Tin-Yam Chan

Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia: Pleistocene isolation, population expansion and secondary contact.

We examined the impact of Pleistocene glacial cycles on geographical distribution and genetic structure of the mitten crab Eriocheir sensu stricto in East Asia using sequence variation of mitochondrial cytochrome c oxidase I and cytochrome b gene segments. Phylogenies revealed four distinct but shallow structured lineages in Eriocheir s. s. Three lineages dominated the East China Sea-Yellow Sea, the Sea of Japan and the South China Sea on the margins of the region, and one lineage occurred on Okinawa Island. This geographical distribution represents a general phylogeographic pattern in East Asia, which is closely associated with the fluctuations of marginal seas and islands during the Pleistocene. The four lineages are estimated to have diverged during the mid-Pleistocene. Demographic expansions were observed in each lineage, starting within the second-to-latest interglacial period in the marginal sea lineages ( approximately 70-130ka) and within the last glacial period in the Okinawa lineage ( approximately 25-80ka). Expansions have probably taken place northward along the coast of the East China Sea-Yellow Sea, following the rise of sea levels. Centered on the southern Korean Peninsula, expansions have likely occurred northward along the west coast and eastward along the south coast of the Sea of Japan. Each marginal sea has served as a single refugium during glacial periods. Two secondary contact regions were identified, one of the East China Sea-Yellow Sea and South China Sea lineages, and another of the East China Sea-Yellow Sea and Sea of Japan lineages. Phylogeography of Eriocheir s. s. provides insights into the evolutionary history and mechanism for generating biodiversity in East Asia.

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes

BackgroundThe evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders.ResultsWe present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis.ConclusionsPhylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

Unweaving hippolytoid systematics (Crustacea, Decapoda, Hippolytidae): resurrection of several families

The Hippolytidae is the fourth largest family within the Caridea, currently containing over 330 described species in 37 genera, and the classification of this family has been rather controversial. In this study, sequences of two nuclear protein‐coding genes, enolase and sodium‐potassium ATPase α‐subunit, and the mitochondrial 16S rRNA gene (totalling 1405 bp) from 29 hippolytid species in 20 genera plus 17 species from eight other caridean families were used to examine the phylogenetic status of Hippolytidae sensu lato. Our results clearly reject the monophyly of Hippolytidae and support the recognition of the Lysmatidae Dana, 1852, Thoridae Kingsley, 1879, Bythocarididae Christoffersen and Merguiidae Christoffersen .

On the different forms of Panulirus longipes femoristriga (von Martens, 1872) (Crustacea: Decapoda: Palinuridae), with description of a new species

Material previously identified as Panulirus longipes femoristriga (von Martens, 1872) is found to have two forms of coloration, namely the banded whisker form and the white whisker form. Careful comparisons of fresh lobsters reveal that the two forms differ in morphological characters. Data from allozyme analysis also shows that they are genetically distinct. To stabilize the confused taxonomy of these species, a neotype for P. longipes femoristriga is selected from a specimen of the banded whisker form from the type-locality Amboina. The white whisker form is shown to be a new species.

Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes

Ma, K. Y., Chan, T. ‐Y & Chu, K. H. (2011). Refuting the six‐genus classification of Penaeus s.l. (Dendrobranchiata, Penaeidae): a combined analysis of mitochondrial and nuclear genes. —Zoologica Scripta, 40, 498–508.

TWO UNUSUAL SPECIES OF ALPHEIDAE (DECAPODA: CARIDEA) ASSOCIATED WITH UPOGEBIID MUDSHRIMPS IN THE MUDFLATS OF TAIWAN AND VIETNAM

Abstract Descriptions are provided for Athanas dentirostris, new species, and Chelomalpheus crangonus, new species, two alpheid shrimps collected from the burrows of the upogebiids Upogebia aff. takaoensis Sakai and Turkay, 1995, and Upogebia edulis Ngoc-Ho and Chan, 1992, respectively. Athanus dentirostris, known only from northern Vietnam, is unique among all Alpheidae in having the superior margin of the rostrum dentate. Adult males of C. crangonus are immediately recognizable by the peculiar, subcheliform first pereiopods, which show superficial resemblance to the chelipeds of Crangonidae.

