Evaluating the efficacy of continuous quantitative characters for reconstructing the phylogeny of a morphologically homogeneous spider taxon (Araneae, Mygalomorphae, Antrodiaetidae, Antrodiaetus)

The use of continuous quantitative characters for phylogenetic analyses has long been contentious in the systematics literature. Recent studies argue for and against their use, but there have been relatively few attempts to evaluate whether these characters provide an accurate estimate of phylogeny, despite the fact that a number of methods have been developed to analyze these types of data for phylogenetic inference. A tree topology will be produced for a given methodology and set of characters, but little can be concluded with regards to the accuracy of phylogenetic signal without an independent evaluation of those characters. We assess the performance of continuous quantitative characters for the mygalomorph spider genus Antrodiaetus, a group that is morphologically homogeneous and one for which few discrete (morphological) characters have been observed. Phylogenetic signal contained in continuous quantitative characters is compared to an independently derived phylogeny inferred on the basis of multiple nuclear and mitochondrial gene loci. Tree topology randomizations, regression techniques, and topological tests all demonstrate that continuous quantitative characters in Antrodiaetus conflict with the phylogenetic signal contained in the gene trees. Our results show that the use of continuous quantitative characters for phylogenetic reconstruction may be inappropriate for reconstructing Antrodiaetus phylogeny and indicate that due caution should be exercised before employing this character type in the absence of other independently derived sources of characters.     

The phylogenetic position of the Clitellata and the Echiura - on the problematic assessment of absent characters*

Absent characters (negative characters) are difficult to assess and their correct interpretation as symplesiomorphies, synapomorphies or convergencies (homoplasies) is one of the greatest challenges in phylogenetic systematics. Different phylogenetic assessments often result in contradictory phylogenetic hypotheses, in which the direction of evolutionary changes is diametrically opposed. Especially in deciding between primary (plesiomorphic) and secondary (apomorphic) absence, false conclusions may be reached if only the outgroup comparison and the principle of parsimony are employed without attempting any biological evaluation or interpretation of characters. For example, in the higher‐level systematization of the Annelida and related taxa different assessments of absent characters have led to conflicting hypotheses about the phylogenetic relationships and the ground pattern of the annelid stem species. Varying phylogenetic interpretations regarding the absence of the chemosensory nuchal organs in the clitellates and their presence in polychaetes initiated a controversy that produced two alternative phylogenetic hypotheses: (1) the Clitellata are highly derived Annelida related to a subtaxon within the, in this case, paraphyletic ‘Polychaeta’ or (2) the Clitellata are comparatively primitive Annelida representing the sister group of a monophyletic taxon Polychaeta. In the former, the absence of nuchal organs in the Clitellata is regarded as a secondary character, in the latter as primary. As most Clitellata are either limnetic or terrestrial, we must ask which characters are plesiomorphies, taken from their marine stem species without changes. In addition to a thorough investigation and evaluation of clitellate characters, a promising approach to these questions is to look for such characters in limnetic and terrestrial annelids clearly not belonging to the Clitellata. A similar problem applies to the evaluation of the position of the Echiura, which lack both segmentation and nuchal organs. Evidence is presented that in both taxa these absent characters represent derived, apomorphic character states. The consequences for their phylogenetic position and the questionable monophyly of the Polychaeta are discussed. The conclusion drawn from morphological character assessments is in accordance with recently published hypotheses based on molecular data.     

Neurobiological constraints and fly systematics: how different types of neural characters can contribute to a higher level dipteran phylogeny

Much uncertainty still exists regarding higher level phylogenetic relationships in the insect order Diptera, and the need for independent analyses is apparent. In this paper, I present a parsimony analysis that is based on details of the nervous system of flies. Because neural characters have received little attention in modern phylogenetic analyses and the stability of neural traits has been debated, special emphasis is given to testing the robustness of the analysis itself and to evaluating how neurobiological constraints (such as levels of neural processing) influence the phylogenetic information content. The phylogenetic study is based on 14 species in three nematoceran and nine brachyceran families. All characters used in the analysis are based on anatomical details of the neural organization of the fly visual system. For the most part they relate to uniquely identifiable neurons, which are cells or cell types that can be confidently recognized as homologues among different species and thus compared. Parsimony analysis results in a phylogenetic hypothesis that favors specific previously suggested phylogenetic relationships and suggests alternatives regarding other placements. For example, several heterodactylan families (Bombyliidae, Asilidae, and Dolichopodidae) are supported in their placement as suggested by Sinclair et al. (1993), but Tipulidae and Syrphidae are placed differently. Tipulidae are placed at a derived rather than ancestral position within the Nematocera, and Syrphidae are placed within the Schizophora. The analysis suggests that neural characters generally maintain phylogenetic information well. However, by "forcing" neural characters onto conventional phylogenetic analyses it becomes apparent that not all neural centers maintain such information equally well. For example, neurons of the second-order visual neuropil, the medulla, contain stronger phylogenetic "signal" than do characters of the deeper visual center, the lobula plate. These differences may relate to different functional constraints in the two neuropils.     

