Mitochondrial DNA analysis of the geographic structure of Indian scad mackerel in the Indo-Malay archipelago

Sequence analysis of a fragment of the cytochrome b gene in Decapterus russelli sampled from the Indo-Malay archipelago revealed two distinct mitochondrial clades (mean nucleotide divergence=2·2%) whose geographic distribution was heterogeneous (Nei's G _ST=0·416). This pointed to a complex pattern of genetic differentiation and demonstrated limited genetic exchange between populations in this highly mobile species.     

Genetic and Morphological Differentiation of the Indo-West Pacific Intertidal Barnacle Chthamalus malayensis

Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses.     

Phylogeography study of Ammodytes personatus in Northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact

To assess the role of historical process and contemporary factors in shaping population structures in Northwestern Pacific, mitochondrial control region sequences were analyzed to characterize the phylogeography and population structure of the Japanese sand lance Ammodytes personatus. A total of 429 individuals sampled from 17 populations through the species' range are sequenced. Two distinct lineages are detected, which might have been divergent in the Sea of Japan and Pacific costal waters of Japanese Island, during the low sea level. Significant genetic structure is revealed between the Kuroshio and Oyashio Currents. However, significant genetic structure is also detected in the Sea of Japan, contracting expected homogenization hypothesis in Tsushima Current. The haplotype frequency of lineages in both sides of Japanese Island and significant genetic structure between north and south groups revealed that the distribution of lineage B and north group were highly limited by the annual sea temperature. The lack of lineage B in Qingdao population with low sea temperature reflects the sea temperature barrier. Lack of genetic structure in the south group and north group populations indicated that ocean currents within groups facilitated the dispersal of A. personatus.     

Genetic diversity enhanced by ancient introgression and secondary contact in East Pacific black mangroves

Regional distribution of genetic diversity in widespread species may be influenced by hybridization with locally restricted, closely related species. Previous studies have shown that Central American East Pacific populations of the wide-ranged Avicennia germinans , the black mangrove, harbour higher genetic diversity than the rest of its range. Genetic diversity in this region might be enhanced by introgression with the locally restricted Avicennia bicolor . We tested the hypotheses of ancient hybridization using phylogenetic analysis of the internal transcribed spacer region (ITS) of the nuclear ribosomal DNA and intergenic chloroplast DNA; we also tested for current hybridization by population level analysis of nuclear microsatellites. Our results unveiled ancient ITS introgression between a northern Pacific Central American A. germinans lineage and A. bicolor . However, microsatellite data revealed contemporary isolation between the two species. Polymorphic ITS sequences from Costa Rica and Panama are consistent with a zone of admixture between the introgressant ITS A. germinans lineage and a southern Central American lineage of A. germinans . Interspecific introgression influenced lineage diversity and divergence at the nuclear ribosomal DNA; intraspecific population differentiation and secondary contact are more likely to have enhanced regional genetic diversity in Pacific Central American populations of the widespread A. germinans .     

Genetic variation and stock structure of school mackerel and spotted mackerel in northern Australian waters

The total mean sample heterozygosity calculated from eight polymorphic loci was 0·172 (0·047 S.E.) (F_st 0·025) for school mackerel Scomberomorus queenslandicus , and for spotted mackerel S. munroi was 0·110 (0·074 S.E.) (F_st 0·038). There was no evidence of temporal variation for either species as significant genetic differences were not detected between months or year classes within areas. Spatially, school mackerel have a complex stock structure, with stocks being associated with large embayments. In contrast, spotted mackerel appear to comprise a single stock in Australian east coast waters. Both species showed a significant pattern of stock structure between Australian east coast and northern (Arafura Sea) samples.     

