Late Quaternary marginal marine palaeoenvironments of northern Australia as inferred from cluster analysis of coccolith assemblages

Cluster analyses (R- and Q-mode) were applied to upper Quaternary coccolith assemblages in a sediment core (MD972132) collected in the Gulf of Carpentaria, northern Australia. This shallow gulf is influenced by the Australian monsoon, is tectonally stable and represents an important link between marine and terrestrial palaeoenvironments. The Gulf of Carpentaria is linked to the Pacific Ocean to the east by Torres Strait (12 m water depth) and to the Indian Ocean to the west by the Arafura Sill (53 m water depth), and therefore has been separated from both oceans during sea-level low-stands, resulting in the formation of Lake Carpentaria. Coccolith assemblages in the gulf are similar to modern assemblages in the region, and correspond to typical assemblages in marginal seas. The cluster analysis defines six species assemblages (R-mode), and six groups of samples (i.e., defined by depth in core depth; Q-mode), some with sub-groups, which were deposited under similar environmental conditions. We thus recognised, four major environmental facies over the past 125 ka, corresponding to closed Lake Carpentaria stages, the transitional periods while active channels sporadically connected Lake Carpentaria to the Indian Ocean, and the opening of the Gulf of Carpentaria to the ocean over either one, or both of the sills. Lake Carpentaria was isolated from both oceans through Marine Isotope Stages (MIS) 5d, MIS 4 and MIS 2, and the Gulf of Carpentaria was connected to both oceans during MIS 5c and MIS 1. Torres Strait was emergent during MIS 5b, was flooded again during MIS 5a and persisted as land bridge from MIS 4 to MIS 1. The Arafura Sill was opened from MIS 5c to MIS 5a and episodically connected the Gulf to the Indian Ocean during MIS 3.     

Diatoms in surface sediments of the Indonesian Archipelago and their relation to hydrography

Diatoms from 53 surface sediments (water depth 350–7200 m) of the Indonesian Archipelago were studied to determine the recent distribution of important assemblages. Three significant assemblages were distinguished, each related to hydrographic parameter(s) of the overlying water mass. The first assemblage is related to the warm saline surface waters of Pacific and Indian Ocean origin; the second assemblage reflects the low-salinity lobe in Makassar Strait; and the third corresponds to major seasonal upwelling areas in the Arafura Sea and south of Java.The normalized ratio of typically Pacific Ocean and Indian Ocean species reflects the fluctuations of the Pacific versus Indian Ocean inflow during the Late Quaternary.Absolute diatom abundances (ADA; in valves g^–1 carbonate-free dry wt) and diatom accumulation rates (DAR; in valves CM^–2 ka^–1) of autochthonous species did not correspond to daily rates of primary production in the photic zone and consequently cannot be used for paleoproductivity estimates.Besides vertical transport some lateral transport of diatoms occurs, as was demonstrated by the presence of three groups of allochthonous species. They are indicators of productivity in the littoral environment, bottom currents and river outflow.     

Vicariance and dispersal across an intermittent barrier: population genetic structure of marine animals across the Torres Strait land bridge

Biogeographic barriers, some transitory in duration, are likely to have been important contributing factors to modern marine biodiversity in the Indo-Pacific region. One such barrier was the Torres Strait land bridge between continental Australia and New Guinea that persisted through much of the late Pleistocene and separated Indian and Pacific Ocean taxa. Here, we examine the patterns of mitochondrial DNA diversity for marine animals with present-day distributions spanning the Torres Strait. Specifically, we investigate whether there are concordant signatures across species, consistent with either vicariance or recent colonization from either ocean basin. We survey four species of reef fishes (Apogon doederleini, Pomacentrus coelestis, Dascyllus trimaculatus, and Acanthurus triostegus) for mtDNA cytochrome oxidase 1 and control region variation and contrast these results to previous mtDNA studies in diverse marine animals with similar distributions. We find substantial genetic partitioning (estimated from F-statistics and coalescent approaches) between Indian and Pacific Ocean populations for many species, consistent with regional persistence through the late Pleistocene in both ocean basins. The species-specific estimates of genetic divergence, however, vary greatly and for reef fishes we estimate substantially different divergence times among species. It is likely that Indian and Pacific Ocean populations have been isolated for multiple glacial cycles for some species, whereas for other species genetic connections have been more recent. Regional estimates of genetic diversity and directionality of gene flow also vary among species. Thus, there is no apparent consistency among historical patterns across the Torres Strait for these co-distributed marine animals.     

