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.

Convergent adaptation of true crabs (Decapoda: Brachyura) to a gradient of terrestrial environments.

For much of terrestrial biodiversity, the evolutionary pathways of adaptation from marine ancestors are poorly understood, and have usually been viewed as a binary trait. True crabs, the decapod crustacean infraorder Brachyura, comprise over 7,600 species representing a striking diversity of morphology and ecology, including repeated adaptation to non-marine habitats. Here, we reconstruct the evolutionary history of Brachyura using new and published sequences of 10 genes for 344 tips spanning 88 of 109 brachyuran families. Using 36 newly vetted fossil calibrations, we infer that brachyurans most likely diverged in the Triassic, with family-level splits in the late Cretaceous and early Paleogene. By contrast, the root age is underestimated with automated sampling of 328 fossil occurrences explicitly incorporated into the tree prior, suggesting such models are a poor fit under heterogeneous fossil preservation. We apply recently defined trait-by-environment associations to classify a gradient of transitions from marine to terrestrial lifestyles. We estimate that crabs left the marine environment at least seven and up to 17 times convergently, and returned to the sea from non-marine environments at least twice. Although the most highly terrestrial- and many freshwater-adapted crabs are concentrated in Thoracotremata, Bayesian threshold models of ancestral state reconstruction fail to identify shifts to higher terrestrial grades due to the degree of underlying change required. Lineages throughout our tree inhabit intertidal and marginal marine environments, corroborating the inference that the early stages of terrestrial adaptation have a lower threshold to evolve. Our framework and extensive new fossil and natural history datasets will enable future comparisons of non-marine adaptation at the morphological and molecular level. Crabs provide an important window into the early processes of adaptation to novel environments, and different degrees of evolutionary constraint that might help predict these pathways.

Shift in symbiotic lifestyle as the major process shaping the evolution of pea crabs (Decapoda: Brachyura: Pinnotheroidea).

The pea crabs, superfamily Pinnotheroidea, are exceptional among brachyuran crabs in their diverse symbiotic associations involving both inquilinism and protective symbiosis. While this group presents a rare opportunity for evolutionary comparative study of host switching and morphological evolution in marine macroinvertebrates, previous phylogenetic studies have been focused on systematics. Here, we reconstructed the most extensive phylogeny of Pinnotheroidea based on two mitochondrial and six nuclear markers, with the aim of elucidating the host switching pathways and the correlation between symbiotic lifestyles and selected morphological adaptations. Ancestral state reconstruction of host association revealed a monophyletic origin of symbiosis in the form of inquilinism. Subsequent shifts in microhabitat preference for burrows or worm tubes, and the move to protective symbiosis, primarily in the switch to mollusc endosymbiosis, contributed to radiation in Pinnotheridae. Further parallel colonisations of echinoderms and tunicates occurred but did not lead to extensive diversification, except in the Clypeasterophilus + Dissodactylus lineage, which experienced a unique switch to echinoderm ectosymbiosis. The evolution of the third maxillipeds, carapace shape and ambulatory pereiopods suggests a rather strong coupling with the symbiotic lifestyle (whether inquilinism or protective symbiosis). Phenotypic diversity of these characters was higher among species engaged in protective symbiosis, with convergence in form (or function) among those sharing the same host affiliation. Species having different host affiliations or symbiotic lifestyles might also exhibit convergence in the form of the three morphological traits, suggesting a common adaptive value of the specialisations. Pinnotherid crabs overall exhibited a lower trait diversity than the also symbiotic palaemonid shrimps with comparable species diversity. This may plausibly be attributed to differences in potential for morphological modification to serve additional functions among the traits analysed in the two groups, the less frequent host switching and the less diverse host affiliations, and thus a less complicated evolutionary history in pinnotherids.

Tightening the requirements for species diagnoses would help integrate DNA-based descriptions in taxonomic practice.