Genetic variation in central and peripheral populations of Excoecaria agallocha from Indo-West Pacific

Genetic diversity and differentiation were studied in Excoecaria agallocha L., a mangrove species growing on the coastlines of the Indo-West Pacific region. Twenty natural populations of E. agallocha were sampled from the Malay Peninsula (central population), and in Southern China, North Australia, Sri Lanka and Southern Japan (peripheral populations). Our results showed that central populations from Malay Peninsula possessed significantly higher genetic diversity than the peripheral ones (P < 0.05). Analysis of molecular variation (AMOVA) revealed that genetic variability was partitioned at 22.9% among regions, 23.6% among populations within regions, and 53.5% within populations. Genetic differentiation (G_ST = 0.300) among the six central populations was stronger than those from peripheral regions. Populations from North Australia clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Southern Japan, Southern China and Sri Lanka also clustered closely together, respectively. However, populations from Malay Peninsula did not cluster by region. The east coast populations of Malay Peninsula (including Pasir population) were more genetically similar to the populations from Southern China than those from the west coastline of Malay Peninsula. Our study suggests that ocean currents, land barriers, limited dispersal ability of seeds, and founder effect may play important roles in the distribution of genetic diversity in E. agallocha.     

Fishy Business: The High Seas Boarding and Inspection Regime in the Western and Central Pacific Ocean

The Western and Central Pacific Fisheries Commission (WCPFC) was created in 2004 to more effectively conserve and manage the region's tuna fishery. One of the Commission's principal enforcement tools is the high seas boarding and inspection regime, which authorizes each member state to board and inspect fishing vessels engaged in a regulated fishery to verify compliance with the Commission's conservation and management measures. This article examines the structure of the WCPFC's high seas boarding and inspection regime and analyzes its effectiveness in furthering the Commission's conservations and management mandate.     

Genetic diversity and population structure of silver pomfret (Pampus argenteus) in the Indo-West Pacific revealed by mitochondrial control region sequences

Sequence variation of the mitochondrial control region in silver pomfret (Pampus argenteus) among six populations from the Indo-West Pacific region was analyzed. A total of 309 polymorphic sites were detected in the 464–466 bp segment of the control region among 165 individuals which defined 72 haplotypes. Haplotype diversity was ranged from 0.800 to 0.943 and nucleotide diversity ranged from 0.333% to 1.886%. Genetic distance and the fixation index indicated significant differences among populations in different geographical groups (P < 0.05). Median-joining network analysis data showed distinct patterns of phylogeographic structure. The present results suggested that P. argenteus populations have developed significant genetic structure, especially among geographically isolated groups.     

Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia

Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c . 400 000 years before present ( bp ): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (≥ 99% Bayesian posterior probability); two that were more recently derived (rho estimate c . 20 000 bp ) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c . 45 000 bp ) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300 000–130 000 bp ), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100 000–10 000 bp ). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.     

Migration of Pacific Rim Chum Salmon on the High Seas: Insights from Genetic Data

Wild stocks of chum salmon, Oncorhynchus keta, have experienced recent declines in some areas of their range. Also, the release of hatchery chum salmon has escalated to nearly three billion fish annually. The decline of wild stocks and the unknown effects of hatchery fish combined with the uncertainty of future production caused by global climate change have renewed interest in the migratory patterns of chum salmon on the high seas. We studied the composition of high-seas mixtures of maturing and immature individuals using baseline data for 20 allozyme loci from 356 populations from throughout the Pacific Rim. Composition estimates were made from three time series. Two of these time series were from important coastal migratory corridors: the Shumagin Islands south of the Alaska Peninsula and the east coast of the Kamchatka Peninsula. The third was from chum salmon captured incidentally in the Bering Sea trawl fishery for walleye pollock. We also analyzed geographically dispersed collections of chum salmon captured in the month of July. The time series show dynamic changes in stock composition. The Shumagin Island corridor was used primarily by Northwest Alaskan and Asian populations in June; by the end of July stocks from the Alaska Peninsula and southern North America dominated the composition. The composition along the Kamchatka coast changed dramatically from primarily Russian stocks in May to primarily Japanese stocks in August; the previously undocumented presence of stocks from the Alaska Peninsula and Gulf of Alaska was also demonstrated. Immature chum salmon from throughout the Pacific Rim, including large proportions of southern North American stocks, contributed to the Bering Sea bycatch during the months of September and October. The migration routes of North American stocks is far more widespread than previously observed, and the Bering Sea is an important rearing area for maturing and immature chum salmon from throughout the species' range.     