Oceanic interchange and nonequilibrium population structure in the estuarine dependent Indo-Pacific tasselfish,Polynemus sheridani

We assayed mtDNA haplotype [300 base pairs (bp) control region] geography and genealogy in the Indo-Pacific tasselfish, Polynemus sheridani from its contiguous estuarine distribution across northern Australia (n = 169). Eight estuaries were sampled from three oceanographic regions (Timor Sea, Gulf of Carpentaria and the Coral Sea) to assess the impact of Pleistocene sea level changes on the historical connectivity among P. sheridani populations. Specifically, we investigated the genetic consequences of disruption to Indian-Pacific Ocean connectivity brought about by the closure of the Torres Strait. Overall there was significant population subdivision among estuaries (FST = 0.161, PhiST = 0.187). Despite a linear distribution, P. sheridani did not show isolation by distance over the entire sampled range because of genetic similarity of estuaries greater than 3000 km apart. However, significant isolation by distance was detected between estuaries separated by less than 3000 km of coastline. Unlike many genetic studies of Indo-Pacific marine species, there was no evidence for an historical division between eastern and western populations. Instead, phylogeographical patterns were dominated by a starlike intraspecific phylogeny coupled with evidence for population expansion in both the Gulf of Carpentaria and the Coral Sea but not the Timor Sea. This was interpreted as evidence for recent west to east recolonization across of northern Australia following the last postglacial marine advance. We argue that although sufficient time has elapsed postcolonization for populations to approach gene flow-drift equilibrium over smaller spatial scales (< 3000 km), the signal of historical colonization persists to obscure the expected equilibrium pattern of isolation by distance over large spatial scales (> 3000 km).     

SPINNER DOLPHINS (STENELLA LONGIROSTRIS) OF THE WESTERN PACIFIC AND SOUTHEAST ASIA: PELAGIC AND SHALLOW-WATER FORMS1

A dwarf form of the spinner dolphin has been reported from the Gulf of Thailand, while more typical large spinner dolphins have been described from Japanese waters and other localities in the western Pacific. These reports have been based on very few specimens. Our purpose in this study was to determine the affinities of spinner dolphins throughout the region based on larger samples and to review their taxonomic status, with an hypothesis of two widespread ecotypic forms, or subspecies. We examined 213 osteological specimens, from a tuna gillnet fishery in the Philippines, from the former Taiwanese shark gillnet fishery in the Timor and Arafura Seas off northern Australia, from the Gulf of Thailand, from other areas in the western Pacific and Southeast Asia, from the eastern Indian Ocean, and from the Central and South Pacific. Results show that spinner dolphins from the deep inner waters of the Philippines conform to the large pelagic type of spinner dolphin that inhabits the Central and South Pacific, the western Pacific and the eastern Indian Ocean. The skull is similar in size and shape to the holotype specimen of S. longirostris (from unknown locality). This form feeds primarily on small mesopelagic fishes and squids. Spinner dolphins from the shallow waters of inner Southeast Asia represented in the sample, including the Gulf of Thailand, Timor Sea and Arafura Sea, are smaller in body and skull size, have fewer teeth and vertebrae, and feed mainly on benthic and coral reef fishes and invertebrates. We hypothesize that this form also inhabits the Java Sea and other shallow waters throughout inner Indonesia and Malaysia. We redescribe a subspecies corresponding to the small form and based on Delphinus roseiventris Wagner 1846 from the Arafura Sea, designating a neotype and paraneotype specimens.     