Modern advances in DNA sequencing hold the promise of facilitating descriptions of new organisms at ever finer precision but have come with challenges as the major Codes of bionomenclature contain poorly defined requirements for species and subspecies diagnoses (henceforth, species diagnoses), which is particularly problematic for DNA-based taxonomy. We, the commissioners of the International Commission on Zoological Nomenclature, advocate a tightening of the definition of "species diagnosis" in future editions of Codes of bionomenclature, for example, through the introduction of requirements for specific information on the character states of differentiating traits in comparison with similar species. Such new provisions would enhance taxonomic standards and ensure that all diagnoses, including DNA-based ones, contain adequate taxonomic context. Our recommendations are intended to spur discussion among biologists, as broad community consensus is critical ahead of the implementation of new editions of the International Code of Zoological Nomenclature and other Codes of bionomenclature.

On the identity of Pronotonyx laevis (Miers, 1884) (Crustacea: Brachyura: Pilumnidae).

The poorly known brachyuran crab, Pronotonyx laevis Ward, 1936, from northern Australia, is redescribed based on type and other material. We document adults of both sexes and confirm the taxonomic placement of the Pronotonyx in the Pilumnidae. Pronotonyx is most similar to the Australian Pseudocryptocoeloma parvum Ward, 1936, differing in features of the carapace and pereopods.

Genomic analysis reveals strong population structure in the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)).

Australia is home to over 140 species of freshwater crayfish (Decapoda: Parastacidae), representing a centre of diversity for this group in the Southern Hemisphere. Species delimitation in freshwater crayfish is difficult because many species show significant variation in colouration and morphology. This is particularly evident in the genus Euastacus, which exhibits large variations in colour and spination throughout its putative range. To understand this variation, we investigated the genetic diversity, population structure, phylogeny, and evolutionary timescale of the Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)). Our data set is sampled from over 70 individuals from across the ∼600 km range of the species, and includes a combination of two mitochondrial markers and more than 7000 single-nucleotide polymorphisms (SNPs) from the nuclear genome. Data were also obtained for representatives of the close relative, Euastacus vesper McCormack and Ahyong, 2017. Genomic SNP analyses revealed strong population structure, with multiple distinct populations showing little evidence of gene flow or migration. Phylogenetic analyses of mitochondrial data revealed similar structure between populations. Taken together, our analyses suggest that E. spinifer, as currently understood, represents a species complex, of which E. vesper is a member. Molecular clock estimates place the divergences within this group during the Pleistocene. The isolated and highly fragmented populations identified in our analyses probably represent relict populations of a previously widespread ancestral species. Periodic flooding events during the Pleistocene are likely to have facilitated the movement of these otherwise restricted freshwater crayfish within and between drainage basins, including the Murray-Darling and South East Coast Drainages. We present evidence supporting the recognition of populations in the southern parts of the range of E. spinifer as one or two separate species, which would raise the number of species within the E. spinifer complex to at least three. Our results add to the growing body of evidence that many freshwater crayfish exhibit highly fragmented, range-restricted distributions. In combination with the life-history traits of these species, the restricted distributions exacerbate the threats already placed on freshwater crayfish, which are among the five most endangered animal groups globally.

Phylogenetic Appraisal of Lysiosquillidae Giesbrecht, 1910, and a New Species of Lysiosquilloides Manning, 1977, from Taiwan (Crustacea: Stomatopoda: Lysiosquilloidea).

The mantis shrimp family Lysiosquillidae includes the largest known stomatopods and presently includes three genera: Lysiosquilla Dana, 1852, Lysiosquillina Manning, 1995, and Lysiosquilloides Manning, 1977. Since 1995, new species assigned to all three lysiosquilloid genera have been recognised: Lysiosquilla manningi Boyko, 2000, Lysiosquillina lisa Ahyong & Randall, 2001, Lysiosquilla colemani Ahyong, 2001, Lysiosquilla suthersi Ahyong, 2001, and Lysiosquilloides mapia Erdmann & Boyer, 2003, and Lysiosquilla isos Ahyong, 2004. Lysiosquillina lisa, Lysiosquilla campechiensis Manning, 1962 and Lysiosquilla suthersi, however, proved problematical to assign to genera owing to the possession of characters intermediate between Lysiosquilla sensu stricto and Lysiosquillina sensu stricto. In particular, species that are transitional between Lysiosquilla and Lysiosquillina challenge the validity of the latter genus. Here, we reassess the status and composition of the lysiosquillid genera by cladistic analysis of all known species in the family. Lysiosquillina is synonymized with Lysiosquilla and a new species of Lysiosquilloides is described from Taiwan. A key to the species of Lysiosquilloides is provided.

