Phylogenetic analysis of the Rhabdocoela (Platyhelminthes) with emphasis on the Neodermata and relatives

Phylogenetic systematic analysis of 24 taxa representing the rhabdocoel platyhelminths, based on a suite of 89 morphological characters, produced two equally parsimonious trees, 181 steps long, with a consistency index (CI) of 0.69 and a rescaled consistency index (RCI) of 0.56, differing only with respect to that portion of the tree containing Umagillidae, Acholadidae, Graffillinae, Pseudograffillinae, Pterastericolidae and Hypoblepharinidae. Our results accommodate all previously proposed sister taxa to the Neodermata in a single clade in which ((Dalyelliidae + Temnocephalida) Typhloplanidae) is the sister group of ((Fecampiidae +  Urastoma ) ( Udonella ((Aspidogastrea + Digenea) (Monogenea (Gyrocotylidea (Amphilinidea + Eucestoda)))))). Bootstrap and jackknife analyses indicate that the groupings of ((Dalyelliidae + Temnocephalida) Typhloplanidae) and of ((Fecampiidae +  Urastoma ) ( Udonella ((Aspidogastrea + Digenea) (Monogenea (Gyrocotylidea (Amphilinidea + Eucestoda)))))) are highly robust, with the latter clade having a CI of 90% and RCI of 82%. Disagreements among previous analyses of these taxa have been due to the influence of missing data for critical characters in key taxa and differences in the taxa analysed, rather than any inherent weakness in the morphological data. Non-phylogenetic systematic approaches to homology assessment and misconceptions regarding phylogenetic systematic methodology are discussed. Recent analyses combining sequence data with a subset of approximately 60% of the morphological characters should be re-assessed using the entire morphological database. Even if Udonella is a monogenean, it is most parsimonious to suggest that the common ancestor of the Neodermata had a vertebrate–arthropod two-host life cycle.     

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.     

Diversity in the Monogenea and Digenea: does lifestyle matter?

If the cestodes are excluded, then the parasitic platyhelminths of fishes divide neatly into the external and monoxenous Monogenea and the internal and heteroxenous Digenea. Both groups have apparently had long associations of coevolution, host switching and adaptation with fishes and have become highly successful in their respective habitats. Current estimates of species richness for the two groups suggest that they may be remarkably similar. Here we consider the nature of the diversity of the Monogenea and Digenea of fishes in terms of richness of species and higher taxa to determine what processes may be responsible for observed differences. The Monogenea includes at least two super-genera (Dactylogyrus and Gyrodactylus) each of which has hundreds of species; no comparable genera are found in the Digenea. Possible reasons for this difference include the higher host specificity of monogeneans and their shorter generation time. If allowance is made for the vagaries of taxonomic 'lumping' and 'splitting', then there are probably comparable numbers of families of monogeneans and digeneans in fishes. However, the nature of the families differ profoundly. Richness in higher taxa (families) in the Digenea is explicable in terms of processes that appear to have been unimportant in the Monogenea. Readily identifiable sources of diversity in the Digenea are: recolonisation of fishes by taxa that arose in association with tetrapods; adoption of new sites within hosts; adoption of new diets and feeding mechanisms; adaptations relating to the exploitation of ecologically similar groups of fishes and second intermediate hosts; and adaptations relating to the exploitation of phylogenetic lineages of molluscs. In contrast, most higher- level monogenean diversity (other than that associated with the subclasses) relates principally to morphological specialisation for attachment by the haptor.     

