Ancestor-descendant Relationships Research Articles

Phylogeny modulates the effects of ecological conditions on group living across hystricognath rodents

The evolution of group living in animals has been linked both to ecological and phylogenetic drivers or constraints. However, available evidence supporting each factor remains equivocal. In this study, we evaluated the influence of both scenarios across 98 species of hystricognath rodents using phylogenetic approaches that included a statistical model of trait evolution. We first estimated the hypothetical ancestral forms of several clades within the hystricognath phylogeny. Secondly, we examined evolutionary correlations between habitat conditions in terms of vegetation cover and group living to determine general macroevolutionary trends on social behaviour. Given the contrasting modes of life that characterize these rodents, we also examined whether subterranean habits influence group living. Our results support the hypothesis that group living in Old World Phiomorpha and New World Caviomorpha had an early origin. The best-fitted and well-supported model of evolution for group living was the equal rate model, implying an equal rate of gains and losses of group living. Logistic regression analyses that included phylogenetic relationships revealed significant correlation between habitats used (i.e. vegetation cover) and absence or presence of group living. The loss of group living across the phylogeny was associated with the use of closed habitat conditions. No association was found between changes in group living and subterranean mode of life. We conclude that ancestor–descendant relationships mediate the effect of changes in habitat use on the evolution of group living across -hystricognath rodents.

An Implementation of Tree Pattern Matching Algorithms for Enhancement of Query Processing Operations in Large XML Trees

Now-a-days XML has become a defacto standard for storing, sharing and exchanging the information across the various domains. Interoperability is achieved using XML. Due to the increasing popularity of XML enterprises are generating and exchanging the data across the various domains. This paper presents a wide analysis to identify the efficiency of XML Tree pattern matching algorithms. Previous years many methods have been proposed to match XML Tree queries efficiently. In particularly TwigStack , OrderedTJ, TJFast and TreeMatch algorithms. All algorithms to achieve something through these own ways like structural relationship including Parent-Child (P-C) relationship (denoted as ‘/’) and Ancestor-Descendant (AD) relationships (denoted as ‘//’) and more. Finally, we report our results to show that which algorithm is superior to previous approaches in terms of the performance.

A study on parallelizing XML path filtering using accelerators

Publish-subscribe systems present the state of the art in information dissemination to multiple users. Such systems have evolved from simple topic-based to the current XML-based systems. XML-based pub-sub systems provide users with more flexibility by allowing the formulation of complex queries on the content as well as the structure of the streaming messages. Messages that match a given user query are forwarded to the user. This article examines how to exploit the parallelism found in XPath filtering. Using an incoming XML stream, parsing and matching thousands of user profiles are performed simultaneously by matching engines. We show the benefits and trade-offs of mapping the proposed filtering approach onto FPGAs, processing streams of XML at wire speed, and GPUs, providing the flexibility of software. This is in contrast to conventional approaches bound by the sequential aspect of software computing, associated with a large memory footprint. By converting XPath expressions into custom stacks, our solution is the first to provide support for complex XPath structural constructs, such as parent-child and ancestor descendant relations, whilst allowing wildcarding and recursion. The measured speedups resulting from the GPU and FPGA accelerations versus single-core CPUs are up to 6.6X and 2.5 orders of magnitude, respectively. The FPGA approaches are up to 31X faster than software running on 12 CPU cores.

A XML Pattern Match Algorithm of Structural Index

XML query processing needs to search an XML document and return results that satisfy a request. In this paper, we proposed an effective pattern match algorithm based on structural index. This algorithm uses a suitable labeling scheme and an efficient structural index by identifying parent-child, ancestor-descendant and sibling relationships among nodes. Due to the algorithm avoids invalid immoderate results to be pushed stacks, So, It reduces the amount of joint and improves the performance of Query. Experiment results proved that our algorithm, TwigM performs about 15% better compared to TwigStack [ and 10% better than TwigINLAB[ for all types of queries.

