An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods

An integrative phylogeography for inferring cryptic speciation in the Alpheus lottini species complex, an important coral mutualist

We use molecular analyses, color patterns, and records of distribution of mating pairs to reconstruct the global phylogeography of Alpheus lottini, a complex of cryptic coral-associated snapping shrimp species. Molecular data support the delineation of ancestral clades A, B, and C, and suggest five additional subdivisions within clades A and B. Clades A, B1, B2, and C exhibit color pattern differences and/or evidence of assortative mating, and thus merit species-level recognition. There is no evidence for assortative mating within clades A and B1, with likely reproductive compatibility (i.e., fertile clutches) in areas of sympatry. The clade diversity peaks in the Mariana Islands and the early branching clade C is restricted to the northern periphery of the Central and Western Pacific suggesting a Pacific origin of this group outside of the Coral Triangle. These findings underscore the prevalence of allopatric processes with possible ecological or microallopatric speciation in areas where clades overlap.

The language of light: a review of bioluminescence in deep-sea decapod shrimps

In the dark, expansive habitat of the deep sea, the production of light through bioluminescence is commonly used among a wide range of taxa. In decapod crustaceans, bioluminescence is only known in shrimps (Dendrobranchiata and Caridea) and may occur in different modes, including luminous secretions that are used to deter predators and/or from specialised light organs called photophores that function by providing camouflage against downwelling light. Photophores exhibit an extensive amount of morphological variation across decapod families: they may be internal (of hepatic origin) or embedded in surface tissues (dermal), and may possess an external lens, suggesting independent origins and multiple functions. Within Dendrobranchiata, we report bioluminescence in Sergestidae, Aristeidae, and Solenoceridae, and speculate that it may also be found in Acetidae, Luciferidae, Sicyonellidae, Benthesicymidae, and Penaeidae. Within Caridea, we report bioluminescence in Acanthephyridae, Oplophoridae, Pandalidae, and new observations for Pasiphaeidae. This comprehensive review includes historic taxonomic literature and recent studies investigating bioluminescence in all midwater and deep benthic shrimp families. Overall, we report known or suspected bioluminescence in 157 species across 12 families of decapod shrimps, increasing previous records of bioluminescent species by 65%. Mounting evidence from personal observations and the literature allow us to speculate the presence of light organs in several families thought to lack bioluminescence, making this phenomenon much more common than previously reported. We provide a detailed discussion of light organ morphology and function within each group and indicate future directions that will contribute to a better understanding of how deep-sea decapods use the language of light.

Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns

Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.

Salmoneus shojaei, a new species of mangrove-dwelling alpheid shrimp (Decapoda: Caridea) from Iran

During a survey of the mangrove infauna on the Iranian side of the Persian Gulf and the Gulf of Oman several specimens of a new alpheid shrimp, Salmoneus shojaei sp. nov., were collected around pneumatophores of mangrove trees, mostly in association with the larger burrowing snapping shrimps of the genus Alpheus Fabricius, 1798. The new species appears to be a member of the S. gracilipes species group and is morphologically closest to S. colinorum De Grave, 2004 and S. alpheophilus Anker & Marin, 2006. However, a unique combination of morphological characters, such as the carapace without rostral carina, the unarmed ischium of the major cheliped, the armed ischia of the minor cheliped and second pereiopod, the very slender dactyli of the fourth and third pereiopods, and the posterior margin of the telson with a deep U-shaped notch, distinguishes the new species from all other members of the S. gracilipes group. In addition, S. shojaei sp. nov. presents a diagnostic, albeit very faint, banding of the pleon, which separates it from most other species of the S. gracilipes group with known colour patterns. A DNA barcode (a partial fragment of the mitochondrial gene, CO1), as well as partial fragments of the mitochondrial 16S rRNA and the nuclear H3 genes, are provided to genetically characterise the new taxon.  