Avian higher-level phylogeny: well-supported clades and what we can learn from a phylogenetic analysis of 2954 morphological characters

It has been shown that increased character sampling betters the accuracy of phylogenetic reconstructions in the case of molecular data. A recently published analysis of avian higher-level phylogenetics based on 2954 morphological characters now provides an empirical example to test whether this is also true in the case of morphological characters. Several clades are discussed which are supported by multiple analyses of mutually independent molecular data (sequences of nuclear genes on different chromosomes and mitochondrial genes) as well as morphological apomorphies, but did not result from parsimony analysis of the large morphological data set. Incorrect character scorings in that analysis notwithstanding, it is concluded that in the case of morphological data, increased character sampling does not necessarily better the accuracy of a phylogenetic reconstruction. Because morphological characters usually have a strongly varying complexity, many simple and homoplastic characters may overrule fewer ones of greater phylogenetic significance in large data sets, thus producing a low ratio of phylogenetic signal to 'noise' in the data.     

Comparison of phylogenetic signal between male genitalia and non-genital characters in insect systematics

It is generally accepted that male genitalia evolve more rapidly and divergently relative to non-genital traits due to sexual selection, but there is little quantitative comparison of the pattern of evolution between these character sets. Moreover, despite the fact that genitalia are still among the most widely used characters in insect systematics, there is an idea that the rate of evolution is too rapid for genital characters to be useful in forming clades. Based on standard measures of fit used in cladistic analyses, we compare levels of homoplasy and synapomorphy between genital and non-genital characters of published data sets and demonstrate that phylogenetic signal between these two character sets is statistically similar. This pattern is found consistently across different insect orders at different taxonomic hierarchical levels. We argue that the fact that male genitalia are under sexual selection and thus diverge rapidly does not necessarily equate with the lack of phylogenetic signal, because characters that evolve by descent with modification make appropriate characters for a phylogenetic analysis, regardless of the rate of evolution. We conclude that male genitalia are a composite character consisting of different components diverging separately, which make them ideal characters for phylogenetic analyses, providing information for resolving varying levels of hierarchy.
© The Willi Hennig Society 2009.     

Strong character incongruence and character choice in phylogeny of sea stars of the Asterinidae

Abstract. Historically, characters from early animal development have been a potentially rich source of phylogenetic information, but many traits associated with the gametes and larval stages of animals with complex life cycles are widely suspected to have evolved frequent convergent similarities. Such convergences will confound true phylogenetic relationships. We compared phylogenetic inferences based on early life history traits with those from mitochondrial DNA sequences for sea stars in the genera Asterina, Cryptasterina , and Patiriella (Valvatida: Asterinidae). Analysis of these two character sets produced phylogenies that shared few clades. We quantified the degree of homoplasy in each character set when mapped onto the phylogeny inferred from the alternative characters. The incongruence between early life history and nucleotide characters implies more homoplasy in the life history character set. We suggest that the early life history traits in this case are most likely to be misleading as phylogenetic characters because simple adaptive models predict convergence in early life histories. We show that adding early life history characters may slightly improve a phylogeny based on nucleotide sequences, but adding nucleotide characters may be critically important to improving inferences from phylogenies based on early life history characters.     

