Molecular Tuning of Rhodopsins for High Visual Sensitivity in Different Light Environments : Variation in Absorbance Spectrum and Opsin Sequence within and between Species

Visual pigments of different animal species must have evolved at some stage to match the prevailing light environments, since all visual functions depend on their ability to absorb available photons and transduce the event into a reliable neural signal. There is a large literature on correlation between the light environment and spectral sensitivity between different fish species. However, little work has been done on evolutionary adaptation between separated populations within species. More generally, little is known about the rate of evolutionary adaptation to changing spectral environments. The objective of this thesis is to illuminate the constraints under which the evolutionary tuning of visual pigments works as evident in: scope, tempo, available molecular routes, and signal/noise trade-offs. Aquatic environments offer Nature s own laboratories for research on visual pigment properties, as naturally occurring light environments offer an enormous range of variation in both spectral composition and intensity. The present thesis focuses on the visual pigments that serve dim-light vision in two groups of model species, teleost fishes and mysid crustaceans. The geographical emphasis is in the brackish Baltic Sea area with its well-known postglacial isolation history and its aquatic fauna of both marine and fresh-water origin. The absorbance spectrum of the (single) dim-light visual pigment were recorded by microspectrophotometry (MSP) in single rods of 26 fish species and single rhabdoms of 8 opossum shrimp populations of the genus Mysis inhabiting marine, brackish or freshwater environments. Additionally, spectral sensitivity was determined from six Mysis populations by electroretinogram (ERG) recording. The rod opsin gene was sequenced in individuals of four allopatric populations of the sand goby (Pomatoschistus minutus). Rod opsins of two other goby species were investigated as outgroups for comparison. Rod absorbance spectra of the Baltic subspecies or populations of the primarily marine species herring (Clupea harengus membras), sand goby (P. minutus), and flounder (Platichthys flesus) were long-wavelength-shifted compared to their marine populations. The spectral shifts are consistent with adaptation for improved quantum catch (QC) as well as improved signal-to-noise ratio (SNR) of vision in the Baltic light environment. Since the chromophore of the pigment was pure A1 in all cases, this has apparently been achieved by evolutionary tuning of the opsin visual pigment. By contrast, no opsin-based differences were evident between lake and sea populations of species of fresh-water origin, which can tune their pigment by varying chromophore ratios. A more detailed analysis of differences in absorbance spectra and opsin sequence between and within populations was conducted using the sand goby as model species. Four allopatric populations from the Baltic Sea (B), Swedish west coast (S), English Channel (E), and Adriatic Sea (A) were examined. Rod absorbance spectra, characterized by the wavelength of maximum absorbance (λmax), differed between populations and correlated with differences in the spectral light transmission of the respective water bodies. The greatest λmax shift as well as the greatest opsin sequence difference was between the Baltic and the Adriatic populations. The significant within-population variation of the Baltic λmax values (506-511 nm) was analyzed on the level of individuals and was shown to correlate well with opsin sequence substitutions. The sequences of individuals with λmax at shorter wavelengths were identical to that of the Swedish population, whereas those with λmax at longer wavelengths additionally had substitution F261F/Y in the sixth transmembrane helix of the protein. This substitution (Y261) was also present in the Baltic common gobies and is known to redshift spectra. The tuning mechanism of the long-wavelength type Baltic sand gobies is assumed to be the co-expression of F261 and Y261 in all rods to produce ≈ 5 nm redshift. The polymorphism of the Baltic sand goby population possibly indicates ambiguous selection pressures in the Baltic Sea. The visual pigments of all lake populations of the opossum shrimp (Mysis relicta) were red-shifted by 25 nm compared with all Baltic Sea populations. This is calculated to confer a significant advantage in both QC and SNR in many humus-rich lakes with reddish water. Since only A2 chromophore was present, the differences obviously reflect evolutionary tuning of the visual protein, the opsin. The changes have occurred within the ca. 9000 years that the lakes have been isolated from the Sea after the most recent glaciation. At present, it seems that the mechanism explaining the spectral differences between lake and sea populations is not an amino acid substitution at any other conventional tuning site, but the mechanism is yet to be found.

