Sharma, P.P., et al., 2013.
Distal-less and dachshund pattern both plesiomorphic and apomorphic structures in chelicerates: RNAinterference in the harvestman Phalangium opilio (Opiliones).
Evolution & Development , 15 , pp. 228-242.
AbstractThe 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.
Sharma, P.P., et al., 2013.
Into the deep: A phylogenetic approach to the bivalve subclass Protobranchia.
Molecular Phylogenetics and Evolution , 69 , pp. 188-204.
AbstractA 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.
Salvatierra, L., Tourinho, A.L. & Giribet, G., 2013.
Description of the male, larva and nymphal stages of Cryptocellus iaci (Arachnida, Ricinulei), with an overview of tarsal sensilla and other integumental structures.
Zootaxa , 3709 , pp. 149-161.
AbstractThe male, larva and nymphal stages of Cryptocellus iaci Tourinho, Lo Man-Hung & Bonaldo, 2010, a species previously known only from a single female, are described based on specimens from around the type locality, in an area of both Terra Firme forest and igapó (flooded forests), at the Jufari River, Roraima State, Brazil. The specimens were illustrated using live photography, stereomicroscopy, and scanning electron microscopy, allowing us to examine and describe the large di- versity of tarsal sensilla and other integumental structures in Cryptocellus and to compare them to those of the previously studied Pseudocellus. Based on the male somatic characters Cryptocellus iaci is placed in the foedus species-group. Cryp- tocellus iaci has two sensilla of type 1 on the distal tarsomeres of legs III (DT III), while only one has been reported for Pseudocellus spp., suggesting a potential value in this type of character for systematic studies of the group.
Clouse, R.M., et al., 2013.
Elongation factor-1α, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid.
Molecular Phylogenetics and Evolution , 68 , pp. 471-481.
Abstractdentification of paralogy in candidate nuclear loci is an important prerequisite in phylogenetics and sta- tistical 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-1a (EF-1a). To test this hypothesis, we systematically cloned EF-1a in three disjunct populations of the har- vestman Metasiro americanus. Here we show that EF-1a 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-1a 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-1a 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-1a 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.
Novo, M., et al., 2013.
Pheromone evolution, reproductive genes, and comparative transcriptomics in Mediterranean earthworms (Annelida, Oligochaeta, Hormogastridae).
Molecular Biology and Evolution , 30 , pp. 1614-1629.
AbstractAnimals 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.
Murienne, J., et al., 2013.
Forest refugia in Western and Central Africa as 'museums' of Mesozoic biodiversity.
Biology Letters , 9 , pp. 20120932.
AbstractThe 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 phy- logenetic 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.
