Shane T. Ahyong

Phylogeny of Decapoda using two nuclear protein-coding genes: Origin and evolution of the Reptantia

The phylogeny of Decapoda is contentious and many hypotheses have been proposed based on morphological cladistic analyses. Recent molecular studies, however, yielded contrasting results despite their use of similar data (nuclear and mitochondrial rDNA). Here we present the first application of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, to reconstruct the phylogeny of major infraorders within Decapoda. A total of 64 species representing all infraorders of Pleocyemata were analyzed with five species from Dendrobranchiata as outgroups. Maximum likelihood and Bayesian inference reveal that the Reptantia and all but one infraorder are monophyletic. Thalassinidea, however, is polyphyletic. The nodal support for most of the infraordinal and inter-familial relationships is high. Stenopodidea and Caridea form a clade sister to Reptantia, which comprises two major clades. The first clade, consisting of Astacidea, Achelata, Polychelida and three thalassinidean families (Axiidae, Calocarididae and Eiconaxiidae), corresponds essentially to the old taxon suborder Macrura Reptantia. Polychelida nests within Macrura Reptantia instead of being the most basal reptant as suggested in previous studies. The high level of morphological and genetic divergence of Polychelida from Achelata and Astacidea justifies its infraorder status. The second major reptant clade consists of Anomura, Brachyura and two thalassindean families (Thalassinidae and Upogebiidae). Anomura and Brachyura form Meiura, with moderate support. Notably thalassinidean families are sister to both major reptant clades, suggesting that the stem lineage reptants were thalassinidean-like. Moreover, some families (e.g. Nephropidae, Diogenidae, Paguridae) are paraphyletic, warranting further studies to evaluate their status. The present study ably demonstrates the utility of nuclear protein-coding genes in phylogenetic inference in decapods. The topologies obtained are robust and the two molecular markers are informative across a wide range of taxonomic levels. We propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics.

A new hypothesis of decapod phylogeny

A cladistic analysis based on external morphology was carried out on 60 taxa of decapod crustaceans. An analysis with unordered characters and one with ordered characters were both in agreement regarding the major relationships. The ordered analysis gave better resolution of more advanced clades, while the unordered analysis gave better resolution of more basal clades. None of the traditional groups Palinura, Anomura, and Macrura is monophyletic. A new classie cation of decapod crustaceans is proposed. Homarida and Astacida are closely related, as shown by the unique process on the ischium of their e rst pereiopods. Glypheoidea forms the sister group to Astacura, within an enlarged Astacidea. Achelata is the sister group to Meiura (Anomala + Brachyura) in a new clade, Eurysternalia, characterized by a unique antennular morphology and by the eponymous wide sternum of its members. Thalassinida emerge as the sister group to Eurysternalia, in a new clade, Sterropoda, characterized by fusion of the e rst segments of the thoracic limbs. The fractostern is interpreted to be a eureptant feature, and a possible burrowing habitus is posited for the ancestral Eureptantia.

Morphological phylogeny of alpheid shrimps : Parallel preadaptation and the origin of a key morphological innovation, the snapping claw

