Root causes of phylogenetic incongruence observed within basal sauropodomorph interrelationships

The relationships among basal sauropodomorphs are controversial. Results of cladistic analyses vary from a fully paraphyletic assemblage to a monophyletic core‐prosauropod. We apply the comparative cladistics method to three published cladistic analyses of sauropodomorph dinosaurs, in order to identify root causes for differences between phylogenetic results. Except for three taxa (Saturnalia, Thecodontosaurus, and Efraasia) and one clade (Gravisauria), the remaining genera are recovered with conflicting positions. The comparative method is based on indices that allow for the quantification of the degree of similarity in characters and character states among analyses. A comparison of primary data, character selection, and scoring highlights significant discrepancies in data sets. Our results suggest that one character out of two varies from one analysis to the other. These are the root causes for the phylogenetic incongruence observed. The hurdle of the phylogenetic definition of the clade Sauropoda, which has been defined in four different ways, is also treated. We concur with several recent papers following the first node‐based definition of Sauropoda. © 2015 The Linnean Society of London     

分支分类学中和谐性概念与和谐性分析方法

和谐性是分支分类学中的一个基本概念。本文给出一个和谐性的数学定义,称为Kexue和谐性。并在Kexue和谐性的基础上开发出一个新的和谐性分析方法。并对该方法在分支分类研究中的应用进行讨论。     

Parsimony with and without Scientific Justification

Brower's (2000, Cladistics 16, 143–154) pursuit of a nonevolutionary cladistics, like those of others (e.g., Scotland, 2000, Syst. Biol. 49, 480–500), fails for lack of a scientific justification. His operational explication of parsimony does not necessarily rule out the use of other criteria on which to base the identification of a hierarchical branching pattern, nor does he give a compelling reason for why just that one kind of pattern is sought. In the absence of evolutionary theory, such as the descent of species, and the modification of character states, one from another, there is no scientific reason to seek congruence among character hierarchies whose origins, functions, and fates are not necessarily the same. Brower's operational parsimony is no substitute for phylogenetic parsimony, where requirements for ad hoc hypotheses of homoplasy are justifiably minimized, assuming only "descent, with modification." In addition to maximizing explanatory power, that most parsimonious cladogram is the least disconfirmed, most highly corroborated, hypothesis.     

Ontogenetic variations in characters of Euchone analis (Krøyer, 1856) (Polychaeta, Sabellidae, Sabellinae) from Spitsbergen, and new assignments of Oriopsis ingelorae Plate, 1995 and O. liefdefjordensis Plate, 1995

Euchone analis, the type species of its genus, was collected in high densities and in different size classes from Kongsfjorden, west Spitsbergen. This material has provided the basis for an investigation of the size dependence of characters. Almost all characters used in diagnoses were highly variable, especially the number of abdominal chaetigers forming the anal depression and the shape of the depression. The only relatively constant features are the number of chaetigers anterior to the anal depression and the branchial crown‐to‐body length ratio. A branchial skeleton extension of the radiolar appendages of the dorsal lips was found for the first time within Euchone, and this character has been added to the diagnosis of Euchone. Oriopsis liefdefjordensis and small specimens of E. analis agree in all characters, and O. liefdefjordensis is proposed to be a junior synonym of E. analis. Characters found in O. ingelorae are in accordance with those described for Chone, and we propose assigning O. ingelorae to this genus. The significance of ontogenetic character variations in the Sabellidae is discussed.     

Connectivity,Not Frequency,Determines the Fate of a Morpheme

Morphemes are the smallest meaningful parts of words and therefore represent a natural unit to study the evolution of words. To analyze the influence of language change on morphemes, we performed a large scale analysis of German and English vocabulary covering the last 200 years. Using a network approach from bioinformatics, we examined the historical dynamics of morphemes, the fixation of new morphemes and the emergence of words containing existing morphemes. We found that these processes are driven mainly by the number of different direct neighbors of a morpheme in words (connectivity, an equivalent to family size or type frequency) and not its frequency of usage (equivalent to token frequency). This contrasts words, whose survival is determined by their frequency of usage. We therefore identified features of morphemes which are not dictated by the statistical properties of words. As morphemes are also relevant for the mental representation of words, this result might enable establishing a link between an individual’s perception of language and historical language change.     