The Identity of Homoioplax haswelli (Miers, 1884) (Crustacea: Decapoda: Brachyura).

The brachyuran crab Pseudorhombila haswelli Miers, 1884, described on the basis of two juveniles from the Arafura Sea, is a poorly known species of uncertain systematic position. It was made the type and only species of Homoioplax Rathbun, 1914, and assigned to the Prionoplacinae (Goneplacidae). Subsequent revisions of the goneplacids showed Prionoplacinae to be a junior synonym of Eucratopsinae Stimpson, 1871, as a member of the Panopeidae Ortmann, 1893, but no one has re-evaluated the position of Homoioplax. As a result, Homoioplax has remained in the Panopeidae as the only Indo-West Pacific representative of the family. This study assesses the systematic status of Homoioplax haswelli based on a re-examination of the type and other material of the species. Homoioplax haswelli is here attributed to Carcinoplax H. Milne Edwards, 1852 (Goneplacidae), justifying the recognition of the species described by Miers as C. haswelli. Moreover, Carcinoplax haswelli is shown to be a senior synonym of C. sinica Chen, 1984, described from the South China Sea. Therefore, C. haswelli is now known to range from southern Taiwan and the Philippines, through the South China Sea, northern Vietnam, the eastern waters of Singapore to the Madura Straits in eastern Java and Arafura Sea, northern Australia, at 25-187 m, but usually less than 100 m depth.

Evaluating the effectiveness of drones for quantifying invasive upside-down jellyfish (Cassiopea sp.) in Lake Macquarie, Australia.

Upside-down jellyfish (Cassiopea sp.) are mostly sedentary, benthic jellyfish that have invaded estuarine ecosystems around the world. Monitoring the spread of this invasive jellyfish must contend with high spatial and temporal variability in abundance of individuals, especially around their invasion front. Here, we evaluated the utility of drones to survey invasive Cassiopea in a coastal lake on the east coast of Australia. To assess the efficacy of a drone-based methodology, we compared the densities and counts of Cassiopea from drone observations to conventional boat-based observations and evaluated cost and time efficiency of these methods. We showed that there was no significant difference in Cassiopea density measured by drones compared to boat-based methods along the same transects. However, abundance estimates of Cassiopea derived from scaling-up transect densities were over-inflated by 319% for drones and 178% for boats, compared to drone-based counts of the whole site. Although conventional boat-based survey techniques were cost-efficient in the short-term, we recommend doing whole-of-site counts using drones. This is because it provides a time-saving and precise technique for long-term monitoring of the spatio-temporally dynamic invasion front of Cassiopea in coastal lakes and other sheltered marine habitats with relatively clear water.

Redescription of Euastacus clydensis Riek, 1969 (Crustacea: Parastacidae), a valid species of spiny crayfish from southern New South Wales, Australia.

The Giant Sydney Crayfish (Euastacus spinifer (Heller, 1865)) was thought to have a wide range in New South Wales, Australia, spanning some 600 km north-south. A recent extensive molecular phylogenetic and population genomic analysis of E. spinifer across its geographical range revealed strong population structure corresponding to several major geographically correlated clades, the southernmost clade being the most genetically divergent and clearly a separate species. This southern clade corresponds to the junior synonym E. clydensis Riek, 1969 and is sister to the clade comprising the remaining populations of E. spinifer and Euastacus vesper. We formally remove E. clydensis from the synonymy of E. spinifer, increasing the recognised number of species of Euastacus to 54. Euastacus clydensis is redescribed based on type and other material, and is distinguished from E. spinifer by differences in abdominal spination and the form of the antennal scaphocerite. Euastacus clydensis has a restricted southern New South Wales range in the Shoalhaven and Jervis Bay-Clyde River catchments, from Moss Vale south to the vicinity of Clyde Mountain; much of the known range of E. clydensis was burnt in the 2019-2020 eastern Australian megafires.

Hawaiian larval stomatopods: molecular and morphological diversity.

