Phylogeography of Long-spined Sea Urchin Diadema setosum Across the Indo-Malay Archipelago

Widely distributed, broadcast-spawning Diadema sea urchins have been used as model invertebrate species for studying the zoogeography of the tropical Indo-Pacific. So far, the Indo-Malay archipelago, a wide and geographically complex maritime region extending from the eastern Indian Ocean to the western Pacific Ocean, has been under-sampled. This study aims to fill this sampling gap and uncover the phylogeographic structure of the long-spined sea-urchin D. setosum in the central Indo-West pacific region. D. setosum samples (total N = 718) were collected in 13 sites throughout the Indo-Malay archipelago. We sequenced over 1157 bp of COI gene. The Phylogeographic structure was derived from pairwise ФST estimates using multidimensional scaling and hierarchical clustering analysis; biogeographic hypotheses were tested by AMOVA; genetic relationships between haplotypes were summarised in the form of a minimum-spanning network; and pairwise mismatch distributions were compared to the expectations from demographic and spatial expansion models. All samples from the Indo-West Pacific were of the previously uncovered D. setosum-a lineage. Phylogeographic structure was evident: the Andaman Sea population and the northern New Guinea population were genetically distinct. Subtler but significant haplotype-frequency differences distinguished two populations within the Indonesian seas, distributed in a parapatric-like fashion. The phylogeographic partition observed was insufficiently explained by previous biogeographic hypotheses. The haplotype network showed a series of closely related star-shaped haplogroups with a high proportion of singletons. Nucleotide-pairwise mismatch patterns in the two populations from the Indonesian seas were consistent with both demographic and spatial expansion models. While geographic barriers to gene flow were inferred at the western and eastern extremities of the Indo-Malay archipelago, the subtler parapatric pattern observed within the Indonesian seas indicated restriction in gene flow, in a fashion that can hardly be explained by geographic isolation given the dynamic current systems that cross this region. Our results thus raise the hypothesis of subtle reproductive isolation between ecologically incompatible populations. While the coalescence pattern of the Andaman-Sea population suggested demographic stability over evolutionary timescales, that of the two populations from the Indonesian seas indicated recent population expansion, possibly linked to the rapid changes in available D. setosum habitat caused by sea-level oscillations in the late Pleistocene. The phylogeographic patterns observed in this study point to likely allopatric differentiation in the central Indo-West Pacific region. Genetic differences between populations were likely reinforced during interglacials by some form of reproductive isolation.

Stepping up to genome scan allows stock differentiation in the worldwide distributed blue shark Prionace glauca

The blue shark Prionace glauca is a top predator with one of the widest geographical distributions of any shark species. It is classified as Critically Endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population. The blue shark was proposed as a possible archetype of the "grey zone of population differentiation," coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific RAD method (DArTseq), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and northern Atlantic samples (Northern population) differentiated significantly from the Indo-west Pacific samples (Southern population). Significant pairwise F_ST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested divergence between Northern and Southern populations occurred about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. Given that the management plans of the blue shark (targeted or bycatch) fisheries currently assume panmictic regional stocks, we strongly recommend that the results presented here be considered in future stock assessments and conservation strategies.

Modelling Marine Predator Habitat Using the Abundance of Its Pelagic Prey in the Tropical South-Western Pacific

Understanding the ecological mechanisms underpinning distribution patterns is vital in managing populations of mobile marine species. This study is a first step towards an integrated description of the habitats and spatial distributions of marine predators in the Natural Park of the Coral Sea, one of the world’s largest marine-protected areas at about 1.3 million km2, covering the entirety of New Caledonia’s pelagic waters. The study aims to quantify the benefit of including a proxy for prey abundance in predator niche modelling, relative to other marine physical variables. Spatial distributions and relationships with environmental data were analysed using catch per unit of effort data for three fish species (albacore tuna, yellowfin tuna and dolphinfish), sightings collected from aerial surveys for three cetacean guilds (Delphininae, Globicephalinae and Ziphiidae) and foraging locations identified from bio-tracking for three seabird species (wedge-tailed shearwater, Tahiti petrel and red-footed booby). Predator distributions were modelled as a function of a static covariate (bathymetry), oceanographic covariates (sea surface temperature, chlorophyll-a concentration and 20 °C-isotherm depth) and an acoustically derived micronekton preyscape covariate. While distributions were mostly linked to bathymetry for seabirds, and chlorophyll and temperature for fish and cetaceans, acoustically derived prey abundance proxies slightly improved distribution models for all fishes and seabirds except the Tahiti petrel, but not for the cetaceans. Predicted spatial distributions showed that pelagic habitats occupied by predator fishes did not spatially overlap. Finally, predicted habitats and the use of the preyscapes in predator habitat modelling were discussed.

Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods

DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.

