Shifts In Allele Frequencies Research Articles

Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod

Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.

Spatio-temporal population genetic structure and mating system of red king crab (Paralithodes camtschaticus) in Alaska

Red king crab, Paralithodes camtschaticus Tilesius, 1815, an economically and culturally important species in the state of Alaska, experienced drastic reductions in abundance over large portions of their Alaskan range by 1980. Abundance of crabs in some of the most important historical fishing areas have failed to rebound, some even in the absence of fishing, highlighting the need for additional research to infer genetic structure and reproductive biology of the species that can then be used to inform management efforts. Red king crab samples were collected from eleven locations throughout Alaska ( n = 845 ), of these, six locations were sampled at least one generation apart. Results of this study suggest moderate rates of gene flow within the Gulf of Alaska/Western Alaska region. Levels of genetic differentiation among populations within Southeast Alaska were higher than seen elsewhere, and there was strong evidence of multiple distinct populations. Red king crab in Bristol Bay and in two areas in Southeast Alaska show signs of recent population bottlenecks and shifts in allele frequencies not observed in previous studies that used less polymorphic genetic markers. In addition to population genetic structure analyses, 24 female red king crab and their broods were collected for purposes of inferring mating system. There was no evidence of multiple paternity in any brood. The results of this study support continued management of distinct geographic groups within the Gulf of Alaska/Western Alaska region and suggest that finer-scale management may be beneficial in Southeast Alaska.

Molecular markers in management of ex situ PGR – A case study

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of longterm- stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50 years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement.

Qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles

Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection, copy number analysis, cancer gene expression and methylation profiling. Tumour cellularity is traditionally estimated by pathological review of sectioned specimens; however this method is both subjective and prone to error due to heterogeneity within lesions and cellularity differences between the sample viewed during pathological review and tissue used for research purposes. In this paper we describe a statistical model to estimate tumour cellularity from SNP array profiles of paired tumour and normal samples using shifts in SNP allele frequency at regions of loss of heterozygosity (LOH) in the tumour. We also provide qpure, a software implementation of the method. Our experiments showed that there is a medium correlation 0.42 (-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (-value 2.2e-16) between cellularity estimates by qpure and deep Ion Torrent sequencing of known somatic KRAS mutations; and a weaker correlation 0.32 (-value = 0.004) between IonTorrent sequencing and pathology review. This suggests that qpure may be a more accurate predictor of tumour cellularity than pathology review. qpure can be downloaded from https://sourceforge.net/projects/qpure/.

Temporal Genetic Similarity Among Year-Classes of the Pacific Geoduck Clam (Panopea generosaGould 1850): A Species Exhibiting Spatial Genetic Patchiness

A previous study revealed genetic differences among collections of the commercially exploited geoduck clam (Panopea generosa) in Puget Sound, WA, but this heterogeneity did not follow an isolation-by-distance model. In this study, we investigated whether these differences were ephemeral or stable and tested predictions of the sweepstakes recruitment hypothesis, in which individuals show a high variance in reproductive success. We genotyped 11 allozyme and 7 microsatellite loci in 2,021 geoducks from 2 sites in Puget Sound and aged individuals by counting annuli in thin-section chondrophores under light microscopy. Genotypic data were then collated by year-class to test predictions of the sweepstakes recruitment hypothesis with allele count rarefaction, year-class relatedness, and 3 estimators of efective population size (Ne) using temporal shifts in allele frequencies. Although estimates of Ne were similar among year-classes, spatial shifts in allele frequencies and year-class strengths were detected among stations at 1 site, indicating that patchy settlement may be the result of an interaction between larval behavior during dispersal and hydrology.

Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population.

Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (N(e)) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean N(e) is estimated as 74. We find indications that N(e) varies over time, but there is no obvious temporal trend. We also estimated N(e) using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an N(e) estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (N(b)) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.

Passage of Campylobacter jejuni through the chicken reservoir or mice promotes phase variation in contingency genes Cj0045 and Cj0170 that strongly associates with colonization and disease in a mouse model

