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J M Pemberton

Publications and source records attributed to J M Pemberton.

At least 37 records · Page 2Linked to original sources
PubMed2002

A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus).

Recent empirical evidence indicates that although fitness and fitness components tend to have low heritability in natural populations, they may nonetheless have relatively large components of additive genetic variance. The molecular basis of additive genetic variation has been investigated in model organisms but never in the wild. In this article we describe an attempt to map quantitative trait loci (QTL) for birth weight (a trait positively associated with overall fitness) in an unmanipulated, wild population of red deer (Cervus elaphus). Two approaches were used: interval mapping by linear regression within half-sib families and a variance components analysis of a six-generation pedigree of >350 animals. Evidence for segregating QTL was found on three linkage groups, one of which was significant at the genome-wide suggestive linkage threshold. To our knowledge this is the first time that a QTL for any trait has been mapped in a wild mammal population. It is hoped that this study will stimulate further investigations of the genetic architecture of fitness traits in the wild.

Animals↗
PubMed2001

Age, sex, density, winter weather, and population crashes in Soay sheep.

Quantifying the impact of density, extrinsic climatic fluctuations, and demography on population fluctuations is a persistent challenge in ecology. We analyzed the effect of these processes on the irregular pattern of population crashes of Soay sheep on the St. Kilda archipelago, United Kingdom. Because the age and sex structure of the population fluctuates independently of population size, and because animals of different age and sex respond in different ways to density and weather, identical weather conditions can result in different dynamics in populations of equal size. In addition, the strength of density-dependent processes is a function of the distribution of weather events. Incorporating demographic heterogeneities into population models can influence dynamics and their response to climate change.

Aging↗
PubMed2001

A microsatellite polymorphism in the gamma interferon gene is associated with resistance to gastrointestinal nematodes in a naturally-parasitized population of Soay sheep.

Free-living Soay sheep (Ovis aries) on the island of Hirta, St Kilda, Scotland, are naturally parasitized by gastrointestinal nematodes, predominantly Teladorsagia circumcincta. In this paper we show that reduced faecal egg counts (FEC) are associated with an allele at a microsatellite locus located in the first intron of the interferon gamma gene (o(IFN)-gamma) in Soay sheep lambs and yearlings, measured at approximately 4 and 16 months of age, respectively. The same allele was also associated with increased T. circumcincta-specific antibody (IgA) in lambs, but not associated significantly in yearlings. Flanking control markers failed to show a significant association with either FEC or IgA. These results suggest that a polymorphic gene conferring increased resistance to gastrointestinal nematode parasites is located at or near the interferon gamma gene, and support previous reports which have mapped a quantitative trait locus (QTL) for resistance to this region in domestic sheep. Our data are consistent with the idea that a functional polymorphism leading to reduced expression or efficacy of (IFN)-gamma could enhance the immune response to gastrointestinal nematodes by favouring the activity of the Th2 cell subset and antibody associated immune mechanisms.

Animals↗
PubMed2001

Bottlenecks, drift and differentiation: the population structure and demographic history of sika deer (Cervus nippon) in the Japanese archipelago.

We assessed genetic differentiation and diversity in 14 populations of sika deer (Cervus nippon) from Japan and four populations of sika deer introduced to the UK, using nine microsatellite loci. We observed extreme levels of differentiation and significant differences in diversity between populations. Our results do not support morphological subspecies designations, but are consistent with previous mitochondrial DNA analyses which suggest the existence of two genetically distinct lineages of sika deer in Japan. The source of sika introduced to the UK was identified as Kyushu. The underlying structure of Japanese populations probably derives from drift in separate glacial refugia and male dispersal limited by distance. This structure has been perturbed by bottlenecks and habitat fragmentation, resulting from human activity from the mid-nineteenth century. Most current genetic differentiation and differences in diversity among populations probably result from recent drift. Coalescent model analysis suggests sika on each of the main Japanese islands have experienced different recent population histories. Hokkaido, which has large areas of continuous habitat, has maintained high levels of gene flow. In Honshu the population is highly fragmented and is likely to have been evolving by drift alone. In Kyushu there has been a balance between gene flow and drift but all the populations have experienced high levels of drift. Habitat fragment size was not significantly associated with genetic diversity in populations but there was a significant correlation between habitat fragment size and effective population size.