Community structure and biogeography of shore fishes in the Gulf of Aqaba,Red Sea

Shore fish community structure off the Jordanian Red Sea coast was determined on fringing coral reefs and in a seagrass-dominated bay at 6 m and 12 m depths. A total of 198 fish species belonging to 121 genera and 43 families was recorded. Labridae and Pomacentridae dominated the ichthyofauna in terms of species richness and Pomacentridae were most abundant. Neither diversity nor species richness was correlated to depth. The abundance of fishes was higher at the deep reef slope, due to schooling planktivorous fishes. At 12 m depth abundance of fishes at the seagrass-dominated site was higher than on the coral reefs. Multivariate analysis demonstrated a strong influence on the fish assemblages by depth and benthic habitat. Fish species richness was positively correlated with hard substrate cover and habitat diversity. Abundance of corallivores was positively linked with live hard coral cover. The assemblages of fishes were different on the shallow reef slope, deep reef slope and seagrass meadows. An analysis of the fish fauna showed that the Gulf of Aqaba harbours a higher species richness than previously reported. The comparison with fish communities on other reefs around the Arabian Peninsula and Indian Ocean supported the recognition of an Arabian subprovince within the Indian Ocean. The affinity of the Arabian Gulf ichthyofauna to the Red Sea is not clear. Received in revised form: 2 November 2001 Electronic Publication     

Paleobiogeographical implications of inner bay Ostracoda during the Late Pleistocene Shimosueyoshi transgression,central Japan,with significance of its migration and disappearance in eastern Asia

A total of 79 ostracode species were recognized from the embayment sediments deposited during the Late Pleistocene Shimosueyoshi transgression in central Japan. The most dominant species was Neomonoceratina delicata, now abundant in tropical inner bays of the Ryukyu Islands, the South China Sea and southeastern Asia. Bicornucythere bisanensis, widely dominant species in enclosed middle muddy bays of temperate climatic zones in Japan and northern China, was also abundant in the middle and upper sequences. Most of the other main species were assigned to the “Japonic elements” and are presently common in tropical or subtropical and temperate shallow seas near the Japanese Islands. Four ostracode biofacies were identified using the Q-mode cluster analysis. A change in water depth was clearly revealed in the study sequence, based on the vertical changes in the biofacies and the relative abundances of fossil ostracode species. The single most dominant species, N. delicata, does not currently exist in the Japanese Islands north of the Tokara Strait (Watase's line: one of zoological lines of demarcation), in southern Japan. Based on a compilation of fossil and recent distribution records, it is believed that N. delicata migrated from the south of the Tokara Strait by the marine oxygen isotope stage (MIS) 11 (～ 430 ka), dominated other species in enclosed muddy bays and then spread to the northernmost areas during the MIS 5. However, almost all populations of this species probably disappeared north of the Tokara Strait during the Last Glacial Maximum due to a decrease in water temperature. This species could not survive colder water temperature and could not migrate north through the Tokara Strait during the postglacial transgression because the strait has been deep and wide since the Early Pleistocene. We conclude that this species lived commonly during the glacial stages of MIS 10, 8 and 6 north of the Tokara Strait because of the favorable water temperature for reproduction.     

Late glacial to recent deep-sea benthic foraminifera from the northeastern Atlantic (Cadiz Gulf) and western Mediterranean (Alboran Sea): Paleooceanographic results

Deep-sea benthic foraminifera of the region of water exchange between the Mediterranean and the Atlantic Ocean, at the Gibraltar Strait, show significant water-mass relationships for the past 18,000 years.Cores used in this benthic foraminifera analysis were selected, according to the context of the distribution of various deep bottom water masses, on each side of the Gibraltar Strait:

• 1.(1) on the Atlantic side of the Strait, two cores (KS 8228, KS 8229) are located in the present day NADW, and one (KC 8221) in the upper part of the present Mediterranean outflow water,
• 2.(2) on the Mediterranean side of Gibraltar, two cores (KC 8241, SU 8107) are located in the deep water mass, and one (KS 8230) in the intermediate water mass.

