Sharma, P. P., E. E. Schwager, G. Giribet, E. L. Jockusch, and C. G. Extavour. 2013. “Distal-less and dachshund pattern both plesiomorphic and apomorphic structures in chelicerates: RNA interference in the harvestman Phalangium opilio (Opiliones).” Evol Dev 15: 228-42. Abstract

The discovery of genetic mechanisms that can transform a morphological structure from a plesiomorphic (=primitive) state to an apomorphic (=derived) one is a cardinal objective of evolutionary developmental biology. However, this objective is often impeded for many lineages of interest by limitations in taxonomic sampling, genomic resources, or functional genetic methods. In order to investigate the evolution of appendage morphology within Chelicerata, the putative sister group of the remaining arthropods, we developed an RNA interference (RNAi) protocol for the harvestman Phalangium opilio. We silenced the leg gap genes Distal-less (Dll) and dachshund (dac) in the harvestman via zygotic injections of double-stranded RNA (dsRNA), and used in situ hybridization to confirm RNAi efficacy. Consistent with the conserved roles of these genes in patterning the proximo-distal axis of arthropod appendages, we observed that embryos injected with Dll dsRNA lacked distal parts of appendages and appendage-like structures, such as the labrum, the chelicerae, the pedipalps, and the walking legs, whereas embryos injected with dac dsRNA lacked the medial podomeres femur and patella in the pedipalps and walking legs. In addition, we detected a role for these genes in patterning structures that do not occur in well-established chelicerate models (spiders and mites). Dll RNAi additionally results in loss of the preoral chamber, which is formed from pedipalpal and leg coxapophyses, and the ocularium, a dorsal outgrowth bearing the eyes. In one case, we observed that an embryo injected with dac dsRNA lacked the proximal segment of the chelicera, a plesiomorphic podomere that expresses dac in wild-type embryos. This may support the hypothesis that loss of the cheliceral dac domain underlies the transition to the two-segmented chelicera of derived arachnids.

Clouse, R.M., P. P. Sharma, G. Giribet, and W.C. Wheeler. 2013. “Elongation factor-1alpha, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid.” Mol Phylogenet Evol 68: 471-81. Abstract

Identification of paralogy in candidate nuclear loci is an important prerequisite in phylogenetics and statistical phylogeography, but one that is often overlooked. One marker commonly assumed to be a single-copy gene and claimed to harbor great utility for inferring recent divergences is elongation factor-1alpha (EF-1alpha). To test this hypothesis, we systematically cloned EF-1alpha in three disjunct populations of the harvestman Metasiro americanus. Here we show that EF-1alpha has a large number of paralogs in this species. The paralogs do not evolve in a concerted manner, and the paralogs diverged prior to the population divergence. Moreover, the paralogs of M. americanus are not comparable to the highly divergent EF-1alpha paralogs found in bees and spiders, which are easily recognized and separated through the use of specific primers. We demonstrate statistically that our detection of paralogs cannot be attributed to amplification error. The presence of EF-1alpha paralogs in M. americanus prevents its use in statistical phylogeography, and the presence of out-paralogs argues against its use in phylogenetic inference among recently diverged clades. These data contradict the common assumption that EF-1alpha is for most or all taxa a single-copy gene, or that it has a small number of paralogs that are homogenized through gene conversion, unequal crossing over, or other processes.

Murienne, J., L. R. Benavides, L. Prendini, G. Hormiga, and G. Giribet. 2013. “Forest refugia in Western and Central Africa as 'museums' of Mesozoic biodiversity.” Biol Lett 9: 20120932. Abstract

The refugial speciation model, or 'species pump', is widely accepted in the context of tropical biogeography and has been advocated as an explanation for present species distributions in tropical Western and Central Africa. In order to test this hypothesis, a phylogeny of the cryptic arachnid order Ricinulei, based on four nuclear and mitochondrial DNA markers, was inferred. This ancient clade of litter-dwelling arthropods, endemic to the primary forests of Western and Central Africa and the Neotropics, might provide insights into the mode and tempo of evolution in Africa. Twenty-six African ricinuleid specimens were sampled from eight countries spanning the distribution of Ricinulei on the continent, and analysed together with Neotropical samples plus other arachnid outgroups. The phylogenetic and molecular dating results suggest that Ricinulei diversified in association with the fragmentation of Gondwana. The early diversification of Ricinoides in Western and Central Africa around 88 (+/-33) Ma fits old palaeogeographical events better than recent climatic fluctuations. Unlike most recent molecular studies, these results agree with fossil evidence, suggesting that refugia may have acted as 'museums' conserving ancient diversity rather than as engines generating diversity during successive episodes of climatic fluctuation in Africa.