Human illness due to Camplyobacter jejuni infection is closely associated with consumption of poultry products. We previously demonstrated a 50 % shift in allele frequency (phase variation) in contingency gene Cj1139 (wlaN) during passage of C. jejuni NCTC11168 populations through Ross 308 broiler chickens. We hypothesized that phase variation in contingency genes during chicken passage could promote subsequent colonization and disease in humans. To test this hypothesis, we passaged C. jejuni strains NCTC11168, 33292, 81-176, KanR4 and CamR2 through broiler chickens and analysed the ability of passaged and non-passaged populations to colonize C57BL6 IL-10-deficient mice, our model for human colonization and disease. We utilized fragment analysis and nucleotide sequence analysis to measure phase variation in contingency genes. Passage through the chicken reservoir promoted phase variation in five specific contingency genes, and these 'successful' populations colonized mice. When phase variation did not occur in these same five contingency genes during chicken passage, these 'unsuccessful' populations failed to colonize mice. Phase variation during chicken passage generated small insertions or deletions (indels) in the homopolymeric tract (HT) in contingency genes. Single-colony isolates of C. jejuni strain KanR4 carrying an allele of contingency gene Cj0170 with a10G HT colonized mice at high frequency and caused disease symptoms, whereas single-colony isolates carrying the 9G allele failed to colonize mice. Supporting results were observed for the successful 9G allele of Cj0045 in strain 33292. These data suggest that phase variation in Cj0170 and Cj0045 is strongly associated with mouse colonization and disease, and that the chicken reservoir can play an active role in natural selection, phase variation and disease.

Allele frequency covariance among cohorts and its use in estimating effective size of age‐structured populations

A general expression for the covariance of allele frequencies among cohorts in age-structured populations is derived. The expression is used to extend the so-called temporal method for estimating effective population size from allele frequency shifts among samples from cohorts born any number of years apart. Computer simulations are used to check on the accuracy and precision of the method, and an application to coastal Atlantic cod is presented.

Genetic Variation in Picea mariana × P. rubens Hybrid Populations Assessed with ISSR and RAPD Markers

Interspecific hybridization can result in significant shifts in allele frequencies. The objective of the present study was to assess the level of genetic variation in populations of P. mariana × P. rubens hybrids derived from artificial crosses. Progenies from backcross populations created through a series of controlled pollinations among P. mariana and P. rubens trees across the hybridization index were analyzed. Several Inter Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) primers were used to amplify genomic DNA samples from each population. ISSR primers produced from 30% to 52% polymorphic loci. The level of polymorphism was higher with RAPD markers, ranging from 57% to 76%. Overall, the two marker systems generated similar levels of polymorphic loci for P. mariana and P. rubens populations. No significant differences were found among the P. mariana × P. rubens populations analyzed and between the hybrids and the parental populations regardless of the molecular marker used. This confirms the genetic closeness of P. mariana and P. rubens species.

Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations.

The genes of the major histocompatibility complex are the most polymorphic genes in vertebrates, with more than 1,000 alleles described in human populations. How this polymorphism is maintained, however, remains an evolutionary puzzle. Major histocompatibility complex genes have a crucial function in the adaptive immune system by presenting parasite-derived antigens to T lymphocytes. Because of this function, varying parasite-mediated selection has been proposed as a major evolutionary force for maintaining major histocompatibility complex polymorphism. A necessary prerequisite of such a balancing selection process is rapid major histocompatibility complex allele frequency shifts resulting from emerging selection by a specific parasite. Here we show in six experimental populations of sticklebacks, each exposed to one of two different parasites, that only those major histocompatibility complex alleles providing resistance to the respective specific parasite increased in frequency in the next host generation. This result demonstrates experimentally that varying parasite selection causes rapid adaptive evolutionary changes, thus facilitating the maintenance of major histocompatibility complex polymorphism.

A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks

Genes underlying repeated adaptive evolution in natural populations are still largely unknown. Stickleback fish (Gasterosteus aculeatus) have undergone a recent dramatic evolutionary radiation, generating numerous examples of marine-freshwater species pairs and a small number of benthic-limnetic species pairs found within single lakes [1]. We have developed a new genome-wide SNP genotyping array to study patterns of genetic variation in sticklebacks over a wide geographic range, and to scan the genome for regions that contribute to repeated evolution of marine-freshwater or benthic-limnetic species pairs. Surveying 34 global populations with 1,159 informative markers revealed substantial genetic variation, with predominant patterns reflecting demographic history and geographic structure. After correcting for geographic structure and filtering for neutral markers, we detected large repeated shifts in allele frequency at some loci, identifying both known and novel loci likely contributing to marine-freshwater and benthic-limnetic divergence. Several novel loci fall close to genes implicated in epithelial barrier or immune functions, which have likely changed as sticklebacks adapt to contrasting environments. Specific alleles differentiating sympatric benthic-limnetic species pairs are shared in nearby solitary populations, suggesting an allopatric origin for adaptive variants and selection pressures unrelated to sympatry in the initial formation of these classic vertebrate species pairs.

