Palaeoglacial and palaeoclimatic conditions in the NW Pacific, as revealed by a morphometric analysis of cirques upon the Kamchatka Peninsula

The distribution of glacial cirques upon the Kamchatka peninsula, Far Eastern Russia, is systematically mapped from satellite images and digital elevation model data. A total of 3,758 cirques are identified, 238 of which are occupied by active glaciers. The morphometry of the remaining 3,520 cirques is analysed. These cirques are found to show a very strong N bias in their azimuth (orientation), likely resulting from aspect-related variations in insolation. The strength of this N bias is considered to indicate that former glaciation upon the peninsula was often ‘marginal’, and mainly of cirque-type, with peaks extending little above regional equilibrium-line altitudes. This is supported by the fact that S and SE-facing cirques are the highest in the dataset, suggesting that glacier-cover was rarely sufficient to allow S and SE-facing glaciers to develop at low altitudes. The strength of these azimuth-related variations in cirque altitude is thought to reflect comparatively cloud-free conditions during former periods of glaciation. It is suggested that these characteristics, of marginal glaciation and comparatively cloud-free conditions, reflect the region’s former aridity, which was likely intensified at the global Last Glacial Maximum, and during earlier periods of ice advance, as a result of the development of negative pressure anomalies over the North Pacific (driven by the growth of the Laurentide Ice Sheet), combined with other factors, including an increase in the extent and duration of sea ice, a reduction in global sea levels, cooler sea surface temperatures, and the localised growth of mountain glaciers. There is published evidence to suggest extensive glaciation of the Kamchatka Peninsula at times during the Late Quaternary, yet the data presented here appears to suggest that such phases were comparatively short-lived, and that smaller cirque-type glaciers were generally more characteristic of the period.

Exploring the Transcriptome of Atlantic Salmon (Salmo salar) Skin, a Major Defense Organ

The skin of fish is the first line of defense against pathogens and parasites. The skin transcriptome of the Atlantic salmon is poorly characterized, and currently only 2,089 expressed sequence tags (ESTs) out of a total of half a million sequences are generated from skin-derived cDNA libraries. The primary aim of this study was to enhance the transcriptomic knowledge of salmon skin by using next-generation sequencing (NGS) technology, namely the Roche-454 platform. An equimolar mixture of high-quality RNA from skin and epidermal samples of salmon reared in either freshwater or seawater was used for 454-sequencing. This technique yielded over 600,000 reads, which were assembled into 34,696 isotigs using Newbler. Of these isotigs, 12 % had not been sequenced in Atlantic salmon, hence representing previously unreported salmon mRNAs that can potentially be skin-specific. Many full-length genes have been acquired, representing numerous biological processes. Mucin proteins are the main structural component of mucus and we examined in greater detail the sequences we obtained for these genes. Several isotigs exhibited homology to mammalian mucins (MUC2, MUC5AC and MUC5B). Mucin mRNAs are generally > 10 kbp and contain large repetitive units, which pose a challenge towards full-length sequence discovery. To date, we have not unearthed any full-length salmon mucin genes with this dataset, but have both N- and C-terminal regions of a mucin type 5. This highlights the fact that, while NGS is indeed a formidable tool for sequence data mining of non-model species, it must be complemented with additional experimental and bioinformatic work to characterize some mRNA sequences with complex features.

Influence of the Pacific Decadal Oscillation, El Niño-Southern Oscillation and solar forcing on climate and primary productivity changes in the northeast Pacific

Evidence of 11-year Schwabe solar sunspot cycles, El Niño-Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO) were detected in an annual record of diatomaceous laminated sediments from anoxic Effingham Inlet, Vancouver Island, British Columbia. Radiometric dating and counting of annual varves dates the sediments from AD 1947-1993. Intact sediment slabs were X-rayed for sediment structure (lamina thickness and composition based on gray-scale), and subsamples were examined for diatom abundances and for grain size. Wavelet analysis reveals the presence of ~2-3, ~4.5, ~7 and ~9-12-year cycles in the diatom record and an w11e13 year record in the sedimentary varve thickness record. These cycle lengths suggest that both ENSO and the sunspot cycle had an influence on primary productivity and sedimentation patterns. Sediment grain size could not be correlated to the sunspot cycle although a peak in the grain size data centered around the mid-1970s may be related to the 1976-1977 Pacific climate shift, which occurred when the PDO index shifted from negative (cool conditions) to positive (warm conditions). Additional evidence of the PDO regime shift is found in wavelet and cross-wavelet results for Skeletonema costatum, a weakly silicified variant of S. costatum, annual precipitation and April to June precipitation. Higher spring (April/May) values of the North Pacific High pressure index during sunspot minima suggest that during this time, increased cloud cover and concomitant suppression of the Aleutian Low (AL) pressure system led to strengthened coastal upwelling and enhanced diatom production earlier in the year. These results suggest that the 11-year solar cycle, amplified by cloud cover and upwelling changes, as well as ENSO, exert significant influence on marine primary productivity in the northeast Pacific. The expression of these cyclic phenomena in the sedimentary record were in turn modulated by the phase of PDO, as indicated by the change in period of ENSO and suppression of the solar signal in the record after the 1976-1977 regime shift. © 2013 Elsevier Ltd and INQUA. All rights reserved.