Estimating stomatopod species diversity using morphology alone has long been difficult; though over 450 species have been described, new species are still being discovered regularly despite the cryptic behaviors of adults. However, the larvae of stomatopods are more easily obtained due to their pelagic habitat, and have been the focus of recent studies of diversity. Studies of morphological diversity describe both conserved and divergent traits in larval stomatopods, but generally cannot be linked to a particular species. Conversely, genetic studies of stomatopod larvae using DNA barcoding can be used to estimate species diversity, but are generally not linked to known species by analyses of morphological characters. Here we combine these two approaches, larval morphology and genetics, to estimate stomatopod species diversity in the Hawaiian Islands. Over 22 operational taxonomic units (OTUs) were identified genetically, corresponding to 20 characterized morphological types. Species from three major superfamilies of stomatopod were identified: Squilloidea (4 OTUs, 3 morphotypes), Gonodactyloidea (9, 8), and Lysiosquilloidea (6, 7). Among these, lysiosquilloids were more diverse based on larval morphotypes and OTUs as compared to previously documented Hawaiian species (3), while squilloids had a lower diversity of species represented by collected larvae as compared to the seven species previously documented. Two OTUs / morphotypes could not be identified to superfamily as their molecular and morphological features did not closely match any available information, suggesting they belong to poorly sampled superfamilies. The pseudosquillid, Pseudosquillana richeri, was discovered for the first time from Hawai'i. This study contributes an updated estimate for Hawaiian stomatopod diversity for a total of 24 documented species, provides references for identification of larval stomatopods across the three major superfamilies, and emphasizes the lack of knowledge of species diversity in more cryptic stomatopod superfamilies, such as Lysiosquilloidea.

Stomatopod Crustacea of Lord Howe Island.

Prior to the present study, five species in four genera of the mantis shrimp superfamily Gonodactyloidea were known from Lord Howe Island, Australia. The 2017 Australian Museum expedition to Lord Howe Island made a small but significant collection of stomatopods, comprising four species: Chorisquilla tweediei (Serène, 1950), Gonodactylaceus falcatus (Forskål, 1775), Pseudosquilla ciliata (Fabricius, 1787) and a new species of Acaenosquilla, representing the first record of the superfamily Lysiosquilloidea from Lord Howe Island. The new species of Acaenosquilla is formally described and a key to the stomatopods of Lord Howe Island is provided.

First records of two species of reef-associated mantis shrimps (Crustacea: Stomatopoda) from India.

The coastal marine environments in the Indian Exclusive Economic Zone harbour a rich diversity of mantis shrimps. However, several regions have not been adequately surveyed for their stomatopod faunal composition. In this paper, we report the first records of two species, Gonodactylopsis drepanophora (de Man, 1902) and Cloridina malaccensis (Manning, 1968) from Indian waters. Samples were collected using a chain dredge deployed by the Fishery Oceanographic Research Vessel Sagar Sampada on the shallow reefs (5356 m depths) of the Andaman Sea and Bay of Bengal during AugustNovember 2019. Gonodactylopsis drepanophora was previously known only from Indonesia, and Cloridina malaccensis from Southeast Asia, New Caledonia and Madagascar.

Is it time to describe new species without diagnoses?A comment on Sharkey et al. (2021).

New methods in taxonomy and systematics can influence the overall practice of formally naming and describing biodiversity. DNA barcoding has been controversial since its emergence, but now, large scale species descriptions exclusively based on barcodes have created what can be called a 'new quality of performance. Its limitations are discussed from different perspectives: nomenclature, general pragmatism, and problems of DNA-based species delimitation in the light of the central aim of achieving a robust and stable nomenclature of organisms, essential for all applications of biodiversity research. This issue needs to be addressed to prevent restraining the progress of taxonomy and its ability to contribute to modern science.

Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae).

