A maximum entropy criterion of filtering and coding for stationary autoregressive signals: Its physical interpretations and suggestions for its application to neural information transmission

The operations of encoding and decoding in communication agree with filtering operations of convolution and deconvolution for Gaussian signal processing. In an analogy with power transmission in thermodynamics, an autoregressive model of information transmission is proposed for representing a continuous communication system which requires a pair of an internal noise source and a signal source to encode or decode a message. In this model transinformation (informational entropy) equals the increase in stationary nonequilibrium organization formed through the amplification of white noise by a positive feedback system. The channel capacity is finite due to the existence of inherent noise in the system. The maximum entropy criterion in information dynamics corresponds to the 2^nd law of thermodynamics. If the process is stationary, the communication system is invertible, and has the maximum efficiency of transformation. The total variation in informational entropy is zero in the cycle of the invertible system, while in the noninvertible system the entropy of decoding is less than that of encoding. A noisy autoregressive coding which maximizes transinformation is optimum, but is also ideal.     

Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae

The identification and application of reliable fossil calibrations represents a key component of many molecular studies of evolutionary timescales. In studies of plants, most paleontological calibrations are associated with macrofossils. However, the pollen record can also inform age calibrations if fossils matching extant pollen groups are found. Recent work has shown that pollen of the myrtle family, Myrtaceae, can be classified into a number of morphological groups that are synapomorphic with molecular groups. By assembling a data matrix of pollen morphological characters from extant and fossil Myrtaceae, we were able to measure the fit of 26 pollen fossils to a molecular phylogenetic tree using parsimony optimisation of characters. We identified eight Myrtaceidites fossils as appropriate for calibration based on the most parsimonious placements of these fossils on the tree. These fossils were used to inform age constraints in a Bayesian phylogenetic analysis of a sequence alignment comprising two sequences from the chloroplast genome (matK and ndhF) and one nuclear locus (ITS), sampled from 106 taxa representing 80 genera. Three additional analyses were calibrated by placing pollen fossils using geographic and morphological information (eight calibrations), macrofossils (five calibrations), and macrofossils and pollen fossils in combination (12 calibrations). The addition of new fossil pollen calibrations led to older crown ages than have previously been found for tribes such as Eucalypteae and Myrteae. Estimates of rate variation among lineages were affected by the choice of calibrations, suggesting that the use of multiple calibrations can improve estimates of rate heterogeneity among lineages. This study illustrates the potential of including pollen-based calibrations in molecular studies of divergence times.     

What Does Palaeontology Contribute to Systematics in a Molecular World?

Palaeontology provides the only direct record for morphological and genetic change through time and uniquely contributes to systematics in two ways: by providing access to denser taxon sampling than is otherwise possible and by dating divergence times. Claims that ancient DNA has survived millions of years in certain fossils suggested the possibility that palaeontology could contribute directly to molecular systematic studies. Unfortunately, none of the supposed geologically ancient DNA records stands up to detailed scrutiny and fossils therefore contribute primarily through the morphological information they preserve. Denser taxon sampling can improve the accuracy of phylogenetic estimates primarily through allowing better discrimination of homoplasy from homology. This in turn leads to more accurate hypotheses of character transformation. Denser taxon sampling also offers the opportunity for more accurate rooting, since more characters can be polarized by reference to a stem-group taxon than to an extant sister-group taxon. Missing data can be a problem for fossils, but is not crippling. Finally the temporal order of clade appearances in the fossil record can provide ancillary evidence for selecting a working phylogeny from among a number of equally most parsimonious cladograms.     

Stability of classification of filamentous fungi under changes in character coding strategy

The characteristics of a number of filamentous fungal cultures were obtained from two previously published numerical taxonomic studies on Penicillium and Phoma. The coding strategies for some of the physiological and morphological properties employed in the original studies were re-examined and the data was re-coded by combining sets of characters into single ordered multistate characters. The different coding procedures were compared by generating average linkage (UPGMA) dendrograms which were in turn compared by calculating correlation coefficients between the final similarity matrices implied by these dendrograms. The character conversions had no significant effect on the final outcome of the clustering.     

