The position of the Arthropoda in the phylogenetic system

Traditionally, Panarthropoda (Euarthropoda, Onychophora, Tardigrada) are regarded as being closely related to Annelida in a taxon Articulata, but this is not supported by molecular analyses. Comparisons of gene sequences suggest that all molting taxa (Panarthropoda, Nematoda, Nematomorpha, Priapulida, Kinorhyncha, Loricifera) are related in a monophyletic taxon Ecdysozoa. An examination of the characters supporting Articulata reveals that only segmentation with a teloblastic segment formation and the existence of segmental coelomic cavities with nephridia support the Articulata, whereas all other characters are modified or reduced in the panarthropod lineage. Another set of characters is presented that supports the monophyly of Ecdysozoa: molting under influence of ecdysteroid hormones, loss of locomotory cilia, trilayered cuticle and the formation of the epicuticle from the tips of epidermal microvilli. Comparative morphology suggests Gastrotricha as the sister group of Ecdysozoa with the synapomorphies: triradiate muscular sucking pharynx and terminal mouth opening. Thus there are morphological characters that support Articulata, but molecular as well as morphological data advocate Ecdysozoa. Comparison of both hypotheses should prompt further thorough and targeted investigations. J. Morphol. 238:263–285, 1998. © 1998 Wiley-Liss, Inc.     

Molecules, development and fossils in the study of metazoan evolution; Articulata versus Ecdysozoa revisited

Two conflicting hypotheses of protostome relationships, Articulata and Ecdysozoa, are reviewed by evaluating the evidence in favor and against each one of them. Understanding early embryonic development and segmentation in non-arthropod non-annelid protostomes seems crucial to the debate. New ways of coding metazoan matrices, avoiding ground-patterns and higher taxa, and incorporating fossil evidence seems the best way to avoid circular debates. Molecular data served as the catalyzer for the Ecdysozoa hypothesis, although morphological support had been implicitly suggested. Most molecular analyses published so far have shown some support for Ecdysozoa, whereas none has ever supported Articulata. Here, new analyses of up to four nuclear loci, including 18S rRNA, myosin heavy chain II, histone H3 and elongation factor 1- are conducted to test the molecular support for Ecdysozoa, and, at least under some parameter sets, most data sets show a clade formed by the molting animals. In contrast, support for Articulata is not found under any analytical conditions.     

Ecdysozoa versus Articulata: clades, artifacts, prejudices

The claim that monophyly of the Ecdysozoa is caused by chance similarities in 18S rDNA sequences ( Wägele et al., J. Zool. Syst. Evol. Res. 37, 211–223, 1999 ) is re-analysed from the cladistic point of view. It is shown that the molecular characters supporting the Ecdysozoa do not behave as 'noisy' in empirical studies that use the sensitivity analysis and character congruence approaches. The 'anti-noise' methodology proposed by Wägele et al. (1999) is unable to identify true misinformative data. The monophyly of the Articulata (= Annelida + Panarthropoda), proposed by Wägele et al. (1999) , is contradicted by all molecular data that support either Ecdysozoa (including Panarthropoda), or Lophotrochozoa (including Annelida), or usually both.     

The Articulata hypothesis – or what is a segment?

The long held view that annelids and arthropods are closely related (Articulata) has been challenged recently by phylogenetic analyses using molecular data. The outcome of these studies is a clade of moulting animals (Ecdysozoa) comprising arthropods and some taxa of the nemathelminth worms. Monophyly of the Ecdysozoa has not yet been shown convincingly on morphological evidence, but is strongly supported by molecular data. The implication of the Ecdysozoa hypothesis is that the type of segmentation found in annelids and arthropods must be either convergent or an ancestral feature of protostomes or even bilaterians. The present review discusses aspects of segmentation in annelids and arthropods at the genetic, cellular, morphogenetic and morphological levels. Based on numerous similarities not shared with other bilaterian taxa it is suggested that segmentation of annelids and arthropods is homologous and apomorphic for a monophyletic Articulata. However, the challenge provided by the molecular analyses should stimulate research programmes gaining more data such as on additional genes, cleavage patterns, molecular developmental biology, and the comparison of nervous systems at the level of single neurons.     

