Systematics and spicule evolution in dictyonal sponges (Hexactinellida: Sceptrulophora) with description of two new species

In this paper we report on recently collected specimens of glass sponges belonging to Farreidae Gray, 1872, and Tretodictyidae Schulze, 1886 (Porifera: Hexactinellida: Hexactinosida). All specimens represent new geographical records for their genera: Coral Sea for Aspidoscopulia Reiswig, 2002 (Farreidae) and Psilocalyx Ijima, 1927 (Tretodictyidae); north‐west Atlantic for Sarostegia Topsent, 1904 (Farreidae). Two new species, Aspidoscopulia australia Dohrmann, Göcke & Janussen sp. nov. and Aspidoscopulia ospreya Dohrmann, Göcke & Janussen sp. nov. , are described. To investigate further the evolution of hexactinosidan sponges, we sequenced two nuclear (18S and 28S rDNA) and two mitochondrial [16S ribosomal rDNA, cytochrome oxidase subunit I (COI)] genes from these specimens, as well as from a recently described new species of Lonchiphora Ijima, 1927 (Farreidae). Besides corroborating the monophyly of Tretodictyidae, our molecular phylogenetic analyses support a clade of clavule‐bearing sponges with a farreoid dictyonal framework (i.e. Farreidae sensu stricto). In contrast, Sarostegia, which lacks these features, appears unrelated to this clade – instead our data are consistent with an earlier placement of this genus in Euretidae Zittel, 1877. We introduce formally the taxon Sceptrulophora Mehl 1992, and emend the classification of Hexactinosida to reflect this move and our new findings regarding the position of Sarostegia. Finally, we discuss implications of the molecular phylogeny for the evolution of sceptrules, the defining autapomorphy of Sceptrulophora. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1003–1025.     

Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA

Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge 'classes,' Demospongiae and Hexactinellida. The division of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon sampling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.     

Evidence of constrained phenotypic evolution in a cryptic species complex of agamid lizards

Lineages that exhibit little morphological change over time provide a unique opportunity to explore whether nonadaptive or adaptive processes explain the conservation of morphology over evolutionary time scales. We provide the most comprehensive evaluation to date of the evolutionary processes leading to morphological similarity among species in a cryptic species complex, incorporating two agamid lizard species (Diporiphora magna and D. bilineata). Phylogenetic analysis of mitochondrial (ND2) and nuclear (RAG-1) gene regions revealed the existence of eight deeply divergent clades. Analysis of morphological data confirmed the presence of cryptic species among these clades. Alternative evolutionary hypotheses for the morphological similarity of species were tested using a combination of phylogenetic, morphological, and ecological data. Likelihood model testing of morphological data suggested a history of constrained phenotypic evolution where lineages have a tendency to return to their medial state, whereas ecological data showed support for both Brownian motion and constrained evolution. Thus, there was an overriding signature of constrained evolution influencing morphological divergence between clades. Our study illustrates the utility of using a combination of phylogenetic, morphological, and ecological data to investigate evolutionary mechanisms maintaining cryptic species.     

Rates of morphological evolution are correlated with species richness in salamanders

The tempo and mode of species diversification and phenotypic evolution vary widely across the tree of life, yet the relationship between these processes is poorly known. Previous tests of the relationship between rates of phenotypic evolution and rates of species diversification have assumed that species richness increases continuously through time. If this assumption is violated, simple phylogenetic estimates of net diversification rate may bear no relationship to processes that influence the distribution of species richness among clades. Here, we demonstrate that the variation in species richness among plethodontid salamander clades is unlikely to have resulted from simple time-dependent processes, leading to fundamentally different conclusions about the relationship between rates of phenotypic evolution and species diversification. Morphological evolutionary rates of both size and shape evolution are correlated with clade species richness, but are uncorrelated with simple estimators of net diversification that assume constancy of rates through time. This coupling between species diversification and phenotypic evolution is consistent with the hypothesis that clades with high rates of morphological trait evolution may diversify more than clades with low rates. Our results indicate that assumptions about underlying processes of diversity regulation have important consequences for interpreting macroevolutionary patterns.     