Isolation by distance and vicariance drive genetic structure of a coral reef fish in the Pacific Ocean

We studied the genetic diversity of a coral reef fish species to investigate the origin of the differentiation. A total of 727 Acanthurus triostegus collected from 15 locations throughout the Pacific were analyzed for 20 polymorphic loci. The genetic structure showed limited internal disequilibrium within each population; 3.7% of the loci showed significant Hardy-Weinberg disequilibrium, mostly associated with Adh*, and we subsequently removed this locus from further analysis of geographic pattern. The genetic structure of A. triostegus throughout the tropical Pacific Ocean revealed a strong geographic pattern. Overall, there was significant population differentiation (multilocus F(ST) = 0.199), which was geographically structured according to bootstraps of neighbor-joining analysis on Nei's unbiased genetic distances and AMOVA analysis. The genetic structure revealed five geographic groups in the Pacific Ocean: western Pacific (Guam, Philippines, Palau, and Great Barrier Reef); central Pacific (Solomons, New Caledonia, and Fiji); and three groups made up of the eastern populations, namely Hawaiian Archipelago (north), Marquesas (equatorial), and southern French Polynesia (south) that incorporates Clipperton Island located in the northeastern Pacific. In addition, heterozygosity values were found to be geographically structured with higher values grouped within Polynesian and Clipperton populations, which exhibited lower population size. Finally, the genetic differentiation (F(ST)) was significantly correlated with geographic distance when populations from the Hawaiian and Marquesas archipelagos were separated from all the other locations. These results show that patterns of differentiation vary within the same species according to the spatial scale, with one group probably issued from vicariance, whereas the other followed a pattern of isolation by distance. The geographic pattern for A. triostegus emphasizes the diversity of the evolutionary processes that lead to the present genetic structure with some being more influential in certain areas or according to a particular spatial scale.     

Molecular evidence for co-occurring cryptic lineages within the Sepioteuthis cf. lessoniana species complex in the Indian and Indo-West Pacific Oceans

The big-fin reef squid, Sepioteuthis cf. lessoniana (Lesson 1930), is an important commodity species within artisanal and near-shore fisheries in the Indian and Indo-Pacific regions. While there has been some genetic and physical evidence that supports the existence of a species complex within S. cf. lessoniana, these studies have been extremely limited in scope geographically. To clarify the extent of cryptic diversity within S. cf. lessoniana, this study examines phylogenetic relationships using mitochondrial genes (cytochrome oxidase c, 16s ribosomal RNA) and nuclear genes (rhodopsin, octopine dehydrogenase) from nearly 400 individuals sampled from throughout the Indian, Indo-Pacific, and Pacific Ocean portions of the range of this species. Phylogenetic analyses using maximum likelihood methods and Bayesian inference identified three distinct lineages with no clear geographic delineations or morphological discriminations. Phylogeographic structure analysis showed high levels of genetic connectivity in the most widespread lineage, lineage C and low levels of connectivity in lineage B. This study provides significant phylogenetic evidence for cryptic lineages within this complex and confirms that cryptic lineages of S. cf. lessoniana occur in sympatry at both small and large spatial scales. Furthermore, it suggests that two closely related co-occurring cryptic lineages have pronounced differences in population structure, implying that underlying differences in ecology and/or life history may facilitate co-occurrence. Further studies are needed to assess the range and extent of cryptic speciation throughout the distribution of this complex. This information is extremely useful as a starting point for future studies exploring the evolution of diversity within Sepioteuthis and can be used to guide fisheries management efforts.     

Inferring the mode of speciation in Indo-West Pacific Conus (Gastropoda: Conidae)

