Wagner Parsimony Research Articles

GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.

Testing Empirical Support for Evolutionary Models that Root the Tree of Life

Trees of life (ToLs) can only be rooted with direct methods that seek optimization of character state information in ingroup taxa. This involves optimizing phylogenetic tree, model and data in an exercise of reciprocal illumination. Rooted ToLs have been built from a census of protein structural domains in proteomes using two kinds of models. Fully-reversible models use standard-ordered (additive) characters and Wagner parsimony to generate unrooted trees of proteomes that are then rooted with Weston’s generality criterion. Non-reversible models directly build rooted trees with unordered characters and asymmetric stepmatrices of transformation costs that penalize gain over loss of domains. Here, we test the empirical support for the evolutionary models with character state reconstruction methods using two published proteomic datasets. We show that the reversible models match reconstructed frequencies of character change and are faithful to the distribution of serial homologies in trees. In contrast, the non-reversible models go counter to trends in the data they must explain, attracting organisms with large proteomes to the base of the rooted trees while violating the triangle inequality of distances. This can lead to serious reconstruction inconsistencies that show model inadequacy. Our study highlights the aprioristic perils of disposing of countering evidence in natural history reconstruction.

Parsimony-based test for identifying changes in evolutionary trends for quantitative characters: implications for the origin of the amniotic egg.

The origin of the amniotic egg was a major event in vertebrate evolution and is thought to have contributed to the spectacular evolutionary radiation of amniotes. We test one of the most popular scenarios proposed by Carroll in 1970 to explain the origin of the amniotic egg using a novel method based on an asymmetric version of linear parsimony (aka Wagner parsimony) for identifying the most parsimonious split of a tree into two parts between which the evolution of the character is allowed to differ. The new method evaluates the cost of splitting a phylogenetic tree at a given node as the integral, over all pairs of asymmetry parameters, of the most parsimonious costs that can be achieved by using the first parameter on the subtree pending from this node and the second parameter elsewhere. By testing all the nodes, we then obtain the most parsimonious split of a tree with regard to the character values at its tips. Among the nine trees and two characters tested, our method yields a total of 517 parsimonious trend changes in Permo-Carboniferous stegocephalians, a single one of which occurs in a part of the tree (among stem-amniotes) where Carroll's scenario predicts that there should have been distinct changes in body size evolutionary trends. This refutes the scenario because the amniote stem does not appear to have elevated rates of evolutionary trend shifts. Our nodal body size estimates offer less discriminating power, but they likewise fail to find strong support for Carroll's scenario.

Diversification of insects since the Devonian: a new approach based on morphological disparity of mouthparts

The majority of the analyses of the evolutionary history of the megadiverse class Insecta are based on the documented taxonomic palaeobiodiversity. A different approach, poorly investigated, is to focus on morphological disparity, linked to changes in the organisms’ functioning. Here we establish a hierarchy of the great geological epochs based on a new method using Wagner parsimony and a ‘presence/absence of a morphological type of mouthpart of Hexapoda’ dataset. We showed the absence of major rupture in the evolution of the mouthparts, but six epochs during which numerous innovations and few extinctions happened, i.e., Late Carboniferous, Middle and Late Triassic, ‘Callovian-Oxfordian’, ‘Early’ Cretaceous, and ‘Albian-Cenomanian’. The three crises Permian-Triassic, Triassic-Jurassic, and Cretaceous-Cenozoic had no strong, visible impact on mouthparts types. We particularly emphasize the origination of mouthparts linked to nectarivory during the Cretaceous Terrestrial Revolution. We also underline the origination of mouthparts linked to phytophagy during the Middle and the Late Triassic, correlated to the diversification of the gymnosperms, especially in relation to the complex ‘flowers’ producing nectar of the Bennettitales and Gnetales.

Reconciliation With Nonbinary Gene Trees Revisited

By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence to annotate orthologs and paralogs. The currently available reconciliation methods for nonbinary gene trees are computationally expensive for genome-scale applications. We present four O (| G |+| S |) algorithms to reconcile an arbitrary gene tree G with a binary species tree S in the duplication, loss, duploss (also known as mutation), and deep coalescence cost models, where |· | denotes the number of nodes in a tree. The improvement is achieved through two innovations: a linear-time computation of compressed child-image subtrees and efficient reconstruction of irreducible duplication histories. Our technique for child-image subtree compression also results in an order of magnitude speedup in runtime for the dynamic programming and Wagner parsimony--based methods for tree reconciliation in the affine cost model.

Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.

The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

Implementation as theory, hierarchy as transformation, homology as synapomorphy.

Presently cladistics is based on, and justified by, a computer implementation (Wagner Parsimony) rather than sound methodological or theoretical foundations. In this paper, the recent goals of cladistics that are derived from computer implementations and 'tree-thinking' are discussed. The discussion raises a critical point, namely whether one can dispense with these recent goals and adopt a wholly systematic approach, one herein termed systematic thinking.