The origins of parasitism in the platyhelminthes

Symbiotic associations have arisen independently in several groups of the largely free-living turbellarians. Morphological adaptations of turbellarians to a symbiotic way of life include suckers and adhesive glands for attachment, elaborate systems of microvilli and other epidermal structures for absorption of food, glands for the formation of cysts, cocoons and cement material, and lack of a pharynx and intestine in some species. However, many species closely resemble their free-living relatives. Egg production is greatly increased at least in some species, and life cycles are always direct. Food of symbiotic turbellarians consists of host food and/or host tissue. Ectosymbiotes show fewer physiological adaptations than entosymbiotes. The major groups of parasitic Platyhehninthes (Trematoda Aspidogastrea, Trematoda Digenea, Monogenea, Udonellidea, Cestoda including Gyrocotylidea, Amphilinidea and Eucestoda), form one monophylum, the Neodermata, characterized by a neodermis (tegument) replacing the larval epidermis, epidermal cilia with a single horizontal rootlet, sensory receptors with electron-dense collars, spermatozoa with axonemes incorporated in the sperm body by proximodistal fusion, and protonephridial flame bulbs formed by two cells each contributing a row of longitudinal ribs to the filtration apparatus. The sister group of the Neodermata is unknown but is likely to be a large taxon including the Proseriata and some other turbellarian groups. Among the Neodennata, the Aspidogastrea is likely to be the most archaic group, as indicated by DNA studies, morphology, life cycles and physiology. Aspidogastreans can survive for many days or even weeks outside a host in simple media, they show little host specificity, and have an astonishingly complex nervous system and many types of sensory receptors, both in the larva and the adult. It is suggested that Aspidogastrea were originally parasites of mlluscs (and possibly arthropods and other invertebrates) and that they are archaic forms which have remained at a stage where vertebrates represent facultative hosts or obligatory final hosts into which only the very last stages of the life cycle (maturation of the gonads) have been transferred. The complex life cycles of Digenea have evolved from the simple aspidogastrean ones by intercalation of multiplicative larval stages (sporocysts, rediae) in the mollusc host, and of cercarial stages ensuring dispersal to the now obligatory final host. Monogenea may have lost the molluscan host or evolved before the early neodermatans had acquired it. Cestoda either replaced the original molluscan with an arthropod host, retained an original arthropod host or evolved from an early neodermatan before molluscan hosts had been acquired, newly acquiring an arthropod host. Horizontal gene transfer and implications for mosaic evolution in the Platyhehninthes are discussed.     

ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non-iterative and does not require independent estimations of weights. It is based on searching trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as a logical implication of the trees being compared. The "fittest" trees imply that the characters are maximally reliable and, given character conflict, have fewer steps for the characters which fit the tree better. If other trees save steps in some characters, it will be at the expense of gaining them in characters with less homoplasy.     

Homoplasy and homology: dichotomy or continuum?

Homology is the presence of the same feature in two organisms whose most recent common ancestor also possessed the feature. I discuss the bases on which we can tell that two features being compared share sufficient elements of sameness to allow them to be treated as homologous and therefore to be legitimately compared with one another in a way that informs comparative, evolutionary, and phylogenetic analysis. To do so, I discuss the relationship(s) between homology and homoplasy to conclude that we are dealing neither with a dichotomy between homoplasy as parallelism/convergence and homology as common descent nor with a dichotomy of homoplasy as the interrupted presence of the character in a lineage and homology as the continuous presence of the character. Rather, we are dealing with common descent with varying degrees of modification. Homoplasy and homology are not dichotomies but the extremes of a continuum, reflecting deep or more recent shared ancestry based on shared cellular mechanisms and processes and shared genes and gene pathways and networks. The same genes can be used to initiate the development of homoplastic and homologous structures. Consequently, structures may be lost but their developmental bases retained, providing the potential for homoplasy. It should not be surprising that similar features persist when a feature is present in the nearest common ancestor (homology). Neither should it be surprising to find that different environments or selective pressures can trigger the reappearance of similar features in organisms that do not share a recent common ancestor (homoplasy).     

Spermiogenesis and sperm ultrastructure of Cyathocephalus truncatus (Pallas, 1781) Kessler, 1868 (Cestoda: Spathebothriidea)

Spermiogenesis and sperm ultrastructure of adult Cyathocephalus truncatus, a member of presumably basal group of "true" cestodes (Eucestoda), have been examined for the first time by using transmission electron microscopy. The process of sperm formation corresponds in basic pattern to that of the Pseudophyllidea. In addition, the 2 pairs of electron-dense attachment zones are present in median cytoplasmic process of C. truncatus. However, mature spermatozoa of C. truncatus differ significantly from those of the pseudophyllideans, especially in the morphology of the proximal and distal spermatozoon extremities. The proximal extremity of the mature spermatozoon lacks a crested body, which is present in more derived cestodes and some pseudophyllideans. The distal end of the mature spermatozoa exhibits different morphology in the gametes from testes and those from receptaculum seminis. New for the Eucestoda is a finding that a lateral cytoplasmic extension creates the distal end of the spermatozoa from testes, resembling sperm of some Monogenea and Digenea. In contrast, the distal extremity of the spermatozoa from receptaculum seminis contains only a nucleus. Despite the above-mentioned peculiarities, the ultrastructural data on sperm/spermiogenesis suggest close relationships of the Spathebothriidea and Pseudophyllidea.     

