Phenetic relationships inClerodendrum (Verbenaceae) and some phylogenetic considerations

Cluster analyses by different methods and a minimum spanning tree were used to study phenetic relationships in the genusChlerodendrum. 129 species were scored for 52 morphological characters corresponding to 119 character states. The phenetic results suggest a classification into 7 distinct groups, which may be grouped into two subgenera. This classification is supported by the iridoid distribution as well as by some phylogenetic considerations.     

Using randomly amplified polymorphic DNA for evaluating genetic relationships among papaya cultivars

Summary We have applied the recently developed technique of random amplification of polymorphic DNA (RAPD) to the analysis of the relationships among ten cultivars of papaya (Carica papaya L.). Eleven ten-base synthetic oligonucleotides were chosen that gave multiple PCR amplification products using papaya DNA as template. These 11 primers amplified a total of 102 distinct fragments. Cultivars were scored for presence or absence of RAPD fragments and grouped by cluster analysis using simple matching coefficients of similarity. A dendrogram of the ten cultivars was constructed. Of the ten cultivars seven were of the Hawaiian type, and all of these grouped to one branch of the tree. Divisions within the Hawaiian, branch were mostly consistent with the known genetic background of these cultivars. Three non-Hawaiian, cultivars were also analyzed. The minimum similarity detected was 0.7 suggesting that the domesticated papaya germ plasm is quite narrow. Our results show that RAPD technology is a rapid, precise and sensitive technique for genomic analysis.Journal series No. 3692 of the Hawaii Institute of Tropical Agriculture and Human Resources     

Food web's backbones and energy delivery in ecosystems

A food web can be seen as a collection of pathways distributing energy to the ecological community. Because of thermodynamical as well as ecological constraints, some pathways are more important than others, as they carry a much larger share of the energy flow. Such pathways, composed of ‘strong’ links, might be hidden in the tangled network of trophic interactions. Due to thermodynamic efficiency, leading to considerable loss at every passage, we expect these important pathways to be short – i.e. of minimal length. Minimum length spanning trees, which are trees formed by the minimum number of links to keep food webs connected, have been indicated as main energy routes. To test this hypothesis, we analyzed 30 well‐resolved, weighted empirical food webs. From each food web, we extracted the minimum length spanning tree (MLST), and compared it to the maximum weight spanning tree (MWST) – a tree composed of connections of maximum strength. To have a robust comparison, we also computed the minimum weight spanning tree (MinWST), composed of the links of minimal strength. Finally, we extracted from each web 1000 random weighted spanning trees (RWSTs) to serve as a null model. We contrasted the different tree structures, and found that MWSTs are significantly shorter than random trees and MinWSTs, but always longer than MLSTs. In addition, MinWSTs are significantly longer than what expected from random trees. Our results show that in food webs, the bulk of energy travels along pathways that tend to be short, although they never coincide with the minimum length spanning trees.     

Inference of trajectory presence by tree dimension and subset specificity by subtree cover

The complexity of biological processes such as cell differentiation is reflected in dynamic transitions between cellular states. Trajectory inference arranges the states into a progression using methodologies propelled by single-cell biology. However, current methods, all returning a best trajectory, do not adequately assess statistical significance of noisy patterns, leading to uncertainty in inferred trajectories. We introduce a tree dimension test for trajectory presence in multivariate data by a dimension measure of Euclidean minimum spanning tree, a test statistic, and a null distribution. Computable in linear time to tree size, the tree dimension measure summarizes the extent of branching more effectively than globally insensitive number of leaves or tree diameter indifferent to secondary branches. The test statistic quantifies trajectory presence and its null distribution is estimated under the null hypothesis of no trajectory in data. On simulated and real single-cell datasets, the test outperformed the intuitive number of leaves and tree diameter statistics. Next, we developed a measure for the tissue specificity of the dynamics of a subset, based on the minimum subtree cover of the subset in a minimum spanning tree. We found that tissue specificity of pathway gene expression dynamics is conserved in human and mouse development: several signal transduction pathways including calcium and Wnt signaling are most tissue specific, while genetic information processing pathways such as ribosome and mismatch repair are least so. Neither the tree dimension test nor the subset specificity measure has any user parameter to tune. Our work opens a window to prioritize cellular dynamics and pathways in development and other multivariate dynamical systems.     

Chloroplast DNA study in wild populations and some cultivars of Prunus avium L.