Diversity, phylogeny, and historical biogeography of large-eye seabreams (Teleostei: Lethrinidae)

The large-eye seabreams or Monotaxinae is one of two subfamilies in the Lethrinidae, a family of perch-like coral reef fishes. Despite its widespread occurrence and its commercial interest in the tropical Indo-West Pacific (IWP), this subfamily has traditionally been considered a taxonomically difficult group. Based on 268 samples collected from all 15 known large-eye seabream species throughout their distribution ranges, we investigated the taxonomic diversity and phylogenetic relationships in the subfamily. From the results of multiple analyses on four gene markers, we confirmed the monophyly of all four genera in the subfamily (Gnathodentex, Gymnocranius, Monotaxis and Wattsia). We confirmed the occurrence of two species in the genus Monotaxis. We reported 15 delimited species within the most speciose genus Gymnocranius, four of which are potentially new species. The time-calibrated phylogenetic reconstruction enabled us to clarify the evolutionary history of the large-eye seabreams and to infer past patterns of species distribution. The most recent common ancestor to the Monotaxinae likely occurred in the central IWP ca. 32 million years ago. A burst of species diversification likely took place during the Mid- to Late Miocene, coinciding with tectonic change in the central IWP region. This gave rise to most extant lineages in Gymnocranius. The observed geographic distribution patterns in the subfamily most likely point to the central IWP as the area of origin and diversification. This was followed by multiple events of centrifugal range expansion towards either the Indian Ocean or the western Pacific Ocean, or both. Our results thus provide new support for S. Ekman's center-of-origin hypothesis.

Neotrygon indica sp. nov., the Indian Ocean blue-spotted maskray (Myliobatoidei, Dasyatidae)

The blue-spotted maskray, previously N. kuhlii, consists of up to eleven lineages representing separate species. Nine of these species (N. australiae, N. bobwardi, N. caeruleopunctata, N. malaccensis, N. moluccensis, N. orientale, N. vali, N. varidens, N. westpapuensis) have already been formally described and two (Indian Ocean maskray and Ryukyu maskray) remain undescribed. Here, the Indian Ocean maskray is described as a new species, Neotrygon indica sp. nov. Specimens of the new species were generally characterized on their dorsal side by a moderately large number of small ocellated blue spots, a low number of medium-sized ocellated blue spots, the absence of large ocellated blue spots, a high number of dark speckles, a few dark spots, and a conspicuous occipital mark. The new species formed a distinct haplogroup in the tree built from concatenated nucleotide sequences at the CO1 and cytochrome b loci. A diagnosis based on colour patterns and nucleotide sequences at the CO1 and cytochrome b loci is proposed. The distribution of N. indica sp. nov. includes the Indian coast of the Bay of Bengal, the Indian coast of the Laccadives Sea, and Tanzania. Considerable sampling effort remains necessary for an in-depth investigation of the phylogeographic structure of the Indian Ocean maskray.

Characterization of genome-wide microsatellite markers in rabbitfishes, an important resource for artisanal fisheries in the Indo-West Pacific

Rabbitfishes are reef-associated fishes that support local fisheries throughout the Indo-West Pacific region. Sound management of the resource requires the development of molecular tools for appropriate stock delimitation of the different species in the family. Microsatellite markers were developed for the cordonnier, Siganus sutor, and their potential for cross-amplification was investigated in 12 congeneric species. A library of 792 repeat-containing sequences was built. Nineteen sets of newly developed primers, and 14 universal finfish microsatellites were tested in S. sutor. Amplification success of the 19 Siganus-specific markers ranged from 32 to 79% in the 12 other Siganus species, slightly decreasing when the genetic distance of the target species to S. sutor increased. Seventeen of these markers were polymorphic in S. sutor and were further assayed in S. luridus, S. rivulatus, and S. spinus, of which respectively 9, 10 and 8 were polymorphic. Statistical power analysis and an analysis of molecular variance showed that subtle genetic differentiation can be detected using these markers, highlighting their utility for the study of genetic diversity and population genetic structure in rabbitfishes.

Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes

On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species.

Multiple cryptic species in the blue-spotted maskray (Myliobatoidei: Dasyatidae: Neotrygon spp.): An update

Previous investigations have uncovered divergent mitochondrial clades within the blue-spotted maskray, previously Neotrygon kuhlii (Müller and Henle). The hypothesis that the blue-spotted maskray may consist of a complex of multiple cryptic species has been proposed, and four species have been recently described or resurrected. To test the multiple cryptic species hypothesis, we investigated the phylogenetic relationships and coalescence patterns of mitochondrial sequences in a sample of 127 new individuals from the Indian Ocean and the Coral Triangle region, sequenced at both the CO1 and cytochrome b loci. The maximum-likelihood (ML) tree of concatenated CO1+cytochrome b gene sequences, rooted by the New Caledonian maskray N. trigonoides, yielded 9 strongly supported, main clades. Puillandre's ABGD algorithm detected gaps in nucleotide distance consistent with the ML phylogeny. The general mixed Yule-coalescent algorithm partitioned the dataset into putative species generally consistent with the ML phylogeny. Nuclear markers generally confirmed that distinct mitochondrial clades correspond to genetically isolated lineages. The nine main lineages identified by ML analysis were geographically distributed in a parapatric fashion, indicating reproductive isolation. The hypothesis of multiple cryptic species is thus validated.