Soft anatomy, diffuse homoplasy, and the relationships of lizards and snakes

Most previous phylogenetic analyses of squamates (‘lizards’ and snakes) employing large character sets have focused on osteology. Soft anatomical traits bearing on this problem have usually been considered in small subsets. Here, a comprehensive phylogenetic analysis of squamate soft anatomy is attempted. 126 informative characters are assessed for 23 squamate lineages, representing snakes, amphisbaenians, dibamids, and all the traditionally recognized ‘families’ of lizards. The traditionally recognized groupings Iguania, Scleroglossa, Gekkota, Scincomorpha, Anguimorpha and Varanoidea are corroborated in this analysis. More controversial taxa are resolved as follows. Xantusiids, amphisbaenians and dibamids cluster with gekkotans, and snakes are strongly allied with anguimorphs in general, and varanids in particular. Nearly all these clades are congruent with those found in a recent comprehensive osteological analysis; the strong support for snake‐varanid relationships found in both studies is particularly notable. This congruence is surprising given that previous studies of soft anatomy tended to give differing and often heterodox results. These previous results can be attributed to overrepresentation of misleading characters in small isolated data sets. Such misleading signals are minimized when data sets are combined. For instance, the snake‐varanid clade is contradicted by many characters, and analyses of particular organ systems therefore give differing results. However, characters that are incongruent with the snake‐varanid clade also disagree with each other (diffuse homoplasy), rather than forming coherent support for some particular alternative clade (concerted homoplasy). In a combined analysis these incongruent but diffuse characters cancel each other out to leave a very strong (and orthodox) phylogenetic signal. These results underscore the view that the raw amount of homoplasy — as revealed by consistency and retention indices — is not the only determinant of phylogenetic signal; the distribution of that homoplasy is also important. Thus, questioning a phylogenetic hypothesis (e.g. the snake‐varanid clade) by identifying numerous conflicting characters is insufficient — the structure of the conflicting characters should be assessed in a rigorous phylogenetic analysis.     

Adaptation and functional integration in primate phylogenetics

In two areas of phylogenetics, contrary predictions have been developed and maintained for character analysis and weighting. With regard to adaptation, many have argued that adaptive characters are poorly suited to phylogenetic analysis because of a propensity for homoplasy, while others have argued that complex adaptive characters should be given high weight because homoplasy in complex characters is unlikely. Similarly, with regard to correlated sets of characters, one point of view is that such sets should be collapsed into a single character-a single piece of phylogenetic evidence. Another point of view is that a suite of correlated characters should be emphasized in phylogenetics, again because recurrence of detailed similarity in the same suite of features is unlikely. In this paper, I discuss the theoretical background of adaptation and functional integration with respect to phylogenetic systematics of primates. Several character examples are reviewed with regard to their functional morphology and phylogenetic signal: postorbital structures, tympanic morphology, fusion of the mandibular symphysis, the tooth comb, strepsirrhine talar morphology, and the prehensile tail. It is clear when considering characters such as these that some characters are synapomorphic of major clades and at the same time functionally important. This appears particularly to be the case when characters are integrated into a complex and maintained as stable configurations. Rather than being simply a problem in character analysis, processes of integration may help to explain the utility of phylogenetically informative characters. On the other hand, the character examples also highlight the difficulty in forming a priori predictions about a character's phylogenetic signal. Explanations of patterns of character evolution are often clade-specific, which does not allow for a simple framework of character selection and/or weighting.     

类群取样与系统发育分析精确度之探索

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.     

Phylogenetic relationships of the genus Dugesia (Platyhelminthes, Tricladida, Paludicola)

A phylogenetic analysis was performed on the genera and subgenera within the freshwater triclad family Dugesiidae, based on 19 terminal taxa and 17 morphological characters. The phylogenetic tree proposed has length of 27 steps and consistency index of 0.66. This phylogenetic hypothesis implies that the current genus Dugesia is paraphyletic and that its subgenera Girardia, Schmidiea and Dugesia S.S. should be elevated to the rank of genus. The genera Cura, Spathula and Neppia are presumed monophyletic by default because the database was unable to provide autapomorphies for any of these genera. The genera Dugesia S.S. and Neppia share sistergroup relationship. Several characters are discussed which were previously considered to be of phylogenetic importance but were not included in the present analysis. It is emphasized that sensory organs form potentially useful set of phylogenetic characters for the Dugesiidae.     

Phylogeny of the family Congiopodidae (Perciformes: Scorpaenoidea), with a proposal of new classification

The phylogenetic relationships of the family Congiopodidae are inferred based on morphological characters. The monophyly of this family is supported by 13 unambiguous apomorphic characters, including four autapomorphies among the superfamily Scorpaenoidea. The Congiopodidae shares 26 apomorphic characters with other scorpaenoid taxa, and these characters are considered to also support the monophyly of the family. Upon completion of the phylogenetic analysis using the characters in 39 transformation series, it was assumed that the family is unambiguously supported by five characters (and also by three and one characters when ACCTRAN and DELTRAN are used, respectively) and is branched into two major clades, including Congiopodus and Alertichthys plus Zanclorhynchus, respectively. Based on the phylogenetic relationships, a new classification, recognizing two subfamilies (Congiopodinae and Zanclorhynchinae) in the family Congiopodidae, is proposed. The genus Perryena, that was recently inferred being closely related to the Tetrarogidae (although many authors included it in the Congiopodidae), is provisionally placed into the Congiopodidae as incertae sedis.     