Abstract The Alpheidae—possibly the most diverse family of recent decapod crustaceans—offers attractive opportunities to study the evolution of many intriguing phenomena, including key morphological innovations like spectacular snapping claws, highly specialized body forms, facultative and obligate symbioses with many animal groups, and sophisticated behaviors like eusociality. However, studies of these remarkable adaptations remain hampered by insufficient phylogenetic information. We present the first phylogenetic hypothesis of relationships among 36 extant genera of alpheid shrimps, based on a cladistic analysis of 122 morphological characters from 56 species, and we use this hypothesis to explore evolutionary trends in morphology and species diversity. Our results strongly supported a monophyletic Alpheidae that included two hitherto difficult-to-place genera (Yagerocaris and Pterocaris). Of 35+ nodes among genera, all were supported by at least one morphological character (24 were supported by two or more) and 17 received greater than 50% jackknife support. Unfortunately, many basal nodes were only weakly supported. Six genera appeared nonmonophyletic, including the dominant genus Alpheus (paraphyletic due to inclusion of one clade with three minor genera). Evolutionary trends in alpheid claw form shed some revealing light on how key innovations evolve. First, several functionally significant features of the cheliped (claw bearing leg) evolved independently multiple times, including: asymmetry, folding, inverted orientation, sexual dimorphism, adhesive plaques that enhance claw cocking, and tooth-cavity systems on opposing claw fingers, a preadaptation for snapping. Many conspicuous features of alpheid claw form therefore appear prone to parallel evolution. Second, although tooth-cavity systems evolved multiple times, a functional snapping claw, which likely facilitated an explosive radiation of over 550 species, evolved only once (in Synalpheus + [Alpheus + satellite genera]). Third, adhesive plaques (claw cocking aids) also evolved multiple times, and within snapping alpheids are associated with the most diverse clade (Alpheus + derivative genera). This pattern of parallel preadaptation—multiple independent evolutionary origins of precursors (preadaptations) to what ultimately became a key innovation (adaptation)—suggests alpheid shrimp claws are predisposed to develop features like tooth-cavity and adhesive plaque systems for functional or developmental reasons. Such functional/developmental predisposition may facilitate the origin of key innovations. Finally, moderate orbital hoods—anterior projections of the carapace partly or completely covering the eyes—occur in many higher Alpheidae and likely evolved before snapping claws. They are unique among decapod crustaceans, and their elaboration in snapping alpheids suggests they may protect the eyes from the stress of explosive snaps. Thus one key innovation (orbital hoods) may have facilitated evolution of a second (snapping claws).

A comprehensive and integrative reconstruction of evolutionary history for Anomura (Crustacea: Decapoda).

BackgroundThe infraorder Anomura has long captivated the attention of evolutionary biologists due to its impressive morphological diversity and ecological adaptations. To date, 2500 extant species have been described but phylogenetic relationships at high taxonomic levels remain unresolved. Here, we reconstruct the evolutionary history—phylogeny, divergence times, character evolution and diversification—of this speciose clade. For this purpose, we sequenced two mitochondrial (16S and 12S) and three nuclear (H3, 18S and 28S) markers for 19 of the 20 extant families, using traditional Sanger and next-generation 454 sequencing methods. Molecular data were combined with 156 morphological characters in order to estimate the largest anomuran phylogeny to date. The anomuran fossil record allowed us to incorporate 31 fossils for divergence time analyses.ResultsOur best phylogenetic hypothesis (morphological + molecular data) supports most anomuran superfamilies and families as monophyletic. However, three families and eleven genera are recovered as para- and polyphyletic. Divergence time analysis dates the origin of Anomura to the Late Permian ~259 (224–296) MYA with many of the present day families radiating during the Jurassic and Early Cretaceous. Ancestral state reconstruction suggests that carcinization occurred independently 3 times within the group. The invasion of freshwater and terrestrial environments both occurred between the Late Cretaceous and Tertiary. Diversification analyses found the speciation rate to be low across Anomura, and we identify 2 major changes in the tempo of diversification; the most significant at the base of a clade that includes the squat-lobster family Chirostylidae.ConclusionsOur findings are compared against current classifications and previous hypotheses of anomuran relationships. Many families and genera appear to be poly- or paraphyletic suggesting a need for further taxonomic revisions at these levels. A divergence time analysis provides key insights into the origins of major lineages and events and the timing of morphological (body form) and ecological (habitat) transitions. Living anomuran biodiversity is the product of 2 major changes in the tempo of diversification; our initial insights suggest that the acquisition of a crab-like form did not act as a key innovation.