Alleles↗
PubMed2001

Positive genetic correlation between parasite resistance and body size in a free-living ungulate population.

Parasite resistance and body size are subject to directional natural selection in a population of feral Soay sheep (Ovis aries) on the island of St. Kilda, Scotland. Classical evolutionary theory predicts that directional selection should erode additive genetic variation and favor the maintenance of alleles that have negative pleiotropic effects on other traits associated with fitness. Contrary to these predictions, in this study we show that there is considerable additive genetic variation for both parasite resistance, measured as fecal egg count (FEC), and body size, measured as weight and hindleg length, and that there are positive genetic correlations between parasite resistance and body size in both sexes. Body size traits had higher heritabilities than parasite resistance. This was not due to low levels of additive genetic variation for parasite resistance, but was a consequence of high levels of residual variance in FEC. Measured as coefficients of variation, levels of additive genetic variation for FEC were actually higher than for weight or hindleg length. High levels of additive genetic variation for parasite resistance may be maintained by a number of mechanisms including high mutational input, balancing selection, antagonistic pleiotropy, and host-parasite coevolution. The positive genetic correlation between parasite resistance and body size, a trait also subject to sexual selection in males, suggests that parasite resistance and growth are not traded off in Soay sheep, but rather that genetically resistant individuals also experience superior growth.

Alleles↗
PubMed2000

Inbreeding depression influences lifetime breeding success in a wild population of red deer (Cervus elaphus).

Evolutionary and conservation biologists have a long-standing interest in the consequences of inbreeding. It is generally recognized that inbred individuals may experience reduced fitness or inbreeding depression. By the same token, relatively outbred individuals can have greater than average fitness, i.e. heterosis. However, nearly all of the empirical evidence for inbreeding depression comes from laboratory or domestic species. Inbreeding depression and heterosis are difficult to detect in natural populations due to the difficulties in establishing pedigrees. An alternative method is to correlate heterozygosity, which is measured using genetic markers, with a trait related to fitness. The typically studied traits, such as juvenile survival and growth rates, either cover only early life or are weakly correlated with lifetime breeding success (LBS). In this paper we show that heterozygosity is positively associated with male and female adult LBS in a wild population of red deer (Cervus elaphus) on the Isle of Rum, Scotland. To the authors' knowledge, this is the first time that inbreeding depression and/or heterosis have been detected for a trait highly correlated with overall fitness in both sexes in a wild population.

Animals↗
PubMed2000

Heritability of fitness in a wild mammal population.

Classical population genetics theory predicts that selection should deplete heritable genetic variance for fitness. We show here that, consistent with this prediction, there was a negative correlation between the heritability of a trait and its association with fitness in a wild population of red deer (Cervus elaphus) and there was no evidence of significant heritability of total fitness. However, the decline in heritability was caused, at least in part, by increased levels of residual variance in longevity and, hence, in total fitness: in this population, longevity is known to be heavily influenced by environmental factors. Other life history traits that were not associated with longevity, such as average annual breeding success, had higher heritabilities. Coefficients of additive genetic variance differed markedly between traits, but highly skewed measures, such as male breeding success, generally had greater coefficients of variance than morphometric traits. Finally, there were significant maternal effects in a range of traits, particularly for females.

Animals↗
PubMed2000

Estimating variance components in natural populations using inferred relationships.

