Prashant P. Sharma

A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores

The internal phylogeny of the arachnid order Opiliones is investigated by including molecular data from five molecular markers for ca. 140 species totalling 43 families of Opiliones. The phylogenetic analyses consisted of a direct optimization (DO) approach using POY v. 4 and sophisticated tree search algorithms as well as a static alignment analysed under maximum likelihood. The four Opiliones suborders were well‐supported clades, but subordinal relationships did not receive support in the DO analysis, with the exception of the monophyly of Palpatores (=Eupnoiu2003+u2003Dyspnoi). Maximum‐likelihood analysis strongly supported the traditional relationship of Phalangida and Palpatores: (Cyphophthalmi ((Eupnoiu2003+u2003Dyspnoi) Laniatores)). Relationships within each suborder are well resolved and largely congruent between direct optimization and maximum‐likelihood approaches. Age estimates for the main Opiliones lineages suggest a Carboniferous diversification of Cyphophthalmi, while its sister group, Phalangida, diversified in the Early Devonian. Diversification of all suborders predates the Triassic, and most major lineages predate the Cretaceous. The following taxonomic changes are proposed. Dyspnoi: Hesperonemastoma is transferred to Sabaconidae. Insidiatores: Sclerobunidae stat. nov. is erected as a family for Zuma acuta.

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

IntroductionTraditionally, genomic or transcriptomic data have been restricted to a few model or emerging model organisms, and to a handful of species of medical and/or environmental importance. Next-generation sequencing techniques have the capability of yielding massive amounts of gene sequence data for virtually any species at a modest cost. Here we provide a comparative analysis of de novo assembled transcriptomic data for ten non-model species of previously understudied animal taxa.ResultscDNA libraries of ten species belonging to five animal phyla (2 Annelida [including Sipuncula], 2 Arthropoda, 2 Mollusca, 2 Nemertea, and 2 Porifera) were sequenced in different batches with an Illumina Genome Analyzer II (read length 100 or 150 bp), rendering between ca. 25 and 52 million reads per species. Read thinning, trimming, and de novo assembly were performed under different parameters to optimize output. Between 67,423 and 207,559 contigs were obtained across the ten species, post-optimization. Of those, 9,069 to 25,681 contigs retrieved blast hits against the NCBI non-redundant database, and approximately 50% of these were assigned with Gene Ontology terms, covering all major categories, and with similar percentages in all species. Local blasts against our datasets, using selected genes from major signaling pathways and housekeeping genes, revealed high efficiency in gene recovery compared to available genomes of closely related species. Intriguingly, our transcriptomic datasets detected multiple paralogues in all phyla and in nearly all gene pathways, including housekeeping genes that are traditionally used in phylogenetic applications for their purported single-copy nature.ConclusionsWe generated the first study of comparative transcriptomics across multiple animal phyla (comparing two species per phylum in most cases), established the first Illumina-based transcriptomic datasets for sponge, nemertean, and sipunculan species, and generated a tractable catalogue of annotated genes (or gene fragments) and protein families for ten newly sequenced non-model organisms, some of commercial importance (i.e., Octopus vulgaris). These comprehensive sets of genes can be readily used for phylogenetic analysis, gene expression profiling, developmental analysis, and can also be a powerful resource for gene discovery. The characterization of the transcriptomes of such a diverse array of animal species permitted the comparison of sequencing depth, functional annotation, and efficiency of genomic sampling using the same pipelines, which proved to be similar for all considered species. In addition, the datasets revealed their potential as a resource for paralogue detection, a recurrent concern in various aspects of biological inquiry, including phylogenetics, molecular evolution, development, and cellular biochemistry.