Evolution and palaeosynecology of the Mesozoic earwigs (Insecta: Dermaptera)

Sinoprotodiplatys zhangi gen. et sp. nov. is described from the Lower Cretaceous Yixian Formation in Liaoning Province, near Beipiao City, China. It is one of the most recent representatives of the suborder Archidermaptera. The classification and synonymies among the archidermapteran families are reassessed. The palaeosynecological evolution of the Mesozoic earwigs is analysed using the new tool of the ‘Wagner Parsimony using Morphological Characters’ method (‘WAPUM’), suggesting that the evolution of the morphology of these insects was very progressive, perhaps owing to their way of life in the soil.

Phylogeny of the genus Palmanura (Collembola: Neanuridae).

In order to assess the phylogenetic structure of the springtail genus Palmanura, as well as to test the monophyly of the tribe Sensillanurini (Neanuridae: Neanurinae), a data matrix of morphological (chaetotactic and other) characters of members of this group was assembled and analysed in the light of Wagner parsimony. The data matrix included all the known members of the Neotropical genus Palmanura, plus representatives of Sensillanura and Americanura. Although not all the clades obtained were highly supported by bootstrap resampling, some structures were relatively constant under different approaches. Alternative analyses (unordered and ordered character states, rescaled weighting procedure) were applied. While alternative solutions were obtained, a number of structures were shared by the results irrespective of the method used. On this basis, the results suggest that some further reassessment is required to confirm formally the monophyly of the tribe Sensillanurini. The genera Palmanura and Americanura are mutually poly/paraphyletic; we thus suggest that Palmanura should be considered as a synonym of Americanura, although some character reassessment and more varied outgroup species may be necessary before a formal generic redefinition can be proposed. Finally, a comparison of the performance of the characters under Wagner parsimony analysis indicated that differences in the characters' retention indexes are due not to the topological (tagmal) position of the traits involved, but to character coding: the characters describing quantitative features (generally numbers of setae) generally performed worse than other types of characters under parsimony. An updated list of the known members of the Sensillanurini (Collembola: Neanuridae: Neanurinae) is presented. © The Willi Hennig Society 2009.

Freshwater invertebrates and Wagner's parsimony method (WPM): Tools for the submersion time estimation of a cadaver found in a natural aquatic environment. Description of a sampling protocol

The forensic investigations are generally very difficult when a body is discovered immersed for an ignored period in freshwater. Due to long periods of immersion and a high level of putrefaction, the estimation of the time since death is problematic. Classical forensic entomology is based on existing links between necrophagous insects and the state of decomposition, in order of appearance of necrophagous insects on the cadaver. This science does not allow a pertinent evaluation of the time since the death for a crime scene technician. It is indeed impossible to reach any conclusions based on the underwater colonisation process once the cadaver has resurfaced. The purpose of this work was to analyze from February 2001 to October 2002, the different cases of cadavers’ discoveries in order to isolate pertinent bioindicators. We created a simple but effective sampling protocol to get a real solution to the problem of estimating the post mortem submersion interval (PMSI) of a cadaver found in lotic or lentic water. Les enquêtes médicolégales sont généralement très difficiles quand on découvre un cadavre immergé en eau douce pendant une durée indéterminée. En raison des longues périodes d’immersion et du haut niveau de putréfaction, l’évaluation de l’heure du décès est problématique. L’entomologie médicolégale classique est basée sur des liaisons existantes entre des insectes nécrophages et l’état de décomposition, par ordre d’apparition sur le cadavre . Mais cette science ne permet pas d’évaluation pertinente du laps de temps écoulé depuis la mort pour un technicien de scène de crime. Il est, en effet, impossible d’arriver à des conclusions fiables sur le processus de colonisation sous-marin une fois que le cadavre a refait surface. Le but de ce travail était d’analyser de février 2001 à octobre 2002 différents cadavres pour isoler des indicateurs pertinents. Nous avons créé un protocole d’échantillonnage pour évaluer l’intervalle d’immersion post-mortem d’un cadavre trouvé dans une eau agitée ou stagnante.

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

Count is a software package for the analysis of numerical profiles on a phylogeny. It is primarily designed to deal with profiles derived from the phyletic distribution of homologous gene families, but is suited to study any other integer-valued evolutionary characters. Count performs ancestral reconstruction, and infers family- and lineage-specific characteristics along the evolutionary tree. It implements popular methods employed in gene content analysis such as Dollo and Wagner parsimony, propensity for gene loss, as well as probabilistic methods involving a phylogenetic birth-and-death model. Count is available as a stand-alone Java application, as well as an application bundle for MacOS X, at the web site http://www.iro.umontreal.ca/ approximately csuros/gene_content/count.html. It can also be launched using Java Webstart from the same site. The software is distributed under a BSD-style license. Source code is available upon request from the author.