Integrative taxonomy of calcareous sponges (subclass Calcinea) from the Peruvian coast: morphology,molecules, and biogeography

Understanding of evolution and systematics of Calcarea (Porifera) have not yet met a corresponding increase in the knowledge of diversity and distribution of these sponges in several parts of the world. Peru is an emblematic example of this lack of taxonomic knowledge, as only three shallow‐water species of sponges have hitherto been reported from its 3000 km coast. With the aim of studying sponges of Peru, an integrative taxonomy approach (morphology, molecules, and biogeography) was used in order to achieve sound species identifications. The first findings of Peruvian calcareous sponges are presented here. Eight species are described in the subclass Calcinea, of which five are new to science. The retrieved biogeographical patterns are either locally endemic, widespread, or discontinuous over large areas. Clathrina antofagastensis was previously known from Chile, while C. aurea and Ernstia tetractina had been reported from the Atlantic (Brazil), and thus represent the first genetically confirmed tropical amphi‐American distributions of species not yet found on both sides of the Isthmus of Panama. Our results reveal a richer Tropical East Pacific sponge fauna than the Warm Temperate South‐Eastern Pacific one. © 2015 The Linnean Society of London     

Ultrastructure and embryonic development of a syconoid calcareous sponge

Abstract. Recent molecular data suggest that the Porifera is paraphyletic (Calcarea+Silicea) and that the Calcarea is more closely related to the Metazoa than to other sponge groups, thereby implying that a sponge‐like animal gave rise to other metazoans. One ramification of these data is that calcareous sponges could provide clues as to what features are shared among this ancestral metazoan and higher animals. Recent studies describing detailed morphology in the Calcarea are lacking. We have used a combination of microscopy techniques to study the fine structure of Syconcoactum Urban 1905, a cosmopolitan calcareous sponge. The sponge has a distinct polarity, consisting of a single tube with an apically opening osculum. Finger‐like chambers, several hundred micrometers in length, form the sides of the tube. The inner and outer layers of the chamber wall are formed by epithelia characterized by apical–basal polarity and occluding junctions between cells. The outer layer—the pinacoderm—and atrial cavity are lined by plate‐like cells (pinacocytes), and the inner choanoderm is lined by a continuous sheet of choanocytes. Incurrent openings of the sponge are formed by porocytes, tubular cells that join the pinacoderm to the choanoderm. Between these two layers lies a collagenous mesohyl that houses sclerocytes, spicules, amoeboid cells, and a progression of embryonic stages. The morphology of choanocytes and porocytes is plastic. Ostia were closed in sponges that were vigorously shaken and in sponges left in still water for over 30 min. Choanocytes, and in particular collar microvilli, varied in size and shape, depending on their location in the choanocyte chamber. Although some of the odd shapes of choanocytes and their collars can be explained by the development of large embryos first beneath and later on top of the choanocytes, the presence of many fused collar microvilli on choanocytes may reflect peculiarities of the hydrodynamics in large syconoid choanocyte chambers. The unusual formation of a hollow blastula larva and its inversion through the choanocyte epithelium are suggestive of epithelial rather than mesenchymal cell movements. These details illustrate that calcareous sponges have characteristics that allow comparison with other metazoans—one of the reasons they have long been the focus of studies of evolution and development.     

Relatedness, phylogeny, and evolution of the fungi

Recent advances in fungal systematics are reviewed in relation to our previous studies. The usefulness of the integrated analysis of genotypic (especially 18S rRNA gene sequence comparisons) and phenotypic (especially ultrastructural and chemotaxonomic data) characters has been emphasized for the major groups and selected taxa of the fungi, and the impact to fungal systematics and evolution is discussed. Our noteworthy studies and findings are: 1) polyphyly of the chytridiomycetes and zygomycetes, 2) phylogenetic origin of the entomophthoralean fungi includingBasidiobolus, 3) detection of a major new lineage “Archiascomycetes,” comprisingTaphrina, Protomyces andSaitoella, Schizosaccharomyces, andPneumocystis, within the Ascomycota, and its phylogenetic and evolutionary significance, 4) polyphyletic origins of species in the anamorphic genusGeosmithia, and 5) phylogenetic placement ofMixia osmundae, species correctly and incorrectly assigned to the genusTaphrina, and basidiomyceotus yeasts. The newest 18S rDNA sequence-based neighbor-joining trees of the Ascomycota are demonstrated. “Traditional studies of evolution have amply demonstrated that evolution at the phenotypic level is characterized by adaptation and opportunism, irregularity in pace, and inequality of rates among lineages. In contrast, studies of molecular evolution have revealed quite different features characterized by changes that are conservative in nature, random in pattern (independent of phenotypic characters), and quite regular in pace with equal rates among diverge [sic] lineages for a given protein”. (Kimura, M. 1983. The neutral theory of molecular evolution, pp. 308–309, Cambridge University Press, Cambridge.) Recipient of the 2nd Mycological Society of Japan's Excellent Achievement Award, 1998; the awarding lecture was given at the 42nd Annual Meeting of the Mycological Society of Japan, 16 May, 1998, Kyoto University, Kyoto. This review is based mainly on the publications intended for the Award.     