Next generation sequencing yields complete mitogenomes of Leopard whipray (Himantura leoparda) and Blue-spotted stingray (Neotrygon kuhlii) (Chondrichthyes: Dasyatidae)

The Leopard whipray (Himantura leoparda) and Blue-spotted stingray (Neotrygon kuhlii) are distributed in the Indian and West Pacific Ocean and considered as complex species based on morphological and molecular evidences. In this study, we used the next-generation sequencing method to decode two complete mitogenomes of H. leoparda and N. kuhlii. The assembled mitogenome, consisting lengths of 17,690 bp for H. leoparda and 17,974 bp for N. kuhlii, shows 78% identity to each other. Both mitogenomes follow the typical vertebrate arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop with the lengths 1931 bp (H. leoparda) and 2243 bp (N. kuhlii) is located between tRNA-Pro and tRNA-Phe. The overall GC content is 40.3% for H. leoparda and 39.8% for N. kuhlii. The complete mitogenome of H. leoparda and N. kuhlii provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses for stingray species complex.

Does natural selection explain the fine scale genetic structure at the nuclear exon Glu-5' in blue mussels from Kerguelen?

The Kerguelen archipelago, isolated in the Southern Ocean, shelters a blue mussel Mytilus metapopulation far from any influence of continental populations or any known hybrid zone. The finely carved coast leads to a highly heterogeneous habitat. We investigated the impact of the environment on the genetic structure in those Kerguelen blue mussels by relating allele frequencies to habitat descriptors. A total sample comprising up to 2248 individuals from 35 locations was characterized using two nuclear markers, mac-1 and Glu-5', and a mitochondrial marker (COI). The frequency data from 9 allozyme loci in 9 of these locations were also reanalyzed. Two other nuclear markers (EFbis and EFprem's) were monomorphic. Compared to Northern Hemisphere populations, polymorphism in Kerguelen blue mussels was lower for all markers except for the exon Glu-5'. At Glu-5', genetic differences were observed between samples from distinct regions (F CT = 0.077), as well as within two regions, including between samples separated by <500 m. No significant differentiation was observed in the AMOVA analyses at the two other markers (mac-1 and COI). Like mac-1, all allozyme loci genotyped in a previous publication, displayed lower differentiation (Jost's D) and F ST values than Glu-5'. Power simulations and confidence intervals support that Glu-5' displays significantly higher differentiation than the other loci (except a single allozyme for which confidence intervals overlap). AMOVA analyses revealed significant effects of the giant kelp Macrocystis and wave exposure on this marker. We discuss the influence of hydrological conditions on the genetic differentiation among regions. In marine organisms with high fecundity and high dispersal potential, gene flow tends to erase differentiation, but this study showed significant differentiation at very small distance. This may be explained by the particular hydrology and the carved coastline of the Kerguelen archipelago, together with spatially variable selection at Glu-5'.

Mitochondrial haplotypes indicate parapatric-like phylogeographic structure in blue-spotted maskray (Neotrygon kuhlii) from the Coral Triangle region

Phylogeographic structure was investigated in the blue-spotted maskray, Neotrygon kuhlii, focusing on the Coral Triangle region. We used as genetic marker a 519-bp fragment of the cytochrome c-oxidase subunit I (COI) gene, sequenced in a total of 147 individuals from 26 sampling locations. The parsimony network of COI haplotypes was split into seven distinct clades within the Coral Triangle region. Different clades had exclusive but contiguous geographic distributions, indicating parapatric-like phylogeographic structure. Strong genetic differences were also inferred between local populations within a clade, where reciprocal monophyly between geographically adjacent samples was observed on several instances. Nearly 25% of the total molecular variance could be ascribed to differences between geographic samples within a clade, whereas interclade variation accounted for >65% of the total variance. The strong phylogeographic structure observed within a clade can be explained by either sedentarity or female philopatry. We interpret the parapatric distribution of clades as the joint result of 1) expansion from refuge populations at times of low sea level, and 2) possible enhanced competition between individuals from different clades, or assortative mating, or hybrid zones, along lines of secondary contact. The parapatric-like structure uncovered in the present study parallels regional differences at nuclear marker loci, thus pointing to incipient speciation within Coral Triangle N. kuhlii.

