Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

Molecular phylogeny of deep-sea blind lobsters of the family Polychelidae (Decapoda: Polychelida), with implications for the origin and evolution of these "living fossils"

A comprehensive molecular analysis of the deep-sea blind lobsters of the family Polychelidae, often referred to as "living fossils", is conducted based on all six modern genera and 27 of the 38 extant species. Using six genetic markers from both mitochondrial and nuclear genomes, the molecular phylogenetic results differ considerably from previous morphological analyses and reveal the genera Polycheles and Pentacheles to be para- or polyphyletic. As the splitting of Polycheles has strong support from both molecular and morphological data, two new genera, Dianecheles and Neopolycheles, are erected for those species excluded from the clade containing the type species of Polycheles. The pattern of polyphyly of Pentacheles, however, is not robustly resolved, so it is retained as a single genus. Fossil evidence suggests that fossil polychelids inhabited deep-sea environments as early as the Early to Middle Jurassic, demonstrating the enduring adaptation of extant polychelid species to the deep-sea. Time-calibrated phylogeny suggested that modern polychelids probably had an Atlantic origin during the Jurassic period. Since their emergence, this ancient lobster group has continued to diversify, particularly in the West Pacific, and has colonized the abyssal zone, with the deepest genus, Willemoesia, representing the more 'derived' members among extant polychelids. Differences in eye reduction among extant polychelid genera highlight the necessity for ongoing investigations to ascertain the relative degree of functionality of their eyes, if they indeed retain any function.

Checklist of decapod crustaceans from the coast of the São Paulo state (Brazil) supported by integrative molecular and morphological data: V. Dendrobranchiata and Pleocyemata [Achelata, Astacidea, Axiidea, Caridea (Alpheoidea and Processoidea excluded), Gebiidea, Stenopodidea]

This checklist is the fifth and last compilation on the decapod crustaceans reported to São Paulo (Brazil) coastal area, resulting from long-term multidisciplinary projects, which combined morphological analyses and molecular techniques. The current research includes 75 decapod species, herein referred as shrimps/lobsters-like (shrimps, ghost-shrimps, lobsters, and related groups), reported to São Paulo coastal area. These species occur in marine, estuarine, and amphidromous habitats and are classified into 21 families as follow: Aristeidae (2 spp., 2 genera), Atyidae (4 spp., 2 genera), Axianassidae (1 sp., 1 genus), Callianassidae (1 sp., 1 genus), Callichiridae (6 spp., 4 genera), Crangonidae (1 sp., 1 genus), Glyphocrangonidae (1 sp., 1 genus), Luciferidae (2 spp., 2 genera), Nephropidae (4 spp., 2 genera), Palaemonidae (15 spp., 9 genera), Palinuridae (2 spp., 1 genus), Pandalidae (1 sp., 1 genus), Pasiphaeidae (1 sp., 1 genus), Penaeidae (10 spp., 6 genera), Sergestidae (3 spp., 3 genera), Sicyoniidae (4 spp., 1 genus), Scyllaridae (5 spp., 3 genera), Solenoceridae (4 spp., 3 genera), Stenopodidae (2 spp., 1 genus), and Upogebiidae (6 spp., 1 genus). We generated new sequences of cytochrome oxidase subunit I (barcode region) and 16S genes (51 and 54, respectively) of 54 species. Our examination concluded that 75 shrimps/lobsters-like species are reported to the São Paulo coast. We excluded Leander tenuicornis (Palaemonidae), Penaeus setiferus (Penaeidae), Philocheras gorei (Crangonidae), and Rhynchocinetes typus (Rhynchocinetidae) from this list.  