The Wagner Parsimony using morphological characters: a new method for palaeosynecological studies

The limits and difficulties related to the tools currently in use for palaeosynecological comparisons of faunas or floras of different geological periods are discussed. The new method of the Wagner parsimony Applied to Palaeosynecology Using Morphology (WAPUM method), is defined and tested on morphological characters gathered from two insect groups Odonatoptera and Thripida. The difficulties related to the monophyly of the taxonomic groups used in the more traditional approaches are no longer a problem when using the WAPUM method. In the WAPUM a character is ‘presence versus absence of species bearing a morphological structure’. The results obtained from use of the WAPUM minimize the number of changes among character states. Application of the WAPUM could reveal signals to confirm or object the currently available scenarios for the global changes in the evolution of past diversity and disparity of organisms (major changes or global crises of diversity).

Phylogenetic analysis of Artemisia L. (Asteraceae) based on micromorphological traits of pollen grains

The phylogenetic relationships within the genus Artemisia have been very controversial. In order to recognize the systematic inference of pollen grains in this genus, the micromorphological characteristics of pollens from 22 taxa were examined by means of light microscopy (LM) and scanning electron microscopy (SEM). A phylogenetic analysis of Artemisia based on 9 micromorphological characters of pollens was conducted using Wagner parsimony method. In the resulting phylogenetic tree, relationships among different Artemisia species are shown. This study also presents the phylogenetic associations among 4 sections within the genus Artemisia. The reunion of genus Seriphidum with Artemisia was also confirmed.

Phylogenetic analysis of Artemisia L. (Asteraceae) based on micromorphological traits of pollen grains

The phylogenetic relationships within the genus Artemisia have been very controversial. In order to recognize the systematic inference of pollen grains in this genus, the micromorphological characteristics of pollens from 22 taxa were examined by means of light microscopy (LM) and scanning electron microscopy (SEM). A phylogenetic analysis of Artemisia based on 9 micromorphological characters of pollens was conducted using Wagner parsimony method. In the resulting phylogenetic tree, relationships among different Artemisia species are shown. This study also presents the phylogenetic associations among 4 sections within the genus Artemisia. The reunion of genus Seriphidum with Artemisia was also confirmed.

Adequacy of numerical taxonomic methods

A simulation model, GENESIS, was developed to examine the relative merits of several phylocenetic and phenetic methods. For a description of the model and the results of a sensitivity analysis, see Heijerman (1988, 1990). GENESIS was designed to generate artificial data sets of ‘species’ with known phylogenies. These datasets were subjected to character analysis b various numerical taxonomic methods (UPGMA clustering, Wagner parsimony analysis and compo nent-comparibility analysis). The results of analysis were compared with the true phylogeny. The agreement between the true tree and the reconstructed tree was used as a measure of quality (adequacy). By varying the input parameters of GENESIS, output produced under different evolutionary scenarios was obtained and the relative adequacies of the methods in relation to these evolutionary conditions were evaluated. The overall differences in adequacy between Wagner parsimony as performed by PAUP, PHYLIP (MIX) and HENNIG86, and UPGMA clustering with product-moment correlations of standardized characters, were rather small. These methods were more adequate than Wagner parsimony with WAGNER78 and group com patibility with CAFCA. The adequacy of the trees as estimated by WAGNER78, PAUP, PHYLIP and CAFCA depended on several tree properties, the consistency index being the most important one.

Studies in cave life evolution: a rationale for future theoretical developments using phylogenetic inference

As in every field of comparative biology, phylogeny provides an independent reference system in studies on cave life evolution to test current theoretical proposals. Using phylogeny, sound hypotheses on the ancestral states of characters and their subsequent changes can be made by polarizing the characters between related taxa. Hypotheses on evolutionary processes can also be tested by comparing the patterns they imply with independently inferred phylogenetic patterns. The power of the tests relies upon the independence of phylogenetic patterns (built with cladistics using Wagner parsimony) and the theoretical proposals under study. Classical assumptions on the evolution of troglobitic life are analysed with this methodology. The following points are discussed: what is a troglobitic taxon? Are there features characteristic of troglobitic taxa? Is troglobitic life an evolutionary dead end? What circumstances favour troglobitic evolution? Using phylogenetic analysis, the presence or absence of so-called troglomorphic features were inferred in troglobitic taxa. In fact these taxa can be characterized only by their behavioural ecology. Pre-adaptations (exaptations) can also be precisely defined. Cave living does not appear to be an evolutionary dead end. Two patterns subsequent to cave life appearance have been documented: speciation of troglobitic taxa in the subterranean environment, and reversal to an epigean habitat. Troglobitic life thus turns out to be one step in the diversification of clades. Troglobitic life is usually explained as an evolution under the pressure of unfavourable environmental conditions, or the conquest of a new resource, or the result of biological interactions (competition, predation). Phylogenetic analyses show that none of these hypotheses propose clear alternatives on cave life evolution. Moreover most of their a priori statements cannot easily be falsified. As such they have only limited explanatory power.