The PCR-RFLP technique was used to detect chloroplast DNA diversity in wild populations of Prunus avium from five European deciduous forests and some cultivars. A study of 10.8% of the total chloroplast genome detected eight insertion-deletion (indel) mutations, distributed over 12 haplotypes. Six haplotypes (H1, H2, H3, H4, H5 and H6) were found in wild populations and eight (H2, H6, H7, H8, H9, H10, H11 and H12) in the cultivars. Only two haplotypes (H2 and H6) are shared by the wild populations and the cultivars. The most-abundant and frequent haplotype in wild populations is H2 (frequency=78%). The wider geographical distribution along with the high frequency reflects its ancient origin. Of the five populations, three are polymorphic. Populations GA (Scotland) and KE (Germany) have unique haplotypes. The total cpDNA diversity in wild populations is h_T=0.40, and a major portion of it is within populations (h_S=0.37). The genetic differentiation among populations was low (G_STC=0.08) and no genetic structure among wild populations was observed. A minimum-length spanning tree, demonstrating relationships among the haplotypes in wild populations, indicated two possible chloroplast lineages. The ten identified cultivars were represented by seven haplotypes; this result proposes the possible utilisation of the PCR-RFLP technique for the characterisation of sweet cherry cultivars. The cpDNA diversity in P. avium should be considered carefully for phylogenetic studies involving this species. Received: 10 July 2000 / Accepted: 19 October 2000     

Unsupervised clustering and centroid estimation using dynamic competitive learning

In this paper, an unsupervised learning algorithm is developed. Two versions of an artificial neural network, termed a differentiator, are described. It is shown that our algorithm is a dynamic variation of the competitive learning found in most unsupervised learning systems. These systems are frequently used for solving certain pattern recognition tasks such as pattern classification and k-means clustering. Using computer simulation, it is shown that dynamic competitive learning outperforms simple competitive learning methods in solving cluster detection and centroid estimation problems. The simulation results demonstrate that high quality clusters are detected by our method in a short training time. Either a distortion function or the minimum spanning tree method of clustering is used to verify the clustering results. By taking full advantage of all the information presented in the course of training in the differentiator, we demonstrate a powerful adaptive system capable of learning continuously changing patterns.     

Genetic relationships within avocado (Persea americana Mill) cultivars and between Persea species

The origin of avocado (Persea americana Mill) cultivars, as well as the genetic relationships between Persea species, are not well defined and are based mainly on morphological parameters. Minisatellite DNA markers were used to analyze 24 P. americana cultivars in an attempt to define their racial allocation. DNA mixes representing the three races were evaluated and used for analysis. The allocation of 19 of the above cultivars was substantiated by the DNA markers, while new suggestions were offered regarding the remaining five. Eight cultivars, of unknown racial origin, were also examined, and a phylogenetic tree suggesting their origin is offered. Selfing progeny of five cultivars were analyzed for six morphological traits which differentiate the three races, and were compared to their parents in order to assess their origin. Eleven Persea species were analyzed, using DNA fingerprint patterns and SSR (simple sequence repeat) alleles, in order to identify the genetic relationships among the Persea species, and between them and the three P. americana races. The phylogenetic tree obtained is presented. The high value of variation between the avocado cultivars and Persea species observed in this work, suggests that the validity of race and species definition within Persea be treated with caution. Received: 3 August 1996 / Accepted: 23 August 1996     

A comparison of phylogenetic network methods using computer simulation

Background

We present a series of simulation studies that explore the relative performance of several phylogenetic network approaches (statistical parsimony, split decomposition, union of maximum parsimony trees, neighbor-net, simulated history recombination upper bound, median-joining, reduced median joining and minimum spanning network) compared to standard tree approaches, (neighbor-joining and maximum parsimony) in the presence and absence of recombination.

Principal Findings

In the absence of recombination, all methods recovered the correct topology and branch lengths nearly all of the time when the substitution rate was low, except for minimum spanning networks, which did considerably worse. At a higher substitution rate, maximum parsimony and union of maximum parsimony trees were the most accurate. With recombination, the ability to infer the correct topology was halved for all methods and no method could accurately estimate branch lengths.

Conclusions

Our results highlight the need for more accurate phylogenetic network methods and the importance of detecting and accounting for recombination in phylogenetic studies. Furthermore, we provide useful information for choosing a network algorithm and a framework in which to evaluate improvements to existing methods and novel algorithms developed in the future.     

Construction of physical maps of the Hor1 locus of two barley cultivars by pulsed field gel electrophoresis.

