No longer Demospongiae: Homoscleromorpha formal nomination as a fourth class of Porifera

Over the past few years, there has been growing interest among the sponge community in the phylogenetic position of the Homoscleromorpha (i.e. within or outside the class Demospongiae). Recent molecular analyses clearly show that the Homoscleromorpha forms a distinct clade separated from the Demospongiae and is composed of two families, Oscarellidae and Plakinidae. Within the currently more widely accepted hypothesis of a monophyletic Porifera, we formally propose here to raise Homoscleromorpha to the class rank (the fourth one). We, therefore, provide a definition and a formal diagnosis. In the supplementary materials, we also present an alternative classification of the Homoscleromorpha, following the PhyloCode.     

Inferring the ancestral sexuality and reproductive condition in sponges (Porifera)

Considerable diversity abounds among sponges with respect to reproductive and developmental biology. Their ancestral sexual mode (gonochorism vs. hermaphroditism) and reproductive condition (oviparity vs. viviparity) however remain unclear, and these traits appear to have undergone correlated evolution in the phylum. To infer ancestral traits and investigate this putative correlation, we used DNA sequence data from two loci (18S ribosomal RNA and cytochrome c oxidase subunit I) to explore the phylogenetic relationships of 62 sponges whose reproductive traits have been previously documented. Although the inferred tree topologies, using the limited data available, favoured paraphyly of sponges, we also investigated ancestral character‐state reconstruction on a phylogeny with constrained sponge monophyly. Both parsimony‐ and likelihood‐based ancestral state reconstructions indicate that viviparity (brooding) was the likely reproductive mode of the ancestral sponge. Hermaphroditism is favoured over gonochorism as the sexual condition of the sponge ancestor under parsimony, but the reconstruction is ambiguous under likelihood, rendering the ancestry of sexuality unresolved in our study. These results are insensitive to the constraint of sponge monophyly when tracing the reproductive characters using parsimony methods. However, the maximum likelihood analysis of the monophyletic hypothetical tree rendered gonochorism as ancestral for the phylum. A test of trait correlation unambiguously favours the concerted evolution of sexuality and reproductive mode in sponges (hermaphroditism/viviparity, gonochorism/oviparity). Although testing ecological hypotheses for the pattern of sponge reproduction is beyond the scope of our analyses, we postulate that certain physiological constrains might be key causes for the correlation of reproductive characters.     

DID EGG‐LAYING BOAS BREAK DOLLO'S LAW? PHYLOGENETIC EVIDENCE FOR REVERSAL TO OVIPARITY IN SAND BOAS (ERYX: BOIDAE)

Re-evolution of lost complex morphological characters has been proposed for several characters, including insect wings, limbs, eyes in snakes, and digits in lizards, among others. There has also been much interest in whether the transition from oviparity to viviparity is reversible, particularly in squamate reptiles where the transition to viviparity has occurred more times than in any other lineage. Here, we present a phylogenetic analysis of boid snakes based on a concatenated multigene study of all genera of erycines, New and Old World boines, plus other groups thought to be closely related with boines such as monotypic species Calabaria and Casarea . We reconstruct ancestral parity mode on this phylogeny and present statistical evidence that oviparity reevolved in a species of Old World sand boa in the genus Eryx nearly 60 million years after the initial boid transition to viviparity. Remarkably, like other viviparous boas hatchlings of oviparous Eryx lack an egg-tooth providing independent evidence that oviparity is a derived state in these species.     

Phylogeny and evolution of glass sponges (porifera, hexactinellida)

Reconstructing the phylogeny of sponges (Porifera) is one of the remaining challenges to resolve the metazoan Tree of Life and is a prerequisite for understanding early animal evolution. Molecular phylogenetic analyses for two of the three extant classes of the phylum, Demospongiae and Calcarea, are largely incongruent with traditional classifications, most likely because of a paucity of informative morphological characters and high levels of homoplasy. For the third class, Hexactinellida (glass sponges)--predominantly deep-sea inhabitants with unusual morphology and biology--we present the first molecular phylogeny, along with a cladistic analysis of morphological characters. We collected 18S, 28S, and mitochondrial 16S ribosomal DNA sequences of 34 glass sponge species from 27 genera, 9 families, and 3 orders and conducted partitioned Bayesian analyses using RNA secondary structure-specific substitution models (paired-sites models) for stem regions. Bayes factor comparisons of different paired-sites models against each other and conventional (independent-sites) models revealed a significantly better fit of the former but, contrary to previous predictions, the least parameter-rich of the tested paired-sites models provided the best fit to our data. In contrast to Demospongiae and Calcarea, our rDNA phylogeny agrees well with the traditional classification and a previously proposed phylogenetic system, which we ascribe to a more informative morphology in Hexactinellida. We find high support for a close relationship of glass sponges and Demospongiae sensu stricto, though the latter may be paraphyletic with respect to Hexactinellida. Homoscleromorpha appears to be the sister group of Calcarea. Contrary to most previous findings from rDNA, we recover Porifera as monophyletic, although support for this clade is low under paired-sites models.     