Until recently, the estimation of the heritability of a trait has required knowledge of the pedigree within a population. In natural populations such knowledge is often unknown. Two techniques have been developed which use marker information to estimate heritabilities without reference to the exact nature of the relationships: a regression-based estimator that regresses phenotypic similarity for a pair of individuals against an estimate of their relationship and a likelihood-based estimator that maximizes the probability of the genotypic and phenotypic data given a known population structure. Computer simulation was used to compare the behaviour of these estimators. Bias in estimates of heritability decreased with increasing marker information, decreasing simulated heritability, increasing relatedness and increasing sample size. The techniques displayed reasonable tolerance to the percentage of missing data. The regression-based technique shows least average bias, but largest variance over simulations. Likelihood-based techniques show larger average bias, but smaller variances over estimates. A modified form of the likelihood technique, requiring fewer initial assumptions about population parameters, is presented. The modified form shows less bias in its estimates of heritability than the likelihood technique originally proposed.

Analysis of Variance↗
PubMed2000

Domain structure, oligomeric state, and mutational analysis of PpsR, the Rhodobacter sphaeroides repressor of photosystem gene expression.

The transcription factor PpsR from the facultative photoheterotroph Rhodobacter sphaeroides is involved in repression of photosystem gene expression under aerobic growth conditions. We have isolated a number of spontaneous mutations as well as constructed directed mutations and deletions in ppsR. Repressor activities and the oligomeric state of the wild-type and mutant proteins were assayed. Our results suggest that the wild-type PpsR exists in cell extracts as a tetramer. Analysis of the PpsR mutants confirmed that the carboxy-terminal region of PpsR (residues 400 to 464) is involved in DNA binding. The central region of the protein (residues 150 to 400) was found to contain two PAS domains (residues 161 to 259 and 279 to 367). PAS domains are ubiquitous protein modules involved in sensory transduction as well as in protein-protein interactions. All spontaneously isolated mutations, which significantly impaired repressor activity and which mapped outside the DNA binding region, were positioned in the PAS domains. None of these, however, affected the overall oligomeric state. This implies that the conformation of the PAS domains within the tetramer is critical for repressor activity. Upstream of the first PAS domain resides a putative glutamine-rich hinge (residues 127 to 136) that connects the first PAS domain to the amino-terminal region (residues 1 to 135). The role of the amino terminus of PpsR is not obvious; however, extended deletions within this region abolish repressor activity, thus suggesting that the amino terminus is essential for structural integrity of the protein. We present a model of the domain architecture of the PpsR protein according to which PpsR is comprised of three regions: the carboxy terminus responsible for DNA binding, the central region primarily involved in protein oligomerization and possibly signal sensing, and the amino terminus of unknown function. This model may prove useful for determining the mode of PpsR action.

Amino Acid Sequence↗
PubMed2000

Sequence analysis and functional characterization of the violacein biosynthetic pathway from Chromobacterium violaceum.

Violacein is a purple-colored, broad-spectrum antibacterial pigment that has a dimeric structure composed of 5-hydroxyindole, oxindole and 2-pyyrolidone subunits formed by the condensation of two modified tryptophan molecules. The violacein biosynthetic gene cluster from Chromobacterium violaceum was characterized by DNA sequencing, transposon mutagenesis, and chemical analysis of the pathway intermediates produced heterologously in Escherichia. coli. The violacein biosynthetic gene cluster spans eight kilobases and is comprised of the four genes, vioABCD, that are necessary for violacein production. Sequence analysis suggests that the products of vioA, vioC and vioD are nucleotide-dependent monooxygenases. Disruption of vioA or vioB completely abrogates the biosynthesis of violacein intermediates, while disruption of the vioC or vioD genes results in the production of violacein precursors.

Amino Acid Sequence↗
PubMed1999

Heritable variation in resistance to gastro-intestinal nematodes in an unmanaged mammal population.