In the two deep basins (1500–2800 m depth in the Gulf of Cadiz, 1200–1300 m depth in the Alboran Sea), the paleooceanographic changes appear to be in an opposite way for the past 18,000 years. The Alboran basin shows a paleooceanographic evolution from a well-oxygenated, nutrient-rich environment at about 18,000 yr B.P. to a nutrient-poor, oxygen-depleted environment from 13,000 to the present time; moreover, for the time-span synchronous with the well-known development of sapropels in the eastern Mediterranean basins between 10,000 and 7000 yr B.P., the faunal assemblage shows most unusual characteristics implying drastic environmental conditions. Conversely, in the Gulf of Cadiz, the environment pass as from a biotope occupied by an oxygen-depleted, nutrient-poor water mass at about 18,000 years B.P. to a biotope occupied by NADW since the Younger Dryas; this agrees with previous data obtained in the northeastern Atlantic Ocean (Caralp, 1987).In the epibathyal zones (550–800 m depth), on both sides of the Gibraltar Strait, paleohydrographic changes do not seem so important. According to the present and very late Holocene assemblages, which are similar on both sides of the Strait with a strong east-west flow, two other stratigraphic episodes have shown the same conditions of water exchanges: the end of the isotopic stage 2 and the Younger Dryas. Conversely, during the last glacial maximum, the Bølling-Allerød and the lower Holocene, westward water fluxes were probably lower. At no time, the hypothesis of a reversal or a stop in the east-west exchanges between Mediterranean and Atlantic Ocean may be justified.     

Radiolaria as a reflection of environmental conditions in the eastern and southern sectors of the Indian Ocean: A new statistical approach

Cluster analysis and species abundance plots of radiolarian abundance counts from core tops from the eastern Indian Ocean between 12° S and 31° S, and the southern Indian Ocean between 31° S and 62.5° S, demonstrate the existence of environmentally-related provinces supporting distinct taxa assemblages. These provinces are closely associated with currents in the eastern sector of the Indian Ocean and with fronts in the southern sector.The radiolarian assemblages correlate strongly with salinity-normalised total alkalinity (NTA) at the sea-surface, with temperature, salinity, and density from the sea-surface to 300 m, and with dissolved oxygen and nitrate and phosphate concentrations from the sea-surface to 100 m. Palaeo-reconstructions of these parameters at the sea-surface have been made for six Last Glacial Maximum (LGM) samples from five eastern Indian Ocean cores. The LGM sea-surface temperature estimates are comparable with those based on planktonic foraminiferal counts of the same samples obtained by other researchers. The reconstructions show that, since the LGM, density increased markedly along the Western Australian coast south of 20° S but changed little further from the Western Australian coast. By contrast, phosphate concentrations were marginally lower than modern values along the Western Australian coast south of 20° S but more than twice modern values in the other LGM samples.The utility of various regression and calibration techniques is discussed. It is concluded that, probably due to the effects of differences in radiolarian habitat, ocean currents, and/or environmental gradients, only one method, weighted averaging — partial least squares, is reliable in a study area of this size and complexity. If other methods are to be used, the study area must be partitioned into at least two separate regions with the major split between the eastern and southern sectors of the Indian Ocean.     

The warm interglacial Marine Isotope Stage 31: Evidences from the calcareous nannofossil assemblages at Site 1090 (Southern Ocean)

Calcareous nannofossil assemblages have been investigated at Ocean Drilling Program (ODP) Site 1090 located in the modern Subantarctic Zone, through the Pleistocene Marine Isotope Stages (MIS) 34–29, between 1150 and 1000 ka. A previously developed age model and new biostratigraphic constraints provide a reliable chronological framework for the studied section and allow correlation with other records. Two relevant biostratigraphic events have been identified: the First Common Occurrence of Reticulofenestra asanoi, distinctly correlated to MIS 31–32; the re-entry of medium Gephyrocapsa at MIS 29, unexpectedly similar to what was observed at low latitude sites.The composition of the calcareous nannofossil assemblage permits identification of three intervals (I–III). Intervals I and III, correlated to MIS 34–32 and MIS 30–29 respectively, are identified as characteristic of water masses located south of the Subtropical Front and reflecting the southern border of Subantarctic Zone, at the transition with the Polar Front Zone. This evidence is consistent with the hypothesis of a northward shift of the frontal system in the early Pleistocene with respect to the present position and therefore a northernmost location of the Subantarctic Front. During interval II, which is correlated to MIS 31, calcareous nannofossil assemblages display the most significant change, characterized by a distinct increase of Syracosphaera spp. and Helicosphaera carteri, lasting about 20 ky. An integrated analysis of calcareous nannofossil abundances and few mineralogical proxies suggests that during interval II, Site 1090 experienced the influence of subtropical waters, possibly related to a southward migration of the Subtropical Front, coupled with an expansion of the warmer Agulhas Current at the core location. This pronounced warming event is associated to a minimum in the austral summer insolation. The present results provide a broader framework on the Mid-Pleistocene dynamic of the ocean frontal system in the Atlantic sector of the Southern Ocean, as well as additional evidence on the variability of the Indian–Atlantic ocean exchange.     