MITOCHONDRIAL DNA SEQUENCE-BASED PHYLOGENY AND THE EVOLUTION OF VIVIPARITY IN THE SCELOPORUS SCALARIS GROUP (REPTILIA,SQUAMATA)

The lizard genus Sceloporus contains both oviparous and viviparous species. The scalaris complex is the only monophyletic group within the genus that includes both reproductive modes, thus it is particularly well suited for studies of the evolution of viviparity. Approximately 874 nucleotides of mtDNA sequence data, collected from 38 specimens, comprising 25 populations of all five recognized species within the group, were used in a phylogenetic analysis of the origin of viviparity. Viviparity appears to have evolved twice in this group: once in S. goldmani, included in a clade formed by a northern group consisting of S. scalaris, S. chaneyi, and S. goldmani, and one more time in S. bicanthalis, included in the southern group formed by S. bicanthalis and S. aeneus. An oviparous population of S. bicanthalis nested within that viviparous clade, indicates that reversal from viviparity to oviparity may be possible. Degree of sequence divergence among several S. bicanthalis individuals pertaining to a population in which both parity modes occur, was no larger between oviparous and viviparous lizards than among viviparous lizards. This suggests that this population is a single species, and it may represent a transition from oviparity to viviparity or vice-versa.     

Interleukin‐1 in reproductive strategies

SUMMARY Evolutionary studies on different classes of vertebrates could help clarify the role of cytokines in acceptance of the embryo by the maternal tissues. This review focuses on the cytokine interleukin‐1 (IL‐1) and reports on its presence in the female reproductive tract of species with different reproductive strategies, that is, viviparity, oviparity, and ovuliparity. Unlike oviparity and viviparity, ovuliparity does not involve any contact between paternal‐derived fetal antigens and maternal tissues, because eggs are released unfertilized in the external environment. Therefore, we consider ovuliparity a natural negative control for mechanisms of materno‐fetal immunotolerance. The goal of this review is to discuss the role of the IL‐1 system in the acquisition of the ability to retain the embryo in the female genital tract during the transition from ovuliparity to viviparity.     

Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classification

The infraorder Thalassinidea is a group of cryptic marine burrowing decapods of which the higher taxonomy is often contentious. The present analysis attempts to reconstruct phylogenetic relationship among 12 of the 13 currently recognized families using partial nuclear 18S, 28S rDNA and mitochondrial 16S rDNA sequences. The infraorder is divided into two distinct clades, with the first clade consisting of Thalassinidae, Laomediidae, Axianassidae and Upogebiidae, and the second clade including Axiidae, Calocarididae, Eiconaxiidae, Callianassidae, Ctenochelidae, Micheleidae, Strahlaxiidae and Callianideidae. Within the first clade, the Upogebiidae is the basal family. The Axianassidae shows low affinity to other laomediid genera indicating that it is a valid family. The interfamilial relationships are less well resolved in the second clade. The Axiidae is paraphyletic with respect to Calocarididae and Eiconaxiidae. Thus, the status of these two latter families is not supported if the currently defined Axiidae is maintained. All three families appear to be basal in the thalassinidean clade. The Micheleidae is closely related to the Callianideidae and they form a sister group to the Strahlaxiidae. The monophyletic Callianassidae aligns with the Micheleidae + Callianideidae + Strahlaxiidae clade. The relationship among the Axiidae + Calocarididae + Eiconaxiidae clade, Callianassidae + Micheleidae + Callianideidae + Strahlaxiidae clade and the Ctenochelidae cannot be resolved which might be due to a rapid radiation of the three lineages. Our results do not support the generally used classification scheme of Thalassinidea and suggest that the infraorder might be divided into two superfamilies instead of three as suggested based on larval morphology, second pereiopod morphology in adults and gastric mill structure. The two superfamilies are Thalassinoidea (i.e. Thalassinidae, Laomediidae, Upogebiidae and Axianassidae) and Callianassoidea (i.e. Axioidea + Callianassoidea, as defined in Martin and Davis (2001) but excluding Laomediidae and Upogebiidae). It also appears that gill‐cleaning adaptations are important in thalassinidean evolution while the presence of linea thalassinica is a result of parallel evolution.     