The evolutionary and biogeographic history of the armoured harvestmen – Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)

We investigated the internal phylogeny of Laniatores, the most diverse suborder of Opiliones, using sequence data from 10 molecular loci: 12S rRNA, 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I (COI), cytochrome b, elongation factor-1α, histones H3 and H4, and U2 snRNA. Exemplars of all previously described families of Laniatores were included, in addition to two families – Petrobunidae, fam. nov. and Tithaeidae, fam. nov. – that we erect herein. Data analyses were based on maximum likelihood and Bayesian approaches on static alignments, and included phylogenetic tree estimation, molecular dating, and biogeographic analysis of ancestral area reconstruction. The results obtained include the monophyly of Laniatores and the infraorder Grassatores – the focus of this study – as well as support for numerous interfamilial relationships. The two new families described cluster with other South-east Asian families (Podoctidae and Epedanidae). Diversification of Laniatores is estimated at ~348u2009Mya, and origin of most Grassatores superfamilies occurs in a ~25u2009million year span of time immediately after the end-Permian mass extinction (254u2009Mya). Ancestral range reconstruction of the clade (Samooideau2009+u2009Zalmoxoidea) suggests that the ancestral range of Samooidea comprises West Tropical Gondwana (West Africau2009+u2009Neotropics), whereas that of Zalmoxoidea is exclusively Neotropical. The following additional taxonomic changes are proposed: (1) Remyus is transferred to Phalangodidae, and (2) Escadabiidae and Kimulidae are transferred to Zalmoxoidea.

Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous (ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.

A relict in New Caledonia: phylogenetic relationships of the family Troglosironidae (Opiliones: Cyphophthalmi)

The species richness and endemism of New Caledonia are traditionally held to result from the main island’s Gondwanan origin and progressive diversification subsequent to extended isolation. Recent studies have challenged this hypothesis, promoting a scenario of recent origins and diversifications of New Caledonian arthropod groups. In the present study, the phylogeny of the endemic harvestman family Troglosironidae (Opiliones: Cyphophthalmi) is investigated using DNA sequence data from two nuclear ribosomal genes (18S rRNA and 28S rRNA) and two mitochondrial genes (the protein‐coding cytochrome c oxidase subunit I and the ribosomal 16S rRNA). Phylogenetic analyses support the monophyly of Troglosironidae and a scenario of an ancient (>u2003200u2003Ma) origin of the family, with subsequent diversification of extant lineages in the Eocene. These results corroborate the relictual nature of taxa among New Caledonia’s biota while being consistent with diversification in accordance with geological events in the Eocene.

Hox gene expression in the harvestman Phalangium opilio reveals divergent patterning of the chelicerate opisthosoma

Among chelicerates, Hox gene expression has only been investigated in representatives of two arachnid orders to date: Acari (mites and ticks) and Araneae (spiders). Limited data are available for the “primitive” arachnid orders, such as Scorpiones (scorpions) and Opiliones (harvestmen). Here, we present the first data on Hox gene expression in the harvestman Phalangium opilio. Ten Hox genes of this species were obtained from a de novo assembled developmental transcriptome using the Illumina GAII platform. All 10 genes are expressed in characteristic Hox‐like expression patterns, and the expression of the anterior and central Hox genes is similar to those of other chelicerates. However, intriguingly, the three posteriormost genes—Ultrabithorax, abdominal‐A, and Abdominal‐B—share an identical anterior expression boundary in the second opisthosomal segment, and their expression domains extend through the opisthosoma to the posterior growth zone. The overlap in expression domains of the posterior Hox genes is correlated with the absence of opisthosomal organs posterior to the tubular tracheae, which occur on the second opisthosomal segment. Together with the staggered profile of posterior Hox genes in spiders, these data suggest the involvement of abdominal‐A and Abdominal‐B in the evolution of heteronomous patterning of the chelicerate opisthosoma, providing a mechanism that helps explain the morphological diversity of chelicerates.