Geometric morphometrics as a tool for identifying emperor fish (Lethrinidae) larvae and juveniles

The aim of this study was to evaluate the efficiency of geometric morphometrics for describing the body shape of fish larvae and juveniles, and identifying them to species, in comparison with traditional linear measurements. Species of emperor fishes (Perciformes: Lethrinidae, genus Lethrinus) were chosen as the model group, as the late larval and early juvenile stages in this genus are particularly difficult to identify. Forty-five individuals of different species of Lethrinus were collected from the south-western lagoon of New Caledonia between May 2005 and March 2006. The individuals were first identified to species by their partial cytochrome-b gene sequence. They were then morphologically characterized using eight linear measurements and 23 landmarks recorded on digital photographs. Except for a small proportion of individuals, geometric morphometrics gave better results to distinguish the different species than linear measurements. A 'leave one out' approach confirmed the nearly total discrimination of recently settled Lethrinus genivittatus and Lethrinus nebulosus, whereas traditional identification keys failed to distinguish them. Therefore, geometric morphometrics is a promising tool for identifying fish larvae and juveniles to species. An effective approach would require building image databases of voucher specimens associated with their DNA barcodes. These images could be downloaded by the operator and processed with the specimens to be identified.

The coral sea: physical environment, ecosystem status and biodiversity assets

The Coral Sea, located at the southwestern rim of the Pacific Ocean, is the only tropical marginal sea where human impacts remain relatively minor. Patterns and processes identified within the region have global relevance as a baseline for understanding impacts in more disturbed tropical locations. Despite 70 years of documented research, the Coral Sea has been relatively neglected, with a slower rate of increase in publications over the past 20 years than total marine research globally. We review current knowledge of the Coral Sea to provide an overview of regional geology, oceanography, ecology and fisheries. Interactions between physical features and biological assemblages influence ecological processes and the direction and strength of connectivity among Coral Sea ecosystems. To inform management effectively, we will need to fill some major knowledge gaps, including geographic gaps in sampling and a lack of integration of research themes, which hinder the understanding of most ecosystem processes.

Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy

The family Mugilidae comprises mainly coastal marine species that are widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase I, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level.

Pleistocene separation of mitochondrial lineages of Mytilus spp. mussels from Northern and Southern Hemispheres and strong genetic differentiation among southern populations

Smooth-shelled mussels, Mytilus spp., have an antitropical distribution. In the Northern Hemisphere, the M. edulis complex of species is composed of three genetically well delineated taxa: M. edulis, M. galloprovincialis and M. trossulus. In the Southern Hemisphere, morphological characters, allozymes and intron length polymorphisms suggest that Mytilus spp. populations from South America and Kerguelen Islands are related to M. edulis and those from Australasia to M. galloprovincialis. On the other hand, a phylogeny of the 16S rDNA mitochondrial locus demonstrates a clear distinctiveness of southern mussels and suggests that they are related to Mediterranean M. galloprovincialis. Here, we analysed the faster-evolving cytochrome oxidase subunit I locus. The divergence between haplotypes of populations from the two hemispheres was confirmed and was found to predate the divergence between haplotypes of northern M. edulis and M. galloprovincialis. In addition, strong genetic structure was detected among the southern samples, revealing three genetic entities that correspond to (1) South America and Kerguelen Island, (2) Tasmania, (3) New Zealand. Using the trans-Arctic interchange as a molecular clock calibration, we estimated the time since divergence of populations from the two hemispheres to be between 0.5 million years (MY) and 1.3 MY (average 0.84 MY). The contrasting patterns observed for the nuclear and the organelle genomes suggested two alternative, complex scenarios: two trans-equatorial migrations and the existence of differential barriers to mitochondrial and nuclear gene flow, or a single trans-equatorial migration and a view of the composition of the nuclear genome biased by taxonomic preconception.

Expression of two maize putative nitrate transporters in response to nitrate and sugar availability

A full-length cDNA encoding a putative high-affinity nitrate transporter (ZmNrt2.2) from maize was isolated and characterised, together with another previously identified transporter (ZmNrt2.1), in terms of phylogenesis, protein structure prediction and regulation of transcript accumulation in response to nitrate and sugar availability. The expression of both genes was evaluated by quantitative and semi-quantitative RT-PCR in response to nitrate and sugar supply and the in planta localisation of mRNA was studied by in situ hybridisation. Data obtained suggested similar genetic evolution and identical transmembrane structure prediction between the two deduced proteins, and differences in both regulation of their expression and mRNA localisation in response to nitrate, leading us to hypothesise a principal role for ZmNRT2.1 in the influx activity and the major involvement of ZmNRT2.2 in the xylem loading process. Our data suggest opposing sugar regulation by ZmNrt2.1 and ZmNrt2.2 transcription in the presence or absence of nitrate and the existence of both hexokinase-dependent and hexokinase-independent transduction mechanisms for the regulation of ZmNrt2.1 and ZmNrt2.2 expression by sugars.