Mitochondrial cytochrome oxidase I sequence divergence in some Chinese species of Charybdis (Crustacea: Decapoda: Portunidae)

Analysis of the mitochondrial cytochrome oxidase subunit I sequences of four species of Charybdis crabs reveals genetic differences between them and the phylogenetic affinities among them. In C. affinis and C. japonica, no sequence divergence was observed between samples from Taiwan and the Zhujiang estuary. The two species are closely related but genetically distinct and may represent sibling species. The present result is consistent with results based on morphological and allozyme analyses.

Origin and diversification of the clawed lobster genus Metanephrops (Crustacea: Decapoda: Nephropidae)

A phylogenetic analysis of all 17 extant species of the clawed lobster genus Metanephrops based on mitochondrial 12S rRNA, 16S rRNA and cytochrome c oxidase I, and nuclear histone H3 gene sequences supports the morphological groupings of two of the traditional groups of the genus (the binghami and japonicus groups) but refutes monophyly of the other two groups (the arafurensis and thomsoni groups). The results in general support a recent morphology-based cladistic analysis of this genus except that this study suggests M. neptunus to be a basal rather than a derived species as indicated in the morphological analysis. This species is genetically diverse over its geographical range. Moreover, the two color forms of M. thomsoni are genetically distinct, most likely representing different species. The molecular phylogeny and current distribution pattern of the extant species, together with the fossil record, suggest that the genus originated in the Antarctica in the Cretaceous, followed by diversification and dispersal along the continental shelf of different continents as a result of the vicariant events associated with the breakup of the Southern Temperate Gondwana since Late Cretaceous.

Phylogenetic relationships among genera of the Periclimenes complex (Crustacea: Decapoda: Pontoniinae) based on mitochondrial and nuclear DNA

The genus Periclimenes Costa, 1844 is the most species-rich genus in the subfamily Pontoniinae. Recent studies have suggested that it might be a polyphyletic taxon and could be further subdivided. In this study, three protein-coding nuclear genes and one mitochondrial ribosomal gene were used to analyze the phylogenetic relationships among the genera of the Periclimenes complex, includes the genus Periclimenes and 15 related genera, viz. Ancylomenes, Brucecaris, Crinotonia, Cuapetes, Harpiliopsis, Harpilius, Laomenes, Leptomenaeus, Manipontonia, Palaemonella, Periclimenella, Philarius, Phycomenes, Unguicaris and Vir. Based on both independent and combined data analyses, the results support that the genus Periclimenes is a polyphyletic group. Furthermore, the studied Periclimenes species could be divided into several independent groups, and the taxonomic status of P. commensalis, P. brevicarpalis and P. digitalis may need to be reconsidered. Besides, the majority of the related genera of Periclimenes are suggested to be monophyletic. Our analyses also reveal that these genera approximately form two main clades, despite some deep relationships are still obscure.

Phylogenetic and transcriptomic analyses reveal the evolution of bioluminescence and light detection in marine deep-sea shrimps of the family Oplophoridae (Crustacea: Decapoda)

Bioluminescence is essential to the survival of many organisms, particularly in the deep sea where light is limited. Shrimp of the family Oplophoridae exhibit a remarkable mechanism of bioluminescence in the form of a secretion used for predatory defense. Three of the ten genera possess an additional mode of bioluminescence in the form of light-emitting organs called photophores. Phylogenetic analyses can be useful for tracing the evolution of bioluminescence, however, the few studies that have attempted to reconcile the relationships within Oplophoridae have generated trees with low-resolution. We present the most comprehensive phylogeny of Oplophoridae to date, with 90% genera coverage using seven genes (mitochondrial and nuclear) across 30 oplophorid species. We use our resulting topology to trace the evolution of bioluminescence within Oplophoridae. Previous studies have suggested that oplophorid visual systems may be tuned to differentiate the separate modes of bioluminescence. While all oplophorid shrimp possess a visual pigment sensitive to blue-green light, only those bearing photophores have an additional pigment sensitive to near-ultraviolet light. We attempt to characterize opsins, visual pigment proteins essential to light detection, in two photophore-bearing species (Systellaspis debilis and Oplophorus gracilirostris) and make inferences regarding their function and evolutionary significance.