Phylogenetic analysis of the Pinnotheridae (Crustacea, Brachyura) based on larval morphology, with emphasis on the Dissodactylus species complex

Comparative larval morphology was used to elucidate phylogenetic relationships within the Pinnotheridae and the Dissodactylus species complex. Within the family, seven zoeal and six megalopal characters suggested two equally parsimonious phylogenetic hypotheses for pinnotherid larvae, both with Ostracotheres tridacnae representing the sister group for the Dissodactylus complex. Results indicated that the genus Pinnotheres is a polyphyletic taxon, and that the traditional subfamilial arrangement comprises paraphyletic taxa within the subfamilies Pinnotherinae and Pinnothereliinae. Certain evidence has suggested that Fabia and Juxtafubia should be excluded from the Pinnotherinae and placed into the Pinnothereliinae. Larval and adult morphology suggested that Pinnotheres politus should be included within Tumidotheres. The phylogenetic analysis within the Dissodactylus complex involved one zoeal and 16 megalopal characters. Results suggested a single phylogenetic hypothesis based on larval morphology. Combining adult morphology with larval evidence resulted in two equally parsimonious phylogenetic hypotheses, one of which agreed with a previously suggested hypothesis based only on adult characters.     

Testing phylogenetic implications of eggshell characters in side-necked turtles (Testudines: Pleurodira)

Amniote egg and eggshell morphology is a rich source of characters to link aspects of reproductive biology with systematics. Extensive work concerning both anatomy and phylogenetic assignability has been done on fossil bird and dinosaur eggs, but little is known for extant sauropsids. The utility of eggshell characters for phylogenetic analyses is tested and discussed for extant side-necked turtles (Pleurodira), and the diversity of egg ultrastructure is examined in several species. Egg gross morphology and eggshell ultrastructure of 12 species of extant side-necked turtles was documented using scanning electron microscopy. Thirteen eggshell characters were scored and mapped on a composite phylogeny and ancestral character states were reconstructed. Many of the characters do not show a phylogenetic signal according to a test comparing the number of steps on the chosen phylogeny with that on randomly generated trees. The presence of conservative, clade-supporting features could be demonstrated, and the following clades are supported by several characters: the Elseya-Emydura entity, short-necked Australasian chelids, is backed by two characters, and two additional characters could potentially support this group. Three characters support the monophyly of South American chelids, whereas two characters argue for the exclusion of Hydromedusa, a long-necked form resembling Australian chelids rather than South American forms, from this clade.     

Comparative leaf anatomy and phylogenetic relationships of 11 species of Laeliinae with emphasis on Brassavola (Orchidaceae)

Brassavola inhabits a wide altitude range and habitat types from Northern Mexico to Northern Argentina. Classification schemes in plants have normally used vegetative and floral characters, but when species are very similar, as in this genus, conflicts arise in species delimitation, and alternative methods should be applied. In this study we explored the taxonomic and phylogenetic value of the anatomical structure of leaves in Brassavola; as ingroup, seven species of Brassavola were considered, and as an outgroup Guarianthe skinneri, Laelia anceps, Rhyncholaelia digbyana and Rhyncholaelia glauca were evaluated. Leaf anatomical characters were studied in freehand cross sections of the middle portion with a light microscope. Ten vegetative anatomical characters were selected and coded for the phylogenetic analysis. Phylogenetic reconstruction was carried out under maximum parsimony using the program NONA through WinClada. Overall, Brassavola species reveal a wide variety of anatomical characters, many of them associated with xeromorphic plants: thick cuticle, hypodermis and cells of the mesophyll with spiral thickenings in the secondary wall. Moreover, mesophyll is either homogeneous or heterogeneous, often with extravascular bundles of fibers near the epidermis at both terete and flat leaves. All vascular bundles are collateral, arranged in more than one row in the mesophyll. The phylogenetic analysis did not resolve internal relationships of the genus; we obtained a polytomy, indicating that the anatomical characters by themselves have little phylogenetic value in Brassavola. We concluded that few anatomical characters are phylogenetically important; however, they would provide more support to elucidate the phylogenetic relantionships in the Orchidaceae and other plant groups if they are used in conjunction with morphological and/or molecular characters.     

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. “Thaliacea” is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic “Ascidiacea”. Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.     

Estimating phylogenetic inertia in Tithonia (Asteraceae): a comparative approach

Abstract.— Phylogenetic inertia is a difficult issue in evolutionary biology because we have yet to reach a consensus about how to measure it. In this study a comparative approach is used to evaluate phylogenetic inertia in 14 demographic and morphological characters in 10 species and one subspecies of the genus Tithonia (Asteraceae). Three different methods, autocorrelational analysis, phylogenetic correlograms, and ancestor-state reconstruction, were used to evaluate phylogenetic inertia in these traits. Results were highly dependent on the method applied. Autoregression and phylogenetic eigenvector regression (PVR) methods found more inertia in morphological traits. In contrast, phylogenetic correlograms and ancestor-state reconstruction suggest that morphological characters exhibit less phylogenetic inertia than demographic ones. The differences between results are discussed and methods are compared in an effort to understand phylogenetic inertia more thoroughly.     