Marine Biodiversity of Aotearoa New Zealand

The marine-biodiversity assessment of New Zealand (Aotearoa as known to Māori) is confined to the 200 nautical-mile boundary of the Exclusive Economic Zone, which, at 4.2 million km2, is one of the largest in the world. It spans 30° of latitude and includes a high diversity of seafloor relief, including a trench 10 km deep. Much of this region remains unexplored biologically, especially the 50% of the EEZ deeper than 2,000 m. Knowledge of the marine biota is based on more than 200 years of marine exploration in the region. The major oceanographic data repository is the National Institute of Water and Atmospheric Research (NIWA), which is involved in several Census of Marine Life field projects and is the location of the Southwestern Pacific Regional OBIS Node; NIWA is also data manager and custodian for fisheries research data owned by the Ministry of Fisheries. Related data sources cover alien species, environmental measures, and historical information. Museum collections in New Zealand hold more than 800,000 registered lots representing several million specimens. During the past decade, 220 taxonomic specialists (85 marine) from 18 countries have been engaged in a project to review New Zealands entire biodiversity. The above-mentioned marine information sources, published literature, and reports were scrutinized to give the results summarized here for the first time (current to 2010), including data on endemism and invasive species. There are 17,135 living species in the EEZ. This diversity includes 4,315 known undescribed species in collections. Species diversity for the most intensively studied phylum-level taxa (Porifera, Cnidaria, Mollusca, Brachiopoda, Bryozoa, Kinorhyncha, Echinodermata, Chordata) is more or less equivalent to that in the ERMS (European Register of Marine Species) region, which is 5.5 times larger in area than the New Zealand EEZ. The implication is that, when all other New Zealand phyla are equally well studied, total marine diversity in the EEZ may be expected to equal that in the ERMS region. This equivalence invites testable hypotheses to explain it. There are 177 naturalized alien species in New Zealand coastal waters, mostly in ports and harbours. Marine-taxonomic expertise in New Zealand covers a broad number of taxa but is, proportionately, at or near its lowest level since the Second World War. Nevertheless, collections are well supported by funding and are continually added to. Threats and protection measures concerning New Zealands marine biodiversity are commented on, along with potential and priorities for future research.

Feral populations of the Australian Red-Claw crayfish (Cherax quadricarinatus von Martens) in water supply catchments of Singapore

The Red-Claw crayfish, Cherax quadricarinatus von Martens, is native to freshwater habitats of northern Australia and Papua New Guinea. Owing to its large size and suitability for aquaculture, C. quadricarinatus has been widely translocated around the world. Unfortunately, C. quadricarinatus is also recognised as invasive, having already established feral populations in South Africa, Mexico, Jamaica and Puerto Rico. The hardiness and conspicuous colouration of C. quadricarinatus has also made it popular in the aquarium trade worldwide, including Singapore. Here, we report the establishment of feral populations of C. quadricarinatus in the water supply catchments of Singapore.

CLADISTIC ANALYSIS OF DASYUROMORPHIAN (MARSUPIALIA) PHYLOGENY USING CRANIAL AND DENTAL CHARACTERS

Abstract Dasyuromorphian relationships were investigated using cladistic analysis for 24 species using 77 cranial and dental features. Among the 7 extinct taxa used were 6 recently described fossil species, each well represented by cranial and dental material (3 ameridelphians, 1 peramelemorphian, and 2 dasyuromorphians). Monophyly for the Dasyuromorphia and several clades widely recognized therein is supported, but in many instances, relationships among extant dasyurids departs greatly from general consensus. Where congruence with previous investigations is evident, few taxa are united by unique synapomorphies within Marsupialia. Many clades are united by combinations of locally derived features only. Bootstrap and Bremer support is weak for most clades. Thus, although supported by cladistic analysis, the status of many synapomorphies identified in the course of this study are tentative. However, for some groups, notably Dasyuridae and a dasyurid clade inclusive of all modern subfamilies, the synapomorphic nature of some derived features appears to be robust, even where they also are present in some outgroup taxa. This argument applies to shared apomorphies of the basicranium in particular. No potential sister taxon to Dasyuromorphia is favored. The case for australidelphian and microbiotheriid affinity of some American and Antarctic fossil taxa was considered to be highly equivocal.

Galatheoidea are not monophyletic - molecular and morphological phylogeny of the squat lobsters (Decapoda: Anomura) with recognition of a new superfamily.

The monophyletic status of the squat lobster superfamily Galatheoidea has come under increasing doubt by studies using evidence as diverse as larval and adult somatic morphology, sperm ultrastructure, and molecular data. Here we synthesize phylogenetic data from these diverse strands, with the addition of new molecular and morphological data to examine the phylogeny of the squat lobsters and assess the status of the Galatheoidea. A total of 64 species from 16 of the 17 currently recognised anomuran families are included. Results support previous work pointing towards polyphyly in the superfamily Galatheoidea and Paguroidea, specifically, suggesting independent origins of the Galatheidae+Porcellanidae and the Chirostylidae+Kiwaidae. Morphological characters are selected that support clades resolved in the combined analysis and the taxonomic status of Galatheoidea sensu lato is revised. Results indicate that Chirostylidae are more closely related to an assemblage including Aegloidea, Lomisoidea and Paguroidea than to the remaining Galatheoidea and are referred to the superfamily Chirostyloidea to include the Chirostylidae and Kiwaidae. A considerable amount of research highlighting morphological differences supporting this split is discussed. The Galatheoidea sensu stricto is restricted to the families Galatheidae and Porcellanidae, and diagnoses for both Chirostyloidea and Galatheoidea are provided. Present results highlight the need for a detailed revision of a number of taxa, challenge some currently used morphological synapomorphies, and emphasise the need for integrated studies with wide taxon sampling and multiple data sources to resolve complex phylogenetic questions.