Biosystematics of the aphid genus Cryptomyzus (Hornoptera, Aphididae): an electrophoretic analysis

The aphid genus Crypromyzus was studied using starch. el electrophoresis in order to establish differences between the various taxa and to estimate their paylogenetic relationships. A low degree of polymorphism and heterozyosity was observed. Taxa previously assumed to be homogeneous appeared to consist of different tost-secific forms. Polymorphism at the PGI locus was used to assess the degree of isolation. It was founf to range from complete separation to a reduction in gene flow. Three methods of estimating hylogenetic relationships were employed: the UPGMA clustering method using Nei's genetic distance; the Rogers distance together with the distance Wagner method and the independent allele model of Mickevich and Mitter (1981) combined with the Wagner parsimony method. The results of all three methods agree that several of the taxa are closely related but assign different lower branching points to the phylogenetic tree. The independent allele model is discussed in more detail because it is not often applied.

Forensic entomology: a new hypothesis for the chronological succession pattern of necrophagous insect on human corpses

Forensic entomology can help to estimate the time elapsed since death, by studying the necrophagous species collected on a cadaver and its surroundings. The determination of the so- called post mortem interval (PMI or period of first oviposition) is based on the development time of necrophagous dipterans and on the chronological pattern of insects’ succession on the corpse throughout the decaying process. In the present study, authors investigated this succession by the analysis of the database of the Department of Forensic Entomology of the French Gendarmerie over 12 years (1992–2003) in order to propose a new approach and a new hypothsesis of the dynamic of necrophagous-insects’ populations present on a human cadaver over time. For all treated cases, the presence/absence and the oldest development stage of the species were recorded. Data were analyzed by statistical and Wagner parsimony methods. The statistic results allowed the association of groups of species with typical developmental stages. The Wagner parsimony analysis showed that the dynamic of the necrophagous insect population present on a cadaver could be characterised by specific species. Together, they allowed establishing hypotheses of succession of necrophagous insects on human cadavers over time that could be usefull in the PMI estimation.

Phylogenetic analysis in some Diospyros spp. (Ebenaceae) and Japanese persimmon using chloroplast DNA PCR-RFLP markers

Ten universal primer pairs of chloroplast genome were used to amplify non-coding regions of chloroplast DNA (cpDNA) in 7 Diospyros L. species including 29 genotypes and approximately 20.4 kb, 12.6% of the chloroplast genome were analyzed. The amplified products were digested by seven restriction enzymes. The results showed that there were abundant polymorphisms in inter-specific cpDNA within the genus Diospyros. However, it was not observed intra-species variations in 22 tested genotypes of Diospyros kaki (Japanese persimmon), except for ‘Male strain No. 9’. Persimmon had close relationship with Diospyros lotus and Diospyros glaucifolia, but distantly with Diospyros virginiana and Diospyros rhombifolia in diagram based on principal coordinates analysis and Wagner parsimony method. The discrepancy of digesting pattern in cpDNA suggested that the genotype Jinzaoshi was distinct with the remaining Diospyros spp., which revealed that Jinzaoshi may be a new species of the genus Diospyros.

AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae)

The genus Rosa has a complex evolutionary history caused by several factors, often in conjunction: extensive hybridization, recent radiation, incomplete lineage sorting, and multiple events of polyploidy. We examined the applicability of AFLP markers for reconstructing (species) relationships in Rosa, using UPGMA clustering, Wagner parsimony, and Bayesian inference. All trees were well resolved, but many of the deeper branches were weakly supported. The cluster analysis showed that the rose cultivars can be separated into a European and an Oriental cluster, each being related to different wild species. The phylogenetic analyses showed that (1) two of the four subgenera (Hulthemia and Platyrhodon) do not deserve subgeneric status; (2) section Carolinae should be merged with sect. Cinnamomeae; (3) subsection Rubigineae is a monophyletic group within sect. Caninae, making sect. Caninae paraphyletic; and (4) there is little support for the distinction of the five other subsections within sect. Caninae. Comparison of the trees with morphological classifications and with previous molecular studies showed that all methods yielded reliable trees. Bayesian inference proved to be a useful alternative to parsimony analysis of AFLP data. Because of their genome-wide sampling, AFLPs are the markers of choice to reconstruct (species) relationships in evolutionary complex groups.