Aim This study aims to initially explore the mode of speciation in Indo‐West Pacific Conus. Location The Indo‐West Pacific island arc, Indian and Pacific Oceans. Methods Relating evolutionary divergence in a molecular phylogeny [T.F. Duda & S.R. Palumbi (1999) Proceedings of the National Academy of Science USA, 96 , 10272] using node height with modern range extents as a possible measure of allopatric or sympatric speciation following that of T.G. Barraclough, A.P. Vogler & P.H. Harvey [(1999) Evolution of Biological Diversity. Oxford University Press, Oxford] models of sympatric and allopatric speciation. Results The analysis seems to indicate that the relationship of sympatry with node height is not informative. Species that have diverged quite recently show 100% sympatry with the sister species. A clearer signal of recent allopatric speciation is observed in species whose distribution is at the edge of the Indian and Pacific Ocean basins. In the widely distributed Conus ebraeus clade, the relationships of node heights and range extents of the member species support a key prediction of sympatric speciation. In highly ecologically specialized species, there is a smaller degree of sympatry than those species that are less specialized. Main conclusions The modes of speciation models presented in this study are not informative. This suggests that there had been large and possibly rapid changes in range size after speciation in the various clades. This could have been due to the fact that the wide dispersal life‐history strategy in the genus had been largely conserved in Conus evolution. There is evidence of sympatric and parapatric speciation in one Conus clade. Overall, the patterns of phylogeny and range distribution when related to the timing of speciation lend circumstantial support to a Neogene centre of origin hypothesis but not to speciation on the Pacific Plate. Speciation is likely to have been associated with the Tethys Sea closure event, with rapid speciation occurring after closure.     

Quantitative biochronology of Pliocene and early Pleistocene calcareous nannofossils from the Atlantic,Indian and Pacific oceans

Semi-quantitative methods have been used to refine the precision with which Pliocene and early Pleistocene nannofossil datums may be applied for biostratigraphic purposes. Using these methods, the datums may be applied with a precision of between 0.01 m.y. (e.g.Calcidiscus macintyrei andDiscoaster brouweri) and 0.2 m.y. (e.g.Discoaster asymmetricus). The age of each datum is estimated by interpolation between magnetic reversals, so that the uncertainty in each age estimate is a function of proximity to the nearest reversal as well as of uncertainties in the reversal chronology but is probably better than 0.1 m.y. for all the datums studied here.The following ages are estimated for biostratigraphically useful datums: LADHelicosphaera sellii, 1.37 Ma (diachronous; earlier outside the equatorial zone); LADCalcidiscus macintyrei, 1.45 Ma; LADDiscoaster brouweri, 1.88 Ma; LADDiscoaster asymmetricus, 2.2 Ma; LAD DisDiscoaster pentaradiatus, 2.35 Ma; LADDiscoaster surculus, 2.41 Ma; LADDiscoaster tamalis, 2.65 Ma; LADDiscoaster variabilis, 2.90 Ma; LADSphenolithus spp., 3.45 Ma; LADReticulofenestra pseudoumbilica, 3.56 Ma; LADAmaurolithus delicatus, 3.66 Ma; FADCeratolithus rugosus, 4.62 Ma.The final 0.15 m.y. of the range ofDiscoaster brouweri is characterised by a high (about 20%) proportion of the triradiate form, which is a useful pointer for the extinction of this species even in the presence of considerable reworking.     

Characterization of the Bacterial Diversity in Indo-West Pacific Loliginid and Sepiolid Squid Light Organs

Loliginid and sepiolid squid light organs are known to host a variety of bacterial species from the family Vibrionaceae, yet little is known about the species diversity and characteristics among different host squids. Here we present a broad-ranging molecular and physiological analysis of the bacteria colonizing light organs in loliginid and sepiolid squids from various field locations of the Indo-West Pacific (Australia and Thailand). Our PCR-RFLP analysis, physiological characterization, carbon utilization profiling, and electron microscopy data indicate that loliginid squid in the Indo-West Pacific carry a consortium of bacterial species from the families Vibrionaceae and Photobacteriaceae. This research also confirms our previous report of the presence of Vibrio harveyi as a member of the bacterial population colonizing light organs in loliginid squid. pyrH sequence data were used to confirm isolate identity, and indicates that Vibrio and Photobacterium comprise most of the light organ colonizers of squids from Australia, confirming previous reports for Australian loliginid and sepiolid squids. In addition, combined phylogenetic analysis of PCR-RFLP and 16S rDNA data from Australian and Thai isolates associated both Photobacterium and Vibrio clades with both loliginid and sepiolid strains, providing support that geographical origin does not correlate with their relatedness. These results indicate that both loliginid and sepiolid squids demonstrate symbiont specificity (Vibrionaceae), but their distribution is more likely due to environmental factors that are present during the infection process. This study adds significantly to the growing evidence for complex and dynamic associations in nature and highlights the importance of exploring symbiotic relationships in which non-virulent strains of pathogenic Vibrio species could establish associations with marine invertebrates.     

