Polymerase chain reaction (PCR) primers for the amplification of five nuclear introns in vertebrates

[Extract] Advancements in evolutionary genetics, as well as the conservation of biodiversity, increasingly require direct analyses of sequence variation in nuclear DNA. Recent studies indicate that nuclear introns have variabilities useful for both phylogenetics and population genetics (reviewed in Friesen 2000); however, use of introns is currently limited by the paucity of polymerase chain reaction (PCR) primers that have been demonstrated to have broad taxonomic utility (although several primers with less general or uncertain utilities have been published; reviewed in Friesen 2000). We have designed 30 general PCR primers for nuclear introns for vertebrates

Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms

Combination of the targeted amplification of nuclear introns and the analysis of single-stranded conformational polymorphisms has the potential to provide an inexpensive, rapid, versatile and sensitive genetic assay for evolutionary studies and conservation. We are developing primers and protocols to analyse nuclear introns in vertebrates, and are testing them in a population genetic study of marbled murrelets Brachyramphus marmoratus. Here we present protocols and results for introns for aldolase B, α-enolase, glyceraldehyde-3-phosphate dehydrogenase and lamin A. Results suggest that this approach presents a potentially powerful method for detecting genetic variation within and among local populations and species of animals: (i) a variety of genes can be surveyed, including genes of special interest such as those involved in disease resistance; (ii) assays are rapid and relatively inexpensive; (iii) large numbers of genes can be assayed, enabling accurate estimation of variation in the total genome; (iv) almost any mutation can be detected in the genes amplified; (v) the exact nature of variation can be investigated by sequence analysis if desired; (vi) statistical methods previously developed for proteins and/or sequence data can be used; (vii) protocols can be easily transferred to other species and other laboratories; and (viii) assays can be performed on old or degraded samples, blood or museum skins, so that animals need not be killed. Results of analyses for murrelets support earlier evidence that North American and Asiatic subspecies represent reproductively isolated species, and that genetic differences exist among murrelets from different sites within North America

Population genetic structure and conservation of marbled murrelets (Brachyramphus marmoratus)

Marbled murrelets (Brachyramphus marmoratus) are coastal seabirds that nest from California to the Aleutian Islands. They are declining and considered threatened in several regions. We compared variation in the mitochondrial control region, four nuclear introns and three microsatellite loci among194 murrelets from throughout their range except Washington and Oregon. Significant population genetic structure was found: nine private control region haplotypes and three private intron alleles occurred at high frequency in the Aleutians and California; global estimates of FST or ΦST and most pairwise estimates involving the Aleutians and/or California were significant; and marked isolation-by-distance was found. Given the available samples, murrelets appear to comprise five genetic management units: (1) western Aleutian Islands, (2) central Aleutian Islands, (3) mainland Alaska and British Columbia, (4) northern California, and (5) central California

Older and wiser: improvements in breeding success are linked to better foraging performance in European shags

1. An increase in average breeding performance with age and experience among younger age classes has been recorded in numerous studies of iteroparous breeders. An important component of this pattern is thought to be improvements in foraging performance, resulting in delivery of more or better quality food to offspring by older, more experienced individuals. 2. Young, inexperienced breeders may exhibit lower foraging efficiency or foraging effort, and it has been predicted that differences in foraging performance with age and experience will be more marked when environmental conditions are poor. However, as the timing of breeding generally differs with age and experience, intrinsic differences in foraging abilities are typically confounded by variation in extrinsic conditions, and hence food availability. 3. To disentangle these effects, we experimentally manipulated the timing of breeding in European shags, Phalacrocorax aristotelis Linnaeus. We used a cross-fostering protocol, such that naive, young birds reared their chicks at the same time as older, experienced individuals. Our design produced simultaneous chick rearing during two periods in the same breeding season that differed markedly in environmental conditions: early, when conditions were good; and late, when conditions were poorer. We examined foraging efficiency, foraging effort and amount of food delivered to offspring by the two classes of breeder. We predicted that any differences in foraging performance would be more marked under the poorer conditions later in the season. 4. We found that experienced parents delivered more food than naive parents, irrespective of the time of season. This was due partly to the consistently higher foraging efficiency of the experienced parents. In addition, experienced parents adjusted their foraging effort to the environmental conditions. Early in the breeding season, they made less foraging effort than naive parents. Under the poorer foraging conditions, experienced parents increased their foraging effort but naive parents did not, being either unable or unwilling to do so. 5. Our results suggest that an increase in foraging efficiency, and the capacity to adjust foraging effort in response to food availability, are important components of the observed improvements in breeding performance with age and experience

The impact of the sandeel fishery closure in the northwestern North Sea on seabird food consumption, distribution and productivity

In the North Sea, the lesser sandeel (Ammodytes marinus) is the target of an industrial fishery and the principal prey of many top predators. Because of concerns about potential effects on predators, the sandeel fishery off eastern Scotland was closed in 2000, and local sandeel abundance increased subsequently. To examine whether closure benefitted sandeel-dependent seabirds, we compared summer sandeel consumption, at-sea distributions, and breeding success of seven species with fishery removals and abundance of older (1+ group) and young-of-the-year (0 group) sandeels from 1996 to 2003. Breeding success of black-legged kittiwake (Rissa tridactyla), a species that has declined in recent decades, was related to abundance of both 1+ group (the age class targeted by the fishery) and 0 group sandeels. The proportion of 0 group consumed by kittiwakes and proportion of the kittiwake population foraging in the area were linked to 0 group abundance. None of these parameters in the other seabird species were associated with sandeel abundance. Our results suggest that fishery closure can have a beneficial impact on top predators sensitive to variation in abundance of the target species, although environmental conditions before and after closure are also likely to be critically important

From plankton to top predators: bottom-up control of a marine food web across four trophic levels

Abundant mid-trophic pelagic fish often play a central role in marine ecosystems, both as links between zooplankton and top predators and as important fishery targets. In the North Sea, the lesser sandeel occupies this position, being the main prey of many bird, mammal and fish predators and the target of a major industrial fishery. However, since 2003, sandeel landings have decreased by > 50%, and many sandeel-dependent seabirds experienced breeding failures in 2004. Despite the major economic implications, current understanding of the regulation of key constituents of this ecosystem is poor. Sandeel abundance may be regulated 'bottom-up' by food abundance, often thought to be under climatic control, or 'top-down' by natural or fishery predation. We tested predictions from these two hypotheses by combining unique long-term data sets (1973–2003) on seabird breeding productivity from the Isle of May, SE Scotland, and plankton and fish larvae from the Continuous Plankton Recorder survey. We also tested whether seabird breeding productivity was more tightly linked to sandeel biomass or quality (size) of individual fish. The biomass of larval sandeels increased two- to threefold over the study period and was positively associated with proxies of the abundance of their plankton prey. Breeding productivity of four seabirds bringing multiple prey items to their offspring was positively related to sandeel larval biomass with a 1-year lag, indicating dependence on 1-year-old fish, but in one species bringing individual fish it was strongly associated with the size of adult sandeels. These links are consistent with bottom-up ecosystem regulation and, with evidence from previous studies, indicate how climate-driven changes in plankton communities can affect top predators and potentially human fisheries through the dynamics of key mid-trophic fish. However, the failing recruitment to adult sandeel stocks and the exceptionally low seabird breeding productivity in 2004 were not associated with low sandeel larval biomass in 2003, so other mechanisms (e.g. predation, lack of suitable food after metamorphosis) must have been important in this case. Understanding ecosystem regulation is extremely important for predicting the fate of keystone species, such as sandeels, and their predator