A Mysterious World Revealed: Larval-Adult Matching of Deep-Sea Shrimps from the Gulf of Mexico

The identification of deep-sea (>200 m) pelagic larvae is extremely challenging due to the morphological diversity across ontogeny and duration of larval phases. Within Decapoda, developmental stages often differ conspicuously from their adult form, representing a bizarre and mysterious world still left to be discovered. The difficulties with sampling and rearing deep-sea larvae, combined with the lack of taxonomic expertise, argues for the use of molecular methods to aid in identification. Here, we use DNA barcoding combined with morphological methods, to match larval stages with their adult counterpart from the northern Gulf of Mexico and adjacent waters. For DNA barcoding, we targeted the mitochondrial ribosomal large subunit 16S (16S) and the protein coding cytochrome oxidase subunit 1 (COI). These data were combined with previous sequences to generate phylogenetic trees that were used to identify 12 unknown larval and two juvenile species from the infraorder Caridea and the suborder Dendrobranchiata. Once identified, we provide taxonomic descriptions and illustrations alongside the current state of knowledge for all families. For many groups, larval descriptions are missing or non-existent, so this study represents a first step of many to advance deep-sea larval diversity.

Unexpected diversity in the sponge-associated shrimps Onycocaridella Bruce, 1981 (Crustacea : Decapoda : Palaemonidae) revealed by bulk collecting techniques and molecular tools

Multigene molecular revision of a series of specimens of the rare spongobiotic palaemonid shrimp genus, Onycocaridella Bruce, 1981, collected predominantly from Papua New Guinea, has doubled the known species diversity to six. Of the previously known species, O. monodoa (Fujino & Miyake, 1969) and O. stenolepis (Holthuis, 1952) were analysed in the present study, whereas sequenceable specimens of the type species, O. prima Bruce, 1981, were not available. The present molecular analysis (combined COI, 16S, H3 markers) recovered six separate genetic lineages, indicating the presence of four undescribed species. Three of the latter are described in the present study. Remarkably higher known species diversity of Onycocaridella is thus recorded from a single geographic region – Papua New Guinea. The increased diversity reported here was discovered by application of complementary collecting techniques (hand picking, stone brushing, dead-coral sorting, suction sampling). One of the present new species is also reported from Australia, and O. monodoa is newly recorded from New Caledonia. A revised diagnosis of the genus and a key to identification of all known species of Onycocaridella are provided.

Phylogenetic revision of the shrimp genera Ephyrina, Meningodora and Notostomus (Acanthephyridae: Caridea)

The shrimp genera Ephyrina, Meningodora and Notostomus have an unusual carapace strengthened with carinae and a half-serrated mandible, which may suggest a possible monophyly of this group. Here we test this hypothesis and present the first phylogenetic study of these genera based on 95 morphological characters (all valid species coded) and six molecular markers (71% of valid species sequenced). Representatives of all genera of Oplophoridae (sister to Acanthephyridae) were outgroups, 32 species belonging to all genera and potentially different clades of Acanthephyridae were ingroups. Both morphological and molecular analyses retrieve trees with similar topology. Our results reject the hypothesis of a clade formed by Ephyrina + Meningodora + Notostomus. We show that Ephyrina and Notostomus are monophyletic, both on morphological and on molecular trees, Meningodora gains support only on morphological trees. Evolutionary traits in the Ephyrina and Meningodora + Notostomus clades are different. Synapomorphies are mostly linked to adaptations to forward motion in Ephyrina (oar-like meri and ischia of pereopods, stempost-like rostrum) and to progressive strengthening of the carapace and pleon in Meningodora and Notostomus (net of sharp carinae). Unusual mandibles evolved in the clades independently and represent convergent adaptations to feeding on gelatinous organisms.

A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans

Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic-Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.

Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition

The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.