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

A labeled gene tree topology that disagrees with a labeled species tree topology is said to be anomalous if it is more probable under a coalescent model for gene lineage evolution than the labeled gene tree topology that matches the species tree. It has previously been shown that as a consequence of short internal branches of the species tree, for every labeled species tree topology with five or more taxa, and for asymmetric four-taxon species tree topologies, an assignment of species tree branch lengths can be made which gives rise to anomalous gene trees (AGTs). Here, I offer an alternative characterization of this result—a labeled species tree topology produces AGTs if and only if it contains two consecutive internal branches in an ancestor–descendant relationship—and I provide a proof that follows from the change in perspective. The reformulation and alternative proof of the existence result for AGTs provide the insight that it is not merely short internal branches that generate AGTs, but instead, short internal branches that are arranged consecutively.

Assessment of student learning associated with tree thinking in an undergraduate introductory organismal biology course.

Phylogenetic trees provide visual representations of ancestor-descendant relationships, a core concept of evolutionary theory. We introduced "tree thinking" into our introductory organismal biology course (freshman/sophomore majors) to help teach organismal diversity within an evolutionary framework. Our instructional strategy consisted of designing and implementing a set of experiences to help students learn to read, interpret, and manipulate phylogenetic trees, with a particular emphasis on using data to evaluate alternative phylogenetic hypotheses (trees). To assess the outcomes of these learning experiences, we designed and implemented a Phylogeny Assessment Tool (PhAT), an open-ended response instrument that asked students to: 1) map characters on phylogenetic trees; 2) apply an objective criterion to decide which of two trees (alternative hypotheses) is "better"; and 3) demonstrate understanding of phylogenetic trees as depictions of ancestor-descendant relationships. A pre-post test design was used with the PhAT to collect data from students in two consecutive Fall semesters. Students in both semesters made significant gains in their abilities to map characters onto phylogenetic trees and to choose between two alternative hypotheses of relationship (trees) by applying the principle of parsimony (Occam's razor). However, learning gains were much lower in the area of student interpretation of phylogenetic trees as representations of ancestor-descendant relationships.

Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

Local search for the generalized tree alignment problem.

BackgroundA phylogeny postulates shared ancestry relationships among organisms in the form of a binary tree. Phylogenies attempt to answer an important question posed in biology: what are the ancestor-descendent relationships between organisms? At the core of every biological problem lies a phylogenetic component. The patterns that can be observed in nature are the product of complex interactions, constrained by the template that our ancestors provide. The problem of simultaneous tree and alignment estimation under Maximum Parsimony is known in combinatorial optimization as the Generalized Tree Alignment Problem (GTAP). The GTAP is the Steiner Tree Problem for the sequence edit distance. Like many biologically interesting problems, the GTAP is NP-Hard. Typically the Steiner Tree is presented under the Manhattan or the Hamming distances.ResultsExperimentally, the accuracy of the GTAP has been subjected to evaluation. Results show that phylogenies selected using the GTAP from unaligned sequences are competitive with the best methods and algorithms available. Here, we implement and explore experimentally existing and new local search heuristics for the GTAP using simulated and real data.ConclusionsThe methods presented here improve by more than three orders of magnitude in execution time the best local search heuristics existing to date when applied to real data.

Using phylogenetic information and the comparative method to evaluate hypotheses in macroecology

SummaryIt is widely recognized that macroecological patterns are not independent of the evolution of the lineages involved in generating these patterns. While many researchers have begun to evaluate the effect of ancestor–descendant relationships on observed patterns using the phylogenetic comparative method, most macroecological studies only utilize the cross‐sectional comparative method to ‘remove the phylogenetic history’, without considering the option of evaluating its effect without removing it.Currently, most researchers use this method without explicitly evaluating three fundamental evolutionary assumptions of the comparative method: (i) that the phylogeny is constructed without error (which implies evaluating phylogenetic uncertainty); (ii) that more closely related species tend to show more similar characters than expected by chance (which implies evaluating the phylogenetic signal) and; (iii) that the model of the characters' evolution effectively recapitulates their history (which implies comparing the fit of several evolutionary models and evaluating the uncertainty of the estimating model parameters).Macroecological studies will benefit from the use of the comparative method to assess the effect of phylogenetic history without removing its effect. The comparative method will also allow for the simultaneous analysis of trait evolution and its impact on diversification rates; it is important to evaluate these processes together because they are not independent. In addition, explicit evaluations of the assumptions of comparative methods using Bayesian inferences will allow researchers to quantify the uncertainty of specific evolutionary hypotheses accounting for observed macroecological patterns.We illustrate the usefulness of the method using the phylogeny of the genusSebastes(Pisces: Scorpaeniformes), together with data on the body size–latitudinal range relationship to estimate the effect of phylogenetic history on the observed macroecological pattern.