Towards a processual microbial ontology

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities.     

Phylogenetic inference using discrete characters: performance of ordered and unordered parsimony and of three‐item statements

The cladistic literature does not always specify the kind of multistate character treatment that is applied for an analysis. Characters can be treated either as unordered transformation series or as rooted [three‐item analysis (3ia)] or unrooted state trees (ordered characters). We aimed to measure the impact of these character treatments on phylogenetic inference. Discrete characters can be represented either as rows or columns in matrices (e.g. for parsimony) or as hierarchies for 3ia. In the present study, we use simulated and empirical examples to assess the relative merits of each method considering both the character treatment and representation. We measure two parameters (resolving power and artefactual resolution) using a new tree comparison metric, ITRI (inter‐tree retention index). Our results suggest that the hierarchical character representation not only results (with our simulation settings) in the greatest resolving power, but also in the highest artefactual resolution. Our empirical examples provide equivocal results. Parsimony unordered states yield less resolving power and more artefactual resolutions than parsimony ordered states, both with our simulated and empirical data. Relationships between three operational taxonomic units (OTUs), irrespective of their relationships with other OTUs, are called three‐item statements (3is). We compare the intersection tree (which reconstructs a single tree from all of the common 3is of source trees) with the traditional strict consensus and show that the intersection tree retains more of the information contained in the source trees. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 914–930.     

Species concepts and the ontology of evolution

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next.     

Review of methodological problems of 'Computer cladistics' exemplified with a case study on isopod phylogeny (Crustacea: Isopoda)

Using a computerized phylogenetic analysis of the Isopoda (Crustacea: Peracarida) as source of typical errors and misunderstandings, problems that may occur in computer cladistics are reviewed. It is concluded that in addition to the errors that are possible in a conventional Hennigian analysis some specific methodological problems exist in computer cladistics. It is recommended that the OTU be replaced by the groundpattern concept. Tree statistics are not useful for comparing different competing hypotheses. Arguments ought to concentrate on the hypo-thetico-deductive steps of the analysis, i.e. on character analysis. The use of computers does not add objectivity to character analysis. Single outgroup taxa should not be used in assessing the character states of ingroups. Concerning isopod phylogeny, it is argued here that the tail fan of the Isopoda can probably be derived from the eumalacostracan groundpattern and did not evolve de novo within the Isopoda.     

Homology and synapomorphy‐symplesiomorphy—neither synonymous nor equivalent but different perspectives on the same phenomenon

In a recent debate, either synapomorphy and symplesiomorphy or only synapomorphy have been claimed to be synonymous or equivalent to homology. In my view, exactly the same relationship exists between homology supported by a congruence test on the one hand and synapomorphy as well as symplesiomorphy on the other hand. Both conditions become established at the same time with the process of rooting of an unrooted topology. I, however, do not consider the concept of homology equal or synonymous to that of synapomorphy and symplesiomorphy. In my view, they represent different perspectives on the same phenomenon, i.e. correspondence by common origin. Homology has no implication on the direction of transformation, whereas symplesiomorphy as “primitive” condition and synapomorphy as “derived” condition refer directly to phylogenesis, the real historical evolutionary process of speciation and transformation. In addition, synapomorphy and symplesiomorphy might also refer to a character state that refers to the absence of a structure/organ, which creates problems with traditional homology concepts. Hennig's terms synapomorphy and symplesiomorphy are necessary and sufficient for the evolutionary interpretation of character states. For what is corroborated in an unrooted topology as the result of a congruence test, I suggest as a new term “synmorphy” because it can well be applied also to those characters where one state represents the absence of a structure/organ. The place for homology in morphological cladistics, however, is restricted to the characterization of the relationship between different character states of one transformation series (i.e. character).     