Chromate differentially affects the expression of a high-affinity sulfate transporter and isoforms of components of the sulfate assimilatory pathway in Zea mays (L.)

In this study the chromate accumulation and tolerance were investigated in ZEA MAYS L. in relation to sulfur availability since sulfate may interact with chromate for transport into the cells. Chromate inhibited sulfate uptake when supplied to plants for a short-term period, whereas phosphate uptake remained unchanged. Sulfate absorption was also reduced in S-starved (-S) and S-supplied (+S) plants treated for 2 d with 0.2 mM chromate and the concomitant repression of the root high-affinity sulfate root transporter ZMST1;1 transcript accumulation was observed. Conversely, the plasma membrane H (+)-ATPase MHA2 was unaffected by chromate in +S plants, allowing to exclude a general effect of chromate on the active membrane transport. As observed for sulfate uptake, chromate uptake was enhanced in -S condition and decreased in both +S and -S plants after 2 d of Cr treatment. Chromate reduced the concentration of sulfur and sulfate in +S plants to the basal level of -S plants, and maximum chromium accumulation was recorded in S-deprived plants. Analysis of transcript abundance of genes involved in sulfate assimilation revealed differential regulation by chromate, which was only partly related to sulfur availability and to the levels of thiols. This work shows for the first time that chromate specifically represses sulfate uptake, and such repression occurs without the implication of the candidate regulatory metabolites of the sulfate transport system in plants.

Cytochrome b barcoding, molecular systematics and geographic differentiation in rabbitfishes (Siganidae)

The fish genus Siganus (Siganidae) is widely distributed in the coastal habitats of all the tropical Indo-Pacific, with 28 nominal species recognized so far, based on general morphology and coloration patterns. A mitochondrial phylogeny of 16 Siganidae species, based on the partial nucleotide sequences of the cytochome b gene, was produced. Individual haplotypes of given nominal species generally clustered at the extremity of long branches, thus validating the current taxonomy. However, S. lineatus haplotypes formed a paraphyletic group including S. guttatus, while S. fuscescens haplotypes were apparently splitted in two groups, calling for further investigation. S. woodlandi and S. argenteus formed a monophyletic group, as expected from their close morphological relatedness, although they were separated by a substantial, 14.5-16.3% nucleotide distance. Among eight species sampled from different locations across the Indo-West Pacific, S. argenteus and S. spinus showed the lowest degree of geographic differentiation, a result that correlated well with their extended pelagic larval stage. Fixation index estimates were high in all six other species tested (S. doliatus, S. fuscescens, S. lineatus, S. puellus, S. punctatus, S. vulpinus). The cytochrome b gene fragment chosen here proved useful as a barcode in Siganidae.

Marine mammal strandings in the New Caledonia region, Southwest Pacific

Four hundred twenty three marine mammals, in 72 stranding events, were recorded between 1877 and 2005 in New Caledonia, the Loyalty Islands, and Vanuatu in the southwest Pacific. Sixteen species were represented in this count, including: minke whale, Balaenoptera acutorostrata (1 single stranding), sei whale, B. borealis (1 single stranding), blue whale, B. musculus (1 single stranding), humpback whale, Megaptera novaeangliae (2 single strandings), giant sperm whale, Physeter macrocephalus (18 single strandings, 2 pair strandings), pygmy sperm whale, Kogia breviceps (5 single strandings), dwarf sperm whale, K. sima (2 single strandings, 1 triple stranding), Blainville's beaked whale, Mesoplodon densirostris (2 single strandings), short-finned pilot whale, Globicephala macrorhynchus (4 strandings, 56 individuals), melon-headed whale, Peponocephala electra (1 single stranding and 2 mass strandings totalling 231 individuals), common dolphin, Delphinus delphis (1 single stranding), spinner dolphin, Stenella longirostris (1 pair stranding and 2 mass strandings of groups of approximately 30 individuals each), Indian Ocean bottlenose dolphin, Tursiops aduncus (2 single strandings), dugong, Dugong dugon (14 single strandings), and New Zealand fur seal, Arctocephalus forsteri (3 single strandings). A stranded rorqual identified as an Antarctic minke whale (B. bonaerensis), with coloration patterns that did not match known descriptions, was also reported. Sei whale was recorded for the first time in the tropical Southwest Pacific region and Antarctic minke whale, melon-headed whale, and Indian Ocean bottlenose dolphin were recorded for the first time in New Caledonia. Strandings of sperm whales were most frequent in the spring, but also occurred in autumn months, suggesting a seasonal pattern of occurrence possibly related to seasonal migration. One stranded humpback whale bore the scars of a killer whale's attack and one dugong was injured by a shark. Scars left by propellers were noted on several stranded animals including one Antarctic minke whale, one pygmy sperm whale, one dwarf sperm whale, and four dugongs. Collisions with vessels were suspected to be a frequent cause of death for dugong.

