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.

Complex pattern of genetic structuring in the Atlantic salmon (Salmo salar L.) of the River Foyle system in northwest Ireland: disentangling the evolutionary signal from population stochasticity

Little is known about the microevolutionary processes shaping within river population genetic structure of aquatic organisms characterized by high levels of homing and spawning site fidelity. Using a microsatellite panel, we observed complex and highly significant levels of intrariver population genetic substructure and Isolation-by-Distance, in the Atlantic salmon stock of a large river system. Two evolutionary models have been considered explaining mechanisms promoting genetic substructuring in Atlantic salmon, the member-vagrant and metapopulation models. We show that both models can be simultaneously used to explain patterns and levels of population structuring within the Foyle system. We show that anthropogenic factors have had a large influence on contemporary population structure observed. In an analytical development, we found that the frequently used estimator of genetic differentiation, F-ST, routinely underestimated genetic differentiation by a factor three to four compared to the equivalent statistic Jost's D-est (Jost 2008). These statistics also showed a near-perfect correlation. Despite ongoing discussions regarding the usefulness of "adjusted" F-ST statistics, we argue that these could be useful to identify and quantify qualitative differences between populations, which are important from management and conservation perspectives as an indicator of existence of biologically significant variation among tributary populations or a warning of critical environmental damage.

The replacement of a native freshwater amphipod by an invader: roles for environmental degradation and intraguild predation

We assessed the extent to which an invader, Gammarus pulex (Crustacea: Amphipoda), has replaced a native, Gammarus duebeni celticus, over a 13-year period in a European river system and some of the abiotic and biotic factors that could account for this. Between 1988 and 2001, 56% of mixed-species sites had become invader-only sites, whereas no mixed sites had become native only again. The native dominated areas of higher dissolved oxygen and water quality, with the reciprocal true for the invader. Field transplant experiments revealed that native survivorship was lower in areas where it had been replaced than in areas where the invader does not yet occur. In invader-only areas, native survivorship was lower than that of the invader when kept separately and lowest when both species were kept together. We also observed predation of the native by the invader. Laboratory oxygen manipulation experiments revealed that at 30% saturation, the native's survivorship was two thirds that of the invader. We conclude that decreasing water quality favours replacement of the native by the invader.

Limitations of instantaneous water quality sampling in surface-water catchments: Comparison with near-continuous phosphorus time-series data.

The validity of load estimates from intermittent, instantaneous grab sampling is dependent on adequate spatial coverage by monitoring networks and a sampling frequency that re?ects the variability in the system under study. Catchments with a ?ashy hydrology due to surface runoff pose a particular challenge as intense short duration rainfall events may account for a signi?cant portion of the total diffuse transfer of pollution from soil to water in any hydrological year. This can also be exacerbated by the presence of strong background pollution signals from point sources during low flows. In this paper, a range of sampling methodologies and load estimation techniques are applied to phosphorus data from such a surface water dominated river system, instrumented at three sub-catchments (ranging from 3 to 5 km2 in area) with near-continuous monitoring stations. Systematic and Monte Carlo approaches were applied to simulate grab sampling using multiple strategies and to calculate an estimated load, Le based on established load estimation methods. Comparison with the actual load, Lt, revealed signi?cant average underestimation, of up to 60%, and high variability for all feasible sampling approaches. Further analysis of the time series provides an insight into these observations; revealing peak frequencies and power-law scaling in the distributions of P concentration, discharge and load associated with surface runoff and background transfers. Results indicate that only near-continuous monitoring that re?ects the rapid temporal changes in these river systems is adequate for comparative monitoring and evaluation purposes. While the implications of this analysis may be more tenable to small scale ?ashy systems, this represents an appropriate scale in terms of evaluating catchment mitigation strategies such as agri-environmental policies for managing diffuse P transfers in complex landscapes.