Genetic population structure of Indian oil sardine, <Emphasis Type="Italic">Sardinella longiceps</Emphasis> assessed using microsatellite markers

Indian oil sardines, commercially and ecologically important pelagic fishes in Indian waters have not been the focus of major genetic studies as compared to their counter parts in Atlantic and Pacific oceans in spite of several reports suggesting stock complexity and intraspecific diversity. Hence, we investigated the genetic stock structure of Indian oil sardine, Sardinella longiceps using microsatellite markers by collecting a total of 768 individuals from eight locations along the Indian coast and one from Gulf of Oman over a 2 year period (2013–2015). Six polymorphic microsatellite markers revealed significant genetic differentiation between populations with the highest F_ST value (0.055) between Oman and Indian coastline. Within the Indian coastline another major subdivision between Mumbai & Mangalore vs. other regions was detected (F_ST value 0.047) which was also confirmed in Barrier analysis with the presence of two strong barriers between these eco-regions. There exist pronounced differences in oceanographic and environmental features between Gulf of Oman, Western Indian Ocean and Eastern Indian Ocean (Bay of Bengal) which may act as barriers for effective dispersal and gene flow resulting in genetic differentiation. Even though, the samples collected from Calicut, Kollam, Trivandrum, Chennai and Vizag showed the presence of admixed genotypes, the possible presence of distinct populations in some regions was evident in Bayesian analysis which needs to be confirmed further using more widespread sampling design and powerful markers. The present study provided insights into the biocomplexity and intra-specific diversity of Indian oil sardine populations, which needs to be preserved for maintaining resilience of these important fishes to climate change and habitat alterations in the Indian Ocean.     

A 350-ky radiolarian record off Lüderitz,Namibia—evidence for changes in the upwelling regime

The study of radiolarian assemblages from Core MD 962086 provides new information on the variability in the upwelling intensity and origin of upwelled water masses over the past 350 ky in one of the major filamentous regions of the Benguela Upwelling System (BUS), located off Lüderitz, Namibia. The use of key radiolarian species to trace the source of upwelled waters, and the use of a radiolarian-based upwelling index (URI) to reconstruct the upwelling intensity represent the first use of radiolarians for paleoceanographic reconstructions in the BUS. These radiolarian-based proxies indicate strongest upwelling during Marine Isotope Stages (MIS) 3, 5, and 8, which compares well with other studies. While during MIS 3 and 8, the radiolarian-based proxies indicate the influx of waters of Southern Ocean origin, they also point to the increased influence of tropical waters during the lower portion of MIS 5. During MIS 2, 4 and 6 the radiolarian assemblages indicate generally lower upwelling intensities, although this signal is complicated by the increased occurrence of organic carbon in the sediments during these intervals. During MIS 2 there appears to be less of an input of Southern Ocean waters to the BUS, although during the also glacial MIS 4 and 6, there is evidence for an increased influence of cold Antarctic waters. The comparison of the results from Core MD 962086 with other studies in the BUS area indicates a non-uniform pattern of upwelling intensity and advection of cold, southern waters into this system during MIS 2. Weaker upwelling signaled by the radiolarian-based proxy in MIS 4 is in contrast to other studies that indicate higher productivity during this time period. In general, the data show that there is a strong spatiotemporal complexity in upwelling intensity in the BUS and that the advection of water into it is not strongly tied to glacial–interglacial variations in climate.     

Distribution of myctophid resources in the Indian Ocean

Mesopelagics are one of the largest under-exploited marine resources with wide distribution in the world oceans. Lanternfishes are the key members of mesopelagic communities and the total resource in the world oceans is estimated at 600 million tons. Lanternfishes belong to the family Myctophidae which comprises of about 250 species in 35 genera. Myctophids account for about 75% of total global catch of small mesopelagic fishes. They are known to exhibit diel vertical migration, concentrating during the day time between 400 and 1,000 m, and between 5 and 100 m, during the night. In this paper, an attempt is made to review the existing information on the occurrence and distribution of myctophid resources in the Indian Ocean. 137 myctophid species have been reported from the entire Indian Ocean. Studies in the Arabian Sea have indicated that the area is rich in the midwater fish stocks dominated by myctophids with an estimated potential of 100 million tons.     