Systematic analysis of the caridean shrimp superfamily Pandaloidea (Crustacea: Decapoda) based on molecular and morphological evidence

One of the systematically controversial superfamilies in Caridea is the predominately deep-sea or cold water Pandaloidea, largely because this species-rich group of nearly 200 species in 25 genera exhibits a very high diversity of body forms and ecology. Although the relationships amongst the taxa within Pandaloidea have been repeatedly discussed based on morphology, no comprehensive molecular phylogeny exists. In this study, we present the first molecular phylogeny of the group, based on a combined dataset of two mitochondrial (12S and 16S rRNA) and six nuclear (ATP synthase β-subunit, enolase, glyceraldehyde-3-phosphate dehydrogenase, histone 3, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase α-subunit) markers, based on 62 species (about 1/3 of known biodiversity) in 22 genera (88% of genera) of two pandaloid families (Pandalidae, Thalassocarididae) and outgroups from seven other caridean families. With generally high support, the relationships within the clade are fully resolved. Pandalidae is shown to be paraphyletic with Thalassocarididae deeply nested within as a monophyletic group, and the latter is herein considered to be a synonym of Pandalidae. Five major clades are recovered, with the shallow water genera Anachlorocurtis, Chlorocurtis, Chlorotocella and Miropandalus forming a sister clade to the remaining genera. At the genus level, the phylogeny indicates Plesionika, Heterocarpus and Pandalus to be not monophyletic. The validity of Pandalopsis, Stylopandalus and Calipandalus is challenged and these genera are considered herein to be junior synonyms of Pandalus (Pandalopsis) and Plesionika (Stylopandalus and Calipandalus). Although not fully resolved, some evidence potentially considers Nothocaris to be a valid genus. Ancestral State Reconstruction successfully recovered 15 synapomorphies for the major clades, with 11 of them reported to be of systematic significance for the first time.

Freshwater transitions and symbioses shaped the evolution and extant diversity of caridean shrimps

Understanding the processes that shaped the strikingly irregular distribution of species richness across the Tree of Life is a major research agenda. Changes in ecology may go some way to explain the often strongly asymmetrical fates of sister clades, and we test this in the caridean shrimps. First appearing in the Lower Jurassic, there are now ~3500 species worldwide. Carideans experienced several independent transitions to freshwater from marine habitats, while many of the marine species have also evolved a symbiotic lifestyle. Here we use diversification rate analyses to test whether these ecological traits promote or inhibit diversity within a phylogenetic framework. We demonstrate that speciation rates are more than twice as high in freshwater clades, whilst symbiotic ecologies are associated with lower speciation rates. These lower rates amongst symbiotic species are of concern given that symbioses often occur in some of the most diverse, delicately balanced and threatened marine ecosystems.

Katie Davis et al. test the hypothesis that ecological traits are linked to diversification in caridean shrimps. They find that transitions from marine to freshwater habitats contributed to higher diversification rates, whereas symbiosis is associated with a slight decrease in diversification rates.

More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae)

Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.

Ambiguities in the taxonomic assignment and species delineation of botryllid ascidians from the Israeli Mediterranean and other coastlines

Based on mtCOI sequences comparisons, recent studies reassigned the 'dwarf Botrylloides leachii' from the Levant as Botrylloides nigrum. Here we conducted a survey of the literature and of deposited mtCOI sequences of botryllid ascidians, elucidating ambiguities in their taxonomy. We found that the species, dwarf morph of Botrylloides leachii, Botrylloides nigrum, Botryllus aster and Botryllus arenaceus are grouped together on a single molecular taxon. Then, results of three additional markers (18S, 28S, H3) contradicted literature suggestions, revealing minute distances between Botrylloides leachii and the 'dwarf Botrylloides leachii'. Moreover, only Botrylloides leachii and the 'dwarf Botrylloides leachii' develop giant ampullae as an allorecognition response. Our results raise the possibility that inadequate identification, together with faults in molecular assignment, including queries regarding the efficacy of the mtCOI as the exclusive barcoding tool in botryllid ascidians, is the major culprits responsible for the emerged inconsistencies between the mtCOI sequences and traditional taxonomy. Thus, we assign the Levantine dwarf form as Botrylloides aff. leachii.

Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology

Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. In this study, we assessed the diversity of the decapods involved in exosymbiotic assemblages for juvenile and adult Pocillopora damicornis types α and β on reefs of New Caledonia and Reunion Island. This approach revealed complex patterns of association at regional and local scales with a prevalence of assemblages involving crab-shrimp partnerships. Furthermore, the distinction of two lineages in the snapping shrimp Alpheus lottini complex, rarely recognized in ecological studies, reveals a key role for cryptic diversity in structuring communities of mutualists. The existence of partnerships between species that occurred more commonly than expected by chance suggests an increased advantage for the host or a better adaptation of associated species to local environmental conditions. The consideration of cryptic diversity helps to accurately describe the complexity of interaction webs for diverse systems such as coral reefs, as well as the functional roles of dominant associated species for the persistence of coral populations.

Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales

Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.

Morphology of First Zoeal Stage of Four Genera of Alvinocaridid Shrimps from Hydrothermal Vents and Cold Seeps: Implications for Ecology, Larval Biology and Phylogeny

Alvinocaridid shrimps are endemic species inhabiting hydrothermal vents and/or cold seeps. Although indirect evidences (genetic and lipid markers) suggest that their larval stages disperse widely and support large scale connectivity, larval life and mechanisms underlying dispersal are unknown in alvinocaridids. Here we provide for the first time detailed descriptions of the first larval stage (zoea I) of four alvinocaridid species: Rimicaris exoculata and Mirocaris fortunata from the Mid-Atlantic Ridge, Alvinocaris muricola from the Congo Basin and Nautilocaris saintlaurentae from the Western Pacific. The larvae were obtained from onboard hatching of brooding females (either at atmospheric pressure or at habitat pressure in hyperbaric chambers) and from the water column near adult habitats, sampled with plankton pumps or sediment traps. Major characteristics of the alvinocaridid larvae include undeveloped mandible and almost complete absence of setation in the inner margin of the mouth parts and maxillipeds. Although the larvae are very similar between the four species studied, some morphological features could be used for species identification. In addition, undeveloped mouthparts and the large amount of lipid reserves strongly support the occurrence of primary lecithotrophy in the early stage of alvinocaridids. Although lecithotrophy in decapod crustaceans is usually associated with abbreviated larval development, as a mechanism of larval retention, morphological and physiological evidences suggest the occurrence of an extended and lecithotrophic larval stage in the Alvinocarididae. These traits permit the colonization of widely dispersed and fragmented environments of hydrothermal vents and cold seeps. Distribution of larval traits along the phylogenetic reconstruction of the Alvinocarididae and related families suggest that lecithotrophy/planktotrophy and extended/abbreviated development have evolved independently along related families in all potential combinations. However, the Alvinocarididae is the only taxa with a combination of lecithotrophy and extended larval development.

Let's be pals again: major systematic changes in Palaemonidae (Crustacea: Decapoda)

In recent years the systematic position of genera in the shrimp families Gnathophyllidae and Hymenoceridae has been under debate, with phylogenetic studies suggesting the families are not real family level units. Here, we review the molecular evidence as well as the morphological characters used to distinguish both families, leading to the conclusion that neither family is valid. Further, we studied the structural details of the single morphological character which distinguishes the two subfamilies (Palaemoninae, Pontoniinae) in Palaemonidae, as well as their phylogenetic relationship. As the supposed character distinction plainly does not hold true and supported by the phylogenetic results, the recognition of subfamilies in Palaemonidae is not warranted. As a consequence, all three supra-generic taxa (Gnathophyllidae, Hymenoceridae, Pontoniinae) are thus herein formally synonymised with Palaemonidae.

Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences

Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.