REPTILIAN VIVIPARITY AND DOLLO'S LAW

It has been suggested repeatedly that the evolutionary transition from oviparity (egg-laying) to viviparity (live-bearing) in reptiles is irreversible. However, these adaptive arguments have yet to be tested by detailed examination of the phylogenetic distribution of oviparity and viviparity across a broad range of taxa. Using available data on reproductive modes and phylogenetic relationships within reptiles, we here quantify the numbers and directions of evolutionary transitions between oviparity and viviparity. Phylogenetic relationships among three diverse squamate groups (scincid lizards, colubrid snakes, elapid snakes) are currently inadequately known for inclusion in this study Among the remaining reptiles, oviparity has given rise to viviparity at least 35 times. Five possible instances of reversals (from viviparity to oviparity) are identified, but closer examination indicates that all have weak empirical support (i.e., they could be “unreversed” with little loss in parsimony, and/or are based on poorly substantiated phylogenetic hypotheses). Viviparity is clearly more frequently (and presumably easily) gained than lost in several disparate groups so far examined (reptiles, fishes, polychaete worms); this evolutionary bias should be considered when reproductive mode is optimized on a phylogeny or employed in phylogenetic reconstruction.     

Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida)

Newly emerging molecular phylogenetic hypotheses involving the sponge Order Haplosclerida (Class Demospongiae) are far removed from traditional views on their classification using morphology. In the new grouping of marine haplosclerid taxa by molecular data all members of one highly supported clade were found to have three large indels in the 18S rRNA gene. These indels were not found in this gene in other marine haplosclerids or in any other demosponges analysed. These indels were found in the variable V4 and V7 region of the gene, had high GC contents and formed stable double stranded helices in the 18S rRNA secondary structure. These indels are very important synapomorphies, provide high support for an alternative taxonomic scheme and could help resolve the phylogeny of this order in conjunction with other phylogenetically informative characters.     

Life‐history strategies indicate live‐bearing in Nothosaurus (Sauropterygia)

In Sauropterygia, a diverse group of Mesozoic marine reptiles, fossil evidence of viviparity (live‐bearing) only exists for Pachypleurosauria and Plesiosauria, and was assumed to also be the case for nothosaurs. Previous studies have successfully applied an extant squamate model to sauropterygian life‐history traits. In extant squamates, oviparity and viviparity are associated with differences in life‐history trait combinations. We establish growth curves for Nothosaurus specimens based on their humeral histology. We then analyse life‐history traits derived from these curves and compare inferred traits to those of modern squamates and pachypleurosaurs to assess their reproduction mode. We show that birth to adult size ratios (i.e. birth size divided by the mother's size) provide good estimates of clutch sizes in extant squamates and in viviparous extinct marine reptiles, but these ratios cannot discriminate viviparous and oviparous squamates. Thus, large ratios do not indicate viviparity in fossil taxa to which the extant squamate model is applicable. Applying differences in birth size, age at maturation, and maximum longevity that are observed between extant viviparous and oviparous squamates to our Nothosaurus sample, we identified 7 out of 24 specimens as being potentially viviparous. Conversely, they suggested oviparity for many nothosaurs but also for many pachypleurosaur samples. Under the assumption that the entire clade Pachypleurosauria was viviparous, the majority of nothosaurs would also have been viviparous as they comprised trait combinations similar to those seen in pachypleurosaurs. Overall, this suggests that within nothosaurs and pachypleurosaurs both reproduction modes existed in different taxa.     

