Arthropod phylogeny: An overview from the perspectives of morphology,molecular data and the fossil record

Monophyly of Arthropoda is emphatically supported from both morphological and molecular perspectives. Recent work finds Onychophora rather than Tardigrada to be the closest relatives of arthropods. The status of tardigrades as panarthropods (rather than cycloneuralians) is contentious from the perspective of phylogenomic data. A grade of Cambrian taxa in the arthropod stem group includes gilled lobopodians, dinocaridids (e.g., anomalocaridids), fuxianhuiids and canadaspidids that inform on character acquisition between Onychophora and the arthropod crown group. A sister group relationship between Crustacea (itself likely paraphyletic) and Hexapoda is retrieved by diverse kinds of molecular data and is well supported by neuroanatomy. This clade, Tetraconata, can be dated to the early Cambrian by crown group-type mandibles. The rival Atelocerata hypothesis (Myriapoda + Hexapoda) has no molecular support. The basal node in the arthropod crown group is embroiled in a controversy over whether myriapods unite with chelicerates (Paradoxopoda or Myriochelata) or with crustaceans and hexapods (Mandibulata). Both groups find some molecular and morphological support, though Mandibulata is presently the stronger morphological hypothesis. Either hypothesis forces an unsampled ghost lineage for Myriapoda from the Cambrian to the mid Silurian.     

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.     

Phylum Tardigrada: an “individual” approach

Phylum Tardigrada consists of ～1000 tiny, hardy metazoan species distributed throughout terrestrial, limno‐terrestrial and oceanic habitats. Their phylogenetic status has been debated, with current evidence placing them in the Ecdysozoa. Although there have been efforts to explore tardigrade phylogeny using both morphological and molecular data, limitations such as their few morphological characters and low genomic DNA concentrations have resulted in restricted taxonomic coverage. Using a protocol that allows us to identify and extract DNA from individuals, we have sequenced 18S rDNA from 343 tardigrades from across the globe. Using maximum parsimony and Bayesian analyses we have found support for dividing Order Parachela into three super‐families and further evidence that indicates the traditional taxonomic perspective of families in the class Eutardigrada are nonmonophyletic and require re‐working. It appears that conserved morphology within Tardigrada has resulted in conservative taxonomy as we have found cases of several discrete lineages grouped into single genera. Although this work substantially adds to the understanding of the evolution and taxonomy of the phylum, we highlight that inferences gained from this work are likely to be refined with the inclusion of further taxa—specifically representatives of the nine families yet to be sampled. © The Willi Hennig Society 2008.     

A molecular approach to arthrotardigrade phylogeny (Heterotardigrada,Tardigrada)

The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phylum, the phylogenetic relationships of Arthrotardigrada have not been clarified. This study conducted molecular phylogenetic analyses of the order encompassing all families except Neoarctidae using nuclear 18S and 28S rRNA fragments. Data from two rare families, Coronarctidae and Renaudarctidae, were included for the first time. The analyses confirmed the monophyly of Heterotardigrada and inferred Coronarctidae as the sister group to all other heterotardigrade taxa. Furthermore, the results support a monophyletic Renaudarctidae + Stygarctidae clade, which has been previously suggested on morphology. Our data indicated that two subfamilies currently placed in Halechiniscidae are only distantly related to this family. We propose that these taxa are each elevated to family level (Styraconyxidae (new rank) and Tanarctidae (new rank)). The morphology of tardigrades is discussed in the context of the inferred phylogeny.     

The position of Cetacea within mammalia: phylogenetic analysis of morphological data from extinct and extant taxa