IN SEARCH OF HOMOPLASTIC TENDENCIES: STATISTICAL INFERENCE OF TOPOLOGICAL PATTERNS IN HOMOPLASY

The “tendency” for homoplasy to appear in closely related taxa has been widely discussed but rarely quantified. This paper proposes statistical tests that examine the topological distribution of homoplasy within characters in phylogenies. They test whether character changes are localized (confined to some subtree), or clustered (occur in proximity to each other), relative to two null models of character evolution. Null Model I assumes that the observed number of character changes are dispersed randomly among the internodes of the tree, whereas Model II weights the probability that an internode contains a change by the length of that internode—estimated by the total number of character changes along that internode. Localization is measured by the largest furthest-neighbor distance between changes, clustering by the mean nearest neighbor distance. Distances are measured either by the number of intervening branches or the number of intervening character changes. Analyses of four cladistic data sets from the literature reveal very few characters that exhibit significant levels of clustering or localization—no more than would be expected by chance. In every data set a majority of characters exhibited at least weak tendencies, but in only one data set was there a significant excess of such characters. The present findings do not provide compelling evidence for the existence of “tendencies” in homoplasy, at least among characters used to reconstruct phylogenies. They should be sought elsewhere, in cladistic analyses of larger scope, probably among a class of characters defined a priori on a structural or functional basis.     

Ultrastructure of the protonephridial system, of Anoplodiscus cirrusspiralis (Monogenea Monopisthocotylea).

The flame bulb is formed by a terminal cell and a proximal canal cell. The weir consists of interdigitating ribs all of which form one circle, i.e. alternating ribs do not have distinctly 'internal' or 'external' positions. Cytoplasmic cords are absent and all ribs, i.e. those continuous with the proximal canal cell and those continuous with the terminal cell, form external leptotriches. At least some external leptotriches have interconnected branches extending along the flame bulb. Internal leptotriches are not branched and arise from the basal perikaryon of the terminal cell. In the cytoplasmic cylinder at the tip of the flame bulb, structures resembling incomplete septate junctions were seen. However, neither the cytoplasmic cylinder nor the small protonephridial capillaries contain complete septate junctions as found in all other Monogenea Polyopisthocotylea, Monogenea Monopisthocotylea, Trematoda Aspidogastrea and Trematoda Digenea examined to date. In the lack of a septate junction, Anoplodiscus resembles Udonella, Amphilinidea, Gyrocotylidea and Eucestoda. However, the presence in this species of rudimentary septate junctions in the small capillaries and of complete junctions in larger ones indicates that complete junctions have been secondarily lost. Anoplodiscus resembles the Monogenea and Trematoda in the presence of lamellae in the larger protonephridial ducts. For the first time in a monogenean, the ultrastructure of the excretory bladder is described. A nucleated convoluted duct opens through a narrow connecting duct into the bladder, which in turn opens through a narrow connecting duct into the excretory pore lined by tegument. Convoluted duct, connecting ducts and bladder are lined by a lamellated epitheliu.(ABSTRACT TRUNCATED AT 250 WORDS)     

ONTOGENETIC SEQUENCES AND THE PHYLOGENETICS OF PARASITIC FLATWORM LIFE CYCLES

Abstract— Ontogenetic data can be used in phylogenetic analyses (1) as tests of character homology, (2) for polarizing transformation series, and (3) as characters themselves. The ontogenetic sequence of semaphoronts can change by addition, substitution, or deletion of stages which are either terminal or nonterminal. Outgroup comparisons can use life cycle data as well as morphological data to establish a general reference system of inferred genealogy, which can then be used to distinguish which of the six ontogenetic sequence changes has occurred in a particular phylogeny. A cladistic study of the parasitic platyhelminths suggests that the evolution of the Digenea involved a nonterminal addition of ontogenetic stages and a terminal addition of a second host to the ancestral life cycle. The evolution of the Cestoidea appears to have involved a terminal addition of ontogenetic stages and a nonterminal addition of a second host. The "complex life cycles" of the two groups are thus different in nature and etiology. Further cladistic analysis, within the Digenea, suggests that the plesiomorphic state of the intercalated ontogenetic stages was a miracidium-sporocyst-cercariae sequence. Rediae are concluded to have been intercalated between sporocysts and cercariae at a later point. The mutual exclusivity of rediae and daughter sporocysts in a life cycle is noted.     