New Species and New Records of Hydrothermal Vent Shrimps from New Zealand (Caridea: Alvinocarididae, Hippolytidae)

Alvinocaris alexander sp. nov. (Alvinocarididae) and Lebbeus wera sp. nov. (Hippolytidae) are described from hydrothermal vents on the southern Kermadec Ridge, northern New Zealand. Alvinocaris alexander most closely resembles A. williamsi Shank & Martin, 2003 from the Mid-Atlantic Ridge, differing in rostral, antennular, and abdominal features. Alvinocaris alexander is apparently sympatric with A. niwa Webber, 2004, and comprises part of the type series of the latter. Lebbeus wera is the first species of the genus to be recorded from New Zealand waters and is most similar to other deep-water Lebbeus species including Lebbeus washingtonianus (Rathbun, 1902) and L. polyacanthus Komai, Hayashi & Kohtsuka, 2004, but is distinctive in its five dorsal postrostral teeth. The first records of the alvinocaridid, Nautilocaris saintlaurentae Komai & Segonzac, 2004, from Brothers Seamount, New Zealand, are reported, being previously known only from the North Fiji and Lau basins. Three genera and five species of caridean shrimp are now known from New Zealand hydrothermal vents. Alvinocaris alexander sp. nov. (Alvinocarididae) und Lebbeus wera sp. nov. (Hippolytidae) werden im Folgenden von hydrothermalen Quellen des sudlichen Kermadec Ruckens, Nord-Neuseeland, beschrieben. Alvinocaris alexander ahnelt A. williamsi Shank & Martin, 2003 vom Mittelatlantischen Rucken, unterscheidet sich aber in Merkmalen des Rostrums, der Antennen und des Abdomens. Alvinocaris alexander ist scheinbar sympatrisch mit A. niwa Webber, 2004, und stellt einen Teil dessen Typenserie dar. Lebbeus wera ist die erste Art dieser Gattung aus neuseelandischen Gewassern und ahnelt anderen Tiefseearten der Gattung Lebbeus wie Lebbeus washingtonianus (Rathbun, 1902) und L. polyacanthus Komai, Hayashi & Kohtsuka, 2004, unterscheidet sich von diesen allerdings durch seine funf dorsalen postrostralen Zahne. Erstmals wird hier die alvinocaridide Nautilocaris saintlaurentae Komai & Segonzac, 2004, von dem Brothers Seamount, Neuseeland, gemeldet. Bisher war diese Art nur vom Nord-Fidschi-Becken und dem Lau Becken bekannt. Damit sind drei Gattungen und funf Arten carideaner Garnele von neuseelandischen Hydrothermalquellen bekannt.

Semisubmersible oil platforms: understudied and potentially major vectors of biofouling-mediated invasions.

Biofouling has long been recognised as a major pathway for the introduction of non-indigenous species. This study records the decapods and stomatopod crustaceans fouling a semisubmersible oil platform dry docked for hull cleaning in Jurong Port, Singapore. Of the 25 species of decapods identified, 13 were non-indigenous and represent new records to Singapore waters. Of these, the crabs Glabropilumnus seminudus and Carupa tenuipes are known to be invasive in other parts of the world. The stomatopod, Gonodactylaceus randalli, is the first mantis shrimp recorded in a biofouling community. The richness and diversity of this fouling community, consisting of many vagile species, highlights the difference between platforms and ships. With the expansion of maritime oil and gas exploration, the threat posed by an expanded fleet of semisubmersible oil platforms translocating non-indigenous fouling communities across biogeographical boundaries is very serious. Scientists, policy-makers, and stakeholders should turn their attention to this growing problem.