Cyathophycus and the origin of demosponges

The relationships between the poriferan classes are currently obscure. Molecular phylogenies appear to be reaching a consensus that the hexactinellids and demosponges are closely related, despite previous attempts to separate the Hexactinellida from other sponges on cytological grounds, but the details of the transition are unknown. Similarities of spicule morphology and structure are used to infer that the transition probably occurred after the onset of silicification, and should therefore be seen in fossils. The similarity between protosponges and early demosponges has been noted previously, based largely on a thin, reticulated wall of simple spicules (monaxons in Leptomitus, stauracts in Protospongia). A close relationship is, however, unlikely, since the protospongiids possessed a precise geometric arrangement of multiple spicule size orders that is lacking in demosponges. A close morphological similarity exists between the skeletons of transitional protosponge-dictyosponge reticulosids, such as Cyathophycus, and the early hazeliid demosponges. The inner spicule layer of primitive dictyosponges consists of a cross-hatched array of fine monaxons, as seen in the wall of some simple hazeliids. Although most described species of hazeliids were morphologically complex, a simple globose species is here recorded from the Caradoc of Wales. The evolutionary link between the classes is suggested to lie within the dictyospongioid and hazeliid lineages. Although the direction of evolution cannot be certainly fixed, it is conceptually much easier to derive the demosponges from the hexactinellids, rather than vice versa.     

Phylogenetic analysis and the evolution of queen number in eusocial Hymenoptera

Analyses of the evolution of colony queen number in eusocial insects have generally been conducted without specific reference to phylogenetic relationships, leading to incomplete evolutionary explanations for this key attribute of social organization. Consideration of queen number in a phylogenetic context in the highly eusocial Hymenoptera reveals that its evolution has been very conservative in the bees but that it is a highly labile character in most ants. The wasps appear intermediate in this respect, with some large and widespread clades characterized by little or no phylogenetic variability in queen number. This hierarchy of phylogenetic lability suggests that while ant populations may often be responsive to selection on colony queen number linked with local ecology, bees and wasps appear less responsive in this regard, with a significant element of phylogenetic conservatism involved in the expression of this social trait in the latter two groups.     

Phylogenetic network and physicochemical properties of nonsynonymous mutations in the protein-coding genes of human mitochondrial DNA

Theories on molecular evolution predict that phylogenetically recent nonsynonymous mutations should contain more non-neutral amino acid replacements than ancient mutations. We analyzed 840 complete coding-region human mitochondrial DNA (mtDNA) sequences for nonsynonymous mutations and evaluated the mutations in terms of the physicochemical properties of the amino acids involved. We identified 465 distinct missense and 6 nonsense mutations. 48% of the amino acid replacements changed polarity, 26% size, 8% charge, 32% aliphaticity, 13% aromaticity, and 44% hydropathy. The reduced-median networks of the amino acid changes revealed relatively few differences between the major continent-specific haplogroups, but a high variation and highly starlike phylogenies within the haplogroups. Some 56% of the mutations were private, and 25% were homoplasic. Nonconservative changes were more common than expected among the private mutations but less common among the homoplasic mutations. The asymptotic maximum of the number of nonsynonymous mutations in European mtDNA was estimated to be 1,081. The results suggested that amino acid replacements in the periphery of phylogenetic networks are more deleterious than those in the central parts, indicating that purifying selection prevents the fixation of some alleles.     

Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes

Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.     