Leaf anatomical characters and their value in understanding morphoclines in the Araceae

Leaf anatomy and petiole anatomy of the Araceae are discussed in terms of their potential use as character states in a phylogenetic analysis. The characters include leaf venation and structure, leaf epidermis, mesophyll ground tissue, vascular bundles, sclerenchyma, collenchyma, laticifers, secretory ducts, and raphide crystals. Characters that seem to have the greatest potential for use in phylogenetic analysis include those of ground tissue, vascular bundles, fibers, trichosclereids, collenchyma, and laticifers. Other, equally distinguishable, characters have states that are apparently autapomorphies, providing little phylogenetic signal. Therefore, although most leaf and petiole structural variation is useful diagnostically, some characters will probably be less valuable in phylogenetic analysis than originally hoped.     

Phylogenetic implications of the morphology of the braincase of caecilian amphibians (Gymnophiona)

Caecilian morphology is strongly modified in association with their fossorial mode of life. Currently phylogenetic analyses of characters drawn from the morphology of caecilians lack resolution, as well as complementarity, with results of phylogenetic analyses that employ molecular data. Stemming from the hypothesis derived from the mammal literature that the braincase has the greatest potential (in comparison to other cranial units) to yield phylogenetic information, the braincase and intimately associated stapes of 27 species (23 genera) of extant caecilians were examined using images assembled via microcomputed tomography. Thirty‐four new morphological characters pertaining to the braincase and stapes were identified and tested for congruence with previously recognized morphological characters. The results reveal that when added to previous character matrices, characters of the braincase and stapes resolve generic‐level relationships in a way that is largely congruent with the results of molecular analyses. Analysis of a combined data set of molecular and morphological data provides a framework for conducting ancestral character state reconstructions, which resulted in the identification of 95 new synapomorphies for various clades and taxa, 27 of which appear to be unique for the taxa that possess them. Together these data demonstrate the utility of the application of characters of the braincase and stapes for resolving phylogenetic relationships for a group whose morphology is largely confounded by functional modifications. In addition this study provides evidence of the utility of the braincase in resolving problematic morphology‐based phylogeny outside of Amniota, in an amphibian group. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 160–201.     

Developmental characters in phylogenetic inference and their absolute timing information

Despite the recent surge of interest in studying the evolution of development, surprisingly little work has been done to investigate the phylogenetic signal in developmental characters. Yet, both the potential usefulness of developmental characters in phylogenetic reconstruction and the validity of inferences on the evolution of developmental characters depend on the presence of such a phylogenetic signal and on the ability of our coding scheme to capture it. In a recent study, we showed, using simulations, that a new method (called the continuous analysis) using standardized time or ontogenetic sequence data and squared-change parsimony outperformed event pairing and event cracking in analyzing developmental data on a reference phylogeny. Using the same simulated data, we demonstrate that all these coding methods (event pairing and standardized time or ontogenetic sequence data) can be used to produce phylogenetically informative data. Despite some dependence between characters (the position of an event in an ontogenetic sequence is not independent of the position of other events in the same sequence), parsimony analysis of such characters converges on the correct phylogeny as the amount of data increases. In this context, the new coding method (developed for the continuous analysis) outperforms event pairing; it recovers a lower proportion of incorrect clades. This study thus validates the use of ontogenetic data in phylogenetic inference and presents a simple coding scheme that can extract a reliable phylogenetic signal from these data.     

Assembling the Fungal Tree of Life: constructing the structural and biochemical database

A major goal of the Assembling the Fungal Tree of Life project is to create a searchable database of selected ultrastructural and biochemical characters from published and new data for use in phylogenetic and other analyses. While developing this database such issues as evaluating specimen fixation quality in published micrographs, organizing data to accommodate characters that were dependent on location and developmental stage, and requiring accountability of data contributors were addressed. Character states for three traits, septal pore apparatus, nuclear division and spindle pole body cycle, are illustrated, and character states are resolved with maximum parsimony and plotted on a summary cladogram of known phylogenetic relationships of the Fungi. The analysis illustrates the inherent phylogenetic signal of these characters, the paucity of comparable characters and character states in subcellular studies and the challenges in establishing a comprehensive structural and biochemical database of the Fungi.