Climate change and decadal to centennial-scale periodicities recorded in a late Holocene NE Pacific marine record: Examining the role of solar forcing

We present a decadal-scale late Holocene climate record based on diatoms, biogenic silica, and grain size from a 12-m sediment core (VEC02A04) obtained from Frederick Sound in the Seymour-Belize Inlet Complex of British Columbia, Canada. Sediments are characterized by graded, massive, and laminated intervals. Laminated intervals are most common between c. 2948–2708 cal. yr BP and c. 1992–1727 cal. yr BP. Increased preservation of laminated sediments and diatom assemblage changes at this time suggest that cli- mate became moderately drier and cooler relative to the preceding and succeeding intervals. Spectral and wavelet analyses are used to test for statistically significant periodicities in time series of proxies of primary production (total diatom abundance, biogenic silica) and hydrology (grain size) preserved in the Frederick Sound record. Periodicities of c. 42–53, 60–70, 82–89, 241–243, and 380 yrs are present. Results are com- pared to reconstructed sunspot number data of Solanki et al. (2004) using cross wavelet transform to evalu- ate the role of solar forcing on NE Pacific climate. Significant common power of periodicities between c. 42– 60, 70–89, 241–243, and of 380 yrs occur, suggesting that celestial forcing impacted late Holocene climate at Frederick Sound. Replication of the c. 241–243 yr periodicity in sunspot time series is most pronounced be- tween c. 2900 cal. yr BP and c. 2000 cal. yr BP, broadly correlative to the timing of maximum preservation of laminated sedimentary successions and diatom assemblage changes. High solar activity at the Suess/de Vries band may have been manifested as a prolonged westward shift and/or weakening of the Aleutian Low in the mid-late Holocene, which would have diverted fewer North Pacific storms and resulted in the relatively dry conditions reconstructed for the Seymour-Belize Inlet Complex.

Tephra from andesitic Shiveluch volcano, Kamchatka, NW Pacific: chronology of explosive eruptions and geochemical fingerprinting of volcanic glass

The ~16-ka-long record of explosive eruptions from Shiveluch volcano (Kamchatka, NW Pacific) is refined using geochemical fingerprinting of tephra and radiocarbon ages. Volcanic glass from 77 prominent Holocene tephras and four Late Glacial tephra packages was analyzed by electron microprobe. Eruption ages were estimated using 113 radiocarbon dates for proximal tephra sequence. These radiocarbon dates were combined with 76 dates for regional Kamchatka marker tephra layers into a single Bayesian framework taking into account the stratigraphic ordering within and between the sites. As a result, we report ~1,700 high-quality glass analyses from Late Glacial–Holocene Shiveluch eruptions of known ages. These define the magmatic evolution of the volcano and provide a reference for correlations with distal fall deposits. Shiveluch tephras represent two major types of magmas, which have been feeding the volcano during the Late Glacial–Holocene time: Baidarny basaltic andesites and Young Shiveluch andesites. Baidarny tephras erupted mostly during the Late Glacial time (~16–12.8 ka BP) but persisted into the Holocene as subordinate admixture to the prevailing Young Shiveluch andesitic tephras (~12.7 ka BP–present). Baidarny basaltic andesite tephras have trachyandesite and trachydacite (SiO₂ < 71.5 wt%) glasses. The Young Shiveluch andesite tephras have rhyolitic glasses (SiO₂ > 71.5 wt%). Strongly calc-alkaline medium-K characteristics of Shiveluch volcanic glasses along with moderate Cl, CaO and low P₂O₅ contents permit reliable discrimination of Shiveluch tephras from the majority of other large Holocene tephras of Kamchatka. The Young Shiveluch glasses exhibit wave-like variations in SiO₂ contents through time that may reflect alternating periods of high and low frequency/volume of magma supply to deep magma reservoirs beneath the volcano. The compositional variability of Shiveluch glass allows geochemical fingerprinting of individual Shiveluch tephra layers which along with age estimates facilitates their use as a dating tool in paleovolcanological, paleoseismological, paleoenvironmental and archeological studies. Electronic tables accompanying this work offer a tool for statistical correlation of unknown tephras with proximal Shiveluch units taking into account sectors of actual tephra dispersal, eruption size and expected age. Several examples illustrate the effectiveness of the new database. The data are used to assign a few previously enigmatic wide-spread tephras to particular Shiveluch eruptions. Our finding of Shiveluch tephras in sediment cores in the Bering Sea at a distance of ~600 km from the source permits re-assessment of the maximum dispersal distances for Shiveluch tephras and provides links between terrestrial and marine paleoenvironmental records.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5–20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here we compare the fitness of communally-reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically-based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.

Two species of caridean shrimps (Decapoda:Hippolytidae and Nematocarcinidae) newly recorded from hydrothermally vents on the Manus Basin, Southwestern Pacific.

Two species of caridean shrimps are newly recorded from hydrothermal vents on the Manus Basin, southwestern Pacific, at depths of 1540-1577m. Lebbeus manus, new species, is related to L.curvirostris Zarenkov, 1976, L.elegans Komai, Hayashi & Kohtsuka, 2004, L.longipes (Kobjakova, 1936), L.vicinus vicinus (Rathbun, 1902) and L.vicinus motereyensis (Wicksten & Mendez, 1982) because of the lack of strap-like epipods on the second and third pereopods; but characters of the rostrum, carapace and abdomen immediately distinguish the new species from the these five taxa. Subadult and juvenile specimens of Nematocarcinus are referred to N.sp.aff.exilis, but their definite identification is postponed until additional specimens become available for study. There are a few minor differences between the present Manus specimens and European specimens representing N.exilis (Bate, 1888), suggesting that the Manus population may indeed represent a separate species.

Neuroendocrinology of cooperation: the role of neuropeptides on the modulation of mutualistic behaviour of the Indo-Pacific Cleaner Wrasse (Labroides dimidiatus)

Tese de doutoramento, Ciências do Mar, da Terra e do Ambiente, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Meridional mixing of water masses in the Kuroshio Extension: Origins of North Pacific Intermediate Water anomalies

Senior thesis written for Oceanography 445