Knowledge of the phylogenetic position of the order Cetacea (whales, dolphins, and porpoises) within Mammalia is of central importance to evolutionary biologists studying the transformations of biological form and function that accompanied the shift from fully terrestrial to fully aquatic life in this clade. Phylogenies based on molecular data and those based on morphological data both place cetaceans among ungulates but are incongruent in other respects. Morphologists argue that cetaceans are most closely related to mesonychians, an extinct group of terrestrial ungulates. They have disagreed, however, as to whether Perissodactyla (odd-toed ungulates) or Artiodactyla (even-toed ungulates) is the extant clade most closely related to Cetacea, and have long maintained that each of these orders is monophyletic. The great majority of molecule-based phylogenies show, by contrast, not only that artiodactyls are the closest extant relatives of Cetacea, but also that Artiodactyla is paraphyletic unless cetaceans are nested within it, often as the sister group of hippopotamids. We tested morphological evidence for several hypotheses concerning the sister taxon relationships of Cetacea in a maximum parsimony analysis of 123 morphological characters from 10 extant and 30 extinct taxa. We advocate treating certain multistate characters as ordered because such a procedure incorporates information about hierarchical morphological transformation. In all most-parsimonious trees, whether multistate characters are ordered or unordered, Artiodactyla is the extant sister taxon of Cetacea. With certain multistate characters ordered, the extinct clade Mesonychia (Mesonychidae + Hapalodectidae) is the sister taxon of Cetacea, and Artiodactyla is monophyletic. When all fossils are removed from the analysis, Artiodactyla is paraphyletic with Cetacea nested inside, indicating that inclusion of mesonychians and other extinct stem taxa in a phylogenetic analysis of the ungulate clade is integral to the recovery of artiodactyl monophyly. Phylogenies derived from molecular data alone may risk recovering inconsistent branches because of an inability to sample extinct clades, which by a conservative estimate, amount to 89% of the ingroup. Addition of data from recently described astragali attributed to cetaceans does not overturn artiodactyl monophyly.     

Stasis and convergence characterize morphological evolution in eupolypod II ferns

Background and Aims

Patterns of morphological evolution at levels above family rank remain underexplored in the ferns. The present study seeks to address this gap through analysis of 79 morphological characters for 81 taxa, including representatives of all ten families of eupolypod II ferns. Recent molecular phylogenetic studies demonstrate that the evolution of the large eupolypod II clade (which includes nearly one-third of extant fern species) features unexpected patterns. The traditional ‘athyrioid’ ferns are scattered across the phylogeny despite their apparent morphological cohesiveness, and mixed among these seemingly conservative taxa are morphologically dissimilar groups that lack any obvious features uniting them with their relatives. Maximum-likelihood and maximum-parsimony character optimizations are used to determine characters that unite the seemingly disparate groups, and to test whether the polyphyly of the traditional athyrioid ferns is due to evolutionary stasis (symplesiomorphy) or convergent evolution. The major events in eupolypod II character evolution are reviewed, and character and character state concepts are reappraised, as a basis for further inquiries into fern morphology.

Methods

Characters were scored from the literature, live plants and herbarium specimens, and optimized using maximum-parsimony and maximum-likelihood, onto a highly supported topology derived from maximum-likelihood and Bayesian analysis of molecular data. Phylogenetic signal of characters were tested for using randomization methods and fitdiscrete.

Key Results

The majority of character state changes within the eupolypod II phylogeny occur at the family level or above. Relative branch lengths for the morphological data resemble those from molecular data and fit an ancient rapid radiation model (long branches subtended by very short backbone internodes), with few characters uniting the morphologically disparate clades. The traditional athyrioid ferns were circumscribed based upon a combination of symplesiomorphic and homoplastic characters. Petiole vasculature consisting of two bundles is ancestral for eupolypods II and a synapomorphy for eupolypods II under deltran optimization. Sori restricted to one side of the vein defines the recently recognized clade comprising Rhachidosoraceae through Aspleniaceae, and sori present on both sides of the vein is a synapomorphy for the Athyriaceae sensu stricto. The results indicate that a chromosome base number of x =41 is synapomorphic for all eupolypods, a clade that includes over two-thirds of extant fern species.

Conclusions

The integrated approach synthesizes morphological studies with current phylogenetic hypotheses and provides explicit statements of character evolution in the eupolypod II fern families. Strong character support is found for previously recognized clades, whereas few characters support previously unrecognized clades. Sorus position appears to be less complicated than previously hypothesized, and linear sori restricted to one side of the vein support the clade comprising Aspleniaceae, Diplaziopsidaceae, Hemidictyaceae and Rachidosoraceae – a lineage only recently identified. Despite x =41 being a frequent number among extant species, to our knowledge it has not previously been demonstrated as the ancestral state. This is the first synapomorphy proposed for the eupolypod clade, a lineage comprising 67 % of extant fern species. This study provides some of the first hypotheses of character evolution at the family level and above in light of recent phylogenetic results, and promotes further study in an area that remains open for original observation.     