Congruence between nuclear and mitochondrial genes in Demospongiae: a new hypothesis for relationships within the G4 clade (Porifera: Demospongiae)

The current morphological classification of the Demospongiae G4 clade was tested using large subunit ribosomal RNA (LSU rRNA) sequences from 119 taxa. Fifty-three mitochondrial cytochrome oxidase 1 (CO1) barcoding sequences were also analysed to test whether the 28S phylogeny could be recovered using an independent gene. This is the largest and most comprehensive study of the Demospongiae G4 clade. The 28S and CO1 genetrees result in congruent clades but conflict with the current morphological classification. The results confirm the polyphyly of Halichondrida, Hadromerida, Dictyonellidae, Axinellidae and Poecilosclerida and show that several of the characters used in morphological classifications are homoplasious. Robust clades are clearly shown and a new hypothesis for relationships of taxa allocated to G4 is proposed.     

THE EVOLUTION OF OVIPARITY WITH EGG GUARDING AND VIVIPARITY IN LIZARDS AND SNAKES: A PHYLOGENETIC ANALYSIS

This paper investigates the evolution of viviparity and of egg guarding in lizards and snakes in which three modes of reproduction can be described: oviparity without egg guarding, oviparity with egg guarding, and viviparity. All possible transitions of reproductive modes were detected in each taxon using Maddison's method. We then tested two specific hypotheses. First, egg guarding can be regarded as an alternative to viviparity. A relatively frequent association of egg guarding and viviparous species in the same taxon may be due to similar environmental conditions or species characteristics leading to two different solutions. Second, egg guarding may facilitate the evolution of viviparity. This hypothesis is supported by the high frequency of viviparous species in taxa containing egg guarding species and by a tendency for prolonged uterine retention of eggs in brooding squamates. Our analyses demonstrate that the first hypothesis is the best supported. Egg guarding and viviparity most often evolved independently. If a major benefit of egg guarding is the repulsion of potential predators, size is one of the most obvious morphological characters that should be correlated with the evolution of reproductive modes. The two reproductive traits were correlated to a reduction in body size for viviparous species and an increase in body size for egg guarding species. This could partly explain why the evolution of these reproductive modes seems almost antagonist.     

Saccharomycomorpha psychra n. g., n. sp., a Novel Member of Glissmonadida (Cercozoa) Isolated from Arctic and Antarctica

A novel genus and species within the order Glissmonadida (Cercozoa, Rhizaria), Saccharomycomorpha psychra n. g., n. sp., is described from lichen in the Ny-Ålesund region (High Arctic) and moss in the Fildes peninsula of King George Island (Maritime Antarctica). Cells were spherical and did not appear to present flagella in organic-rich Potato Dextrose Agar medium where they were able to feed osmotrophically. Molecular phylogenetic analyses based on 18S rRNA gene sequence demonstrated that Saccharomycomorpha psychra belong to “clade T” within the order Glissmonadida (Cercozoa, Rhizaria). All three investigated strains could grow at 4 °C and had an optimum growth temperature of 12 °C, 20 °C, and 20 °C, while a maximum growth temperature of 20 °C, 20 °C, and 25 °C, respectively. In conclusion, we established the phenotypic identity of “clade T,” which until now was exclusively detected by environmental sequences, and erect a new family Saccharomycomorphidae for “clade T.” Nomenclatural, morphological and ecological aspects of this novel species are discussed.     

Multiple origins of viviparity,or reversal from viviparity to oviparity? The European common lizard (Zootoca vivipara,Lacertidae) and the evolution of parity

The evolution of viviparity in squamates has been the focus of much scientific attention in previous years. In particular, the possibility of the transition from viviparity back to oviparity has been the subject of a vigorous debate. Some studies have suggested this reversal is more frequent than previously thought. However, none of them provide conclusive evidence. We investigated this problem by studying the phylogenetic relationships between oviparous and viviparous lineages of the reproductively bimodal lizard species Zootoca vivipara . Our results show that viviparous populations are not monophyletic, and that several evolutionary transitions in parity mode have occurred. The most parsimonious scenario involves a single origin of viviparity followed by a reversal back to oviparity. This is the first study with a strongly supported phylogenetic framework supporting a transition from viviparity to oviparity.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 87 , 1–11.     