Many species of the gastropod genus Philine have been named from northeastern Asia but scanty descriptions based predominantly on shells make it difficult to determine which are valid. This, plus the sporadic anatomical and genetic information available for many of these species has led to what may be described as an un-integrated taxonomy. In this situation, it is generally preferable to postpone dissection of rare and unusual specimens until relevant diagnostic characters can be established in broader studies. Micro-CT scanning and DNA sequencing were used to examine such a specimen collected recently from deep waters off northeastern Taiwan. Micro-CT examination of the morphology of the internal shell and gizzard plates suggested that, among named species, the sequenced specimen is most similar to P.otukai. It cannot, however, be definitively referred to P.otukai as that species lacks adequate anatomical description or known DNA sequences. Phylogenetic analyses of newly collected DNA sequences show the specimen to be most closely related to, but distinct from the northern Atlantic Ocean and Mediterranean species, Philinequadripartita. The sequences also confirm genetically that five or more species of Philine occur in northeast Asia, including at least three subject to considerable taxonomic uncertainty.

Mitochondrial genome of Sabella spallanzanii (Gmelin, 1791) (Sabellida: Sabellidae).

We report the mitochondrial genome of Sabella spallanzanii, an invasive Mediterranean sabellid introduced to Australia and New Zealand. The mitogenome is 15,581 bp long and consists of 38 genes, including 13 protein coding genes, two rRNA genes, and 23 tRNA genes. It shows deviations from the putative annelid ground pattern, such as gene order re-arrangements and regions encoding on the negative strand. It is, however, very different from the mitogenome of the closely related serpulid, Spirobranchus giganteus. Phylogenetic analyses of the mitochondrial genes support a sister relationship of Sabella spallanzanii and Spirobranchus giganteus.

New species of pinnotherid crabs from Southeast Asia and Papua New Guinea (Crustacea: Decapoda: Brachyura).

Three new Indo-West Pacific species of pinnotherid crabs are described, one each of Arcotheres, Buergeres and Nepinnotheres. Arcotheres pollus, described from Paway Island, Mergui Archipelago, is most similar to A. boninensis (Stimpson, 1858), A. pernicola (Bürger, 1895) and A. purpureus (Alcock, 1900), sharing a transversely ovate carapace and long, slender, almost styliform dactyli of P4 and 5 that are about twice the length of those of P2 and 3. Buergeres choprai, described from Papua New Guinea, is most similar to B. deccanesis (Chopra, 1931) from eastern India but differentiated by segment proportions and setation of the walking legs. Buergeres tenuipes (Bürger, 1895) is synonymised with B. ortmanni (Bürger, 1895), which is also reported for the first time from Indonesia. A male of an undetermined species of Buergeres from the Philippines, possibly B. ortmanni, is figured and described, documenting the gonopod morphology in Buergeres for the first time. A key to the species of Buergeres based on females is provided. Nepinnotheres fulvia sp. nov. is also described from Papua New Guinea, and resembles N. cardii (Bürger, 1895) from the Philippines and Malaysia but can be distinguished by features of the chelipeds and maxilliped 3.

An annotated checklist of the mantis shrimps of India (Crustacea: Stomatopoda).

An annotated checklist of the mantis shrimps (Stomatopoda) occurring in India is compiled from published literature and specimens collected from coastal areas of Gujarat state. A total of 72 species, 35 genera, 10 families and 5 superfamilies reported from Indian waters are listed. Four species were recorded for the first time from Gujarat while one species, Erugosquilla hesperia (Manning, 1968), is confirmed for the first time from India. The maximum number of species was reported from Tamil Nadu (48 species), while fewest species were reported from Karnataka (2 species). The results also suggest that the east coast is more diverse (66 species) than the west coast of India (32 species).

Discovery of Viridotheres Manning, 1996 in the southwestern Pacific and first record of Discorsotheres camposi Ahyong, 2018 from New Caledonia (Crustacea: Brachyura: Pinnotheridae).

The pinnotherid crab genus, Viridotheres Manning, 1996, is recorded for the first time from the southwestern Pacific in the new species, V. asaphis, described based on specimens from Australia and New Caledonia. The new species most closely resembles V. sanguinolariae (Pillai, 1951) from India, differing chiefly in the proportional length of the walking legs; both species are hosted by bivalve molluscs of the family Psammobiidae, but of different genera. The pinnotherid crab Discorsotheres camposi Ahyong, 2018, an associate of the bivalve Spondylus, is recorded for the first time from New Caledonia. Fifteen species of pinnotherid are now known from Australian waters and five from New Caledonia.