The impact of parasites on natural populations has received considerable attention from evolutionary biologists in recent years. Central to a number of theoretical developments during this period is the assumption of additive genetic variation in resistance to parasites. However, very few studies have estimated the heritability of parasite resistance under field conditions, and those that have are mainly restricted to birds and their ectoparasites. In this paper, to our knowledge, we show for the first time in a free-ranging mammal population, Soay sheep (Ovis aries) living on the islands of St Kilda, that there is significant heritable variation in resistance to gastrointestinal nematodes. This result is consistent with earlier studies on this population which have indicated locus-specific associations with parasite resistance. We discuss our results in the context of current studies examining heritable resistance to parasites in domestic sheep and the possible mechanisms of selective maintenance of genetic variation for resistance to gastrointestinal nematodes in the St Kilda Soay sheep population.

Animals↗
PubMed1999

Population density affects sex ratio variation in red deer.

Many mammal populations show significant deviations from an equal sex ratio at birth, but these effects are notoriously inconsistent. This may be because more than one mechanism affects the sex ratio and the action of these mechanisms depends on environmental conditions. Here we show that the adaptive relationship between maternal dominance and offspring sex ratio previously demonstrated in red deer (Cervus elaphus), where dominant females produced more males, disappeared at high population density. The proportion of males born each year declined with increasing population density and with winter rainfall, both of which are environmental variables associated with nutritional stress during pregnancy. These changes in the sex ratio corresponded to reductions in fecundity, suggesting that they were caused by differential fetal loss. In contrast, the earlier association with maternal dominance is presumed to have been generated pre-implantation. The effects of one source of variation superseded the other within about two generations. Comparison with other ungulate studies indicates that positive associations between maternal quality and the proportion of male offspring born have only been documented in populations below carrying capacity.

Adaptation, Physiological↗
PubMed1999

The gene encoding a periplasmic deoxyribonuclease from Aeromonas hydrophila.

A gene encoding a deoxyribonuclease, dnsH, was cloned from Aeromonas hydrophila JMP636. The predicted mature protein was very similar to the previously described extracellular Dns from this organism and an N-terminal region corresponding to a large putative signal sequence was predicted for the JMP636 protein. Inactivation of dnsII demonstrated that the DnsH protein was not present extracellularly in this strain. As DnsH degraded plasmid DNA and was believed to have a periplasmic location, a dnsH mutant was constructed to determine whether electroporation of A. hydrophila with plasmid DNA could be achieved. No transformants were detected. From SDS-PAGE studies, at least two additional DNases remain to be characterised from A. hydrophila JMP636.

Aeromonas hydrophila↗
PubMed1999

Power to detect QTL in a free-living polygynous population.

Evolutionary biologists attempting to detect quantitative trait loci (QTL) in natural populations have thus far had to carry out some kind of cross with their study organism. Such techniques often increase the probability of detecting linkage, but are impossible or undesirable in many populations. A potential way of overcoming this problem is to carry out linkage studies in large complex pedigrees. In this paper we contrast the power to detect linkage in a complex pedigree of red deer (Cervus elaphus) with that of the widely used half-sib design. When a QTL of magnitude 1 phenotypic standard deviation is segregating and completely linked to a marker, the extended pedigree has power of 0.67, whereas the half-sib design has power of just 0.21. We conclude that detecting QTL may be possible in intensively studied natural populations, provided detailed life history data and good pedigree information are available.

Animals↗
PubMed1999

Male reproductive success in a promiscuous mammal: behavioural estimates compared with genetic paternity.