First molecular data on the phylum Loricifera: an investigation into the phylogeny of ecdysozoa with emphasis on the positions of Loricifera and Priapulida

Recent progress in molecular techniques has generated a wealth of information for phylogenetic analysis. Among metazoans all but a single phylum have been incorporated into some sort of molecular analysis. However, the minute and rare species of the phylum Loricifera have remained elusive to molecular systematists. Here we report the first molecular sequence data (nearly complete 18S rRNA) for a member of the phylum Loricifera, Pliciloricus sp. from Korea. The new sequence data were analyzed together with 52 other ecdysozoan sequences, with all other phyla represented by three or more sequences. The data set was analyzed using parsimony as an optimality criterion under direct optimization as well as using a Bayesian approach. The parsimony analysis was also accompanied by a sensitivity analysis. The results of both analyses are largely congruent, finding monophyly of each ecdysozoan phylum, except for Priapulida, in which the coelomate Meiopriapulus is separate from a clade of pseudocoelomate priapulids. The data also suggest a relationship of the pseudocoelomate priapulids to kinorhynchs, and a relationship of nematodes to tardigrades. The Bayesian analysis placed the arthropods as the sister group to a clade that includes tardigrades and nematodes. However, these results were shown to be parameter dependent in the sensitivity analysis. The position of Loricifera was extremely unstable to parameter variation, and support for a relationship of loriciferans to any particular ecdysozoan phylum was not found in the data.     

Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between animals and fungi

To understand the early evolution of the Metazoa, it is necessary to determine the correct phylogenetic status of diploblastic animals. Despite cladistic studies of morphological characters and recent molecular phylogenetic studies, it remains uncertain whether diploblasts are monophyletic or paraphyletic, and how the phyla of diploblasts are phylogenetically related. The heat shock protein 70 (Hsp70) sequences, because of their ubiquity and high degree of conservation, could provide a useful model for phylogenetic analysis. We have sequenced almost the entire nucleic acid sequence of cytoplasmic Hsp70 from eight diploblastic species. Our data support the monophyly of diploblastic animals. However, the phylogenetic relationships of the diploblast groups were not significantly resolved. Our phylogenetic trees also support the monophyly of Metazoa with high bootstrap values, indicating that animals form an extremely robust clade.      

The Ajellomycetaceae, a new family of vertebrate-associated Onygenales

Phylogenies inferred from the analysis of DNA sequence data have shown that the Onygenales contains clades that do not correspond with previously described families. One lineage identified in recent molecular phylogenetic studies includes the dimorphic pathogens belonging to the genera Ajellomyces, Emmonsia and Paracoccidioides. To evaluate the degree of support for this lineage and determine whether it includes additional taxa, we examined relationships among the members of this clade and selected saprobic onygenalean taxa based on maximum-parsimony analyses of partial nuclear large RNA subunit (LSU) and internal transcribed spacer (ITS) sequences. A clade distinct from the Onygenaceae was found to encompass Ajellomyces (including the anamorph genera Blastomyces, Emmonsia and Histoplasma) and Paracoccidioides brasiliensis. The members of this lineage are saprobic and pathogenic vertebrate-associated taxa distinguished by their globose ascomata with coiled appendages, muricate globose or oblate ascospores, and lack of keratinolytic activity. Anamorphs are solitary aleurioconidia or irregular alternate arthroconidia. Based on molecular data and on morphological and physiological similarities among these taxa, we propose the new family, Ajellomycetaceae.     