Nutrient concentrations in Nyanza Gulf, Lake Victoria, Kenya: light limits algal demand and abundance

Nyanza Gulf is a large shallow embayment connected to Lake Victoria by the deep narrow Rusinga Channel. Between December 2000 and May 2002 the gradient of nutrients along the axis of Nyanza gulf into the main lake was determined. Nutrient concentrations in the gulf were found to be different from those in the main lake with phosphorus fractions, SRP and TP being significantly higher in the main lake than in the gulf. Well oxygenated conditions in the gulf keep the PO₄–P strongly bound to mineral particles whereas in the main lake, where deeper depths allows for development of anoxia, it is released into solution. The low TN:TP molar ratio in the gulf and in the main lake indicates many algae may be N-limited and heterocystous N-fixing cyanobacteria may be favored. However, the high mineral turbidity in the gulf reduces light availability and hence limits algal abundance resulting in easily measure concentrations of mineral nutrients and in particular high levels of dissolved reactive silica. The gulf is a net source of dissolved silica and total nitrogen to the main lake while the main lake is potentially a source of P to the gulf depending on interchange through Rusinga Channel.     

The effect of landscape processes upon gene flow and genetic diversity in an Australian freshwater fish, Neosilurus hyrtlii

1. Flow regime and riverine architecture are two important landscape characteristics that influence genetic diversity and gene flow in riverine species.
2. Using population genetic markers (mtDNA, microsatellites and allozymes), this study aimed to investigate genetic diversity and gene flow in the freshwater fish, Neosilurus hyrtlii , across two major drainage divisions in northern and central Australia (the Gulf of Carpentaria and Lake Eyre basins). These basins lie adjacent to each other and differ in their hydrological inputs and riverine structure, providing an ideal opportunity to identify the impact of landscape processes upon population dynamics of freshwater fish.
3. Populations were strongly structured among basins, among catchments within basins and were weakly structured within catchments in the Lake Eyre Basin, providing support for the Stream Hierarchy Model.
4. Interestingly, mtDNA and microsatellite diversity was much higher in the Gulf of Carpentaria Basin compared to the Lake Eyre Basin. It was concluded that this difference was due to the extreme hydrological variability in this basin and boom-bust population cycles resulting in smaller effective population sizes in the Lake Eyre Basin.     

Biodiversity and community structure of Late Pleistocene foraminifera from Kish Island, Persian Gulf (Iran)

The raised coral reef sequences at Kish Island provide a rare window into the depositional setting and paleoenvironment of a high-latitude, shallow-water coral reef that developed under turbid conditions in the Persian Gulf during Marine Isotope Stage 7 (~200 to 250?ka). Six sedimentary facies and eight foraminiferal assemblages can be identified throughout the sequence. A ninth assemblage can be defined for the modern subtidal realm. At the base of the sequence is a marl rich in hyaline foraminifera (Elphidium, Ammonia, Asterorotalia, Bulimina, Nonion, and Quinqueloculina) and ostracods, which was deposited in about 30–40?m water depth in a turbid deltaic setting. Shallowing resulted in the marl becoming sandy, and changing to a mollusc-rich facies with rare foraminifera (mostly smaller miliolid taxa) that formed the substrate for coral recruitment. The coral marl layer contains many large corals embedded in situ in an aggregate and coralline algae-rich marl. Two abundance peaks in the foraminifera occur at the base and mid-way through this layer, which also correspond to a change from Murrayinella-dominated to Placopsilina-dominated assemblages, indicating deepening and more open-marine conditions, but elevated turbidity. Towards the top of the layer, abundance of foraminifera decreases and miliolid foraminifera become dominant. The top-most layer is dominated by coral and mollusc fragments and has an Amphistegina-rich reef-related assemblage. Of the Late Pleistocene foraminiferal assemblages, the Murrayinella-, Pararotalia-, and Placopsilina-dominated assemblages are no longer present in the modern gulf for unknown reasons. Of the other five assemblages, only the Amphistegina assemblage is found within proximity to the modern Kish Island. The Elphidium and Asterorotalia-Bulimina assemblages are from deeper areas of the gulf. The Ammonia and Quinqueloculina assemblages occur in lagoonal sediments on the Arabian side of the gulf. Like the modern Persian Gulf, the diversity of foraminifera was low (~80 common species) during the Pleistocene and does not correlate with foraminiferal abundance.     

Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region

There is convincing geological evidence for the historical existence of an ancient lake on the Australian-New Guinea continental shelf during the late Pleistocene. Lake Carpentaria was a vast fresh- to brackishwater lake that would presumably have provided habitat for, and facilitated gene flow among, aquatic taxa that tolerate low to moderate salinities in this region. Moreover, it has been argued that the outflow of Papua New Guinea's Fly River was diverted westward into Lake Carpentaria during this period, although this hypothesis is controversial. We predicted that these events, if a true history, would have promoted gene flow and population growth via range-expansion events in the giant freshwater prawn (Macrobrachium rosenbergii) and restricted gene flow subsequently by way of a vicariant event as sea levels rose during the late Pleistocene, and a marine environment replaced Lake Carpentaria. We tested these hypotheses using phylogeographical and phylogenetic analyses of mitochondrial DNA variation in M. rosenbergii populations sampled from the Lake Carpentaria region. Our results support the hypothesis that Lake Carpentaria facilitated gene flow among populations of M. rosenbergii that are today isolated, but contest claims of a westward diversion of the Fly River. We inferred the timing of initial expansion in the 'Lake Carpentaria lineage' and found the timing of this event to be broadly concordant with geological dating of the formation of Lake Carpentaria. Reconciling geological and molecular data, as presented here, provides a powerful framework for investigating the influence of historical earth history events on the distribution of biological (i.e. molecular) diversity.     

Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages

Archaea assemblages from the Arctic Ocean and Antarctic waters were compared by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified using the Archaea-specific primers 344f and 517r. Inspection of the DGGE fingerprints of 33 samples from the Arctic Ocean (from SCICEX submarine cruises in 1995, 1996, and 1997) and 7 Antarctic samples from Gerlache Strait and Dallman Bay revealed that the richness of Archaea assemblages was greater in samples from deep water than in those from the upper water column in both polar oceans. DGGE banding patterns suggested that most of the Archaea ribotypes were common to both the Arctic Ocean and the Antarctic Ocean. However, some of the Euryarchaeota ribotypes were unique to each system. Cluster analysis of DGGE fingerprints revealed no seasonal variation but supported depth-related differences in the composition of the Arctic Ocean Archaea assemblage. The phylogenetic composition of the Archaea assemblage was determined by cloning and then sequencing amplicons obtained from the Archaea-specific primers 21f and 958r. Sequences of 198 clones from nine samples covering three seasons and all depths grouped with marine group I Crenarchaeota (111 clones), marine group II Euryarchaeota (86 clones), and group IV Euryarchaeota (1 clone). A sequence obtained only from a DGGE band was similar to those of the marine group III Euryarchaeota:     

Foraminiferal and ostracod ecological patterns in coastal environments of SE Andros Island (Middle Aegean Sea, Greece)

A comparative study of recent epiphytal ostracod and benthic foraminiferal populations was conducted in August 2001, at two gulfs (Korthi and Kastro) located at the southeastern part of Andros Island (middle Aegean Sea, Greece). Thirty samples (representing living macro-benthic algae and seagrasses) from both gulfs were studied and a total of 34 ostracod species and 60 benthic foraminiferal species were identified. In the gulf of Korthi both benthic foraminiferal and epiphytal ostracod assemblages were characterized by high abundances of Amphistegina lessonii and Xestoleberis spp., respectively, therefore the performed Q-mode cluster analysis verified the presence of a Normal Environment Biofacies (NE). Declined Environment (DE) and Stressed (SE) Environment Biofacies were recognized in the gulf of Kastro, an area more affected by anthropogenic activities. Several deformed foraminiferal specimens have been documented in the assemblages from both gulfs, but malformed tests are significantly increased in SE Biofacies of Kastro gulf. This study suggests that great accumulations of A. lessonii (35-60%) associated with high frequencies of Xestoleberis communis and/or Xestoleberis decipiens and high species diversities can be used as bioindicators of coastal health.     

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.