Genetic structure of Indian scad mackerel Decapterus russelli: Pleistocene vicariance and secondary contact in the Central Indo-West Pacific Seas

Major genetic breaks between the Indian and Pacific oceans have been reported for marine fishes and invertebrates. The genetic structure and history of the Indian scad mackerel, Decapterus russelli, in the Indo-Malay archipelago were investigated using the cytochrome b gene sequence as mitochondrial marker and two length-polymorphic introns as nuclear markers. The existence of two major mitochondrial lineages separated by 2.2% average nucleotide divergence, and their heterogeneous geographical distributions, were confirmed. This indicated past geographic isolation, possibly caused by a Pleistocene drop in sea level. The presence, in sympatry, of the two mitochondrial lineages was thought to result from secondary contact. A recent population bottleneck and subsequent rapid population expansion were indicated by low genetic diversities and strongly negative Tajima's D-values. This evidence supports the hypothesis that the habitat available to D. russelli in the Pleistocene was restricted. Taking into account both mitochondrial and nuclear-DNA data, three geographically distinct populations were identified: one sampled in the Makassar Strait and Sulawesi Sea, one in the Arafura Sea and the third from the entire western region of the Indo-Malay archipelago. Considering the high hydrological connectivity of this region of the Indo-Pacific and the species pelagic life-history, the population structure may be maintained by homing behaviour and, perhaps, the association of spawning with retention zones.

Nuclear-DNA markers confirm the presence of two anchovy species in the Mediterranean

Morphometric, allozymic, and mitochondrial DNA variability previously indicated that the Mediterranean anchovy Engraulis encrasicolus includes two distinct forms, one of the inshore habitat, and the other one of the open-sea habitat. Here, we showed that the two forms significantly differ by several morphological characters. To test the hypothesis, proposed previously, that the two forms are distinct biological species, we used length-polymorphic, exon-primed intronic PCR markers from the creatine-kinase multigenic family and genetically characterized anchovy samples collected in the northwestern Mediterranean and in the eastern Atlantic. Large genetic differences were found between the two forms (Weir and Cockerham's theta = 0.397 to 0.586). In contrast, geographic variation in the open-sea form at the scale of the eastern Atlantic/northwestern Mediterranean was weak (theta = -0.006 to 0.042). This again demonstrated considerable restriction to nuclear gene flow between inshore and open-sea anchovy populations. In addition to previous results from allozymes, this confirmed their status as distinct biological species, namely Engraulis albidus sp. nov. and Engraulis encrasicolus L.

Direct selection on allozymes is not required to explain heterogeneity among marker loci across a Mytilus hybrid zone

Unequal differentiation between two types of loci (allozyme and DNA markers) across a Mytilus hybrid zone has recently been claimed as evidence for direct selection on some allozyme loci. We provide here a counter-example: a noncoding DNA locus that exhibits as much differentiation as the incriminated allozymes do. The levels of genetic differentiation varied widely among both allozymes and noncoding DNA markers and no clear difference emerged between the two types of markers. This suggests that the strong interlocus variance in genetic differentiation has been confounded with a discrepancy between marker types as a result of an insufficient and unbalanced locus sampling. Heterogeneity in differentiation among neutral loci can be created by stochastic variance during the allopatric divergence preceding a secondary contact. In hybrid zones, a further source of variance is differential introgression among chromosomal regions after the secondary contact owing to the local influence of selected genes on more or less distant markers. However, the degree of differentiation alone gives no way to distinguish indirect pseudo-selection (a regular and ubiquitous feature of hybrid zones) from direct selection. More generally, we suggest that comparative neutrality tests based on discrepancies among marker types have to be applied with caution when the presence of semi-permeable genetic barriers to gene exchange is suspected.

Introgression patterns in the mosaic hybrid zone between Mytilus edulis and M. galloprovincialis

Hybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine mussels Mytilus edulis and M. galloprovincialis, using three length-polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient from M. galloprovincialis on the Iberian Peninsula to M. edulis populations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical of M. galloprovincialis first decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantly M. edulis-like and M. galloprovincialis-like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre- or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory 'short-cut' connecting M. edulis-like populations of the Charente patch to an external M. edulis population in Normandy and thought to reflect artificial transfer of spat for aquaculture.