Evolution Is Not a Necessary Assumption of Cladistics

Although the point has already been emphasized by various authors that the assumption of descent with modification is not required to justify cladistics, recent debate suggests that there is still confusion surrounding the necessary and sufficient background knowledge underlying the method. Three general axioms necessary to justify cladistics—the discoverability of characters, hierarchy, and parsimony—are reviewed. Although the assumption of evolution is sufficient to justify cladistics, it is also sufficient to justify competing approaches like maximum likelihood, which suggests that the philosophical support for the cladistic approach is strengthened by purging reference to descent with modification altogether.     

The use of hierarchies as organizational models in systematics

A hierarchy is an abstract organizational model of inter-level relationships among entities. When isomorphic with nature, hierarchies are useful for organizing and manipulating our knowledge. Hierarchies have been used in biological systematics to represent several distinct, but interrelated, facets of the evolution of life with different organizational properties, and these distinctions have been confused by the rubric 'the hierarchy of life'. Evolution, as descent with modification, is inherently dualistic. The organizational structure of a hierarchy can be used to represent dualistic properties as inter-level relationships. Cladistics is monistic, with a singular focus on patterns of descent. Descent has conceptual priority over modification, but the organizational relationship is not exclusive. 'Cladistic classification' is an oxymoron because cladistics lacks the class concepts needed to construct a classification, a point recognized by those who suggest abandoning Linnaean classification in favour of a newly devised monophyletic systematization. Cladistic analysis of descent can be supplemented with an analysis of modification that provides the class concepts needed to construct an evolutionary/phylogenetic classification. When a strong monophyletic pattern of modification is detected (in addition to its monophyletic pattern of descent), the criterion of subsequent modification provides the basis for formally recognizing a certain monophyletic group at a given rank, as opposed to a group that is one node more inclusive or one node less. The criterion of subsequent modification also permits detection of strong paraphyletic patterns of modification, when they exist. By setting standards of evidence needed to recognize paraphyletic groups, one concomitandy strengthens the basis for formally recognizing selective monophyletic groups.     

Word Formation Is Aware of Morpheme Family Size

Words are built from smaller meaning bearing parts, called morphemes. As one word can contain multiple morphemes, one morpheme can be present in different words. The number of distinct words a morpheme can be found in is its family size. Here we used Birth-Death-Innovation Models (BDIMs) to analyze the distribution of morpheme family sizes in English and German vocabulary over the last 200 years. Rather than just fitting to a probability distribution, these mechanistic models allow for the direct interpretation of identified parameters. Despite the complexity of language change, we indeed found that a specific variant of this pure stochastic model, the second order linear balanced BDIM, significantly fitted the observed distributions. In this model, birth and death rates are increased for smaller morpheme families. This finding indicates an influence of morpheme family sizes on vocabulary changes. This could be an effect of word formation, perception or both. On a more general level, we give an example on how mechanistic models can enable the identification of statistical trends in language change usually hidden by cultural influences.     

Cladistic analysis of molecular and morphological data

Considerable progress has been made recently in phylogenetic reconstruction in a number of groups of organisms. This progress coincides with two major advances in systematics: new sources have been found for potentially informative characters (i. e., molecular data) and (more importantly) new approaches have been developed for extracting historical information from old or new characters (i. e., Hennigian phylogenetic systematics or cladistics). The basic assumptions of cladistics (the existence and splitting of lineages marked by discrete, heritable, and independent characters, transformation of which occurs at a rate slower than divergence of lineages) are discussed and defended. Molecular characters are potentially greater in quantity than (and usually independent of) more traditional morphological characters, yet their great simplicity (i. e., fewer potential character states; problems with determining homology), and difficulty of sufficient sampling (particularly from fossils) can lead to special difficulties. Expectations of the phylogenetic behavior of different types of data are investigated from a theoretical standpoint, based primarily on variation in the central parameter λ (branch length in terms of expected number of character changes per segment of a tree), which also leads to possibilities for character and character state weighting. Also considered are prospects for representing diverse yet clearly monophyletic clades in larger-scale cladistic analyses, e. g., the exemplar method vs. “compartmentalization” (a new approach involving substituting an inferred “archetype” for a large clade accepted as monophyletic based on previous analyses). It is concluded that parsimony is to be preferred for synthetic, “total evidence” analyses because it appears to be a robust method, is applicable to all types of data, and has an explicit and interpretable evolutionary basis. © 1994 Wiley-Liss, Inc.     