Assessing the Relative Contribution of Molecular and Morphological Characters in Simultaneous Analysis Trees

We examined the contribution of morphological and molecular character information for 15 systematics studies in which these two kinds of data were used in combined or simultaneous analyses. Assessment of the disagreement between these data sources, as measured by the incongruence length difference, reveals substantial conflict for the studies surveyed. In addition, the partitioned Bremer support was used to measure the degree of support provided by each data partition when analyzed together. Despite the significant incongruence found for nearly half the studies, the PBS indices suggest both types of data contribute positively to the combined analyses and that, when standardized by the number of phylogenetically informative characters, morphology data generally provide equal or greater support than do the molecular data. This result, combined with the fact that morphological characters generally exhibit higher consistency, indicates that this source of character information continues to be useful in systematics studies despite the increasing volume of available molecular data.     

A phylogeny of the Platyhelminthes: towards a total-evidence solution

We advocate a total-evidence approach for the reconstruction of working phylogenies for the Turbellaria and the phylum Platyhelminthes. Few morphology-based character matrices are available in the systematic literature concerning flatworms, and molecular-based phylogenies are rapidly providing the only means by which we can estimate phylogenies cladistically. Character matrices based on gross morphology and ultrastructure are required and should be internally consistent, i.e. character coding should follow a set of a priori guidelines and character duplication and contradiction is avoided. In order to test our molecular phylogenies we need complementary data sets from morphology. To understand morphological homology we need phylogenetic evidence from independent (e.g. molecular) data. Fully complementary morphological and molecular data sets enable us to validate phylogenetic hypotheses and the combination of these sets in phylogenetic reconstruction utilises all statements of homology. Working phylogenies which include all phylogenetic information not only shed light on individual character evolution, but form a strong basis for comparative studies investigating the origin and evolutionary radiation of the taxonomic group under scrutiny. This revised version was published online in July 2006 with corrections to the Cover Date.     

Giant taxon‐character matrices: quality of character constructions remains critical regardless of size

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one‐third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re‐analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.     

Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.     

When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss

Molecular and morphological data sets have yielded conflicting phylogenies for the Metazoa. So far, no general explanation for the existence of this conflict has been suggested. However, I believe that a neglected aspect of metazoan cladistics has introduced a systematic and substantial bias into morphological phylogenetic analyses. Most characters used for metazoan cladistics are coded as binary absence/presence characters. For most of these characters, the absence states are assumed to be uninformative default plesiomorphies, if they are defined at all. This character coding strategy could seriously underestimate the number of informative apomorphic absences or secondary character losses. Because nodes in morphological metazoan phylogenies are typically supported by relatively small numbers of characters each with a potentially strong impact on tree topology, failure to distinguish between primary absence and secondary loss of characters before a cladistic analysis may mislead morphological cladistics. This may falsely suggest conflict with molecular phylogenies, which are not sensitive to this bias. To test the existence of this bias, I compare the phylogenetic placement of a variety of metazoan taxa in molecular and morphological trees. In all instances investigated here, phylogenetic conflict can be resolved by allowing for secondary loss of morphological characters, which were assumed to be primitively absent in cladistic analyses. These findings suggest that we should be cautious in interpreting the results of morphological metazoan cladistic analyses and additionally illustrate the value of a more functional approach to comparative morphology in certain circumstances.     

Scorpion higher phylogeny and classification, taxonomic anarchy, and standards for peer review in online publishing