Morphological and mitochondrial-DNA analysis of the Indo-West Pacific rock oysters (Ostreidae: Saccostrea species)

Species of Saccostrea are common oysters on Indo-Pacific rockyshores. The taxonomy of this genus is unclear, however, becauseof morphological plasticity among its constituent species. Oystersamples with distinct morphotypes were collected from shoresexperiencing different degrees of wave exposure in Japan, Taiwan,China, Vietnam, Singapore and Australia. Intraspecific and interspecificvariations in shell characters have been identified. Only S.kegaki could be readily differentiated from S. cucullata-B,S. cucullata-C and S. mordax by multivariate shell allometricanalyses. Phylogenetic analyses using partial mitochondrial16S DNA sequences of approximately 513 base pairs identifiedtwo clades that correspond to superspecies, i.e. putative S.cucullata and putative S. mordax, comprising nine and two lineagesfrom the Indo-West Pacific, respectively. These are S. cucullata-A,B, C, D, E, F, G, S. kegaki and S. glomerata in one clade, andS. mordax-A and B in the other. Interspecific sequence divergence(Kimura-2-parameter values) between lineages ranged from 1.02%to 11.74%. Both S. cucullata-C and S. kegaki are restrictedto the northern hemisphere, whereas S. glomerata seems to bea temperate species from the southern hemisphere. S. cucullata-Doccurs only in Taiwan. Other species, i.e. S. cucullata-A, B,D, E and F and S. mordax-A and B, have a wide range on rockyshores in the tropical and subtropical Western Pacific and inboth northern and southern hemispheres. (Received 7 January 2005; accepted 4 November 2005)     

Genetic structure in the Mediterranean seagrass Posidonia oceanica: disentangling past vicariance events from contemporary patterns of gene flow

The Mediterranean Sea is a two‐basin system, with the boundary zone restricted to the Strait of Sicily and the narrow Strait of Messina. Two main population groups are recognized in the Mediterranean endemic seagrass Posidonia oceanica, corresponding to the Western and the Eastern basins. To address the nature of the East–West cleavage in P. oceanica, the main aims of this study were: (i) to define the genetic structure within the potential contact zone (i.e. the Strait of Sicily) and clarify the extent of gene flow between the two population groups, and (ii) to investigate the role of present water circulation patterns vs. past evolutionary events on the observed genetic pattern. To achieve these goals, we utilized SSR markers and we simulated, with respect to current regime, the possible present‐day dispersal pattern of Posidonia floating fruits using 28‐day numerical Lagrangian trajectories. The results obtained confirm the presence of the two main population groups, without any indices of reproductive isolation, with the break zone located at the level of the Southern tip of Calabria. The populations in the Strait of Sicily showed higher affinity with Western than with Eastern populations. This pattern of genetic structure probably reflects historical avenues of recolonization from relict glacial areas and past vicariance events, but seems to persist as a result of the low connectivity among populations via marine currents, as suggested by our dispersal simulation analysis.     

Lecithotrophic development and metamorphosis in the Indo-West Pacific brittle star Ophiomastix venosa (Echinodermata: Ophiuroidea)

Summary

The larval development of the ophiocomid ophiuroid Ophiomastix venosais described using SEM. The gastrula transforms into a uniformly ciliated early larva which progressively changes into a lecithotrophic late premetamorphic larva with a continuous bilateral ciliated band. This stage is short-lived and equivalent to a highly reduced ophiopluteus. Comparisons between O. venosa and other ophiuroid species whose development has been investigated suggest that, whatever the developmental mode (lecithotrophic or planktotrophic), a pluteus stage always occurs in ophiuroids with planktonic development. Two metamorphic stages were identified, the late metamorphic larva differing from the early one by the closure of the larval mouth. The appearance of the permanent mouth marks the end of the metamorphosis. The postlarva still possesses remnants of larval features. The transformation of the reduced ophiopluteus into a barrel-shaped metamorphic larva with transverse ciliated bands, a vitellaria larva, is followed. The possible occurrence of a unique type of metamorphic larva in non-brooding ophiuroids is discussed. Verification of this, however, needs further SEM investigations on metamorphic larva from species having “regular” planktotrophic development.