Proposing a solution to the Articulata–Ecdysozoa controversy

Recent studies of animal radiation agree on monophyly of the Bilateria, but there is no consensus about the early radiation of the group. Protostomia and Deuterostomia are usually recognized, with two competing theories regarding the division of the Protostomia: one divides them into Spiralia and Cycloneuralia, the other into Lophotrochozoa and Ecdysozoa. The main discrepancy concerns the Arthropoda, which are placed with the Articulata within the Spiralia by the first group, and with the Cycloneuralia within the Ecdysozoa by the second. Here I propose that this discrepancy can be resolved by regarding the Ecdysozoa as the sister group of the Annelida within the Articulata. This implies that segmentation has been lost in phyla such as Nematoda and Priapula, but the Kinorhyncha may show a 'reduced segmentation' with serially arranged muscles associated with a ringed cuticle. Morphological, palaeontological and molecular implications of this theory are discussed. While many morphological and palaeontological data can be interpreted in accordance with the theory, the molecular data remain inconclusive.     

Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis1

As many data as possible must be included in any scientific analysis, provided that they follow the logical principles on which this analysis is based. Phylogenetic analysis is based on the basic principle of evolution, i.e., descent with modification. Consequently, ecological characters or any other nontraditional characters must be included in phylogenetic analyses, provided that they can plausibly be postulated heritable. The claim of Zrzavý (1997, Oikos 80, 186–192) or Luckow and Bruneau (1997, Cladistics 13, 145–151) that any character of interest should be included in the analysis is thus inaccurate. Many characters, broadly defined or extrinsic (such as distribution areas), cannot be considered as actually heritable. It is argued that we should better care for the precise definition and properties of characters of interest than decide a priori to include them in any case in the analysis. The symmetrical claim of de Queiroz (1996, Am. Nat. 148, 700–708) that some characters of interest should better be excluded from analyses to reconstruct their history is similarly inaccurate. If they match the logical principles of phylogenetic analysis, there is no acceptable reason to exclude them. The different statistical testing strategies of Zrzavý (1997) and de Queiroz (1996) aimed at justifying inclusion versus exclusion of characters are ill‐conceived, leading respectively to Type II and Type I errors. It is argued that phylogenetic analyses should not be constrained by testing strategies that are downstream of the logical principles of phylogenetics. Excluding characters and mapping them on an independent phylogeny produces a particular and suboptimal kind of secondary homology, the use of which can be justified only for preliminary studies dealing with broadly defined characters.     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

Ecdysozoa: The Relationship between Cycloneuralia and Panarthropoda

The hypothesis that molting protostomes such as nematodes and arthropods form a monophyletic group known as Ecdysozoa is directly opposed to Articulata, in which some segmented protostomes such as annelids and arthropods form a monophyletic taxon. Ultrastructural and cladistic studies have led to the widely accepted hypothesis that nematodes belong among the protostomes. While early molecular studies suggested that nematodes were basal triploblasts, more recent molecular evidence suggests that this was an artifact of ‘long branch attraction’ and 18S rRNA gene, total evidence and hox gene studies all support the placement of nematodes within Ecdysozoa. The branching pattern within Ecdysozoa has been difficult to elucidate, but it now appears that priapulids and kinorhynchs form the earliest branching clade, followed by nematodes + nematomorphs, and finally the panarthropods. This suggests that Cycloneuralia is paraphyletic and that arthropods are the most derived of the ecdysozoans.     

On the pronymphal stage in the migratory locust (Locusta migratoria, Orthoptera, Acrididae)

The structure of the integument, somatic and visceral muscles, midgut, and Malpighian tubules were investigated at the late stages of the embryonic and early postembryonic development of the migratory locust, Locusta migratoria, to assess the organization of its pronymphal stage. In its morphogenetic features, the vermiform locust larva sometimes called the pronymph corresponds to the first nymphal instar covered with the second embryonic cuticle which has not been shed. Since the first-instar locust nymphs before and after the shedding of this embryonic cuticle differ significantly in many morphological characters, two consecutive phases of this nymphal instar can be distinguished: the first phase existing from the moment of development of the third embryonic cuticle to the shedding of the second one; the second phase existing from the shedding of the second embryonic cuticle to the formation of the cuticle of the second nymphal instar. Since the pronymphal stage should precede the nymph stage, it may be concluded that the pronymph of the locust is fully embryonized and covered with the second embryonic cuticle, which is also typical of other insects with hemimetabolous development (Konopová and Zrzavý, 2005). Therefore, it would be erroneous to refer to the vermiform first-instar nymph as the pronymph, because the two stages are separated by molting and formation of a new cuticle.     