Tracing the evolution of bioluminescent light organs across the deep-sea shrimp family Sergestidae using a genomic skimming and phylogenetic approach

Deep-sea shrimp of the family Sergestidae Dana, 1852 provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores; non-lensed photophores; or internal organs of Pesta. This morphological diversity across the Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (Sergia Stimpson, 1860 and Sergestes Milne Edwards, 1830) into 15. The present study capitalises on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from ~87 individuals belonging to 13 of the 15 newly proposed genera. A ‘genome skimming’ approach was implemented, allowing the capture of mitochondrial genomic data across 19 sergestid species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3 and NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -sergestes group was rendered non-monophyletic and the -sergia group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate that organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -sergia group, but were later lost in the deepest living genus, Sergia. Lensed photophores also evolved once within the genera Prehensilosergia Vereshchaka, Olesen & Lunina, 2014, Lucensosergia Vereshchaka, Olesen & Lunina, 2014 and Challengerosergia Vereshchaka, Olesen & Lunina, 2014. These findings identify preliminary patterns across light organ type and species’ depth distributions; however, future research that incorporates finer-scale depth data and more species is needed to confirm our findings.

Towards a Supertree of Arthropoda: A Species-Level Supertree of the Spiny, Slipper and Coral Lobsters (Decapoda: Achelata)

While supertrees have been built for many vertebrate groups (notably birds, mammals and dinosaurs), invertebrates have attracted relatively little attention. The paucity of supertrees of arthropods is particularly surprising given their economic and ecological importance, as well as their overwhelming contribution to biodiversity. The absence of comprehensive archives of machine-readable source trees, coupled with the need for software implementing repeatable protocols for managing them, has undoubtedly impeded progress. Here we present a supertree of Achelata (spiny, slipper and coral lobsters) as a proof of concept, constructed using new supertree specific software (the Supertree Toolkit; STK) and following a published protocol. We also introduce a new resource for archiving and managing published source trees. Our supertree of Achelata is synthesised from morphological and molecular source trees, and represents the most complete species-level tree of the group to date. Our findings are consistent with recent taxonomic treatments, confirming the validity of just two families: Palinuridae and Scyllaridae; Synaxidae were resolved within Palinuridae. Monophyletic Silentes and Stridentes lineages are recovered within Palinuridae, and all sub-families within Scyllaridae are found to be monophyletic with the exception of Ibacinae. We demonstrate the feasibility of building larger supertrees of arthropods, with the ultimate objective of building a complete species-level phylogeny for the entire phylum using a divide and conquer strategy.

Molecular phylogeny of commercially important lobster species from Indian coast inferred from mitochondrial and nuclear DNA sequences

Lobsters constitute low-volume high-value crustacean fishery resource along Indian coast. For the conservation and management of this declining resource, accurate identification of species and larvae is essential. The objectives of this work were to generate species-specific molecular signatures of 11 commercially important species of lobsters of families Palinuridae and Scyllaridae and to reconstruct a phylogeny to clarify the evolutionary relationships among genera and species included in this study. Partial sequences were generated for all the candidate species from sampling sites along the Indian coast using markers like Cytochrome oxidase I (COI), 16SrRNA, 12SrRNA, and 18SrRNA genes, and analyzed. The genetic identities of widely distributed Thenus species along the Indian coast to be Thenus unimaculatus and the sub-species of Panulirus homarus to be P. homarus homarus were confirmed. Phylogeny reconstruction using the individual gene and concatenated mtDNA data set were carried out. The overall results suggested independent monophyly of Scyllaridae and Stridentes of Palinuridae. The interspecific divergence was found to be highest for the 12SrRNA compared with other genes. Significant incongruence between mtDNA and nuclear 18SrRNA gene tree topologies was observed. The results hinted an earlier origin for Palinuridae compared with Scyllaridae. The DNA sequence data generated from this study will aid in the correct identification of lobster larvae and will find application in research related to larval transport and distribution.

The complete mitochondrial genome of the Japanese fan lobster Ibacus ciliatus (Crustacea, Achelata, Scyllaridae)

Slipper lobsters are a unique group of decapod crustaceans; they have cylindrical or flattened bodies and belong to the family Scyllaridae. The genus Ibacus (Leach, 1815) (Achelata, Scyllaridae, Ibacinae) consists of eight recognized species to date, all of which occur in the Indo-West Pacific Ocean and are commercially important seafood species. The complete mitochondrial genome of the Japanese fan lobster Ibacus ciliatus (Von Siebold, 1824) is 15,696 bp in size and consists of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region of 783 bp. The base composition of I. ciliatus is 35.8% A, 34.7% T, 19.0% C, and 10.5% G, with an overall AT content of 70.5%. The mitogenome of I. ciliatus was found to have gene arrangement and transcriptional polarity identical to that of the American lobster Homarus americanus, showing the pancrustacean ground pattern. Here, we present the complete mitogenome sequence of I. ciliatus; it is the first mitogenome information from the subfamily Ibacinae, and represents the second for the family Scyllaridae.