Summary In order to construct a physical map of the Hor1 locus of barley (Hordeum vulgare) high molecular weight DNA was prepared from leaf mesophyll protoplasts. Seventeen different restriction endonucleases containing CpG or CpXpG motifs in their recognition sequences were tested and ten proved useful for the generation of high molecular weight DNA fragments. Physical maps of the Hor1 region of the barley cultivars IGRI and FRANKA spanning a distance of 370 and 430 kb respectively were constructed. The maps include sites of nine restriction endonucleases in IGRI and of eight in FRANKA. The maximal extent of the Hor1 locus could be limited to a 135 kb DNA fragment occurring in both cultivars. The differences in arrangement of restriction sites and in fragment lengths reveal major differences in the Hor1 flanking region in the two cultivars. The location of a CpG island, however, is highly conserved in both cultivars and reflects similarities to the organization of mammalian genomes.     

MartiTracks: a geometrical approach for identifying geographical patterns of distribution

Panbiogeography represents an evolutionary approach to biogeography, using rational cost-efficient methods to reduce initial complexity to locality data, and depict general distribution patterns. However, few quantitative, and automated panbiogeographic methods exist. In this study, we propose a new algorithm, within a quantitative, geometrical framework, to perform panbiogeographical analyses as an alternative to more traditional methods. The algorithm first calculates a minimum spanning tree, an individual track for each species in a panbiogeographic context. Then the spatial congruence among segments of the minimum spanning trees is calculated using five congruence parameters, producing a general distribution pattern. In addition, the algorithm removes the ambiguity, and subjectivity often present in a manual panbiogeographic analysis. Results from two empirical examples using 61 species of the genus Bomarea (2340 records), and 1031 genera of both plants and animals (100118 records) distributed across the Northern Andes, demonstrated that a geometrical approach to panbiogeography is a feasible quantitative method to determine general distribution patterns for taxa, reducing complexity, and the time needed for managing large data sets.     

矮慈菇居群的数量分类研究

本文运用聚类分析和主成分分析基础上构造最小生成树的方法,对采自中国南方的7个矮慈菇居群用28个形态学性状进行了数量分类研究。结果划分出3个类群,综合反映了各居群间的亲缘关系。本文还简要讨论了数量分类学方法在居群生物学中的应用问题。     

EDENetworks: A user‐friendly software to build and analyse networks in biogeography,ecology and population genetics

The recent application of graph‐based network theory analysis to biogeography, community ecology and population genetics has created a need for user‐friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy‐to‐use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray‐Curtis or Sorensen distance, or population genetic metrics such as F_ST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.     

Phylogeography of Eldana saccharina Walker (Lepidoptera: Pyralidae)

The pyralid moth Eldana saccharina Walker is an indigenous insect widely distributed throughout sub-Saharan Africa. Studies have shown that populations from West Africa have distinct behavioural differences compared to populations from East and southern Africa. In addition, the parasitoid guilds attacking populations in these different regions are markedly different. This marked geographical variation evoked a hypothesis of genetic differentiation. To evaluate this hypothesis a molecular analysis was conducted on populations of E. saccharina from throughout much of the species’ range, using the cytochrome c oxidase subunit I (COI) region of the mitochondrial genome. A minimum spanning network and a maximum parsimony tree separated the 21 specimens into three distinct groups. Results revealed the presence of substantial genetic differentiation that is related to geographic variation.     

Analysis of nonlinear relations between expression profiles by the principal curves of oriented-points approach

DNA microarray technology enables high-throughput gene expression analysis and allows researchers to test the activity of thousands of genes at one time in multiple cellular conditions. This approach is based on principal curves of oriented points (PCOP) analysis and minimum spanning trees to analyze temporal and nontemporal series data to relate the genes. PCOP is a very suitable method, non-hypothesis-driven, for nonlinear relationship recognition between multivariable sets of data. Initially, a gene-relations tree is generated from the correlation between each pair of genes, calculated by PCOP analysis. Next, the researcher can introduce the query genes to be studied into the zoom-in operation, and the system selects the genes which connect the previously provided ones, beyond the activation pathways, using the minimum spanning tree. Thus, this zoom-in operation generates the nonlinear pattern of the intraset expression behavior for the new gene set. This inner expression pattern relates the query and selected genes to study their mutual interdependence in detail. This detailed information is especially useful in the biomedical environment, where such information is not possible to obtain by applying the current analytical methods.     

A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation

The minimum spanning tree (MST) problem is to find minimum edge connected subsets containing all the vertex of a given undirected graph. It is a vitally important NP-complete problem in graph theory and applied mathematics, having numerous real life applications. Moreover in previous studies, DNA molecular operations usually were used to solve NP-complete head-to-tail path search problems, rarely for NP-hard problems with multi-lateral path solutions result, such as the minimum spanning tree problem. In this paper, we present a new fast DNA algorithm for solving the MST problem using DNA molecular operations. For an undirected graph with n vertex and m edges, we reasonably design flexible length DNA strands representing the vertex and edges, take appropriate steps and get the solutions of the MST problem in proper length range and O(3m + n) time complexity. We extend the application of DNA molecular operations and simultaneity simplify the complexity of the computation. Results of computer simulative experiments show that the proposed method updates some of the best known values with very short time and that the proposed method provides a better performance with solution accuracy over existing algorithms.     