Optically Stimulated Luminescence (OSL) Dating of Sediments from Himalaya

Optically Stimulated Luminescence (OSL) dating gives the age of most recent daylight exposure or heating of samples to >400 degrees C or the formation events of authigenic minerals. These correspond to the age of sedimentation and burial, ages of thermal events like contact heating by lava flows and heating during faulting and sand dyke formation, and the formation of a mineral via chemical precipitation. With the first observation of OSL in 1985, this method now occupies centre stage in Quaternary Geochronology. The use of OSL method for sediments from Himalaya began over three decades ago. The method has since provided chronology for a variety of events, such as past glaciation events, formation ages of river terraces, paleo-lacustrine deposits, landslides, floods, seismic events with substantive new insights into timing and style of geological processes. Theoretically, the dating range of method is present to a Million years, and this critically depends on two factors, viz, luminescence properties of mineral and their radiation environments. The general working range using quartz is 200ka, and using feldspars is up to Brunhes Matuyam Boundary. Extensions beyond this limit are currently being explored.

Comparative limnology of waters in a coniferous forest: is a generalisation possible?

The high density of meres and mosses in the Delamere area comes from numerous moraine-hollows formed after the melting of stranded ice-blocks following last glaciation. The main vegetation is of conifers along with some deciduous species and the area was designated as a National Forest Park in 1987. It has been managed since the beginning of the 19th century and is a popular tourist area with walking, orienteering, cycling and educational activities. In recent years this forest park has been attracting over half a million people per year. This paper studies the limnology of different aquatic habitats in the Delamere Forest area in order to give some insight into the waters of a coniferous, temperate forest area, which has so far been largely unexplored. The authors assume therefore, thought that despite apparent large variability in origin, age, surface area, morphometry, catchment size and hydraulic regime, the waters of Delamere Forest might share some revealing chemical and biological features. Seven water-bodies in the Delamere Forest Park area, namely, Black Lake, Blakemere Moss, Delamere Lake, Delamere Quarry, Hatchmere, Windyhowe Farm Spring and Fir Brook were sampled, their water chemistry and dissolved organic carbon and the occurrence of phytoplankton and zooplankton species examined. In a final chapter the authors analyse their findings for patterns.

'The highly nervous system of the English Lakes': aquatic ecosystem sensitivity to external changes, as demonstrated by diatoms.

The author reviews the stratigraphic diatom profile of Cumbrian lakes since the last glaciation. Knowledge of both present and previous interglacials suggests that a natural cycle of change is imposed on all lakes. The nature of inwashed material is dependant on climatic and natural soilcycles and this affects the water quality and sensitive aquatic biota. Anthropogenic effects are superimposed upon this with forest clearance and pollution. Whilst some Cumbrian diatom profiles extend over the entire post glacial, others cover only detailed sections relating to particular problems. Causes and effect of recent changes in lakes can be studied using indicator species but palaeocology contributes greatly to understanding of long term changes.

Population structure of pink salmon (Oncorhynchus gorbuscha) in British Columbia and Washington, determined with microsatellites

Population structure of pink salmon (Oncorhynchus gorbuscha) from British Columbia and Washington was examined with a survey of microsatellite variation to describe the distribution of genetic variation. Variation at 16 microsatellite loci was surveyed for approximately 46,500 pink salmon sampled from 146 locations in the odd-year broodline and from 116 locations in the even-year broodline. An index of genetic differentiation, FST, over all populations and loci in the odd-year broodline was 0.005, with individual locus values ranging from 0.002 to 0.025. Population differentiation was less in the even-year broodline, with a FST value of 0.002 over all loci, and with individual locus values ranging from 0.001 to 0.005. Greater genetic diversity was observed in the odd-year broodline. Differentiation in pink salmon allele frequencies between broodlines was approximately 5.5 times greater than regional differentiation within broodlines. A regional structuring of populations was the general pattern observed, and a greater regional structure in the odd-year broodline than in the even-year broodline. The geographic distribution of microsatellite variation in populations of pink salmon likely ref lects a distribution of broodlines from separate refuges after the last glaciation period.