The complete mitochondrial genome of the onychophoran Epiperipatus biolleyi reveals a unique transfer RNA set and provides further support for the ecdysozoa hypothesis

Onychophora (velvet worms) play a crucial role in current discussions on position of arthropods. The ongoing Articulata/Ecdysozoa debate is in need of additional ground pattern characters for Panarthropoda (Arthropoda, Tardigrada, and Onychophora). Hence, Onychophora is an important outgroup taxon in resolving the relationships among arthropods, irrespective of whether morphological or molecular data are used. To date, there has been a noticeable lack of mitochondrial genome data from onychophorans. Here, we present the first complete mitochondrial genome sequence of an onychophoran, Epiperipatus biolleyi (Peripatidae), which shows several characteristic features. Specifically, the gene order is considerably different from that in other arthropods and other bilaterians. In addition, there is a lack of 9 tRNA genes usually present in bilaterian mitochondrial genomes. All these missing tRNAs have anticodon sequences corresponding to 4-fold degenerate codons, whereas the persisting 13 tRNAs all have anticodons pairing with 2-fold degenerate codons. Sequence-based phylogenetic analysis of the mitochondrial protein-coding genes provides a robust support for a clade consisting of Onychophora, Priapulida, and Arthropoda, which confirms the Ecdysozoa hypothesis. However, resolution of the internal ecdysozoan relationships suffers from a cluster of long-branching taxa (including Nematoda and Platyhelminthes) and a lack of data from Tardigrada and further nemathelminth taxa in addition to nematodes and priapulids.     

Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets

Zrzavý, J. & ?i?ánková, V. (2004). Phylogeny of Recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets. — Zoologica Scripta, 33, 311–333. Phylogenetic relationships within the Canidae are examined, based on three genes (cytb, COI, COII) and 188 morphological, developmental, behavioural and cytogenetic characters. Both separate and combined phylogenetic analyses were performed. To inspect the phylogenetic ‘behaviour’ of individual taxa, basic phylogenetic analysis was followed by experimental cladistic analyses based on different data‐partition combinations and taxon‐removal analyses. The following phylogeny of the Recent Canidae is preferred: (1) Urocyon is the most basal canid; (2) Vulpes is a monophyletic genus (including Fennecus and Alopex); (3) the doglike canids (DC) form a clade (=Dusicyon + Pseudalopex + Lycalopex + Cerdocyon + Atelocynus + Chrysocyon + Speothos + Lycaon + Cuon + Canis), split into two subclades, South American and Afro‐Holarctic, with uncertain position of the Chrysocyon + Speothos subclade; (4) Canis is paraphyletic due to the position of Lycaon and Cuon. Otocyon and Nyctereutes are the most problematic canid genera, causing an unresolved branching pattern of Otocyon, Vulpes, Nyctereutes and DC clades. Reclassification of the two basal species of ‘Canis’ into separate genera is proposed (Schaeffia for ‘C.’ adustus, Lupulella for ‘C.’ mesomelas). Although the morphological dataset ranked poorly in both separate and simultaneous analyses (measured by number of minimum‐length topologies, relative number of resolved nodes in the strict consensus of all minimum‐length topologies, consistency and retention indices, nodal dataset influence, and number of extra steps required by the data partition to reach the topology of the combined tree), the morphological synapomorphies represent nearly one quarter of all synapomorphies in the combined tree. Among the hidden morphological support of the combined tree the developmental and behavioural characters are conspicuously abundant.     

Molecules,morphology, missing data and the phylogenetic position of a recently extinct madtom catfish (Actinopterygii: Ictaluridae)

Taxa missing large amounts of data pose challenges that may hinder the recovery of a well‐resolved, accurate phylogeny and leave questions surrounding their phylogenetic position. Systematists commonly have to contend with one or two species in a group for which there is little or no material available suitable for recovering molecular data. It is unclear whether these taxa can be better placed using analyses based on morphological data only, or should be included in broader analyses based on both morphological and molecular data. The extinct madtom catfish Noturus trautmani is known from few specimens for which molecular data are unavailable. We included this taxon in parsimony and Bayesian analyses of relationships of madtom catfishes based on a combination of morphological and molecular data. Results indicate that using a combination of morphological and molecular data does a better job at providing a phylogenetic placement for N. trautmani than morphology alone, even though it is missing all of its molecular characters. We provide a novel hypothesis of relationships among Noturus species and recommendations for classification within the group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 60–75.     