Can chemical cues from blossom buds influence cultivar preference in the apple blossom weevil (Anthonomus pomorum)?

The post-hibernating adults of the apple blossom weevil, Anthonomus pomorum (L.), show preferences for certain cultivars in mixed apple tree orchards. The degree of infestation of various cultivars was positively correlated with the density of flower buds at a comparable phenological stage, but the numbers of collected beetles were not linearly proportional to the bud density of different cultivars. Hence other possible factors, namely chemical ones, were investigated. Chromatographic analysis of apple tree bud emanations showed that volatiles from two different apple cultivars that show a different attractiveness to the beetles, differed in chemical composition. Several less volatile components of the bud emanation bouquet elicited antennographic responses in both male and female antennae. Four terpene hydrocarbons, namely 3-carene, perillene, caryophyllene and (E,E)--farnesene, were identified among the components that produced distinct electrophysiological responses in the antennae. These findings support a hypothesis that the adult weevils use chemical cues for olfactory discrimination during host-searching behaviour.     

Molecular Characterization of Tree Peony Germplasm Using Sequence-Related Amplified Polymorphism Markers

This study examined 63 tree peony specimens, consisting of 3 wild species and 63 cultivars, using sequence-related amplified polymorphism (SRAP) markers for the purpose of detecting genomic polymorphisms. Bulk DNA samples from each specimen were evaluated with 23 SRAP primer pairs. Among the 296 different amplicons, 262 were polymorphic. The maximum parsimony, neighbor-joining, and unweighted pair-group method using arithmetic average trees were largely in congruence. In the three trees, the wild species Paeonia ludlowii and P. delavayi formed separate clusters with strong bootstrap support, and P. ostii was closely related to all cultivars. The cultivars were divided into groups with various corresponding bootstrap values. The genetic similarity among the genotypes ranged from 0.02 to 0.73. These results demonstrate that SRAP markers are effective in detecting genomic polymorphisms in the tree peony and should be useful for linkage map construction and molecular marker assisted selection breeding. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Molecular AFLP Analysis of the Genotypes of Pepper Capsicum annuum Cultivars

The results of AFLP study of 14 Capsicum annuum cultivars are presented. In spite of the known low genomic variation of large-fruited sweet pepper, AFLP analysis proved to be suitable for detecting polymorphism and genotyping pepper cultivars. Nine primer pairs were selected to allow identification of the cultivars under study. Among-cultivar polymorphism detectable with these primers was estimated at 16.5%. A characteristic AFLP pattern was obtained for each cultivar. Several cultivar-specific fragments were revealed for seven cultivars. On the basis of the AFLP data, genetic distances between cultivars were determined and a tree was constructed by means of hierarchic cluster analysis (UPGMA) with the Jacquard coefficient. It was assumed that this information is useful in breeding programs involving the cultivars examined.     

木芙蓉三个品种及近缘种的叶绿体基因组比较分析

木芙蓉(Hibiscus mutabilis)栽培历史悠久,是原产中国的古老园林树种和药用植物。为了探讨木芙蓉品种及近缘种的进化特征,厘清木芙蓉品种间及其与近缘种间的亲缘关系,以及探究木芙蓉叶绿体基因组(chloroplast DNA, cpDNA)的遗传方式,该文选择了一个杂交组合中的3个木芙蓉栽培品种(‘单瓣白’‘金秋颂’‘牡丹粉’),用高通量测序平台Illumina NovaSeq对其cpDNA进行首次测序。经组装注释后得到3条完整的cpDNA序列,结合该团队已经完成的近缘种台湾芙蓉(H.taiwanensis)和来自基因库的木槿、朱槿的cpDNA,对木槿属4种及木芙蓉种下的3个品种进行了cpDNA组成和结构特征的比较分析,并完成了其系统发育树重建。结果表明：(1)‘单瓣白’‘金秋颂’‘牡丹粉’的cpDNA序列长度分别为160 880、160 879、160 920 bp,基因数目均为130个,其中蛋白编码基因85个、核糖体RNA 8个和转运RNA 37个。(2)比较分析结果显示,木芙蓉的种下3个品种及其近缘种台湾芙蓉在cpDNA上高度保守,反向重复区(IR)均为26 300 b...