Defining and redefining monophyly: Haeckel, Hennig, Ashlock, Nelson and the proliferation of definitions

The various existing definitions of monophyly have resulted in confusion within the systematics community. The divergence in terminology started with the work of Willi Hennig who attempted to introduce a precise definition of phylogenetic relationship in 1950, a term that he had synonymised with monophyly by 1953, thereby creating a new definition. In 1965, Hennig introduced paraphyly to distinguish his version of monophyly from groups based on symplesiomorphies or stem groups. In attempting to resolve the confusion, Ashlock synonymised Hennig’s monophyly as holophyly, resulting in another new term. Ashlock, Mayr and others defended Haeckel’s original use of monophyly, by including holophyly and paraphyly. The result was an unresolved 21-year debate on monophyly and its various uses. A review of the history of monophyly and the origins of its various definitions has resulted in two new terms to distinguish the different versions of monophyly currently in use: diamonophyly, which group definitions based a notion of ancestor-descendant relationships, and synmonophyly, which groups definition based on kinship relationships. The terms ‘reciprocal monophyly’ and ‘oligophyly’ are discussed as being diamonophyletic.

Efficient Streaming Algorithms for Tree Matching Problems

With the growing importance of XML in data exchange, much research has been done in providing flexible query mechanisms to extract data from XML documents. In this paper, we focus on the query evaluation in an XML streaming environment, in which data streams arrive continuously and queries have to be evaluated even before all the data of an XML document are available. Two algorithms will be discussed. One is for the unordered tree matching, by which only ancestor-descendant and parent-child relationships are considered. It requires O(|T'|⋅leafQ) time, where T' is a subtree of document tree T, in which each node matches at least one node in query Q and leafQ is the number of leaf nodes in Q. The other is for the ordered tree matching, by which the left-to-right order of nodes must also be taken into account. It runs in O(|T'|⋅|Q|) time. Furthermore, our algorithms achieve high time performance without trading off space requirements. They have the same caching space and buffering space overhead as state-of-the-art stream-querying algorithm. We show the efficiency and effectiveness of our algorithms by a lot of experiments.

Efficient evaluation of reachability query for directed acyclic XML graph based on a prime number labelling schema

Many schema labelling approaches have been designed to facilitate querying of XML documents. The proposed algorithms are based on the fact that ancestor–descendant relationships among nodes can be quickly determined. Schema labelling is a family of technologies widely used in indexing tree, graph, or structured XML graph, in which a unique identifier is assigned to each node in the tree/graph. The generated identifier is then used in indexing as a reference to the actual node so that structural relationship among the nodes can be quickly captured. In this paper, we extend the prime number schema labelling algorithm for labelling DAG XML graph. Our main contribution is scaling down the original XML graph size substantially based on the Strongly Connected Component (SCC) principles. Labelling each node in DAG with an integer that is the arithmetical multiplication of the prime number associating with the node and its parent label. The schema does not depend on spanning tree. Thus, subsumption hierarchies represented in a DAG can be efficiently explored by checking the divisibility among the labels. Also, it inherits dynamic update ability and compact size features from its predecessors. Our theoretical analysis and the experimental results showed that the generated labelled schema is an efficient and a scalable one for processing reachability queries on large XML graphs.

Parmeliopsis esorediata (Degel.) Nordnes Discovered in North America

Parmeliopsis esorediata (Degel.) Nordnes was first described in 1956 as a non-sorediate variety of the wide-ranging boreal sorediate P. hyperopia. It was considered endemic to subalpine areas of southern Norway until a 2004 collection was made in the Ural Mountains of Russia. Here, we report P. esorediata for the first time for North America, from the Gaff Topsails region of western Newfoundland, Canada. This high-elevation region is similar bioclimatically to those in Norway and Russia where P. esorediata occurs. We review the status of this globally rare lichen and P. hyperopia as a “species pair”. Whether they have an ancestor-descendant relationship, or whether P. esorediata has arisen sporadically and repeatedly, should now be amenable to resolution with molecular phylogenetic methods.