Adding mitochondrial sequence data (16S rRNA and cytochrome c oxidase subunit I) to the phylogeny of centipedes (Myriapoda: Chilopoda): an analysis of morphology and four molecular loci

Relationships within Chilopoda (centipedes) are assessed based on 222 morphological characters, complete 18S rRNA sequences for 70 chilopod terminals, the D3 region of 28S rRNA for 65 terminals, 16S rRNA sequences for 54 terminals and cytochrome c oxidase subunit I sequences for 45 terminals. Morphological and molecular data for seven orders of Diplopoda are used to root cladograms for Chilopoda. Analyses use direct character optimization for 15 gap and substitution models. The Pleurostigmophora and Epimorpha s.l. hypotheses are largely stable to parameter variation for the combined data; the latter clade is formalized as the new taxon Phylactometria. The combined data include parameter sets that support either the monophyly of Epimorpha s.str. (=Scolopendromorpha + Geophilomorpha) or Craterostigmus + Geophilomorpha; the former derives its support from morphology and the nuclear ribosomal genes. Monophyly of Lithobiomorpha and the sister group relationship between Lithobiidae and Henicopidae are stable for morphological and combined data, and are also resolved for the molecular data for 14 of 15 parameter sets. The fundamental split in Scolopendromorpha is between Cryptopidae and Scolopendridae sensu Attems. Blind scolopendromorphs unite as a clade in most molecular and combined analyses, including those that minimize incongruence between data partitions. Geophilomorpha divides into Placodesmata and Adesmata under nine of 15 explored parameter sets.     

Reproduction and development ofSebastes in the context of the evolution of piscine viviparity

Synopsis Selected aspects of the reproduction and development ofSebastes and other rockfishes are reviewed in the context of piscine viviparity. Among the eight subfamilies of the Scorpaenidae, viviparity is confined to the subfamily Sebastinae; gestation is lumenal and the embryos usually develop to term within the egg envelope. Transitional states from oviparity to viviparity are evident in different species within the family. A scenario for the evolutionary origin of viviparity in rockfishes is derived from an analysis of scorpaeniform reproductive biology. Although viviparity is best developed in the genusSebastes, it is still in a primitive, unspecialized state. Rockfish viviparity is essentially lecithotrophic, i.e. embryonic nutrition is dependent on the energy reserves laid down during oogenesis. In other groups of viviparous fishes, lecithotrophy has been shown to be better suited energetically to seasonally unpredictable habitats, whereas matrotrophy requires a predictable food supply. During the evolution of an essentially primitive form of lecithotrophic viviparity in rockfishes, the advantages of high fecundity associated with oviparity were retained while an enormous increase in the survival rate of the developing embryos was acquired. The basic lecithotrophic pattern of oviparous development was not changed since it offered selective advantages both in terms of energetics and as a basis for retaining a large brood size.     

Copulation and egg retention in an oviparous Caecilian (Amphibia: Gymnophiona)

Viviparity (i.e., the bearing of live young) has evolved from oviparity (egg laying) independently in various major vertebrate lineages, and several transitional stages have been described. The transition from oviparity to viviparity requires the retention of fertilised eggs in the female reproductive tract. Caecilian amphibians (Gymnophiona) display a considerable diversity of reproductive modes, including oviparity and viviparity. Among amphibians, caecilians have also modified the process of internal fertilisation through a special intromittent organ, or phallus, in males. Here we report the oviposition of “embryonated” eggs ranging from various gastrula-to-neurula stages by female Ichthyophis cf. kohtaoensis (Ichthyophiidae) from North-eastern Thailand. In addition, we describe a copulation resulting in an oviposition of embryonated eggs. Our findings will have implications for the further understanding of the evolutionary reproductive biology of amphibians.     

Morphological and molecular taxonomy of a new Daptonema (Nematoda,Xyalidae) with comments on the systematics of some related taxa

A new species of Daptonema is described based upon morphological characters and 18S rRNA sequence. Daptonema matrona sp. nov. was collected in Pina Basin (north‐eastern Brazil). It differs from all other species of the genus by the presence of reduced cephalic setae and straight spicules. These features require an adaptation of the generic diagnosis. Moreover, the females are characterized by intra‐uterine development of the offspring, considered herein as their major autapomorphic feature. Molecular systematic analyses supported Daptonema matrona sp. nov. as a distinct genetic and evolutionary lineage. The data also indicate hypotheses of taxonomic synonymies amongst some related taxa from Xyalidae as well as the paraphyly of Daptonema. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 1–15.