan Nature Reserve (33.6% of the reserve). We defined core habitat areas by incorporating a minimum patch-size criterion (5.5 km²) based on home-range size. Percentage of core habitat area was higher in Foping Nature Reserve (41.8% of the reserve) than Guanyinshan Nature Reserve (26.3% of the reserve). Within the larger analysis region, Foping Nature Reserve contained 32.7% of all core habitat areas we identified, indicating regional importance of the reserve. We observed a negative relationship between distribution of core areas and presence of roads and small villages. Protection of giant panda habitat at lower elevations and improvement of habitat linkages among core habitat areas are important in a regional approach to giant panda conservation.     

不同生态保护地植物特征和土壤性质的对比研究——以黑河中游湿地为例

选择黑河中游张掖国家湿地公园和张掖黑河湿地国家级自然保护区为研究对象,对比分析了植物组成、物种多样性、植物生长状态、土壤养分、土壤理化性质及植物土壤间关系。结果显示:湿地公园的植物高度和土壤养分含量(有机碳、全氮、速效氮、全磷、速效钾)显著高于自然保护区,土壤理化性质含量(容重、pH)显著低于自然保护区,表明湿地公园有利于植物生长发育、土壤养分固存、改善土壤质地;自然保护区的植物科属种、多度、物种多样性(多样性指数、丰富度指数、均匀度指数)显著高于湿地公园,表明自然保护区有利于维持植物多样性;两种保护地中影响植物多样性的土壤因子不同,湿地公园物种多样性与土壤全磷和速效磷显著正相关,而自然保护区物种多样性与土壤盐分显著负相关。     

江西井冈山国家级自然保护区蝶类资源研究

2002年至2008年对井冈山国家级自然保护区的蝴蝶种类进行调查,共发现有蝴蝶231种,隶属ll科128属,其中包括国家I级保护动物金斑喙凤蝶Teinopalpus aureus Mell。离斑带蛱蝶Athymaranga Moore、珠翠蛱蝶Euthaliaper MlaChouetWang、斜带缺尾蚬蝶Dodonaouida Moore和花裙陀弄蝶Thoressa submacula（Leech）这4种为江西省新记录,另有135种为保护区首次记载。井冈山国家级自然保护区蝴蝶区系成分以东洋界为主,占总种数的73．26％。     

Constructing a minimum phylogenetic network from a dense triplet set

For a given set L of species and a set T of triplets on L, we seek to construct a phylogenetic network which is consistent with T i.e. which represents all triplets of T. The level of a network is defined as the maximum number of hybrid vertices in its biconnected components. When T is dense, there exist polynomial time algorithms to construct level-0,1 and 2 networks (Aho et al., 1981; Jansson, Nguyen and Sung, 2006; Jansson and Sung, 2006; Iersel et al., 2009). For higher levels, partial answers were obtained in the paper by Iersel and Kelk (2008), with a polynomial time algorithm for simple networks. In this paper, we detail the first complete answer for the general case, solving a problem proposed in Jansson and Sung (2006) and Iersel et al. (2009). For any k fixed, it is possible to construct a level-k network having the minimum number of hybrid vertices and consistent with T, if there is any, in time O(T(k+1)n([4k/3]+1)).