Molecular evolution of the small subunit ribosomal DNA in woodlice (Crustacea, Isopoda, Oniscidea) and implications for Oniscidean phylogeny

Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods

Among the few crustacean taxa that managed to inhabit terrestrial environments, Oniscidea includes the most successful colonizers in terms of species richness and abundance. However, neither morphological traits nor molecular markers have definitively resolved phylogenetic relationships among major Oniscidea clades or established the monophyly of the taxon. Herein, we employed the highly conserved, nuclear protein-coding genes Sodium-Potassium Pump (NAK) and Phosphoenolpyruvate Carboxykinase (PEPCK), along with the traditionally used 18 s and 28 s ribosomal RNA genes, in an attempt to clarify these questions. Our dataset included sequences representing all major Oniscidea clades and closely related aquatic taxa, as suggested by previous studies. We applied Bayesian Inference and Maximum Likelihood methods and produced a robust and fully resolved phylogenetic tree that offers strong evidence against the monophyly of Oniscidea. The amphibious genus Ligia appears to be more closely related to representatives of marine suborders, while the phylogenetic pattern of the remaining Oniscidea implies a complex history of the transition from the marine environment to land. With the exception of the basal clade, all other established major clades have been recovered as monophyletic, even though relationships within these clades call for a revised interpretation of morphological characters used in terrestrial isopod taxonomy.

A molecular phylogeny of Porcellionidae (Isopoda, Oniscidea) reveals inconsistencies with present taxonomy

Porcellionidae is one of the richest families of Oniscidea globally distributed but we still lack a comprehensive and robust phylogeny of the taxa that are assigned to it. Employing five genetic markers (two mitochondrial and three nuclear) we inferred phylogenetic relationships among the majority of Porcellionidae genera. Phylogenetic analyses conducted via Maximum Likelihood and Bayesian Inference resulted in similar tree topologies. The mtDNA genes cytochrome oxidase I (COI) and 16s rRNA (16s) were used for clade dating using previously published mutation rates. Our results provide evidence against the monophyly of both Porcellionidae and the largest genus of the family Porcellio. These results are compared to previous published work based on morphological evidence. The genera Leptotrichus and Brevurus are not grouped with the rest of Porcellionidae whereas Agnaridae are grouped with part of Porcellionidae. Armadillidium and Schizidium (Armadillidiidae) occupy a basal position on the phylogenetic tree. Even though the African genera Tura and Uramba (distributed in East Africa) are grouped together there is no general geographical pattern in other sub-clades. Additional taxonomic issues that arise in this work such as the assignment of the recently described genus Levantoniscus, arealso discussed. The status of Porcellionidae should be further revised and morphological characters traditionally used in Oniscidea taxonomy should be reconsidered in view of molecular evidence. The origin of the monophyletic clade within Porcellionidae as indicated in the present work is dated back to the Oligocene (~32 mya).

Diversity and evolution of sex determination systems in terrestrial isopods

Sex determination systems are highly variable in many taxa, sometimes even between closely related species. Yet the number and direction of transitions between these systems have seldom been characterized, and the underlying mechanisms are still poorly understood. Here we generated transcriptomes for 19 species of terrestrial isopod crustaceans, many of which are infected by Wolbachia bacterial endosymbionts. Using 88 single-copy orthologous genes, we reconstructed a fully resolved and dated phylogeny of terrestrial isopods. An original approach involving crossings of sex-reversed individuals allowed us to characterize the heterogametic systems of five species (one XY/XX and four ZW/ZZ). Mapping of these and previously known heterogametic systems onto the terrestrial isopod phylogeny revealed between 3 and 13 transitions of sex determination systems during the evolution of these taxa, most frequently from female to male heterogamety. Our results support that WW individuals are viable in many species, suggesting sex chromosomes are at an incipient stage of their evolution. Together, these data are consistent with the hypothesis that nucleo-cytoplasmic conflicts generated by Wolbachia endosymbionts triggered recurrent turnovers of sex determination systems in terrestrial isopods. They further establish terrestrial isopods as a model to study evolutionary transitions in sex determination systems and pave the way to molecularly characterize these systems.