Sexual selection uncouples the evolution of brain and body size in pinnipeds

The size of the vertebrate brain is shaped by a variety of selective forces. Although larger brains (correcting for body size) are thought to confer fitness advantages, energetic limitations of this costly organ may lead to trade-offs, for example as recently suggested between sexual traits and neural tissue. Here, we examine the patterns of selection on male and female brain size in pinnipeds, a group where the strength of sexual selection differs markedly among species and between the sexes. Relative brain size was negatively associated with the intensity of sexual selection in males but not females. However, analyses of the rates of body and brain size evolution showed that this apparent trade-off between sexual selection and brain mass is driven by selection for increasing body mass rather than by an actual reduction in male brain size. Our results suggest that sexual selection has important effects on the allometric relationships of neural development.     

First reported occurrence of wewokellid sponges (Calcarea, Heteractinida) from the Permian of central Iran

The new calcisponges Regispongia fluegeli n. sp., and Iranospongia circulara n. gen. n. sp., are described from central Iran. These are the first heteractinid sponges reported from the Permian of the region. These wewokellid sponges are large, irregularly cylindrical forms with a distinct axial spongocoel. The calcareous spicular skeletons of both taxa have been overgrown and are recrystallized. However, the preserved skeleton of Regispongia fluegeli does include large polyactines in the main endosomal layer and small octactines and possibly other polyactine spicules in both the relatively massive dermal layer and the distinct, delicately spiculed, gastral layer. Iranospongia is characterized by a discontinuous ring of vertical exhalant canals interior to the dense dermal layer, and by an interior skeleton net that includes common coarse vertical fibers. Individual spicules in Iranospongia are commonly obscured, but locally some remnants of possible polyactines occur in outer parts of the skeleton.     

Phylogenetic significance of the pseudoparaphyses in Loculoascomycete taxonomy

The ontogeny of the ascostroma, in particular the centrum structures, has always been regarded as an important criterion in the subdivision of the Loculoascomycetideae (ascomycetous fungi). However, the use of pseudoparaphysis type, cellular or trabeculate, to classify taxa at the ordinal level has been contentious due to the lack of information about their evolution. To determine the phylogenetic significance of the pseudoparaphysis and its variants, DNA sequences of the 18S nuclear rRNA genes from representatives of the orders Pleosporales and Melanommatales were obtained and analyzed. Species with pseudoparaphyses formed a monophyletic group with high statistical confidence. The monophyly of a distinct lineage of species with cellular pseudoparaphyses (the order Pleosporales) is rejected. Likewise, monophyly of a distinct lineage of species with trabeculate pseudoparaphyses (the order Melanommatales) is rejected also. The Pleosporales and Melanommatales are, therefore, not natural orders. The Lophiostomataceae, Phaeosphaeriaceae, and Melanommataceae are most probably polyphyletic, as is the genus Massarina.     

Evidence for spicule homology in calcareous and siliceous sponges: biminerallic spicules in Lenica sp. from the Early Cambrian of South China

Botting, J.P., Muir, L.A., Xiao, S., Li, X. & Lin, J.‐P. 2012: Evidence for spicule homology in calcareous and siliceous sponges: biminerallic spicules in Lenica sp. from the Early Cambrian of South China. Lethaia, Vol. 45, pp. 463–475. The relationships of the extant sponge classes, and the nature of the last common ancestor of all sponges, are currently unclear. Early sponges preserved in the fossil record differ greatly from extant taxa, and therefore information from the fossil record is critical for testing hypotheses of sponge phylogenetic relationships that are based on modern taxa. New specimens of the enigmatic sponge Lenica sp., from the Early Cambrian Hetang Biota of South China, exhibit an unusual spicule structure. Each spicule consists of a siliceous core with an axial canal, an organic outer layer and a middle layer interpreted to have been originally calcium carbonate. This finding confirms previous work suggesting the existence of biminerallic spicules in early sponges. Combined with data from other early sponges, the new findings imply that the two fundamental spicule structures of modern sponges were derived from a compound, biminerallic precursor. Spicules are therefore homologous structures in Calcarea and Silicea, and if sponges are paraphyletic with respect to Eumetazoa, then spicules may also have been a primitive feature of Metazoa. □Calcarea, Early Cambrian, Hetang Biota, phylogeny, Silicea, taphonomy.