Numeric-based XML labeling schema by generalized dynamic method

Most efficient indeces and query techniques over XML (extensible markup language) data are based on a certain labeling scheme, which can quickly determine ancestor-descendant and parent-child relationship between two nodes. The current basic labeling schemes such as containment scheme and prefix scheme cannot avoid relabeling when XML documents are updated. After analyzing the essence of existing dynamic XML labels such as compact dynamic binary string (CDBS) and vector encoding, this paper gives a common unifying framework for the numeric-based generalized dynamic label, which can be implemented into a variety of dynamic labels according to the different user-defined value comparison methods. This paper also proposes a novel dynamic labeling scheme called radical sign label. Extensive experiments show that the radical sign label performs well for the initialization, insertion and query operations, and especially for skewed insertion where the storage cost of the radical sign label is better than that of former methods.

Efficiency of TreeMatch Algorithm in XML Tree Pattern Matching

In Recent days exchange XML data more often in organizations and business sectors, so there is an increasing need for effective and efficient processing of queries on XML data. This paper presents a wide analysis to identify the efficiency of XML tree pattern matching algorithms. Previous years many methods have been proposed to match XML tree queries efficiently. In particularly TwigStack, OrderedTJ, TJFast and TreeMatch algorithms. All algorithms to achieve something through these own ways like structural relationship including Parent - Child (P-C) relationship (denoted as '/') and Ancestor-Descendent (A-D) relationships (denoted as '//') and more. Finally, we report our results to show that which algorithm is superior to previous approaches in terms of the performance. Keywords - Efficient TPQ, Efficiency of Tree pattern, XML Tree pattern

TAXONOMIC OVERVIEW AND EVOLUTIONARY HISTORY OF GLOBOTRUNCANITA INSIGNIS (GANDOLFI, 1955)

Globotruncanita insignis (Gandolfi, 1955) is a planktonic species commonly recognized in Late Cretaceous foraminiferal assemblages, but uncertainty about its morphologic variability and phyletic relationships have led to different interpretations of it. The taxon was considered to be morphologically and evolutionary related to Globotruncana rosetta (Carsey, 1926), phyletically linked to Globotruncanita elevata (Brotzen, 1934), or a junior synonym of the latter species. In addition, the neotype that replaced the lost holotype caused a taxonomic debate and compromised the identification of G. insignis , which has been assigned to both Globotruncanita and Globotruncana. This study resolves the taxonomic problems and reconstructs the phyletic lineage of this species on the basis of a continuous sequence of exceptionally well preserved and highly diversified planktonic foraminiferal assemblages in the Contusotruncana plummerae and Radotruncana calcarata zones, recently recovered from southeastern Tanzania drillholes. In addition to common G. insignis that characteristically have a strongly convex umbilical side, we recognized succession of morphotypes intermediate between Globotruncanita stuartiformis and G. insignis that demonstrates an ancestor–descendant relationship between the two taxa and further validates the assignment of G. insignis to Globotruncanita . Moreover, our results confirm that the neotype falls in the same phyletic lineage, but it represents a primitive form of G. insignis .

Detecting Highways of Horizontal Gene Transfer

In a horizontal gene transfer (HGT) event, a gene is transferred between two species that do not have an ancestor-descendant relationship. Typically, no more than a few genes are horizontally transferred between any two species. However, several studies identified pairs of species between which many different genes were horizontally transferred. Such a pair is said to be linked by a highway of gene sharing. We present a method for inferring such highways. Our method is based on the fact that the evolutionary histories of horizontally transferred genes disagree with the corresponding species phylogeny. Specifically, given a set of gene trees and a trusted rooted species tree, each gene tree is first decomposed into its constituent quartet trees and the quartets that are inconsistent with the species tree are identified. Our method finds a pair of species such that a highway between them explains the largest (normalized) fraction of inconsistent quartets. For a problem on n species and m input quartet trees, we give an efficient O(m + n(2))-time algorithm for detecting highways, which is optimal with respect to the quartets input size. An application of our method to a dataset of 1128 genes from 11 cyanobacterial species, as well as to simulated datasets, illustrates the efficacy of our method.