Matrotrophy and placentation in invertebrates: a new paradigm

Matrotrophy, the continuous extra-vitelline supply of nutrients from the parent to the progeny during gestation, is one of the masterpieces of nature, contributing to offspring fitness and often correlated with evolutionary diversification. The most elaborate form of matrotrophy-placentotrophy-is well known for its broad occurrence among vertebrates, but the comparative distribution and structural diversity of matrotrophic expression among invertebrates is wanting. In the first comprehensive analysis of matrotrophy across the animal kingdom, we report that regardless of the degree of expression, it is established or inferred in at least 21 of 34 animal phyla, significantly exceeding previous accounts and changing the old paradigm that these phenomena are infrequent among invertebrates. In 10 phyla, matrotrophy is represented by only one or a few species, whereas in 11 it is either not uncommon or widespread and even pervasive. Among invertebrate phyla, Platyhelminthes, Arthropoda and Bryozoa dominate, with 162, 83 and 53 partly or wholly matrotrophic families, respectively. In comparison, Chordata has more than 220 families that include or consist entirely of matrotrophic species. We analysed the distribution of reproductive patterns among and within invertebrate phyla using recently published molecular phylogenies: matrotrophy has seemingly evolved at least 140 times in all major superclades: Parazoa and Eumetazoa, Radiata and Bilateria, Protostomia and Deuterostomia, Lophotrochozoa and Ecdysozoa. In Cycliophora and some Digenea, it may have evolved twice in the same life cycle. The provisioning of developing young is associated with almost all known types of incubation chambers, with matrotrophic viviparity more widespread (20 phyla) than brooding (10 phyla). In nine phyla, both matrotrophic incubation types are present. Matrotrophy is expressed in five nutritive modes, of which histotrophy and placentotrophy are most prevalent. Oophagy, embryophagy and histophagy are rarer, plausibly evolving through heterochronous development of the embryonic mouthparts and digestive system. During gestation, matrotrophic modes can shift, intergrade, and be performed simultaneously. Invertebrate matrotrophic adaptations are less complex structurally than in chordates, but they are more diverse, being formed either by a parent, embryo, or both. In a broad and still preliminary sense, there are indications of trends or grades of evolutionarily increasing complexity of nutritive structures: formation of (i) local zones of enhanced nutritional transport (placental analogues), including specialized parent-offspring cell complexes and various appendages increasing the entire secreting and absorbing surfaces as well as the contact surface between embryo and parent, (ii) compartmentalization of the common incubatory space into more compact and 'isolated' chambers with presumably more effective nutritional relationships, and (iii) internal secretory ('milk') glands. Some placental analogues in onychophorans and arthropods mimic the simplest placental variants in vertebrates, comprising striking examples of convergent evolution acting at all levels-positional, structural and physiological.

Patterns of taxonomic diversity among terrestrial isopods

The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics.

Molecular phylogenetic analyses reveal a new southern hemisphere oniscidean family (Crustacea : Isopoda) with a unique water transport system

A significant diversity of terrestrial oniscidean isopods was recently discovered in the subterranean ‘calcrete islands’ of Western Australia, but the species and higher-level systematic status of much of the fauna are currently uncertain. Here we focus on one group of species that was initially assigned to the genus Trichorhina (Platyarthridae), based on several shared characters, and investigate the phylogenetic relationships of these species to 21 oniscidean genera, including 13 known families, using 18S rDNA sequence data. We then present phylogenetic analyses using 28S-only and combined 18S, 28S rDNA and mitochondrial cytochrome c oxidase subunit I (COI) data for a more restricted sampling of taxa, and present results for a detailed morphological study of the antennae and other cephalic structures of exemplar taxa. Bayesian and maximum likelihood analyses of the extended 18S-only, the 28S-only and multi-gene datasets provide strong evidence for a distinct well-supported monophyletic group comprising the new Western Australian and one South American taxon. This clade is unrelated to all included members of Platyarthridae, which appears to be polyphyletic, and it forms a distinct group relative to other oniscidean families. Given these findings and the results of the morphological study, a new southern hemisphere oniscidean family, Paraplatyarthridae Javidkar & King, fam. nov. is erected based on Paraplatyarthrus subterraneus Javidkar & King, gen. & sp. nov. (type genus and species), and several undescribed taxa which occur in the arid (terrestrial and subterranean) regions of Western Australia and subtropical South America. Paraplatyarthridae is distinguishable from all other oniscidian families on a combination of character states including, among others, the presence of fan-like scale setae on the dorsal body, and the ventral second antenna with leaf-like scale setae and a furrow containing elongated hair-like capillary setae that form part of a water conducting system unique within Oniscidea. This study has important implications for the higher-level classification of oniscidean crustaceans and points to the need for a more detailed molecular phylogeny that includes a comprehensive sampling of southern hemisphere taxa.