Systematics of the Atlantic–Mediterranean soles Pegusa impar, P. lascaris, Solea aegyptiaca, S. senegalensis, and S. solea (Pleuronectiformes: Soleidae)

Nucleotide-sequence variation at the cytochrome b locus was investigated in five Solea species, with a re appraisal of meristic data and a review of allozyme data pertinent to their systematics. Solea aegyptiaca, considered a synonym of Solea solea, and Solea (Pegusa) impar, considered a synonym of S. (P.) lascaris, are shown to be valid species according to the morphological, phylogenetic, genotypic, and biological species definitions. The validity of the genus Pegusa was examined in the light of both allozyme and cytochrome b gene sequence data.

The zone of sympatry and hybridization of Mytilus edulis and M. galloprovincialis, as described by intron length polymorphism at locus mac-1

Intron-size variation at the actin gene locus mac-1 was used to characterize mussel, Mytilus spp., populations in the approximately 2000-km wide zone of contact and hybridization ('hybrid zone') between M. edulis and M. galloprovincialis in western Europe. Twenty-five samples were collected in 1995-99 in locations within the hybrid zone and from reference populations of each species. We used correspondence analysis on the matrix of allelic frequencies to determine which alleles are characteristic of each species, and to characterize samples along the genetic gradient between M. edulis and M. galloprovincialis. In the hybrid zone, some samples exhibited mac-1 allele frequencies that were typical of M. edulis; other samples were distributed along the M. edulis/M. galloprovincialis gradient and displayed variable levels of intergradation that were not correlated with geography. Some of the latter samples exhibited significant heterozygote deficiencies. The simple admixture hypothesis (Wahlund effect) could not be rejected for two-fifths of the samples. The hybrid zone thus appeared as a mosaic of populations which are either pure M. edulis, or hybrid between M. galloprovincialis and M. edulis, or a mixture of the foregoing with M. galloprovincialis individuals. These results were consistent with published allozyme data, suggesting that they can be extended to the entire nuclear genome. M. edulis mac-1 alleles were present at moderate frequency in Atlantic M. galloprovincialis, and at significantly lower frequency in some Mediterranean samples. This pattern was homogeneous over a broad geographical range within each basin. It was not evident that introgression of M. edulis into M. galloprovincialis presently occurs south of the zone of contact. We propose that the distinctness of the Atlantic M. galloprovincialis population results from past introgression by M. edulis alleles.

Extensive gene flow within sibling species in the deep-sea fish Beryx splendens

Molecular markers allow insights into the population biology and ecology of deep-sea organisms, which are usually hardly accessible to direct observation and poorly known. Such a study was undertaken here for the deep-sea fish Beryx splendens, a species of growing interest to fisheries. B. splendens populations were sampled on seamounts and continental margins in the southwestern Pacific (New Caledonia, New Zealand, southeastern Australia) and in the northeastern Atlantic. Two hundred and fifty individuals were characterised by their single-strand DNA conformation (SSCP) of a approximately 360-base-pair (bp) fragment of the mitochondrial cytochrome b gene, amplified by the polymerase chain reaction (PCR). Two major SSCP haplotypes were observed in New Caledonia, a and w, whose frequencies were negatively correlated along a north-to-south cline. All SSCP haplotypes in the total sample were sequenced on 273 bp. The phylogenetic tree of B. splendens haplotype sequences, rooted by two B. decadactylus sequences, showed that a and w belong to distinct mitochondrial clades, A and W, which are separated by approximately 4-6% nucleotide divergence. Thirty individuals from New Caledonia were characterised by their DNA fingerprint from arbitrary-primed PCR. The distribution of individual-pairwise similarity indices was strongly bimodal. The larger similarity values all corresponded to comparisons within a clade (A or W) while the lower values were all between clades. Therefore, there was a strict association between the mitochondrial type and the DNA (presumably, nuclear DNA) fingerprint of an individual. Altogether, these results point to the existence of two biological species (sp. A and sp. W) within the current taxon B. splendens. No within-species differentiation was detected at the regional scale (New Caledonia). A remarkable result is that the three cytochrome b haplotypes of northeastern Atlantic B. cf. splendens sp. A were also the three commonest in the southwestern Pacific populations of this species. Such a level of homogeneity in the distribution of haplotypes suggests there is, or recently has been, gene flow at the inter-oceanic scale.

Genetic relationships of Mytilus galloprovincialis Lamarck populations worldwide: evidence from nuclear-DNA markers