Sharma, P. P., J. D. Zardus, E. E. Boyle, V. L. Gonzalez, R. M. Jennings, E. McIntyre, W.C. Wheeler, R. J. Etter, and G. Giribet. 2013. “Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia.” Mol Phylogenet Evol 69: 188-204. Abstract

A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.

Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

Novo, M., A. Riesgo, A. Fernandez-Guerra, and G. Giribet. 2013. “Pheromone evolution, reproductive genes, and comparative transcriptomics in mediterranean earthworms (annelida, oligochaeta, hormogastridae).” Mol Biol Evol 30: 1614-29. Abstract

Animals inhabiting cryptic environments are often subjected to morphological stasis due to the lack of obvious agents driving selection, and hence chemical cues may be important drivers of sexual selection and individual recognition. Here, we provide a comparative analysis of de novo-assembled transcriptomes in two Mediterranean earthworm species with the objective to detect pheromone proteins and other reproductive genes that could be involved in cryptic speciation processes, as recently characterized in other earthworm species. cDNA libraries of unspecific tissue of Hormogaster samnitica and three different tissues of H. elisae were sequenced in an Illumina Genome Analyzer II or Hi-Seq. Two pheromones, Attractin and Temptin were detected in all tissue samples and both species. Attractin resulted in a reliable marker for phylogenetic inference. Temptin contained multiple paralogs and was slightly overexpressed in the digestive tissue, suggesting that these pheromones could be released with the casts. Genes involved in sexual determination and fertilization were highly expressed in reproductive tissue. This is thus the first detailed analysis of the molecular machinery of sexual reproduction in earthworms.

Giribet, G., Tourinho. AL, Shih. C, and Ren. D. 2012. “An equisitely preserved harvestman (Arthropoda, Arachnida, Opiliones) from the Middle Jurassic of China.” Organisms, Diversity and Evolution 12: 51-56.
Sharma, PP., Schwager. EE, Extavour. CG, and Giribet. G. 2012. “Evolution of the chelicerae: a dachshund domain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata).” Evolution & Development 14: 522-533.
Giribet, G., Sharma. PP, Benavides. LR, Boyer. SL, Clouse. RM, Bivort. de BL, Dimitrov. D, Kawauchi. GY, Murienne. JY, and Schwendinger. PJ. 2012. “Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement.” Biological Journal of the Linnean Society 105: 92-130.
Stahalavsky, F., Boyer. SL, Harvey. MS, and Giribet. G. 2012. “First cytogenetic study of a member of the harvestman family Pettalidae (Opiliones: Cyphophtalmi).” Australian Journal of Entomology 51: 299-302.
Sharma, PP., Buenavente. PAC, Clouse. RM, Diesmos. AC, and Giribet. G. 2012. “Forgotten gods: Zalmoxidae of the Philippines and Borneo (Opiliones: Laniatores).” Zootaxa 3280: 29-55.
Goodbody-Gringley, G., Woollacott. RM, and Giribet. G. 2012. “Population structure and connectivity in the Atlantic scleractinian coral Montastraea cavernosa (Linnaeus, 1767).” Marine Ecology 33: 32-48.
Edgecombe, GD., Vahtera. V, Stock. SR, Kallonen. A, Xioa. X, Rack. A, and Giribet. G. 2012. “A scolopocryptopid centipede (Chilopoda: Scolopendromorpha) from Mexican amber: synchrotron microtomography and phylogenetic placement using a combined morphological and molecular dataset.” Zoological Journal of the Linnean Society 166: 768-786.
Kawauchi, GY., Sharma. PP, and Giribet. G. 2012. “Sipunculan phylogeny based on six genes, with a new classification and the description of two new families.” Zoologica Scripta 41: 186-210.
Vahtera, V., Edgecombe. GD, and Giribet. G. 2012. “Spiracle structure in scolopendromorph centipedes (Chilopoda: Scolopendromorpha) and its contribution to phylogenetics.” Zoomorphology 131: 225-248.