The geoarchaeology of Paleolithic rivers of southwest Britain

In Britain, the majority of Lower and Middle Paleolithic archaeological finds come from river terrace deposits. The impressive “staircase” terrace sequences of southeast England, and research facilitated by aggregate extraction have provided a considerable body of knowledge about the terrace chronology and associated archaeology in that area. Such research has been essential in considering rates of uplift, climatic cycles, archaeological chronologies, and the landscapes in which hominins lived. It has also promoted the view that southeast England was a major hominin route into Britain. By contrast, the terrace deposits of the southwest have been little studied. The Palaeolithic Rivers of South West Britain (PRoSWEB) project employed a range of geoarchaeological methodologies to address similar questions at different scales, focusing on the rivers Exe, Axe, Otter, and the paleo-Doniford, all of which were located south of the maximum Pleistocene glacial limit (marine oxygen isotope stage [MIS] 4–2). Preliminary analysis of the fieldwork results suggests that although the evolution of these catchments is complex, most conform to a standard staircase-type model, with the exception of the Axe, and, to a lesser extent, the paleo-Doniford, which are anomalous. Although the terrace deposits are less extensive than in southeast Britain, differentiation between terraces does exist, and new dates show that some of these terraces are of great antiquity (MIS 10+). The project also reexamined the distribution of artifacts in the region and confirms the distributional bias to the river valleys, and particularly the rivers draining southward to the paleo–Channel River system. This distribution is consistent with a model of periodic occupation of the British peninsula along and up the major river valleys from the paleo–Channel River corridor. These data have a direct impact on our understanding of the paleolandscapes of the southwest region, and therefore our interpretations of the Paleolithic occupation of the edge of the continental landmass.

Purification capacity of a highly loaded laboratory scale tidal flow reed bed system with effluent recirculation

The purification capacity of a laboratory scale tidal flow reed bed system with final effluent recirculation at a ratio of 1:1 was investigated in this study. In particular, this four-stage reed bed system was highly loaded with strong agricultural wastewater. Under the hydraulic and organic loading rates as high as 0.43 m3/m2d and 1055 gCOD/m2d, respectively, the average removal efficiencies of COD, BOD5, SS, NH4-N and P were 77%, 78%, 66%, 62% and 38%. Even with the high loading rates, approximately 30% of NH4-N was converted into NO2-N and NO3-N from the mid-stage of the system where nitrification took place. The results suggest that the multi-stage reed bed system could be employed to treat strong wastewater under high loading, especially for the substantive mass removal of solids, organic matter and ammoniacal-nitrogen. Tidal flow combined with effluent recirculation is a favourable operation strategy to achieve this objective.

Habitat-specific adaptation of immune responses of stickleback (Gasterosteus aculeatus) lake and river ecotypes

Freshwater populations of three-spined sticklebacks (Gasterosteus aculeatus) in northern Germany are found as distinct lake and river ecotypes. Adaptation to habitat-specific parasites might influence immune capabilities of stickleback ecotypes. Here, naive laboratory-bred sticklebacks from lake and river populations were exposed reciprocally to parasite environments in a lake and a river habitat. Sticklebacks exposed to lake conditions were infected with higher numbers of parasite species when compared with the river. River sticklebacks in the lake had higher parasite loads than lake sticklebacks in the same habitat. Respiratory burst, granulocyte counts and lymphocyte proliferation of head kidney leucocytes were increased in river sticklebacks exposed to lake when compared with river conditions. Although river sticklebacks exposed to lake conditions showed elevated activation of their immune system, parasites could not be diminished as effectively as by lake sticklebacks in their native habitat. River sticklebacks seem to have reduced their immune-competence potential due to lower parasite diversity in rivers

Anti-sized reed bed system for animal wastewater treatment: a comparative study

This paper presents a comparative study on the treatment of high-strength animal wastewater in two parallel lab-scale constructed reed bed systems, progressively-sized system and anti-sized system, which have same configuration but different arrangement of bed media. The reed bed systems were operated in a tidal flow pattern to treat diluted pig slurry. Detailed analyses were carried out for the removal of some key pollutants including COD, BOD5, NH4-N, P and suspended solids. The results showed that both systems have considerable capacity for the removal of solids, organic matter and inorganic nutrients. The formation of biofilms on the surfaces of gravel media in both reed bed systems was monitored by scanning selected gravel samples using scanning electron microscopy. In general, no significant difference was detected with regard to the percentage pollutant removal in the systems. However, the anti-sized system demonstrated a clear advantage in its ability to slow down the clogging of bed media and avoid the impairment of long-term functioning and sustainability of the beds. A conceptual model was developed to predict the occurrence of the clogging. The validity of the model was tested using data from this study and from the literatures.