Soleglad and Fet's (2003a) attempt to reconstruct the phylogeny of Recent (including extant) scorpions, the revised classification derived from it, and recent emendations, mostly published in their self‐edited online journal, Euscorpius, are deficient. Separate analyses of three independent matrices (morphology, 16S rDNA, 18S rDNA) were presented. In the morphological matrix, 52 binary and 10 tristate trichobothrial characters were replaced with one character comprising six ordered states representing trichobothrial “types”. The remaining matrix of 105 characters was further reduced to 33 “fundamental” characters (20% of the morphological dataset), the analysis of which appears to be the basis for the revised classification presented. The taxon sample for the morphological analysis included 14 supraspecific terminal taxa representing genera, the monophyly of only 7 (12.5%) of which has been confirmed. A composite terminal, assembled from the fragments of fossils that may not be confamilial let alone monophyletic, was created for the Palaeopisthacanthidae, employed as the primary outgroup for the analysis. Other important outgroup taxa, notably eurypterids, xiphosurans and other arachnids, were omitted entirely. The morphological characters presented contained numerous unjustifiable assumptions of character polarity and phylogenetic relationship. An approach to character coding, deliberately adopted to reduce “homoplasy”, biased the analysis towards a preconceived result. Structurally and topographically similar features in different taxa were explicitly assigned separate (often autapomorphic) states according to presumed phylogenetic relationships among the taxa in which they were observed. Putative “reversals” were coded as separate characters or states. Character transformation was forced by ordering, additive coding or Sankoff optimization through allegedly intermediate states for which there is no empirical evidence. Many characters were defined in a manner that demonstrates either a lack of understanding of, or disregard for, established methods and standards of morphological character coding. Some states display overlapping variation whereas others subsume variation that is not structurally or topographically similar. Polymorphic “states” were created for terminals with interspecific variation and unknown “states” for terminals that should have been scored unknown. Many characters were not evaluated for particular terminal taxa, but merely scored inapplicable although the structures and, consequently, the characters in question are present and therefore applicable to them. In view of the significant theoretical and empirical problems with the approach to cladistics taken by Soleglad and Fet, we find no justification for accepting either the results of their analyses or the revised classification derived from them. Pending the outcome of a rigorous phylogenetic analysis, published according to acceptable standards of scholarship in a peer‐reviewed journal, we revert to the suprageneric classification of Scorpiones reflected by the most recent peer‐reviewed, published treatments and reject all changes to the classification proposed by Soleglad, Fet and colleagues since 2001. We argue that an analysis and revised classification of the kind presented in various papers by these authors could not survive the peer‐review process of a mainstream scientific journal. The poor scholarship exemplified by these and other papers published in Euscorpius emphasize the importance of quality control associated with the emergent infrastructure of online publishing. A centralized register of taxa may be the only solution for ensuring quality control in the taxonomy of the future. © The Willi Hennig Society 2005.     

ONTOGENY,HOMOLOGY, AND TERMINOLOGY—WALL MORPHOGENESIS AS AN AID TO CHARACTER RECOGNITION AND CHARACTER STATE DEFINITION FOR PENNATE DIATOM SYSTEMATICS1

This article reviews current knowledge of wall morphogenesis in pennate diatoms in relation to the way characters are defined and described for taxonomic and systematic analyses. It argues that an understanding of ontogeny is essential for the accurate identification of character homologies, which in turn must underpin all phylogenetic and systematic analyses. Terminology should reflect character homology, but most diatom terminology fails to do this, with concomitant confusion and potential taxonomic mistakes. Identifying where information is lacking or misinterpreted are first steps toward improving our understanding of diatom structure and relationships. After reviewing the current knowledge on pennate diatom structure and its development, this article briefly discusses the significance of morphological variation, character polarity, and the vital importance of applying diatom terminology correctly.     

Meta-analysis of character utility and phylogenetic information content in cladistic studies of ammonoids

While previous workers have argued persuasively that ammonoid workers should use cladistic approaches to reconstruct phylogeny, relatively few cladistic studies have been published to date. An essential yet challenging part of cladistic analysis is the selection of characters. Are certain types of characters more likely to show homoplasy? Are certain aspects of shell anatomy more likely to contain phylogenetically informative characters? Are datasets with more characters inherently better? To answer these questions, a meta-analysis of character data from published ammonoid phylogenies was performed. I compiled 14 datasets, published between 1989 and 2007, representing parsimony-based phylogenetic analyses of ammonoids. These studies defined a combined total of 323 characters, which were grouped into categories reflecting different aspects of anatomy: shell size and shape, ornament, suture, early ontogeny, body chamber and apertural modifications. Tree searches were re-run to determine overall tree statistics, parsimony permutation tail probability (PTP) tests were calculated to assess the phylogenetic information content of the matrices, and retention and rescaled consistency indices for each character were calculated. My analyses revealed that studies with higher character/taxon ratios did not necessarily produce trees with more information content and less homoplasy, as measured by retention or rescaled consistency indices, because additional characters were often parsimony-uninformative. Rather, studies with relatively few characters could produce high-quality trees if the characters were well-chosen and character states carefully defined. Characters related to the body chamber and adult aperture typically had retention indices of either 0 or 1, rarely in between, indicating that they either worked perfectly or not at all. Suture characters tended to have higher indices than shell shape or ornament characters, suggesting more phylogenetic information and less homoplasy in the suture line than in shell traits. These results should aid in the selection of characters for future cladistic studies of ammonoids.     