Molecular techniques have enabled behavioural ecologists to reassess mating systems from a genetic perspective. Studies of paternity frequently reveal that mating behaviour does not always reflect parentage, and may bring to light alternative mating tactics. Here we present a comparison of behavioural and genetic measures of male reproductive success in a mammalian mating system in which both sexes are highly promiscuous. Rather than having a stable harem social structure, Soay rams (Ovis aries) on the island of Hirta, St Kilda, UK usually consort with individual oestrous ewes sequentially. Not all matings occur between consort pairs, however, and ewes have been seen to mate with up to 10 different rams on the same day. Using locus-specific polymorphism at five protein and 10 microsatellite DNA loci, we determined paternity for 236 lambs born into three cohorts, and compared paternity with estimates of mating success derived from more than one census of rutting behaviour. The correlation between the number of ewes with which each ram was witnessed in consort and the number of paternities assigned was positive and statistically significant, and rams that were observed in consort with a ewe were 18 times more likely to have sired her offspring than other candidate rams. However, most lambs (73%) were not sired by a ram seen in consort with the oestrous mother. Many juveniles, yearlings and some adult rams were rarely seen in consort with ewes, yet were assigned a significant number of paternities. These results suggest that mating tactics differ between age groups, and that alternative mating strategies among adults that do not involve forming consorts with many females also confer mating success. For these reasons, census-based observations of consort associations between individuals cannot be used to accurately estimate individual male reproductive success in this population.

Animals↗
PubMed1999

Density-dependent variation in lifetime breeding success and natural and sexual selection in Soay rams.

Variation in male lifetime breeding success (LBS) is central to understanding selection, yet it has rarely been measured in natural populations of large mammals. Here, we first describe variation in the opportunity for selection in cohorts of Soay rams (Ovis aries) on the archipelago of St. Kilda, Scotland, that were born during years of varying population density. Variation in LBS is closely coupled with demography, as rams born in years of low density following population crashes enjoy greater LBS than do those born in high-density years. Paradoxically, the opportunity for selection was greatest in the largest cohorts, those born in years of high population density, owing to low juvenile breeding success and overwinter survival. Variation in longevity and the contribution of nonbreeders were the most important components of the total variance in LBS in cohorts born in years of high density, while variation in fecundity was more important in cohorts born in low-density years. The opportunity for sexual selection is thus stronger in cohorts born in low-density years, as many rams in these cohorts survive to compete for mates as adults in subsequent ruts. Variation in population density in the year of birth also influenced the intensity of selection. Individuals born in years of high population density underwent strong natural selection in favor of longer hindlimbs over their first winter. In contrast, in cohorts born in low-density years, there was no natural selection on hindlimb in the first year of life. Longer hindlimbs were associated with increased fecundity over the entire lifetime of individuals born in low-density years. Natural and sexual selection thus act on the same trait in the same direction at different life-history stages in Soay rams, depending on the population density experienced in the year of birth.

Journal Article↗
PubMed1999

Introgression through rare hybridization: A genetic study of a hybrid zone between red and sika deer (genus Cervus) in Argyll, Scotland.

In this article we describe the structure of a hybrid zone in Argyll, Scotland, between native red deer (Cervus elaphus) and introduced Japanese sika deer (Cervus nippon), on the basis of a genetic analysis using 11 microsatellite markers and mitochondrial DNA. In contrast to the findings of a previous study of the same population, we conclude that the deer fall into two distinct genetic classes, corresponding to either a sika-like or red-like phenotype. Introgression is rare at any one locus, but where the taxa overlap up to 40% of deer carry apparently introgressed alleles. While most putative hybrids are heterozygous at only one locus, there are rare multiple heterozygotes, reflecting significant linkage disequilibrium within both sika- and red-like populations. The rate of backcrossing into the sika population is estimated as H = 0.002 per generation and into red, H = 0.001 per generation. On the basis of historical evidence that red deer entered Kintyre only recently, a diffusion model evaluated by maximum likelihood shows that sika have increased at approximately 9.2% yr-1 from low frequency and disperse at a rate of approximately 3.7 km yr-1. Introgression into the red-like population is greater in the south, while introgression into sika varies little along the transect. For both sika- and red-like populations, the degree of introgression is 30-40% of that predicted from the rates of current hybridization inferred from linkage disequilibria; however, in neither case is this statistically significant evidence for selection against introgression.

Alleles↗