An upgraded comprehensive multilocus phylogeny of the Tardigrada tree of life

Providing accurate animals’ phylogenies rely on increasing knowledge of neglected phyla. Tardigrada diversity evaluated in broad phylogenies (among phyla) is biased towards eutardigrades. A comprehensive phylogeny is demanded to establish the representative diversity and propose a more natural classification of the phylum. So, we have performed multilocus (18S rRNA and 28S rRNA) phylogenies with Bayesian inference and maximum likelihood. We propose the creation of a new class within Tardigrada, erecting the order Apochela (Eutardigrada) as a new Tardigrada class, named Apotardigrada comb. n. Two groups of evidence support its creation: (a) morphological, presence of cephalic appendages, unique morphology for claws (separated branches) and wide‐elongated buccopharyngeal apparatus without placoids, and (b) phylogenetic support based on molecular data. Consequently, order Parachela is suppressed and its superfamilies erected as orders within Eutardigrada, maintaining their current names. We propose a new classification within the family Echiniscidae (Echiniscoidea, Heterotardigrada) with morphological and phylogenetic support: (a) subfamily Echiniscinae subfam. n., with two tribes Echiniscini tribe n. and Bryodelphaxini tribe n.; (b) subfamily Pseudechiniscinae subfam. n., with three tribes Cornechiniscini tribe n., Pseudechiniscini tribe n. and Anthechiniscini tribe n.; and (c) subfamily Parechiniscinae subfam. n., with two tribes Parechiniscini tribe n. and Novechiniscini tribe n. Reliable biodiversity selection for tardigrades in broad phylogenies is proposed due to biased analyses performed up to now. We use our comprehensive molecular phylogeny to evaluate the evolution of claws in the clawless genus Apodibius and claw reduction across the Tardigrada tree of life. Evolutionary consequences are discussed.     

Ebriid phylogeny and the expansion of the Cercozoa

Ebria tripartita is a phagotrophic flagellate present in marine coastal plankton communities worldwide. This is one of two (possibly four) described extant species in the Ebridea, an enigmatic group of eukaryotes with an unclear phylogenetic position. Ebriids have never been cultured, are usually encountered in low abundance and have a peculiar combination of ultrastructural characters including a large nucleus with permanently condensed chromosomes and an internal skeleton composed of siliceous rods. Consequently, the taxonomic history of the group has been tumultuous and has included a variety of affiliations, such as silicoflagellates, dinoflagellates, 'radiolarians' and 'neomonads'. Today, the Ebridea is treated as a eukaryotic taxon incertae sedis because no morphological or molecular features have been recognized that definitively relate ebriids with any other eukaryotic lineage. We conducted phylogenetic analyses of small subunit rDNA sequences from two multi-specimen isolations of Ebria tripartita. The closest relatives to the sequences from Ebria tripartita are environmental sequences from a submarine caldera floor. This newly recognized Ebria clade was most closely related to sequences from described species of Cryothecomonas and Protaspis. These molecular phylogenetic relationships were consistent with current ultrastructural data from all three genera, leading to a robust placement of ebriids within the Cercozoa.     

Conflicting molecular phylogenies of European long-eared bats (Plecotus) can be explained by cryptic diversity

Conflicting phylogenetic signals of two data sets that analyse different portions of the same molecule are unexpected and require an explanation. In the present paper we test whether (i) differential evolution of two mitochondrial genes or (ii) cryptic diversity can better explain conflicting results of two recently published molecular phylogenies on the same set of species of long-eared bats (genus Plecotus). We sequenced 1714bp of three mitochondrial regions (16S, ND1, and D-loop) of 35 Plecotus populations from 10 European countries. A likelihood ratio test revealed congruent phylogenetic signals of the three data partitions. Our phylogenetic analyses demonstrated that the existence of a previously undetected Plecotus lineage caused the incongruities of previous studies. This lineage is differentiated on the species level and lives in sympatry with its sister lineage, Plecotus auritus, in Switzerland and Northern Italy. A molecular clock indicates that all European Plecotus species are of mid or late Pliocene origin. Plecotus indet. was previously described as an intergrade between P. auritus and Plecotus austriacus since it shares morphological characters with both. It is currently known from elevations above 800 m a.s.l. in the Alps, the Dinarian Alps and the Pindos mountains in Greece. Since we could demonstrate that incongruities of two molecular analyses simply arose from the mis-identification of one lineage, we conclude that molecular phylogenetic analyses do not free systematists from a thorough inclusion of morphological and ecological data.     