Systematics of naviculoid diatoms (Bacillariophyta): A preliminary analysis of protoplast and frustule characters for family and order level classification

The relationships between 49 naviculoid diatoms, currently arranged in 14 families and four orders were investigated using cladistic analysis in order to test the types of characters used in diatom systematics and to assess how well the current classification reflects possible phylogenetic relationships in this group. Some of the families and orders comprise taxa with different protoplast characters, or taxa with similar protoplast arrangements are placed in separate families or orders. Therefore as both cell wall and protoplast characters were used, three analyses were undertaken; total data, protoplast data and frustule data. The analyses support the recognition of the Mastogloiales (unequivocally) and the Cymbellales (largely) but indicate that some of the familial groupings are more ambiguous. The members of the Berkeleyaceae, Berkeleya, Parlibellus and Climaconeis, were never grouped together and Achnanthes brevipes never grouped with the other monoraphid diatoms, but usually with members of the Mastogloiales (total and protoplast data). Similarly, Round et al.’s familial groupings within the Cymbellales do not emerge from our analyses. Our results support the hypothesis that monoraphid genera have arisen independently from different naviculoid diatoms, and that Achnanthes sensu stricto should be transferred to the Mastogloiales. Some of the problems associated with incomplete information and inaccurate terminology are discussed briefly.     

Palaeontological and Molecular Evidence Linking Arthropods, Onychophorans, and other Ecdysozoa

Membership of Arthropoda in a clade of molting animals, the Ecdysozoa, has received a growing body of support over the past 10 years from analyses of DNA sequences from many genes together with morphological characters involving the cuticle and its molting. Recent analyses based on broad phylogenomic sampling strengthen the grouping of cycloneuralian worms and arthropods as Ecdysozoa, identify the velvet worms (Phylum Onychophora) as the closest living relatives of arthropods, and interpret segmentation as having separate evolutionary origins in arthropods and annelid worms. Determining whether the water bears (Phylum Tardigrada) are more closely related to onychophorans and arthropods or to unsegmented cycloneuralians such as roundworms (Nematoda) is an open question. Fossil taxa such as the Cambrian anomalocaridids provide a combination of arthropod and cycloneuralian characters that is not observed in any living ecdysozoan. Fossils break up long branches and help to resolve the sequence of character acquisition at several critical nodes in the arthropod tree, notably in a suite of Cambrian lobopodians that may include the stem groups of each of the major panarthropod lineages.     

On the information content of characters in comparative morphology and molecular systematics

A review of the fundamental difference between single molecular-sequence positions, or numerical characters, and complex morphological characters is the subject of this study. It has been found that transformation series of single complex structures contain enough information to allow a priori determination of character order and that rooting of a dendrogram is possible without out-group comparison, while trees based on less-informative characters can usually only be rooted with out-group comparison. Furthermore, the quality of total information used is decisive in discriminating between hypotheses of relationships. Numerical methods for the inference of phylogenies have been found to be useful for high numbers of characters that have only a low information content, while the Hennigian procedure seems to be preferable for complex characters.     

Haemothermia or Archosauria? The interrelationships of mammals,birds and crocodiles

The recently proposed hypothesis that the living birds and the living mammals are sister groups, together forming a natural taxon Haemothermia, is contrasted with the more traditional view, that birds and crocodiles are living sister groups within the taxon Archosauria. Of the 28 or so characters claimed to be unique to the Haemothermia, several are found to be structurally or developmentally different in birds compared to mammals. Others are found to occur also in crocodiles. In either case the status of the characters as homologues categorizing the group becomes doubtful, and only about eight characters remain as potentially acceptable. In contrast, some 24 characters are identified as potential homologues of birds plus crocodiles and therefore categorizing the group Archosauria, and this hypothesis must be judged preferable. The evidence of the characters of fossils can be used legitimately to test cladograms, but only to a limited extent. Nevertheless, the relevant fossils do support the Archosauria rather than the Haemothermia hypothesis. Cladograms logically may, and methodologically should, be taken as theories of phylogenetic relationships, and are potentially subject to independent evolutionary tests. A priori character weighting is sound in principle but cannot be applied in practice for want of the necessary, independently acquired knowledge of how characters change in evolution. The relative dates of the fossils is shown to be more compatible with the Archosauria than the Haemothermia classification. Finally, the hypothetical common ancestors that are implied by the two respective cladograms are compared. That shared by mammals and birds, as implied by the Haemothermia theory, would have been functionally incongruent, and therefore less probable than that shared by birds and crocodiles. These several lines of evidence all lead to the conclusion that the traditional theory of a relationship between birds and crocodiles, vis à vis mammals is substantially the better supported.     