Population structure of chum salmon (Oncorhynchus keta) across the Pacific Rim, determined from microsatellite analysis

The Pacific Rim population structure of chum salmon (Oncorhynchus keta) was examined with a survey of microsatellite variation to describe the distribution of genetic variation and to evaluate whether chum salmon may have originated from two or more glacial refuges following dispersal to newly available habitat after glacial retreat. Variation at 14 microsatellite loci was surveyed for over 53,000 chum salmon sampled from over 380 localities ranging from Korea through Washington State. An index of genetic differentiation, FST, over all populations and loci was 0.033, with individual locus values ranging from 0.009 to 0.104. The most genetically diverse chum salmon were observed from Asia, particularly Japan, whereas chum salmon from the Skeena River and Queen Charlotte Islands in northern British Columbia and those from Washington State displayed the fewest number of alleles compared with chum salmon in other regions. Differentiation in chum salmon allele frequencies among regions and populations within regions was approximately 18 times greater than that of annual variation within populations. A regional structuring of populations was the general pattern observed, with chum salmon spawning in different tributaries within a major river drainage or spawning in smaller rivers in a geographic area generally more similar to each other than to populations in different major river drainages or geographic areas. Population structure of chum salmon on a Pacific Rim basis supports the concept of a minimum of two refuges, northern and southern, during the last glaciation, but four possible refuges fit better the observed distribution of genetic variation. The distribution of microsatellite variation of chum salmon on a Pacific Rim basis likely reflects the origins of salmon radiating from refuges after the last glaciation period.

Arcabouço estratigráfico e ciclicidade deposicional dos sistemas sedimentares quaternários da plataforma sul da Bacia de Campos (RJ)

A análise sísmica de ~ 3000 km de dados sísmicos sparker de reflexão monocanal permitiu a proposição de um arcabouço estratigráfico englobando a seção rasa (~300 milisegundos) da plataforma continental sul da Bacia de Campos. Cinco sequências sísmicas foram reconhecidas (Sq1-Sq5), limitadas por superfícies erosivas de escala plataformal (superfícies S1-S5), interpretadas como sequências deposicionais formadas por oscilações glacioeustáticas e limites de sequências (discordâncias regionais) esculpidos durante longos períodos de exposição subaérea e total da plataforma, indicando condições de diminuição de nível de base e destruição parcial de espaço de acomodação sedimentar. As sequências Sq1-Sq4 são dominantemente regressivas, compostas principalmente por prismas de regressão forçada de borda de plataforma/talude superior. A sequência superficial Sq5 é constituída essencialmente de unidades retrogradantes restritas à plataforma continental, interpretadas como compondo uma sequência eminentemente transgressiva. A correlação entre dados sísmicos e cronoestratigráficos de um poço exploratório disponível na área permitiu posicionar a deposição desta sucessão estratigráfica entre o Pleistoceno Médio- Holoceno (últimos ~500 ka). Além disso, a correlação entre a base de dados com curvas globais de variações eustáticas, baseadas nas razões isotópicas de 18O (estágios isotópicos marinhos), permitiu ainda sugerir que a sucessão estratigráfica Sq1-Sq4 registra sequências regressivas de quarta ordem, refletindo deposição durante ciclos glacioeustáticos de ~ 100 -120 ka de duração e de alta amplitude de oscilação eustática (100-145m), que caracterizam o sinal eustático nos últimos ~500 ka. A sequência Sq5 seria uma sequência ainda em formação, constituída por depósitos transgressivos e de mar alto formados durante o Pleistoceno Tardio-Holoceno.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