Allozyme surveys of genetic variation in Mytilus galloprovincialis Lamarck throughout the world have identified three groups within this species: a northeastern (NE) Atlantic group that also includes the M. galloprovincialis population of South Africa, a Mediterranean group that also includes the M. galloprovincialis populations from the eastern and the western coasts of the North Pacific, and an Australasian group. Hypotheses that have been proposed to account for the genetic differentiation patterns and disjunct, worldwide distribution of M. galloprovincialis include the recent introduction of this species into the southern hemisphere and the North Pacific through human agency, and an alternative hypothesis that each of the three groups is endemic. In this study, two nuclear-DNA markers (the polyphenolic adhesive protein gene Glu-5′ and the first intron of the actin gene mac-1) were used to investigate in more depth the genetic relationships among M. galloprovincialis populations. Samples were taken between 1996 and 1999 from California, the NE Atlantic, the Mediterranean Sea, South Africa, Korea, Western Australia, Tasmania and New Zealand. NE Atlantic M. edulis L. were used as an outgroup. While all M. galloprovincialis samples were fixed, or nearly so, for the diagnostic G allele at locus Glu-5′, correspondence analysis of mac-1 allele frequency data highlighted the genetic distinctness of Australasian mussels relative to other M. galloprovincialis populations. The latter consisted of two differentiated groups (NE Atlantic and Mediterranean) as formerly reported at allozyme loci. Another sample, from Chile, was nearly identical to Mediterranean M. galloprovincialis. Nuclear-DNA data thus enforce the idea that M. galloprovincialis have probably been introduced from the Mediterranean to the North Pacific (and now Chile), and from the NE Atlantic to South Africa. It is argued in this study that Australasian mussels derive from a proto- M. galloprovincialis population introgressed by M. edulis-like genes, and should be considered as a regional subspecies of M. galloprovincialis.

Intron-length polymorphism at the actin gene locus mac-1: a genetic marker for population studies in the marine mussels Mytilus galloprovincialis Lmk. and M. edulis L

A novel intron-length polymorphism at the actin gene locus mac-1 is here reported and used as a genetic marker for population studies in mussels of the genus Mytilus. Two closely related genes subsequently identified as alleles, mac-1a1 and mac-1b1, from a genomic library of M. galloprovincialis were partially cloned and sequenced. They mainly differed from each other by a 65-bp insertion within their first intron. Polymerase chain reaction (PCR) primers were designed outside the insertion. The PCR analysis of 166 individual mussels from M. galloprovincialis and M. edulis populations revealed three size-classes of alleles or allelomorphs, two of which were of the expected sizes for mac1a1 and mac-1b1. One allelomorph was absent from M. edulis samples, although it was present at substantial frequencies in M. galloprovincialis populations. The frequencies of the two other allelomorphs significantly differed between M. galloprovincialis and M. edulis populations. The comparison of six mac-1 intron sequences over 277 bp showed at once that allelomorphs encompassed alleles differing from one another by substantial numbers of mutations, and that identical alleles were present in both M. galloprovincialis and M. edulis individuals, a probable result of the recent introgression between the two species.

Proprioception following total knee arthroplasty with and without the posterior cruciate ligament

Proprioception was measured in two groups of patients following successful total knee arthroplasty (TKA). In one group, the posterior cruciate ligament was retained and an unconstrained cruciate-retaining total knee component was used; in the other group, the posterior cruciate ligament was excised and a cruciate-substituting design was implanted. Threshold to detection of passive motion was quantified as a measure of proprioception. The degree of preoperative arthritis was objectively classified according to Resnick and Niwoyama. There was no difference in threshold to detection of passive motion in cruciate-retaining versus cruciate-substituting TKA. In patients with a moderate grade of arthritis before surgery, the postoperative scores were virtually identical. When the grade of preoperative arthritis was severe, patients with cruciate-substituting TKAs performed significantly better than those with cruciate-retaining TKAs.

Single-stranded DNA conformation polymorphism at the Rdl locus in Hypothenemus hampei (Coleoptera: Scolytidae)

The homologue of the resistance to dieldrin gene (Rdl) in Drosophila melanogaster was cloned and sequenced in the scolytid beetle Hypothenemus hampei, a coffee pest resistant to cyclodiene insecticides in New Caledonia. The amino acid sequence of the Rdl exon no. 7 protein product in H. hampei was identical to that in D. melanogaster and showed the same amino acid change as that characterizing susceptible vs. resistant D. melanogaster. Samples from natural H. hampei populations (from Asia, the Pacific Islands, Africa and Central America), from reference susceptible (S) and resistant (R) laboratory strains, and from their hybrid progenies, were analysed at the Rdl locus using single-stranded DNA conformation polymorphism on polymerase chain reaction products. The susceptible allele was the only allele present in all samples from natural populations except in the only resistant population known to date (Ponerihouen, New Caledonia). Females and some males obtained at F1 from R x S crosses were heterozygous at the Rdl locus, confirming that this local mate competing species is diplo-diploid.

Seasonal occurrence of the leopard seal, Hydrurga leptonyx, in the Kerguelen Islands

Five consecutive years of observations (1982–1986), mainly along the eastern coast of Kerguelen Island, indicate a seasonal presence of juvenile leopard seals, with a peak in September and October. Smaller numbers of adults are present throughout the year. The occurrence of leopard seals may be related to the presence and period of reproduction of different penguin species (king, gentoo, rockhopper, and macaroni penguins), which are part of the seal diet.