Evolutionary divergence of geographic subspecies within the scalloped spiny lobster Panulirus homarus (Linnaeus 1758)

Panulirus homarus is an economically important spiny lobster that is widespread through the Indo-West Pacific Region, but has an uncertain taxonomic status, with three or four geographic subspecies having been described. This study used mitochondrial (16S, COI and control region) and nuclear (18S, ITS-1) DNA sequences to examine specimens of all putative subspecies and forms from throughout their range, in order to determine their genetic validity, and understand the evolutionary history of this species. Despite the range of diversity present in the loci examined, the results were consistent across genes. P. h. rubellus from the SW Indian Ocean comprised the most divergent lineage that was reciprocally monophyletic with respect to all other P. homarus (approx. 9% divergence in COI), and has likely evolved reproductive barriers. The putative P. h. "Brown" subspecies from the Marquesas Is in the central Pacific also comprised a somewhat divergent monophyletic lineage (approx. 3% in COI), but may simply be an allopatric population. The widespread P. h. homarus was not diverged at all from the described P. h. megasculpta from the NW Indian Ocean. The degree of evolutionary divergence of populations at the extremes distribution of the species is somewhat surprising, given the long pelagic larval stage, but suggests that allopatric speciation has been an important driver in the evolution of the genus.

The emergence of lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (decapoda: achelata, astacidea, glypheidea, polychelida)

Lobsters are a ubiquitous and economically important group of decapod crustaceans that include the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and "living fossil" species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships among the major groups of all lobster families and 94% of the genera using six genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A rich fossil history coupled with dense taxon coverage allowed us to estimate and compare divergence times and origins of major lineages using two drastically different approaches. Age priors were constructed and/or included based on fossil age information or fossil discovery, age, and extant species count data. Results from the two approaches were largely congruent across deep to shallow taxonomic divergences across major lineages. The origin of the first lobster-like decapod (Polychelida) was estimated in the Devonian (∼409-372 Ma) with all infraorders present in the Carboniferous (∼353-318 Ma). Fossil calibration subsampling studies examined the influence of sampling density (number of fossils) and placement (deep, middle, and shallow) on divergence time estimates. Results from our study suggest including at least 1 fossil per 10 operational taxonomic units (OTUs) in divergence dating analyses. [Dating; decapods; divergence; lobsters; molecular; morphology; phylogenetics.].

The ‘giant phyllosoma’ are larval stages of Parribacus antarcticus (Decapoda : Scyllaridae)

Early reports on larval distributions are frustratingly obscure due to ambiguous identification of plankton samples. A particularly striking case is posed by the so-called ‘giant phyllosoma’ which attain 80 mm in total length and are among the largest larvae known in marine invertebrates. Based on the supposition that these giant larvae are produced by local species, Philip Robertson (1968) assigned them to Parribacus. In the present study, 12 phyllosoma larvae collected in the Coral Sea and corresponding to intermediate stages VI to IX are described in detail. The identity of these freshly caught specimens was confirmed as belonging to Parribacus antarcticus (Lund, 1793) by using DNA barcoding methods. This new collection further allowed us to complete the larval series for the genus. The intermediate stage VI, which was missing in previous accounts, is described here for the first time. Besides the Coral Sea larvae, another five phyllosoma specimens previously deposited in UK and German museum collections are also described. Given that no useful DNA could be obtained from the old collection specimens, these larvae were identified as Parribacus sp. based on morphology only. Furthermore, a complete morphometric analysis of Parribacus larvae was undertaken including information from literature dating back to 1830. The first detailed description of all dactyli from a complete phyllosoma of the genus Parribacus is presented, with further comparison with those from other genera of Scyllaridae.