timng of the last glacial maximum from observed sea level minima

During the Last Glacial Maximum, ice sheets covered large areas in northern latitudes, and global temperatures were significantly lower than today. But few direct estimates exist of the volume of the ice sheets, or the timing and rates of change during their advance and retreat. Here we analyze four distinct sediment facies in the shallow, tectonically stable Bonaparte Gulf, Australia - each of which is characteristic of a distinct range in sea level - to estimate the maximum volume of land-based ice during the last glaciation and the timing of the initial melting phase. We use faunal assemblages and preservation status of the sediments to distinguish open marine, shallow marine, marginal marine and brackish conditions, and estimate the timing and the mass of the ice sheets using radiocarbon dating and glacio-hydroisostatic modelling. Our results indicate that from at least 22,000 to 19,000 (calendar) years before present, land-based ice volume was at its maximum, exceeding today's grounded ice sheets by 52.5 x 10 exp 6 cu km. A rapid decrease in ice volume by about 10 percent within a few hundred years terminated the Last Glacial Maximum at 19,000 +/- 250 years.

Benthic foraminifera and bottom water evolution in the middle-southern Okinawa Trough during the last 18 ka

A piston sediment core E017 from the middle-southern Okinawa Trough was investigated. A preliminary study of the deep-water evolution since 18 cal. ka BP was performed based on the quantitative census data of benthic foraminiferal fauna, together with planktonic foraminiferal oxygen and carbon isotope, AMS(14)C dating, and the previous results achieved in the southern Okinawa Trough. The result shows that the benthic fauna was dominated by Bulimina aculeata (d'Orbigny), Uvigerina peregrina (Cushman), Hispid Uvigerina and Uvigerina dirupta (Todd) during the glaciation-deglaciation before 9.2 cal. ka BP, while Epistominella exigua (Brady), Pullenia bulloides (d'Orbigny), Cibicidoides hyalina (Hofker), Sphaeroidina bulloides (d'Orbigny) and Globocassidulina subglobosa (Brady) predominated the fauna in the post-glacial period after 9.2 cal. ka BP. The benthic foraminifera accumulation rate (BFAR), paleoproductivity estimates and benthic foraminiferal assemblage conformably indicate that surface water paleoproductivity and organic matter flux during the glaciation-deglaciation were higher than those of the post-glacial period in the middle-southern Okinawa Trough, and gradually enhanced from the southern to the central Okinawa Trough during the glaciation-deglaciation, which could be caused by the discrepancy of the terrigenous nutrients supply. High abundances of E exigua, an indicator of pulsed organic matter input, after 9.2 cal. ka. BP may indicate that the intensity of seasonally riverine pulsed flux during the post-glacial period was stronger than that of the glaciation-deglaciation period, and the seasonal influx in the central trough might be stronger than in the south. The temporal distributions of the typical species indicating bottom water oxygen content and ventilation condition show that the ventilation of the bottom water during the post-glacial period is more active than the glaciation-deglaciation, which reflects that the evolution of the intermediate and deep waters of the northwestern Pacific during the last glaciation has no evident influence on the deep-water of the middle-southern Okinawa Trough. Additionally, the variations in agglutinated benthic foraminiferal abundance and other carbonate dissolution proxies indicate that carbonate dissolution gradually increased since the last 18 ka in the Okinawa Trough and rapidly enhanced at 9.2 cal. ka BP. The modern shallow carbonate lysocline could form at 3 cal. ka BP.