Wild and Hatchery Populations of Korean Starry Flounder (Platichthys stellatus) Compared Using Microsatellite DNA Markers

Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (FST = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity.

Shifts in Intra-Clonal Dynamics Rather Than Novel Mutations Are the Main Engine Driving Tumor Evolution in Relapsed CLL

Abstract 284Tumor evolution is a complex process, and is the biologic underpinning of disease progression, resistance to therapy and relapse. Using whole-exome sequencing (WES) of sequential samples from patients with relapsed chronic lymphocytic leukemia (CLL) treated with conventional chemotherapy, we studied genetic tumor evolution of cancer relapse.We performed WES using paired-end reads on DNA from two peripheral blood-derived CLL tumor samples at least one year apart and on germline DNA for 20 patients. Here we report the analysis of tumor exomes from the first seven patients, of whom 6 had relapsed disease after chemotherapy and one untreated patient without intervening therapy between samples. All samples had a tumor purity that exceeded 90%. Sequencing coverage was >86% of target territory, with 132x depth obtained for all samples. In total, 187 coding region mutations (124 nonsynonymous, 63 synonymous) were identified (median: 21 somatic mutations/patient; range: 10–64), not including Ig gene mutations which were >80% clonal and remained clonally stable in our cohort.We measured the abundance of specific mutations in each patient tumor to assess clonality. An allelic frequency of 0.3–0.6 likely represents heterozygous mutations in most or all tumor cells (‘clonal’) while a frequency of <0.3 represents mutations in a subset of tumor cells (‘subclonal’). Overall, 118 (63%) somatic mutations were clonal, and their allelic frequency remained unchanged in the relapse samples. 65 (35%) mutations were subclonal (average allelic frequency 0.13±0.075). Ten subclonal mutations, found in 3 of 7 initial samples, evolved into clonal mutations in the relapse samples, compared with only a single opposite occurrence where a clonal mutation became subclonal (p< 0.005, FDR q<0.01). The remaining 4 of 7 tumors showed only minor shifts in allelic frequencies over time, and included the individual who did not receive chemotherapy between samples.In Patient A, a subclone with three mutations appeared to expand to become the dominant clone, with a change in allelic fraction from an average of 0.17 (0.14–0.23) to an average of 0.43 (0.41–0.46) (p<0.000001). Two of three mutations were non-silent and are likely cancer drivers: NRAS (Q61R, found in 38/38 samples in COSMIC- Catalogue of Somatic Mutations in Cancer, Sanger Institute), and a cancer related gene PLK1. The third mutation is likely a passenger mutation as it was a synonymous mutation in ADAM18. In Patient B, a subclone containing a novel, recently identified driver in CLL, SF3B1, became the dominant clone that included additional mutations in cancer-related genes, CSMD1 and KIAA1199 (change in allelic fraction from an average of 0.16 (0.12–0.18) to an average of 0.37 (0.35–0.38) (p<0.001)). In another example, Patient C, a TP53 mutation increased in allelic frequency from 0.18 in the initial sample to 0.69 in the relapse sample (p<0.005). Analysis of copy number variation (CNV) by CapSeg (a novel algorithm that examines CNV from WES) revealed this change in allelic frequency to be coupled with a ploidy change in del(17p) from 0.8 to 0.5, consistent with a loss of both alleles.Only one sample demonstrated the appearance of novel mutations with relapse (Patient C), with 19 new mutations (13 non-silent, 3 Silent) of a total of 46 appearing at relapse. All however were subclonal, and thus less likely to have driven tumor relapse. A comparison of the 10 mutations that were selected by chemotherapy to all other mutations demonstrated an enrichment in mutations seen in the COSMIC database (p<0.05), which hints at a higher proportion of cancer drivers in this set. Our ongoing analyses are focused on the association of clinical features with copy number variation and changes in gene expression.In summary, our analysis of serial exomes from seven patients provided important insights into the genetic evolution of CLL under the selective pressure of chemotherapy. We demonstrate a significant change in clonal dynamics in one half of treated patients, which suggests that relapsed disease following treatment is driven by expansion of subclones under the selective pressure of chemotherapy rather than by novel mutagenesis. This observation may have clinical implications, as it suggests that pre-treatment WES may allow not only for the delineation of current genetic abnormalities, but through investigation of subclonal mutations, may also predict genetic evolution in future relapse. Disclosures:No relevant conflicts of interest to declare.

Successive increases in the resistance of Drosophila to viral infection through a transposon insertion followed by a Duplication.