An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales

Kickxellomycotina is a recently described subphylum encompassing four zygomycete orders (Asellariales, Dimargaritales, Harpellales, Kickxellales). These fungi are united by the formation of disciform septal pores containing lenticular plugs. Morphological diversification and life history evolution has made the relationships within and among the four orders difficult to resolve on those grounds alone. Here we infer the phylogeny of the Kickxellomycotina based on an eight-gene supermatrix including both ribosomal rDNA (18S, 28S, 5.8S) and protein sequences (MCM7, TSR1, RPB1, RPB2, β-tubulin). The results of this study demonstrate that Kickxellomycotina is monophyletic and related to members of the Zoopagomycotina. Eight unique clades are distinguished in the Kickxellomycotina, including the four defined orders (Asellariales, Dimargaritales, Harpellales, Kickxellales) as well as four genera previously placed within two of these orders (Barbatospora, Orphella, Ramicandelaber, Spiromyces). Dimargaritales and Ramicandelaber are the earliest diverging members of the subphylum, although the relationship between these taxa remains uncertain. The remaining six clades form a monophyletic group, with Barbatospora diverging first. The next split divides the remaining members of the subphylum into two subclades: (i) Asellariales and Harpellales and (ii) Kickxellales, Orphella and Spiromyces. Estimation of ancestral states for four potentially informative morphological and ecological characters reveals that arthropod endosymbiosis might have been an important factor in the early evolution of the Kickxellomycotina.

Ultrastructural characterization and multilocus sequence analysis (MLSA) of 'Candidatus Rickettsiella isopodorum', a new lineage of intracellular bacteria infecting woodlice (Crustacea: Isopoda)

The taxonomic genus Rickettsiella (Gammaproteobacteria; Legionellales) comprises intracellular bacteria associated with a wide range of arthropods including insects, arachnids and crustaceans. The present study provides ultrastructural together with genetic evidence for a Rickettsiella bacterium in the common rough woodlouse, Porcellio scaber (Isopoda, Porcellionidae), occurring in Germany, and shows that this bacterium is very closely related to one of the same genus occurring in California that infects the pill bug, Armadillidium vulgare (Isopoda, Armadillidiidae). Both bacterial isolates displayed the ultrastructural features described previously for crustacean-associated bacteria of the genus Rickettsiella, including the absence of well-defined associated protein crystals; occurrence of the latter is a typical characteristic of infection by this type of bacteria in insects, but has not been reported in crustaceans. A molecular systematic approach combining multilocus sequence analysis (MLSA) with likelihood-based significance testing demonstrated that despite their distant geographic origins, both bacteria form a tight sub-clade within the genus Rickettsiella. In the 16S rRNA gene trees, this sub-clade includes other bacterial sequences from woodlice. Moreover, the bacterial specimens from P. scaber and A. vulgare are found genetically or morphologically different from each of the four currently recognized Rickettsiella species. Therefore, the designation 'Candidatus Rickettsiella isopodorum' is introduced for this new lineage of isopod-associated Rickettsiella bacteria.