Heinrich event imprints in the Okinawa Trough: evidence from oxygen isotope and planktonic foraminifera

Planktonic foraminiferal faunas, oxygen isotope and modern analog technique sea surface temperature records were obtained in piston core DGKS9603 (28degrees08.869'N, 127degrees16.238'E, water depth 1100 in) collected from the middle Okinawa Trough. During the last glaciation, four cold events were identified and correlate Heinrich events (HE) H2-5 of the last 45 ka. During the last deglaciation, core DGKS9603 has begun to be influenced by the Kuroshio since about 16 cal ka BP. Three weakenings of this warm current occurred at about 2.8-5.3, 11.4 and 15.5 cal ka BP respectively. Among the three fluctuations, the oldest one is synchronous with HE1 and could be a response to the strong cooling observed in the North Atlantic Ocean. The fluctuation occurring at about 11.4 cal ka ago corresponds to the Younger Dryas within the age error bars. Our observations provide new evidence that the HEs documented from Greenland and the northern North Atlantic had a global climatic impact. Changes in the intensity of the East Asian monsoon could be the main mechanism responsible for the paleoccanographic variations observed in the Okinawa Trough. (C) 2001 Elsevier Science B.V. All rights reserved.

The unique skeleton of siliceous sponges (Porifera; Hexactinellida and Demospongiae) that evolved first from the Urmetazoa during the Proterozoic: a review

Sponges (phylum Porifera) had been considered as an enigmatic phylum, prior to the analysis of their genetic repertoire/tool kit. Already with the isolation of the first adhesion molecule, galectin, it became clear that the sequences of sponge cell surface receptors and of molecules forming the intracellular signal transduction pathways triggered by them, share high similarity with those identified in other metazoan phyla. These studies demonstrated that all metazoan phyla, including Porifera, originate from one common ancestor, the Urmetazoa. The sponges evolved prior to the Ediacaran-Cambrian boundary (542 million years ago [myr]) during two major "snowball earth events", the Sturtian glaciation (710 to 680 myr) and the Varanger-Marinoan ice ages (605 to 585 myr). During this period the ocean was richer in silica due to the silicate weathering. The oldest sponge fossils (Hexactinellida) have been described from Australia, China and Mongolia and are thought to have existed coeval with the diverse Ediacara fauna. Only little younger are the fossils discovered in the Sansha section in Hunan (Early Cambrian; China). It has been proposed that only the sponges possessed the genetic repertoire to cope with the adverse conditions, e.g. temperature-protection molecules or proteins protecting them against ultraviolet radiation. The skeletal elements of the Hexactinellida (model organisms Monorhaphis chuni and Monorhaphis intermedia or Hyalonema sieboldi) and Demospongiae (models Suberites domuncula and Geodia cydonium), the spicules, are formed enzymatically by the anabolic enzyme silicatein and the catabolic enzyme silicase. Both, the spicules of Hexactinellida and of Demospongiae, comprise a central axial canal and an axial filament which harbors the silicatein. After intracellular formation of the first lamella around the channel and the subsequent extracellular apposition of further lamellae the spicules are completed in a net formed of collagen fibers. The data summarized here substantiate that with the finding of silicatein a new aera in the field of bio/inorganic chemistry started. For the first time strategies could be formulated and experimentally proven that allow the formation/synthesis of inorganic structures by organic molecules. These findings are not only of importance for the further understanding of basic pathways in the body plan formation of sponges but also of eminent importance for applied/commercial processes in a sustainable use of biomolecules for novel bio/inorganic materials.

Potential refugium on the Qinghai-Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata (Gentianaceae)