PHYLOGENETIC RELATIONSHIPS AND EVOLUTIONARY HISTORY OF THE PALEOGENE GENUS IGORINA THROUGH PARSIMONY ANALYSIS

Research Article| July 01, 2011 PHYLOGENETIC RELATIONSHIPS AND EVOLUTIONARY HISTORY OF THE PALEOGENE GENUS IGORINA THROUGH PARSIMONY ANALYSIS Dario M. Soldan; Dario M. Soldan 3 1Dipartimento di Scienze della Terra “A. Desio”, Università degli Studi di Milano, via Mangiagalli 34, Milano, Italy 3Correspondence author: E-mail: dario.soldan@unimi.it Search for other works by this author on: GSW Google Scholar Maria Rose Petrizzo; Maria Rose Petrizzo 1Dipartimento di Scienze della Terra “A. Desio”, Università degli Studi di Milano, via Mangiagalli 34, Milano, Italy Search for other works by this author on: GSW Google Scholar Isabella Premoli Silva; Isabella Premoli Silva 1Dipartimento di Scienze della Terra “A. Desio”, Università degli Studi di Milano, via Mangiagalli 34, Milano, Italy Search for other works by this author on: GSW Google Scholar Andrea Cau Andrea Cau 2Museo Geologico “Giovanni Capellini”, via Zamboni 63, Bologna, Italy Search for other works by this author on: GSW Google Scholar Author and Article Information Dario M. Soldan 3 1Dipartimento di Scienze della Terra “A. Desio”, Università degli Studi di Milano, via Mangiagalli 34, Milano, Italy Maria Rose Petrizzo 1Dipartimento di Scienze della Terra “A. Desio”, Università degli Studi di Milano, via Mangiagalli 34, Milano, Italy Isabella Premoli Silva 1Dipartimento di Scienze della Terra “A. Desio”, Università degli Studi di Milano, via Mangiagalli 34, Milano, Italy Andrea Cau 2Museo Geologico “Giovanni Capellini”, via Zamboni 63, Bologna, Italy 3Correspondence author: E-mail: dario.soldan@unimi.it Publisher: Cushman Foundation for Foraminiferal Research Received: 28 Sep 2010 Accepted: 20 Jan 2011 First Online: 03 Mar 2017 Online ISSN: 1943-264X Print ISSN: 0096-1191 © 2011 Journal of Foraminiferal Research Journal of Foraminiferal Research (2011) 41 (3): 260–284. https://doi.org/10.2113/gsjfr.41.3.260 Article history Received: 28 Sep 2010 Accepted: 20 Jan 2011 First Online: 03 Mar 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Get Permissions Search Site Citation Dario M. Soldan, Maria Rose Petrizzo, Isabella Premoli Silva, Andrea Cau; PHYLOGENETIC RELATIONSHIPS AND EVOLUTIONARY HISTORY OF THE PALEOGENE GENUS IGORINA THROUGH PARSIMONY ANALYSIS. Journal of Foraminiferal Research 2011;; 41 (3): 260–284. doi: https://doi.org/10.2113/gsjfr.41.3.260 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyJournal of Foraminiferal Research Search Advanced Search Abstract The evolution of planktic foraminifera in the Paleocene–Eocene time interval is characterized by a high rate of diversification after the major extinction event observed at the Cretaceous/Paleogene boundary. An accelerated speciation rate resulted in the appearance of several new genera. Phylogenetic relationships among many of genera are still poorly understood. This study investigates the origin and phylogeny of the genus Igorina, which is characterized by a thick, nonspinose and incrusted wall. Igorina appears in Subzone P3a (early late Paleocene) and disappears in Zone P11 (middle Eocene). To date, nine species have been assigned to the genus Igorina (I. pusilla, I. trichotrocha, I. tadjikistanensis, I. convexa, I. albeari, I. laevigata, I. lodoensis, I. broedermanni, and I. anapetes) based on both wall texture and morphologic similarities. However, the taxonomic identification at species level is affected by several problems, mainly those resulting from poor descriptions and illustrations of the primary type specimens of several species. This study reconstructs the phylogeny and evolution of the igorinids through cladistic analysis by applying the method of parsimony.Phylogenetic relationships of the species assigned to Igorina are determined through stratocladistic analysis by using a data matrix of 23 taxa (including key species of Acarinina), 31 morphological characters (unordered), and a stratigraphic character (ordered) mapping the first occurrence of the taxa under investigation. The matrix (Appendix 1) was processed with PAUP* 4.0b10 software by using the heuristic search option to discover the most parsimonious trees. Results suggest that I. pusilla is the first representative of the Igorina lineage, and it is followed by I. laevigata, I. convexa, and I. albeari. Morphotypes of uncertain taxonomic identification have been coded and analyzed separately as morphotypes A–F to determine their ancestor-descendant relationships and to evaluate their validity as discrete species. As the result of our analysis, two new species are formally described as I. praecarinata (= morphotype A) and I. paraspiralis (= morphotypes C, E, and F). Finally, our analysis provides evidence that I. lodoensis, I. broedermanni, and I. anapetes are more closely related to Acarinina than to Igorina and clearly belong to a different lineage. You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