Regressive progression,progressive regression or neither? Phylogeny and evolution of the Percopsiformes (Teleostei,Paracanthopterygii)

Dillman, C.B., Bergstrom, D.E., Noltie, D.B., Holtsford, T.P. & Mayden, R.L. (2010). Regressive progression, progressive regression or neither? Phylogeny and evolution of the Percopsiformes (Teleostei, Paracanthopterygii). —Zoologica Scripta, 40, 45–60. Cave animals have fascinated scientists for centuries, and clades consisting primarily of cave‐adapted species are even more intriguing. The percopsiforms are an enigmatic group of fishes comprised of nine species in seven genera, with four species in three genera exhibiting characteristic troglomorphic features, such as a lack of pigmentation and eyes. Nucleotide characters presented here provide the first test of monophyly for both the Percopsiformes and Amblyopsidae with this character type and taxonomic completeness. Characters of ND2 support a monophyletic Percopsiformes and Amblyopsidae and further document phylogeographic subdivision in two stygobitic genera, Amblyopsis and Typhlichthys, in Amblyopsidae. Age estimates from time‐calibrated branch lengths utilizing two independent intra‐lineage fossils indicate that the ancestor to amblyopsids is Eocene in age, and that phylogeographic subdivision in both Amblyopsis and Typhlichthys occurred primarily in the Miocene. Interestingly, ancestral character state reconstruction for the amblyopsids strongly supports the re‐evolution of eyes and body pigment. While certainly unconventional, but supported with this character set, the hypothesis provides continued challenge to Dollo’s Law.     

Description,circumscription and phylogenetics of the new tribe Zaeucoilini (Hymenoptera: Figitidae: Eucoilinae), including a description of a new genus

Abstract Neotropical eucoiline genera that have been included in and allied with the Zaeucoila genus group are redescribed. Following character analysis and phylogenetic reconstruction (25 taxa, 96 morphological characters, 1452 ribosomal and mitochondrial characters), this informal genus group was found to be monophyletic, and hence raised to formal recognition as a tribe of eucoilines, namely Zaeucoilini new tribe . Through phylogenetic reconstruction, Aegeseucoela Buffington was determined to be polyphyletic; the type species of Aegeseucoela, A. grenadensis (Ashmead), is transferred to Agrostocynips comb.n. ; the orphaned species, A. flavotincta (Kieffer), is transferred to Marthiella Buffington gen.n. , comb.n. Based on the examination of the holotype of Diranchis flavipes Ashmead, 1900 , this species is transferred to Rhabdeucoela comb.n. , where it is both a junior, subjective synonym of flavipes ( Ashmead, 1894 ) syn.n. and a junior, secondary homonym. Zaeucoilini contains the following genera: Agrostocynips Diaz, Dettmeria Borgmeier, Dicerataspis Ashmead, Lopheucoila Weld, Marthiella Buffington, Moneucoela Kieffer, Moritiella Buffington, Penteucoila Weld, Preseucoela Buffington, Rhabdeucoela Kieffer, Tropideucoila Ashmead and Zaeucoila Ashmead. Characters and character states applicable specifically to Zaeucoilini are defined and illustrated. Characters supporting the monophyly of each genus are discussed. The plesiomorphic host for members of the Zaeucoilini are postulated as agromyzid leaf‐mining Diptera, with one shift within the clade containing Dettmeria, Dicerataspis and Lopheucoila to fruit‐infesting Diptera. New host records are reported for species of Preseucoela, Rhabdeucoela and Zaeucoila. All known hosts for the species of each genus are reported, as are known distributions and locations of type specimens.     

Spatio-structural granularity of biological material entities

Background  

With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.