Metagentiana striata is an alpine annual herbaceous plant endemic to the east of the Qinghai-Tibet (Q-T) Plateau and adjacent areas. The phylogeography of M. striata was studied by sequencing the chloroplast DNA (cpDNA) trnS-trnG intergenic spacer. Ten haplotypes were identified from an investigation of 232 individuals of M. striata from 14 populations covering the entire geographical range of this species. The level of differentiation amongst populations was very high (G(ST) = 0.746; N-ST = 0.774) and a significant phylogeographical structure was observed (P < 0.05). An analysis of molecular variance found a high variation amongst populations (76%), with F-ST = 0.762 (highly significant, P < 0.001), indicating that little gene flow occurred amongst the different regions; this was explained by the isolation of populations by high mountains along the Q-T Plateau and adjacent areas (N-m = 0.156). Only one ancestral haplotype (A) was common and widespread throughout the distributional range of M. striata. The populations of the Hengduan Mountains region of the south-eastern Q-T Plateau showed high diversity and uniqueness of haplotypes. It is suggested that this region was the potential refugium of M. striata during the Quaternary glaciation, and that interglacial and postglacial range expansion occurred from this refugium. This scenario was in good agreement with the results of nested clade analysis, which inferred that the current spatial distribution of cpDNA haplotypes and populations resulted from range expansion, together with past allopatric fragmentation events. (c) 2008 The Linnean Society of London.

元谋盆地河湖相沉积记录的上新世印度季风转型事件

The Indian monsoon, an integral part of the global climate system, has been extensively investigated during the past decades. Most of the proxy records are derived from marine sediments and focused on time periods of the late Miocene and Pleistocene. The Pliocene represents a period when Earth’s boundary conditions underwent dramatic changes. However, variations of the Indian monsoon during the Pliocene and its forcing mechanisms have remained unclear. The Yuanmou Basin, located in the region of the Indian monsoon, provides an ideal target for understanding the Pliocene history of Indian monsoon variations. Detailed investigations on the lithostratigraphy, magnetostratigraphy and limnology of a 650-m-thick fluvio-lacustrine sedimentary sequence from the basin are carried out in the present study. The clay and clay-plus-fine-silt fractions of the sediments are referred to the midlake-facies components, and changes in the percentages of both fractions generally reflect changes in the water level of the lakes developed in the basin closely related to variations in the intensity of the Indian monsoon. Whereas the greenish-gray lacustrine mud beds represent the environment of deep-water lakes, and the frequency of individual lacustrine mud beds is considered to indicate the frequency of the deep-water lakes developed in the basin associated with the variability of the Indian monsoon. The proxy data suggest that the Indian monsoon experienced abrupt shifts at 3.53, 3.14, 2.78 and 2.42 Ma, respectivey. 1) Since 3.53 Ma, the midlake-facies components displayed a general trend of increase in the concentrations, accompanied by an increase in the sedimentation rate from an average ~10 to 25 cm ka–1. The data suggest that high stands of the lakes in the basin rose progressively, implying a gradual intensification of the Indian monsoon since that time. This shift occurred coeval with the accelerated uplift of the northern Tibetan Plateau, denoting a close link between the Indian monsoon strengthening and the Tibetan Plateau uplifting. 2) 2.78 Ma ago, the concentrations of the midlake-facies components decreased abruptly and the dominant fraction of the sediments turned to fluvial sands. The data indicate that lakes in the basin disappeared, reflecting a dramatic decline in the intensity of the Indian monsoon at that time. This shift coincided with the formation of extensive Northern Hemisphere ice sheets, implying a quick response of the low-latitude monsoon regime to the high-latitude glaciation. 3) At 3.14 Ma, the initial appearance of blackish-grey mud beds with long durations and occasional occurrences of lacustrine mud beds indicate that the basin was overall dominated by shallow lakes, implying a shift to decreased variability of the Indian monsoon at that time. At 2.42 Ma, an increase in the frequency and a decrease in the duration of the lacustrine mud beds suggest that deep-water lakes were frequently developed in the basin, denoting a shift to increased variability of the Indian monsoon at that time. The former shift coincides with the onset of large-scale glaciation in the circum Atlantic region and the latter corresponds to the inception of predominance of the 41 ka periodicity in Northern Hemisphere ice-sheet cover fluctuations, presumably suggesting a physical link between the Indian monsoon system and the high-latitude ice sheets in the Northern Hemisphere.