The evolution of the Ecdysozoa

Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.     

Mitochondrial DNA,morphology, and the phylogenetic relationships of Antarctic icefishes (Notothenioidei: Channichthyidae)

The Channichthyidae is a lineage of 16 species in the Notothenioidei, a clade of fishes that dominate Antarctic near-shore marine ecosystems with respect to both diversity and biomass. Among four published studies investigating channichthyid phylogeny, no two have produced the same tree topology, and no published study has investigated the degree of phylogenetic incongruence between existing molecular and morphological datasets. In this investigation we present an analysis of channichthyid phylogeny using complete gene sequences from two mitochondrial genes (ND2 and 16S) sampled from all recognized species in the clade. In addition, we have scored all 58 unique morphological characters used in three previous analyses of channichthyid phylogenetic relationships. Data partitions were analyzed separately to assess the amount of phylogenetic resolution provided by each dataset, and phylogenetic incongruence among data partitions was investigated using incongruence length difference (ILD) tests. We utilized a parsimony-based version of the Shimodaira-Hasegawa test to determine if alternative tree topologies are significantly different from trees resulting from maximum parsimony analysis of the combined partition dataset. Our results demonstrate that the greatest phylogenetic resolution is achieved when all molecular and morphological data partitions are combined into a single maximum parsimony analysis. Also, marginal to insignificant incongruence was detected among data partitions using the ILD. Maximum parsimony analysis of all data partitions combined results in a single tree, and is a unique hypothesis of phylogenetic relationships in the Channichthyidae. In particular, this hypothesis resolves the phylogenetic relationships of at least two species (Channichthys rhinoceratus and Chaenocephalus aceratus), for which there was no consensus among the previous phylogenetic hypotheses. The combined data partition dataset provides substantial statistical power to discriminate among alternative hypotheses of channichthyid relationships. These findings suggest the optimal strategy for investigating the phylogenetic relationships of channichthyids is one that uses all available phylogenetic data in analyses of combined data partitions.     

Cladistic relationships of extant and fossil hominoids

There is general agreement that the hominoid primates form a monophyletic group, that the extant great apes and humans form a second clade within that group with the gibbons as the sister group, and that the African apes and humans form a third clade. Although it has recently been proposed that humans and orang utans are sister taxa and also that the great apes form a clade to the exclusion of humans, our analysis, particularly of the molecular evidence, supports the existence of an African ape and human clade. The major problem in hominoid phylogeny at present is the relationships of the species within this clade: morphological data generally support the existence of an African ape clade which is the sister group to humans; some molecular data also support this conclusion, but most molecular evidence indicates the existence of a chimpanzee/human clade. We have cladistically re-analysed the DNA and protein sequence data for which apomorphic character states can be assessed. It is clear that there is a high degree of homoplasy whichever branching pattern is produced, with some characters supporting the existence of a chimpanzee/human clade and others supporting an African ape clade. When the cladistic analyses of morphological and molecular data are combined we believe that the most parsimonious interpretation of the data is that the African apes form a clade which is the sister taxon of the human (i.e., Australopithecus, Homo and Paranthropus) clade.This paper is not intended as a survey of all hominoid fossils but as a study of branching points in hominoid evolution and fossils are included which are relevant to this branching pattern. The analysis of fossil taxa in this study leads us to conclude that Proconsul is the sister taxon to the later Hominoidea. A number of middle Miocene forms such as Dryopithecus, Kenyapithecus, Heliopithecus and Afropithecus are shown to share derived characters with great apes and humans and provide evidence for the divergence of that clade from the gibbon lineage prior to 18 Ma. The position that Sivapithecus represents the sister group of the orang utan clade is supported here and shows that the orang utan lineage had diverged from the African ape and human lineage prior to 11·5 Ma. There is unfortunately no definitive fossil cvidence on branching sequences within the African ape and human clade, although a new specimen from Samburu, Kenya may be related to the gorilla.     