Age and palaeoenvironmental significance of an inter-tidal peat bed at Ballywoolen, Bann estuary, Co. Londonderry.

A recently exposed inter-tidal peat bed at Ballywoolen, Bann estuary, Co. Londonderry, has yielded new information about mid-Holocene coastal environmental change in the northeast of Ireland. Pollen analytical data and wood detritus demonstrate that peat accumulation occurred in a terrestrial environment that was free from marine influence. Radiocarbon dates suggest that the peat accumulated rapidly during a period of low relative sea level subsequent to the maximum of Holocene relative sea-level rise along the north coast of Northern Ireland. The absence of marine/brackish indicator taxa at the site suggests that the tidal range was somewhat less than that at present and/or that the channel of the river was located some distance east of its present alignment. The dates indicate that the low stand lasted for at least ~0.2 ka and possibly for ~1.1 ka. Stable, woodland-dominated landscapes are indicated at both this site and neighbouring ones around ~6.4-5.3 cal ka BP. There is no evidence for large-scale aeolian sand movement or human impact on the landscape during the period of peat accumulation.

Technical Note: Assessing a 24/7 solution for monitoring water quality loads in small river catchments

Quantifying nutrient and sediment loads in catchments is dif?cult owing to diffuse controls related to storm hydrology. Coarse sampling and interpolation methods are prone to very high uncertainties due to under-representation of high discharge, short duration events. Additionally, important low-?ow processes such as diurnal signals linked to point source impacts are missed. Here we demonstrate a solution based on a time-integrated approach to sampling with a standard 24 bottle autosampler con?gured to take a sample every 7 h over a week according to a Plynlimon design. This is evaluated with a number of other sampling strategies using a two-year dataset of sub-hourly discharge and phosphorus concentration data. The 24/7 solution is shown to be among the least uncertain in estimating load (inter-quartile range: 96% to 110% of actual load in year 1 and 97% to 104% in year 2) due to the increased frequency raising the probability of sampling storm events and point source signals. The 24/7 solution would appear to be most parsimonious in terms of data coverage and certainty, process signal representation, potential laboratory commitment, technology requirements and the ability to be widely deployed in complex catchments.

UROTENSIN II FROM THE RIVER LAMPREY (LAMPETRA-FLUVIATILIS), THE SEA LAMPREY (PETROMYZON-MARINUS), AND THE PADDLEFISH (POLYODON SPATHULA)

Urotensin II was isolated from extracts of the whole brain of the river lamprey (Lampetra fluviatilis) and the sea lamprey (Petromyzon marinus). The primary structure of the peptide from both species is the same (Asn-Asn-Phe-Ser-Asp-Cys-Phe-Trp-Lys-Tyr-Cys-Val) and this amino acid sequence is identical to that of urotensin II from the dogfish and skate. Consistent with previous morphological studies indicating that the Agnatha lack a caudal neurosecretory system, urotensin II was not detected in an extract of P. marinus spinal cord. The data suggest that the urotensin II may have functioned in the earliest vertebrates as a neurotransmitter/neuromodulator in the central nervous system rather than as a neurohormone of the caudal neurosecretory system. Urotensin II was also isolated from an extract of the spinal cord of a chondrostean fish, the paddlefish (Polyodon spathula). The primary structure of the paddlefish urotensin II (Gly-Ser-Thr-Ser-Glu-Cys-Phe-Trp-Lys-Tyr-Cys-Val) is the same as that of another chondrostean, the sturgeon (Acipenser ruthenus). The study provides further evidence for a widespread distribution of urotensin II in vertebrate species and suggests that the primary structure of the peptide is better conserved in these phylogenetically ancient fish than in teleosts. (C) 1995 Academic Press, Inc.