동적 XML 데이터 관리를 위한 트리 분해 기반의 소수 레이블링 기법

갱신 연산의 허용으로 동적 XML 데이터의 처리 효율성의 요구가 증대하면서 새로운 동적 XML 레이블링 기법들이 연구되어 왔다. 동적 XML 레이블링 기법의 핵심적인 해결 사항으로는 조상-자손-형제 관계 결정, 레이블 저장공간의 절약, 빠른 응답시간, 갱신에 의한 레이블 재작성의 최소화이다. 대표적인 동적 레이블링 기법으로 소수 기반 레이블링 기법이 있다. 소수 기반 레이블링 기법은 소수의 특성을 이용하여 조상-자손 관계를 쉽게 결정한다. 또한 새로운 엘리먼트를 삽입할 때도 기존 노드의 레이블을 재작성하는 비용이 발생되지 않는 장점을 갖고 있다. 하지만 소수를 많이 사용하면 레이블의 값이 상당히 커지게 되는 레이블 오버플로우 문제가 발생된다. 본 논문에서는 레이블 오버플로우 문제를 효과적으로 줄이는 새로운 방법을 소개한다. 제안하는 방법의 핵심 개념은 트리 분해이다. 레이블 오버플로우가 발생하면 트리를 하부 트리들로 분해하고 레이블은 각 하부 트리에 한해서 부여하는 것이다. 실험을 통해 트리 분해 기반의 소수 기반 레이블링 기법의 효과를 보인다. As demand for efficiency in handling dynamic XML data grows, new dynamic XML labeling schemes have been researched. The key idea of the dynamic XML labeling scheme is to find ancestor-descendent-sibling relationships and to minimize memory space to store total label, response time and range of relabeling incurred by update operations. The prime number labeling scheme is a representative scheme which supports dynamic XML documents. It determines the ancestor-descendant relationships between two elements by a simple divisibility test of labels. When a new element is inserted into the XML data using this scheme, it does not change the label values of existing nodes. However, since each prime number must be used exclusively, labels can become significantly large. Therefore, in this paper, we introduce a novel technique to effectively reduce the problem of label overflow. The suggested idea is based on tree decomposition. When label overflow occurs, the full tree is divided into several sub-trees, and nodes in each sub-tree are separately labeled. Through experiments, we show the effectiveness of our scheme.

Extended XML Tree Pattern Matching: Theories and Algorithms

As business and enterprises generate and exchange XML data more often, there is an increasing need for efficient processing of queries on XML data. Searching for the occurrences of a tree pattern query in an XML database is a core operation in XML query processing. Prior works demonstrate that holistic twig pattern matching algorithm is an efficient technique to answer an XML tree pattern with parent-child (P-C) and ancestor-descendant (A-D) relationships, as it can effectively control the size of intermediate results during query processing. However, XML query languages (e.g., XPath and XQuery) define more axes and functions such as negation function, order-based axis, and wildcards. In this paper, we research a large set of XML tree pattern, called extended XML tree pattern, which may include P-C, A-D relationships, negation functions, wildcards, and order restriction. We establish a theoretical framework about “matching cross” which demonstrates the intrinsic reason in the proof of optimality on holistic algorithms. Based on our theorems, we propose a set of novel algorithms to efficiently process three categories of extended XML tree patterns. A set of experimental results on both real-life and synthetic data sets demonstrate the effectiveness and efficiency of our proposed theories and algorithms.