Information Limited Oligonucleotide Amplification Assay for Affinity-Based,Parallel Detection Studies

Molecular communication systems encounter similar constraints as telecommunications. In either case, channel crosstalk at the receiver end will result in information loss that statistical analysis cannot compensate. This is because in any communication channel there is a physical limit to the amount of information that can be transmitted. We present a novel and simple modified end amplification (MEA) technique to generate reduced and defined amounts of specific information in form of short fragments from an oligonucleotide source that also contains unrelated and redundant information. Our method can be a valuable tool to investigate information overflow and channel capacity in biomolecular recognition systems.     

Ephemeroptera egg chorion characters: a test of their importance in assessing phylogenetic relationships

The egg chorion ultrastructures of the Hermanella-Traverella (Insecta: Ephemeroptera) species complex were studied from a comparative point of view and used for the first time in a cladistic analysis. Egg characters, along with other nymphal and adult morphological characters, were used to assess the phylogenetic relationships of the species complex. In order to test the value of egg characters, analyses were performed on three matrices: 1) egg characters alone, 2) adult and nymphal characters, and 3) adult, nymphal, and egg characters. The computer program Pee-Wee was used to carry out the analysis. The cladistic analysis confirmed the value and potential of egg chorionic characters in assessing the phylogenetic relationships among ephemeropteran species. Egg characters, when added to the nymphal and adult character matrix, provided extra support to the monophyletic nature of the Hermanella-Traverella complex. Previously weakly defined clades were also resolved based on the new evidence. In the species studied the egg chorionic structures as well as their shape did not change after oviposition or water immersion, remaining constant through the different maturation stages of each species (mature nymph, subimago, and imago). For this reason, the eggs are a valuable source of information to unambiguously identify and associate a nymph to its correspondent adult stage when rearing is not possible.     

Ancestral State Reconstruction Reveals Rampant Homoplasy of Diagnostic Morphological Characters in Urticaceae,Conflicting with Current Classification Schemes

Urticaceae is a family with more than 2000 species, which contains remarkable morphological diversity. It has undergone many taxonomic reorganizations, and is currently the subject of further systematic studies. To gain more resolution in systematic studies and to better understand the general patterns of character evolution in Urticaceae, based on our previous phylogeny including 169 accessions comprising 122 species across 47 Urticaceae genera, we examined 19 diagnostic characters, and analysed these employing both maximum-parsimony and maximum-likelihood approaches. Our results revealed that 16 characters exhibited multiple state changes within the family, with ten exhibiting >eight changes and three exhibiting between 28 and 40. Morphological synapomorphies were identified for many clades, but the diagnostic value of these was often limited due to reversals within the clade and/or homoplasies elsewhere. Recognition of the four clades comprising the family at subfamily level can be supported by a small number carefully chosen defining traits for each. Several non-monophyletic genera appear to be defined only by characters that are plesiomorphic within their clades, and more detailed work would be valuable to find defining traits for monophyletic clades within these. Some character evolution may be attributed to adaptive evolution in Urticaceae due to shifts in habitat or vegetation type. This study demonstrated the value of using phylogeny to trace character evolution, and determine the relative importance of morphological traits for classification.     

Partially incorrect fossil data augment analyses of discrete trait evolution in living species

Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model. Under simulated phylogenies and data, likelihood-based models are generally accurate when estimating ancestral node values. Analyses with combined fossil and extant data always outperform analyses with extant species alone, even when around one quarter of the fossil information is incorrect. These results are especially pronounced when model assumptions are violated, such as when there is a trend away from the root value. Fossil data are of particular importance when attempting to estimate the root node character state. Attempts should be made to include fossils in analysis of discrete traits under likelihood, even if there is uncertainty in the fossil trait data.