Morphology matches mtDNA lineages in the southern smooth snake (Coronella girondica) from Iberia

The rise of molecular techniques in the study of evolutionary histories has resulted in a gradual abandonment of morphological characters as the only sources of phylogenetic inference. However, morphological characters may be valuable for phylogenetic reconstruction, especially for tracking adaptive changes across phylogeographic groups defined by genetic markers. We examined the discriminative power of morphological characters between four mitochondrial clades covering almost the entire distribution area of the smooth snake Coronella girondica in the Western Mediterranean. We detected three characters showing sexual dimorphism (relative tail length, number of ventral and of subcaudal scale counts) and, more interestingly, two characters (number of subcaudal and of dorsal rows) displaying interclade differences. Almost all C. girondica examined had 21 dorsal rows except those from a narrow coastal belt in the south-eastern Iberian Peninsula, which had 19 dorsal rows. The distribution of these specimens matches a mitochondrial clade that originated approximately 1.4–2.0 million years ago. Both of these morphological characters support a Betic lineage with a rather well-defined contact zone with the other Iberian lineage, which has been maintained even without the existence of current geographic barriers. The long-term survival of the Betic lineage throughout the Pleistocene climatic oscillations suggests a systematic revision within C. girondica.     

Phylogenetic relationships of functionally dioecious FICUS (Moraceae) based on ribosomal DNA sequences and morphology

Figs (Ficus, Moraceae) are either monoecious or gynodioecious depending on the arrangement of unisexual florets within the specialized inflorescence or syconium. The gynodioecious species are functionally dioecious due to the impact of pollinating fig wasps (Hymenoptera: Agaonidae) on the maturation of fig seeds. The evolutionary relationships of functionally dioecious figs (Ficus subg. Ficus) were examined through phylogenetic analyses based on the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and morphology. Forty-six species representing each monoecious subgenus and each section of functionally dioecious subg. Ficus were included in parsimony analyses based on 180 molecular characters and 61 morphological characters that were potentially informative. Separate and combined analyses of molecular and morphological data sets suggested that functionally dioecious figs are not monophyletic and that monoecious subg. Sycomorus is derived within a dioecious clade. The combined analysis indicated one or two origins of functional dioecy in the genus and at least two reversals to monoecy within a functionally dioecious lineage. The exclusion of breeding system and related characters from the analysis also indicated two shifts from monoecy to functional dioecy and two reversals. The associations of pollinating fig wasps were congruent with host fig phylogeny and further supported a revised classification of Ficus.     

Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida,Cycliophora, Plathelminthes,and Chaetognatha: a combined approach of 18S rDNA sequences and morphology

Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, which seems to happen because of the extreme distance that separates diploblastic from triploblastic taxa according to the 18S rDNA data. Multiple phylogenetic analyses performed with variable analysis parameters yield largely inconsistent results for certain groups such as Chaetognatha, Acoela, and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis having the least character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha) (Nematoda + Nematomorpha)) ((Onychophora + Tardigrada) Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda) (Entoprocta (Nemertea (Sipuncula (Mollusca (Pogonophora (Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida (Cycliophora + Syndermata)) (Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, Biol. Rev. 73:203-266, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (= Gnathifera), which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.     

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.     

Diversification of inflorescence development in the PCK clade (Poaceae: Panicoideae: Paniceae)

In grasses, inflorescence diversification and its correlation with species evolution are intriguing and not well understood. Part of this problem lies in our lack of comprehension about the inflorescence morphological complexity of grasses. We focused our study on the PCK clade (named for phosphoenol pyruvate carboxykinase), a well-supported monophyletic group for which the relationships among its taxa are not well resolved. Interestingly, the PCK clade has an extensive diversity of adult inflorescence forms. A comparative developmental approach can help us to understand the basis of such morphological differences as well as provide characters that can be used in phylogenetic studies of the group. Using SEM studies, we demonstrate that inflorescence morphology in this clade is even more complex than what is typically observed in adult forms. We describe a number of new characters, and some classical features previously used for taxonomic purposes are redefined on the basis of development. We also define four morphological groups combining adult inflorescence form and development, and we discuss some of the evolutionary aspects of inflorescence diversification in the PCK clade. Taxonomic delimitation among genera in the PCK clade remains confusing and unclear where molecular and morphological studies support different classifications.