Sandokanid phylogeny based on eight molecular markers—The evolution of a southeast Asian endemic family of Laniatores (Arachnida, Opiliones)

Little is known about the familial and generic level phylogeny of Laniatores, the most diverse suborder of Opiliones. We investigated the internal phylogeny of the family Sandokanidae (formerly Oncopodidae), the putative sister group of the other families of the highly diverse infraorder Grassatores (Opiliones: Laniatores), on the basis of sequence data from eight molecular loci: 18S rRNA, 28S rRNA, 12S rRNA, 16S rRNA, cytochrome c oxidase subunit I (COI), histones H3, H4, and U2 snRNA. Exemplars of all recognized sandokanid genera, as well as a putative new genus from Thailand, were included. Data analyses were based on a direct optimization approach using parsimony, as well as maximum likelihood and Bayesian approaches on static alignments. The results obtained include the monophyly of Sandokanidae and its stability under a variety of parameter sets and methods. The internal phylogeny is relatively robust to parameter choice and demonstrates the monophyly of nearly all described genera, corroborating previous morphological observations. However, conflict among data sets exists with respect to the monophyly of the largest genus Gnomulus. Morphological character evolution, particularly of characters used to define genera, such as tarsal count and male genitalia, is reexamined and the performance of the eight molecular markers in phylogenetic estimation is evaluated.

Evolution of the chelicera: a dachshund domain is retained in the deutocerebral appendage of Opiliones (Arthropoda, Chelicerata)

The proximo‐distal axis of the arthropod leg is patterned by mutually antagonistic developmental expression domains of the genes extradenticle, homothorax, dachshund, and Distal‐less. In the deutocerebral appendages (the antennae) of insects and crustaceans, the expression domain of dachshund is frequently either absent or, if present, is not required to pattern medial segments. By contrast, the dachshund domain is entirely absent in the deutocerebral appendages of spiders, the chelicerae. It is unknown whether absence of dachshund expression in the spider chelicera is associated with the two‐segmented morphology of this appendage, or whether all chelicerates lack the dachshund domain in their chelicerae. We investigated gene expression in the harvestman Phalangium opilio, which bears the plesiomorphic three‐segmented chelicera observed in “primitive” chelicerate orders. Consistent with patterns reported in spiders, in the harvestman chelicera homothorax, extradenticle, and Distal‐less have broadly overlapping developmental domains, in contrast with mutually exclusive domains in the legs and pedipalps. However, unlike in spiders, the harvestman chelicera bears a distinct expression domain of dachshund in the proximal segment, the podomere that is putatively lost in derived arachnids. These data suggest that a tripartite proximo‐distal domain structure is ancestral to all arthropod appendages, including deutocerebral appendages. As a corollary, these data also provide an intriguing putative genetic mechanism for the diversity of arachnid chelicerae: loss of developmental domains along the proximo‐distal axis.

Running WILD: the case for exploring mixed parameter sets in sensitivity analysis

The robustness of clades to parameter variation may be a desirable quality or even a goal in phylogenetic analyses. Sensitivity analyses used to assess clade stability have invoked the incongruence length difference (ILD or WILD) metric, a measure of congruence among datasets, to compare a series of most‐parsimonious results from re‐running analyses under different analytical conditions. It is also common practice to select a single “optimal” parameter set that minimizes WILD across all parameter sets. However, the divergent molecular evolution of ribosomal genes and protein‐encoding genes—specifically the bias against transversion events in coding genes of conserved function—suggests that deployment of multiple parameter sets could outperform the use of a single parameter set applied to all molecules. We explored congruence in five published datasets by including mixed parameter sets in our sensitivity analysis. In four cases, mixed parameter sets outperformed the previously reported, single optimal parameter set. Conversely, multiple parameter sets did not outperform a single optimal parameter set in a case in which actual strong topological conflict exists between data partitions. Exploration of mixed parameter sets may prove useful when combining ribosomal and protein‐encoding genes, due to the relatively higher frequency of single‐ and double‐base pair indel events in the former, and the relatively lower frequency of transversions in the latter.u2028© The Willi Hennig Society 2010.