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.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

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.

Storage of sediment-associated nutrients and contaminants in river channel and floodplain systems

Samples of fine-grained channel bed sediment and overbank floodplain deposits were collected along the main channels of the Rivers Aire (and its main tributary, the River Calder) and Swale, in Yorkshire, UK, in order to investigate downstream changes in the storage and deposition of heavy metals (Cr, Cu, Pb, Zn), total P and the sum of selected PCB congeners, and to estimate the total storage of these contaminants within the main channels and floodplains of these river systems. Downstream trends in the contaminant content of the <63 μm fraction of channel bed and floodplain sediment in the study rivers are controlled mainly by the location of the main sources of the contaminants, which varies between rivers. In the Rivers Aire and Calder, the contaminant content of the <63 μm fraction of channel bed and floodplain sediment generally increases in a downstream direction, reflecting the location of the main urban and industrialized areas in the middle and lower parts of the basin. In the River Swale, the concentrations of most of the contaminants examined are approximately constant along the length of the river, due to the relatively unpolluted nature of this river. However, the Pb and Zn content of fine channel bed sediment decreases downstream, due to the location of historic metal mines in the headwaters of this river, and the effect of downstream dilution with uncontaminated sediment. The magnitude and spatial variation of contaminant storage and deposition on channel beds and floodplains are also controlled by the amount of <63 μm sediment stored on the channel bed and deposited on the floodplain during overbank events. Consequently, contaminant deposition and storage are strongly influenced by the surface area of the floodplain and channel bed. Contaminant storage on the channel beds of the study rivers is, therefore, generally greatest in the middle and lower reaches of the rivers, since channel width increases downstream. Comparisons of the estimates of total storage of specific contaminants on the channel beds of the main channel systems of the study rivers with the annual contaminant flux at the catchment outlets indicate that channel storage represents <3% of the outlet flux and is, therefore, of limited importance in regulating that flux. Similar comparisons between the annual deposition flux of specific contaminants to the floodplains of the study rivers and the annual contaminant flux at the catchment outlet, emphasise the potential importance of floodplain deposition as a conveyance loss. In the case of the River Aire the floodplain deposition flux is equivalent to between ca. 2% (PCBs) and 36% (Pb) of the outlet flux. With the exception of PCBs, for which the value is ≅0, the equivalent values for the River Swale range between 18% (P) and 95% (Pb). The study emphasises that knowledge of the fine-grained sediment delivery system operating in a river basin is an essential prerequisite for understanding the transport and storage of sediment-associated contaminants in river systems and that conveyance losses associated with floodplain deposition exert an important control on downstream contaminant fluxes and the fate of such contaminants. © 2003 Elsevier Science Ltd. All rights reserved.

Fluxes of organic contaminants from the river catchment into, through and out of the Humber Estuary, UK

This paper summarises the work done on the distribution and reactivity of organic contaminants (simazine, atrazine, lindane, fluoranthene, pyrene, PCB 77, PCB 118) in the Humber Estuary and associated major rivers, as part of the LOIS programme. The preliminary flux calculations show that the most important contributors of selected organic contaminants were the rivers Trent (45% of simazine, 20% of atrazine), Aire (30% of simazine and 33% of atrazine), Don (36 and 37% of fluoranthene and pyrene) and Ouse (18% of fluoranthene and pyrene). For lindane and PCBs, the Aire and Ouse were the key sources. The water flow in all the rivers shows strong seasonal variations, as do the contaminant concentrations. As a result, the mean daily fluxes of these contaminants displayed a strong seasonality. Annual mean concentrations of simazine and atrazine decreased by more than 50% over the period 1994-1995 in most of the rivers, probably as a result of their restricted use in the UK. Mass balance calculations show that the Humber is a sink for atrazine, lindane, PCB 77 and PCB 118, although the degree of removal is generally much lower for atrazine and lindane than for PCB 77 and PCB 118. Mass balance results also show that the Humber can either be a source of fluoranthene and pyrene (in the suspended particulate phase), or a sink (in the dissolved phase), although overall the Humber acts as sink. The budget exercise represents an attempt to quantify the input and output of selected organic contaminants from catchment to ocean. However, due to limited data and assumptions involved in calculations, the estimates should be considered as an order of magnitude approximation. Further improvement both in resolution and accuracy is required.

Towards a budget approach to Pleistocene terraces: preliminary studies using the River Exe in South West England, UK

This paper presents a first approach to using a sediment budget methodology for paired terrace staircase sediments in SW England. Although a budget approach has become firmly established in Holocene fluvial studies, it has not been used in Pleistocene sequences due to the problems of temporal resolution, catchment changes and downstream loss from the system. However, this paper uses a budget approach in a paired non-glaciated basin, primarily as a method of interrogating the terrace record concerning the degree of reworking and new sediment input required to produce the reconstructed terrace sequences. In order to apply a budget approach a number of assumptions have to be made and these are justified in the paper. The results suggest that the Exe system can most parsimoniously be explained principally by the reworking of a Middle Pleistocene floodplain system with relatively little input of new resistant clasts required and a cascade-type model in geomorphological terms. Whilst this maybe partially a result of the specific geology of the catchment, it is likely to be representative of many Pleistocene terrace systems in NW Europe due to their litho-tectonic similarities. This cascade-type model of terrace formation has archaeological implications and sets the context for the Palaeolithic terrace record in the UK. Future work will involve the testing of this and similar budget models using a combination of landscape modelling and chronometric dating. ?? 2009 The Geologists' Association.