Systematics and species-specific response to pH of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) from acid mining lakes

We investigated the morphology, phylogeny of the 18S rDNA, and pH response of Oxytricha acidotolerans sp. nov. and Urosomoida sp. (Ciliophora, Hypotricha) isolated from two chemically similar acid mining lakes (pH~2.6) located at Langau, Austria, and in Lusatia, Germany. Oxytricha acidotolerans sp. nov. from Langau has 18 frontal-ventral-transverse cirri but a very indistinct kinety 3 fragmentation so that the assignment to Oxytricha is uncertain. The somewhat smaller species from Lusatia has a highly variable cirral pattern and the dorsal kineties arranged in the Urosomoida pattern and is, therefore, preliminary designated as Urosomoida sp. The pH response was measured as ciliate growth rates in laboratory experiments at pH ranging from 2.5 to 7.0. Our hypothesis was that the shape of the pH reaction norm would not differ between these closely related (3% difference in their SSU rDNA) species. Results revealed a broad pH niche for O. acidotolerans, with growth rates peaking at moderately acidic conditions (pH 5.2). Cyst formation was positively and linearly related to pH. Urosomoida sp. was more sensitive to pH and did not survive at circumneutral pH. Accordingly, we reject our hypothesis that similar habitats would harbour ciliate species with virtually identical pH reaction norm.

Phylogeny as a proxy for ecology in seagrass amphipods: which traits are most conserved?

Increasingly, studies of community assembly and ecosystem function combine trait data and phylogenetic relationships to gain novel insight into the ecological and evolutionary constraints on community dynamics. However, the key to interpreting these two types of information is an understanding of the extent to which traits are phylogenetically conserved. In this study, we develop the necessary framework for community phylogenetics approaches in a system of marine crustacean herbivores that play an important role in the ecosystem functioning of seagrass systems worldwide. For 16 species of amphipods and isopods, we (1) reconstructed phylogenetic relationships using COI, 16S, and 18S sequences and Bayesian analyses, (2) measured traits that are potentially important for assembling species between and within habitats, and (3) compared the degree to which each of these traits are evolutionarily conserved. Despite poor phylogenetic resolution for the order Amphipoda as a whole, we resolved almost all of the topology for the species in our system, and used a sampling of ultrametric trees from the posterior distribution to account for remaining uncertainty in topology and branch lengths. We found that traits varied widely in their degree of phylogenetic signal. Body mass, fecundity, and tube building showed very strong phylogenetic signal, and temperature tolerance and feeding traits showed much less. As such, the degree of signal was not predictable based on whether the trait is related to environmental filtering or to resource partitioning. Further, we found that even with strong phylogenetic signal in body size, (which may have large impacts on ecosystem function), the predictive relationship between phylogenetic diversity and ecosystem function is not straightforward. We show that patterns of phylogenetic diversity in communities of seagrass mesograzers could lead to a variety of interpretations and predictions, and that detailed study of trait similarities and differences will be necessary to interpret these patterns.

Discontinuous ammonia excretion and glutamine storage in littoral Oniscidea (Crustacea: Isopoda): testing tidal and circadian models

A key evolutionary development facilitating land colonization in terrestrial isopods (Isopoda: Oniscidea) is the intermittent liberation of waste nitrogen as volatile ammonia. Intermittent ammonia release exploits glutamine (Gln) as an intermediary nitrogen store. Here, we explore the relationship between temporal patterns of ammonia release and Gln accumulation in three littoral oniscideans from Southern California. Results are interpreted in terms of water availability, habitat, activity patterns, and ancestry. A two-way experimental design was used to test whether ammonia excretion and Gln accumulation follow a tidal or diel periodicity. Ammonia excretion was studied in the laboratory using chambers with or without available seawater and using an acid trap to collect volatile ammonia. Ligia occidentalis releases ammonia directly into seawater and accumulates Gln during low tide (48.9 ± 6.5 μmol g⁻¹ at low tide, 24.1 ± 3.0 μmol g⁻¹ at high tide), indicating that excretion is tidally constrained. Alloniscus perconvexus and Tylos punctatus can excrete ammonia directly into seawater or utilize volatilization. Both species burrow in sand by day and show a diel excretory pattern, accumulating Gln nocturnally (31.8 ± 2.7 μmol g⁻¹ at dawn and 21.8 ± 2.3 μmol g⁻¹ at dusk for A. perconvexus; 85.7 ± 15.1 μmol g⁻¹ at dawn and 25.4 ± 2.9 μmol g⁻¹ at dusk for T. punctatus) and liberating ammonia diurnally. Glutaminase shows higher activity in terrestrial (0.54-0.86 U g⁻¹) compared to intertidal (0.25-0.31 U g⁻¹) species, consistent with the need to generate high PNH₃ for volatilization. The predominant isoform in Armadillidium vulgare is phosphate dependent and maleate independent; phosphate is a plausible regulator in vivo.