Specific features of the seismosensory system and their use in the systematics of five families of the order pleuronectiformes

The structure of the seismosensory system (SSS) was studied in 23 species of 13 genera from the families Rhombosoleidae, Poecilopsettidae, and Samaridae, and a comparison and generalization of the obtained data with those published previously for the families Psettodidae and Pleuronectidae was performed. It was shown that the individual variability of SSS does not concern topography of canals, being manifested in the variation of the number of pores in particular canals. Interspecific differences also concern mainly the number of pores, and revealing these differences requires, as a rule, statistic methods. Considerable differences were found between genera, so that each of the 40 studied genera can be characterized by a unique combination of SSS characters whose polarization was established on the basis of a reduction trend of SSS transformations common for bony fish. The maximum number of plesiomorphies of SSS was found in the genus Psettodes (Psettodidae). In the framework of the family Pleuronectidae, the most generalized structure of SSS was found in representatives of the subfamily Hippoglossinae, and the most advanced, in Pleuronectinae. In the family Rhombosoleidae, the most generalized structure of SSS is in the genus Oncopterus, the remaining representatives of the family Rhombosoleidae are characterized by a different degree of its reduction. In rather closely related families Poecilopsettidae and Samaridae, SSS is considerably reduced, which may be connected with the miniatuarization of their representatives. A small number of considered characters and a high level of homoplasia hinders their use in cladistic study; however, considerable differences between the studied genera and a low interspecific variation permits for the considering of specific features of SSS as valuable diagnostic characters of genera, and the degree of reduction of this system can indicate the relative degree of advancement of a specific taxon of Pleuronectiformes.     

Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans

There has been broad acceptance among evolutionary biologists of the Ecdysozoa hypothesis that, based principally on molecular phylogenetic studies of small and large subunit ribosomal RNA sequences, postulates a close relationship between molting taxa such as arthropods and nematodes. On the other hand, recent studies of as many as 100 additional genes do not support the Ecdysozoa hypothesis and instead favor the older Coelomata hypothesis that groups the coelomate arthropods with the coelomate vertebrates to the exclusion of the nematodes. Here, exploiting completely sequenced genomes, we examined this question using cladistic analyses of the phylogenetic distribution of 1712 orthologous genes and 2906 protein domain combinations; we found stronger support for the Coelomata hypothesis than for the Ecdysozoa hypothesis. However, although arrived at by considering very large data sets, we show that this conclusion is unreliable, biased toward grouping arthropods with chordates by systematic high rate of character loss in the nematode. When we addressed this problem, we found slightly more support for Ecdysozoa than for Coelomata. Our identification of this systematic bias even when using entire genomes has important implications for future phylogenetic studies. We conclude that the results from the intensively sampled ribosomal RNA genes supporting the Ecdysozoa hypothesis provide the most credible current estimates of metazoan phylogeny.     

The skull of the Upper Cretaceous snake Dinilysia patagonica Smith‐Woodward, 1901, and its phylogenetic position revisited

The cranial anatomy of Dinilysia patagonica, a terrestrial snake from the Upper Cretaceous of Argentina, is redescribed and illustrated, based on high‐resolution X‐ray computed tomography and better preparations made on previously known specimens, including the holotype. Previously unreported characters reinforce the intriguing mosaic nature of the skull of Dinilysia, with a suite of plesiomorphic and apomorphic characters with respect to extant snakes. Newly recognized plesiomorphies are the absence of the medial vertical flange of the nasal, lateral position of the prefrontal, lizard‐like contact between vomer and palatine, floor of the recessus scalae tympani formed by the basioccipital, posterolateral corners of the basisphenoid strongly ventrolaterally projected, and absence of a medial parietal pillar separating the telencephalon and mesencephalon, amongst others. We also reinterpreted the structures forming the otic region of Dinilysia, confirming the presence of a crista circumfenestralis, which represents an important derived ophidian synapomorphy. Both plesiomorphic and apomorphic traits of Dinilysia are treated in detail and illustrated accordingly. Results of a phylogenetic analysis support a basal position of Dinilysia, as the sister‐taxon to all extant snakes. The fossil taxa Yurlunggur, Haasiophis, Eupodophis, Pachyrhachis, and Wonambi appear as derived snakes nested within the extant clade Alethinophidia, as stem‐taxa to the crown‐clade Macrostomata. The hypothesis of a sister‐group relationship between Dinilysia and Najash rionegrina, as suggested by some authors, is rejected by the results of our analysis. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 194–238.