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.     

PARSIMONY AND THE CHOICE BETWEEN DIFFERENT TRANSFORMATIONS FOR THE SAME CHARACTER SET

Abstract— When phylogeneticists choose among alternative hypotheses, they choose the one that requires the fewest ad hoc assumptions, i.e. the one that is the most parsimonious. For some systematists, choosing among alternative transformation series for the same set of taxa is equivalent to attaining trees with shorter length and minimal homoplasy. Homoplasy is shown to be composed of hierarchical discordance and scattering, which are recognized and described for the first time. Neither the consistency nor retention indices can be used in assessing different theories of multistate character transformation because both are affected by the shape of the transformation series rather than the character state distribution on a tree. Fits of transformations to a tree are better assessed by comparing the transformation to the cladogram character and the nearest neighbor network. Nearest neighbor networks are graphical representations of the nearest neighbor matrix. Transformations with the closest greatest number of matches between cladogram characters and the least complexity in the nearest neighbor network are preferred. These transformations are shown to make the fewest number of ad hoc statements and hence to be the most parsimonious. A means for obtaining cladogram characters and nearest neighbor matrices using a widely distributed microcomputer program is presented.     

Within-Terminal Steps and Fit Calculation—A Warning to Pee-Wee Users

Because Pee-Wee (version 2.5.1 and earlier versions) treats all within-terminal steps (internal steps) as homoplasies, if the command "ccode = (space).;" is in effect, it reports incorrect, and consistently too low, fit values for characters having states that occur only within polymorphic terminals (WPTO states). For matrices with WPTO states, this property of Pee-Wee may bias tree search in favour of characters having fewer WPTO states, other things being equal. Contrary to the intended purpose of the Goloboff criterion, Pee-Wee may even, in certain cases involving WPTO states, assign higher weight (fit) to characters with more homoplasy and therefore resolve character conflict in favour of less reliable characters.     

Weighting against homoplasy improves phylogenetic analysis of morphological data sets

The problem of character weighting in cladistic analysis is revisited. The finding that, in large molecular data sets, removal of third positions (with more homoplasy) decreases the number of well supported groups has been interpreted by some authors as indicating that weighting methods are unjustified. Two arguments against that interpretation are advanced. Characters that collectively determine few well‐supported groups may be highly reliable when taken individually (as shown by specific examples), so that inferring greater reliability for sets of characters that lead to an increase in jackknife frequencies may not always be warranted. But even if changes in jackknife frequencies can be used to infer reliability, we demonstrate that jackknife frequencies in large molecular data sets are actually improved when downweighting characters according to their homoplasy but using properly rescaled functions (instead of the very strong standard functions, or the extreme of inclusion/exclusion); this further weakens the argument that downweighting homoplastic characters is undesirable. Last, we show that downweighting characters according to their homoplasy (using standard homoplasy‐weighting methods) on 70 morphological data sets (with 50–170 taxa), produces clear increases in jackknife frequencies. The results obtained under homoplasy weighting also appear more stable than results under equal weights: adding either taxa or characters, when weighting against homoplasy, produced results more similar to original analyses (i.e., with larger numbers of groups that continue being supported after addition of taxa or characters), with similar or lower error rates (i.e., proportion of groups recovered that subsequently turn out to be incorrect). Therefore, the same argument that had been advanced against homoplasy weighting in the case of large molecular data sets is an argument in favor of such weighting in the case of morphological data sets. © The Willi Hennig Society 2008.     

On homology

Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology. ©The Will Henning Society 2011.     

A cladistic analysis of the nomadine bees (Hymenoptera: Apoidea)

Abstract. This study compares the results of Rozen's cladistic analysis of the larvae of fifteen genera of cleptoparasitic bees in the subfamily Nomadinae with an independent data set of adult characters for the same genera. Adult characters exhibited considerably higher levels of homoplasy and poorer resolution of cladistic relationships, with multiple equally parsimonious cladograms. However, comparison of a Nelson consensus tree based on adult characters with the cladogram based on larval characters reveals three components consistently supported in both analyses (the tribes Epeolini and Ammobatini, and Neopasites + Neolarra) , one component supported only by adult characters (Isepeolus + Protepeolus) , and one terminal component supported only by larval characters (Nomada + Ammobatini), as well as several more inclusive groupings based on larval characters that are difficult to compare with the adult consensus tree because it shows so much less resolution. When adult and larval characters are combined in a single data matrix, the resulting cladogram closely resembles the cladogram based on larval characters alone, although levels of homoplasy are considerably higher than in the larval analysis.
A preliminary analysis of adult characters for thirty-four genera in the Nomadinae also exhibited high levels of homoplasy and very large numbers of equally parsimonious cladograms. Nevertheless, certain consistent monophyletic groupings, most notably the Epeolini and Ammobatini, were also supported in this analysis. The one currently recognized tribe whose monophyly has received no support from any analysis is the Nomadini.
The relevance of these phylogenetic hypotheses to our understanding of host associations and variable features of egg morphology and oviposition behaviour in nomadine bees is briefly discussed.     