Sea-land transitions in isopods: pattern of symbiont distribution in two species of intertidal isopods Ligia pallasii and Ligia occidentalis in the Eastern Pacific

Studies of microbial associations of intertidal isopods in the primitive genus Ligia (Oniscidea, Isopoda) can help our understanding of the formation of symbioses during sea-land transitions, as terrestrial Oniscidean isopods have previously been found to house symbionts in their hepatopancreas. Ligia pallasii and Ligia occidentalis co-occur in the high intertidal zone along the Eastern Pacific with a large zone of range overlap and both species showing patchy distributions. In 16S rRNA clone libraries mycoplasma-like bacteria (Firmicutes), related to symbionts described from terrestrial isopods, were the most common bacteria present in both host species. There was greater overall microbial diversity in Ligia pallasii compared with L. occidentalis. Populations of both Ligia species along an extensive area of the eastern Pacific coastline were screened for the presence of mycoplasma-like symbionts with symbiont-specific primers. Symbionts were present in all host populations from both species but not in all individuals. Phylogenetically, symbionts of intertidal isopods cluster together. Host habitat, in addition to host phylogeny appears to influence the phylogenetic relation of symbionts.

Host-specificity of environmentally transmitted Mycoplasma-like isopod symbionts

Mycoplasms are known as pathogens of economic and medical interest in plants, animals and man. Here, we show a positive correlation between the presence of Mycoplasma-like symbionts in their isopod hosts and survivorship on low-quality food. Most isopods that survived feeding on a cellulose-based low-quality diet for 90 days harboured 'Candidatus Hepatoplasma' in their midgut glands, while those that died within 90 days mostly either harboured no or other bacterial symbionts. We detected 'Candidatus Hepatoplasma' in all but one of the examined species of terrestrial isopods from different habitats and locations, suggesting an evolutionarily ancient association between terrestrial isopods and their Mycoplasma-like symbionts. Phylogenetic analyses clustered symbionts from different populations of the same isopod species together, and clearly distinguished between symbionts of different isopod species, indicating host-specificity of 'Candidatus Hepatoplasma', although a previous study provided evidence for environmental symbiont transmission. Nonetheless, horizontal exchange of symbionts between species may have been possible in evolutionary earlier stages, as suggested by only limited congruency of phylogenetic trees of hosts and symbionts. Another symbiont, 'Candidatus Hepatincola porcellionum', was only detected in midgut glands of the most terrestrial tribe of isopods (Crinocheta), suggesting an evolutionarily younger host-symbiont association. This symbiont proved to be negatively correlated with host longevity, even on high-quality food.

High mitochondrial haplotype diversity of Coleps sp. (Ciliophora: Prostomatida)

To date the awareness of the temporal population structure in eukaryotic microbes is very limited. This is exemplified in the scarce knowledge about the intraspecific genetic variation in ciliates. To elucidate the genetic variation of Coleps (Ciliophora: Prostomatida), we employed the analysis of the mitochondrial apocytochrome b gene of the Coleps community in a young lake in Germany. The analysis of 111 isolates, sampled from April 2005 to September 2006, revealed a high genetic variation for the two dominant Coleps species (11 mitochondrial haplotypes in Coleps spetai, nine in Coleps hirtus hirtus). The study represents one of the largest datasets of intraspecific diversity in a microbial eukaryote and demonstrates for the first time the suitability of a mitochondrial gene for the detection of genetic variation within populations of eukaryotic microbes. However, the results of our study warrant caution in the application of such an approach, as we amplified some non-orthologous cob-like sequences, whose uncritical acceptance would have led to the erroneous discovery of cryptic species.

Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects

BACKGROUND

Published molecular phylogenies are usually based on data whose quality has not been explored prior to tree inference. This leads to errors because trees obtained with conventional methods suppress conflicting evidence, and because support values may be high even if there is no distinct phylogenetic signal. Tools that allow an a priori examination of data quality are rarely applied.

RESULTS

Using data from published molecular analyses on the phylogeny of crustaceans it is shown that tree topologies and popular support values do not show existing differences in data quality. To visualize variations in signal distinctness, we use network analyses based on split decomposition and split support spectra. Both methods show the same differences in data quality and the same clade-supporting patterns. Both methods are useful to discover long-branch effects. We discern three classes of long branch effects. Class I effects consist of attraction of terminal taxa caused by symplesiomorphies, which results in a false monophyly of paraphyletic groups. Addition of carefully selected taxa can fix this effect. Class II effects are caused by drastic signal erosion. Long branches affected by this phenomenon usually slip down the tree to form false clades that in reality are polyphyletic. To recover the correct phylogeny, more conservative genes must be used. Class III effects consist of attraction due to accumulated chance similarities or convergent character states. This sort of noise can be reduced by selecting less variable portions of the data set, avoiding biases, and adding slower genes.

CONCLUSION

To increase confidence in molecular phylogenies an exploratory analysis of the signal to noise ratio can be conducted with split decomposition methods. If long-branch effects are detected, it is necessary to discern between three classes of effects to find the best approach for an improvement of the raw data.

Morphology and evolution of the respiratory apparatus in the family Eubelidae (Crustacea, Isopoda, Oniscidea)

The morphology of the respiratory apparatus in the pleopodal lungs of the family Eubelidae was investigated. The family is a monophyletic group including more than 240 species in 53 genera (three of which are nomina dubia), mostly distributed in the Afrotropical Region (tropical Africa and Arabian Peninsula). In all the Eubelidae, except for the monospecific genus Parelumoides and two species of the genus Elumoides, the exopods of pleopods have lungs. All the pulmonary morphologies present in the entire suborder Oniscidea are found: 1) uncovered lungs, composed of a pleated respiratory surface, directly exposed to the air (Atracheodillo-type) or partially enclosed within the appendage (Synarmadilloides-type); 2) covered lungs with several spiracles and respiratory trees, housed within the appendages, with spiracles surrounded by a specialized, nonrespiratory, structure (perispiracular area) (Eubelum- and Somaloniscus-types); 3) covered lungs with only one spiracle, with or without perispiracular area, and one respiratory tree (Aethiopopactes- and Periscyphis-types), which in taxa with Periscyphis-type lung crosses the insertion of the appendage and penetrates into the pleon with bundles of respiratory tubules. The evolution of the various types of lungs is discussed. It is concluded that the two main evolutionary lines, i.e., uncovered lungs and covered lungs, originated independently from an ancestral respiratory structure-the semilunar area. A first mechanism of development of the semilunar area by folding of its surface produced the Atracheodillo-type (all folds coplanar with the surface of the exopod) and Synarmadilloides-type (folds partly coplanar and partly intraflexed inside the exopod) uncovered lungs. A second mechanism of development by tubular invagination of the cuticle of the semilunar area produced the polyspiracular Eubelum-type lungs (numerous arborescent invaginations) and the monospiracular Aethiopopactes-type lungs (only one arborescent invagination), probably passing through a common intermediate pattern. From the common pattern, both the poly- and monospiracular types would have inherited the characteristic concave cell arrangement of the perispiracular area. The Somaloniscus-type and Periscyphis-type lungs are forms specialized for arid environments, directly derived from the Eubelum-type and Aethiopopactes-type, respectively.