First evidence of the presence of microtriches in the Gyrocotylidea

The Gyrocotylidea, a small and enigmatic group of intestinal parasites of chimaeras, has been considered to be related either to the Monogenea, or, more frequently, to the most primitive monozoic tapeworms (Cestoda), i.e., the Amphilinidea and Caryophyllidea. The present study, based on transmission electron microscopical observations of a species of Gyrocotyle from the rabbit fish, Chimaera monstrosa, in the North Atlantic, demonstrates for the first time the presence of microtriches as surface structures of gyrocotylideans. Because microtriches are considered to be an autapomorphy of tapeworms (Cestoda), in which they differ from other Neodermata (Monogenea and Trematoda), the present data represent another source of evidence in support of a close relationship between the gyrocotylideans and the tapeworms sensu stricto (Eucestoda). Simple morphology, small size, and shape uniformity of the microtriches of Gyrocotyle sp. may indicate they represent an original (plesiomorphic) form that then evolved in more derived cestode groups into a variety of types present mainly on the scolex. The microtriches of Gyrocotyle sp. resemble those found in caryophyllidean, spathebothriidean, pseudophyllidean, and trypanorhynch cestodes, which are considered to represent the most basal groups of the Eucestoda.     

Higher-Order Homoplasy Tests

The Le Quesne test of character compatibility uses pairwise comparisons of characters to detect homoplasy in phylogenetic character data. If a pair of characters fails this test we can conclude that a minimum of a single extra step is required by the pair of characters. The rationale of the Le Quesne test is extended to comparisons of triplets of characters. The triplet homoplasy test can reveal that that there is a minimum of four extra steps across a triplet of characters and thus that there are at least two extra steps associated with one of the characters. The triplet homoplasy test can thus detect higher orders of homoplasy than can be detected by the pairwise Le Quesne test. The possibility of quartet and other higher-order homoplasy tests is discussed. The utility of higher-order homoplasy tests is discussed. It is suggested higher-order homoplasy tests have potential uses analogous to the uses of the Le Quesne test, particularly with respect to data exploration.     

追溯山茱萸科植物的性状进化和生物地理学历史——方法选择的影响?

This study compares results on reconstructing the ancestral state of characters and ancestral areas of distribution in Cornaceae to gain insights into the impact of using different analytical methods. Ancestral character state reconstructions were compared among three methods (parsimony, maximum likelihood, and stochastic character mapping) using MESQUITE and a full Bayesian method in BAYESTRAITS and inferences of ancestral area distribution were compared between the parsimony-based dispersal-vicariance analysis (DIVA) and a newly developed maximum likelihood (ML) method. Results indicated that among the six inflorescence and fruit characters examined, "perfect" binary characters (no homoplasy, no polymorphism within terminals, and no missing data) are little affected by choice of method, while homoplasious characters and missing data are sensitive to methods used. Ancestral areas at deep nodes of the phylogeny are substantially different between DIVA and ML and strikingly different between analyses including and excluding fossils at three deepest nodes. These results, while raising caution in making conclusions on trait evolution and historical biogeography using conventional methods, demonstrate a limitation in our current understanding of character evolution and biogeography. The biogeographic history favored by the ML analyses including fossils suggested the origin and early radiation of Cornus likely occurred in the late Cretaceous and earliest Tertiary in Europe and intercontinental disjunctions in three lineages involved movements across the North Atlantic Land Bridge (BLB) in the early and mid Tertiary. This result is congruent with the role of NALB for post-Eocene migration and in connecting tropical floras in North America and Africa, and in eastern Asia and South America. However, alternative hypotheses with an origin in eastern Asia and early Trans-Beringia migrations of the genus cannot be ruled out.