To understand the molecular basis of how hosts evolve resistance to their parasites, we have investigated the genes that cause variation in the susceptibility of Drosophila melanogaster to viral infection. Using a host-specific pathogen of D. melanogaster called the sigma virus (Rhabdoviridae), we mapped a major-effect polymorphism to a region containing two paralogous genes called CHKov1 and CHKov2. In a panel of inbred fly lines, we found that a transposable element insertion in the protein coding sequence of CHKov1 is associated with increased resistance to infection. Previous research has shown that this insertion results in a truncated messenger RNA that encodes a far shorter protein than the susceptible allele. This resistant allele has rapidly increased in frequency under directional selection and is now the commonest form of the gene in natural populations. Using genetic mapping and site-specific recombination, we identified a third genotype with considerably greater resistance that is currently rare in the wild. In these flies there have been two duplications, resulting in three copies of both the truncated allele of CHKov1 and CHKov2 (one of which is also truncated). Remarkably, the truncated allele of CHKov1 has previously been found to confer resistance to organophosphate insecticides. As estimates of the age of this allele predate the use of insecticides, it is likely that this allele initially functioned as a defence against viruses and fortuitously “pre-adapted” flies to insecticides. These results demonstrate that strong selection by parasites for increased host resistance can result in major genetic changes and rapid shifts in allele frequencies; and, contrary to the prevailing view that resistance to pathogens can be a costly trait to evolve, the pleiotropic effects of these changes can have unexpected benefits.

Genetic impacts of Anacapa deer mice reintroductions following rat eradication

The Anacapa deer mouse is an endemic subspecies that inhabits Anacapa Island, part of Channel Islands National Park, California. We used mitochondrial DNA cytochrome c oxidase subunit II gene (COII) and 10 microsatellite loci to evaluate the levels of genetic differentiation and variation in ~1400 Anacapa deer mice sampled before and for 4 years after a black rat (Rattus rattus) eradication campaign that included trapping, captive holding and reintroduction of deer mice. Both mitochondrial and microsatellite analyses indicated significant differentiation between Anacapa deer mice and mainland mice, and genetic variability of mainland mice was significantly higher than Anacapa mice even prior to reintroduction. Bayesian cluster analysis and Principal Coordinates Analysis indicated that East, Middle and West Anacapa mice were genetically differentiated from each other, but translocation of mice among islands resulted in the East population becoming less distinct as a result of management. Levels of heterozygosity were similar before and after management. However, numerous private alleles in the founder populations were not observed after reintroduction and shifts in allele frequencies occurred, indicating that the reintroduced populations experienced substantial genetic drift. Surprisingly, two mitochondrial haplotypes observed in an earlier study of Anacapa deer mice were lost in the 20 years prior to the rat eradication program, leaving only a single haplotype in Anacapa deer mice. This study demonstrates how genetic monitoring can help to understand the re-establishment of endemic species after the eradication of invasive species and to evaluate the effectiveness of the management strategies employed.

Considering alternative life history modes and genetic divergence in conservation: a case study of the Oklahoma salamander

Alternative life history strategies can provide important variation for the long-term persistence of a lineage. However, conservation of such lineages can be complicated because each life history mode may have different habitat requirements and may be vulnerable to different environmental perturbations. The Oklahoma salamander (Eurycea tynerensis) is endemic to the Ozark Plateau of North America, and has two discrete life history modes, biphasic (metamorphic) and aquatic (paedomorphic). Until recently, these modes were considered separate species and conservation attention focused only on paedomorphic populations. We perform phylogenetic analyses of the mitochondrial gene cytochrome b (Cytb) and nuclear gene proopiomelanocortin (POMC) to assess patterns of historical isolation in E. tynerensis, and test whether life history mode is randomly distributed with respect to the phylogeny and geography. We find three divergent Cytb lineages and significant shifts in POMC allele frequencies between the eastern, western, and southwestern portions of the distribution. Life history mode varies extensively, but paedomorphosis is largely restricted to the widespread western clade. Therefore, the two most divergent and narrowly distributed clades (southwestern and eastern) were previously overlooked due to their metamorphic life history. Paedomorphosis has allowed E. tynerensis to drastically increase its niche breadth and distribution size. Nevertheless, metamorphosis is also an important attribute, and metamorphic populations are the ultimate source for paedomorphic evolution. Preservation of divergent genetic lineages, and regions that include adjacent habitat for both life history modes, may be the most effective way to maintain historical and adaptive variation and provide gateways for ongoing life history evolution.

Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49; P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

Campylobacter genotypes from poultry transportation crates indicate a source of contamination and transmission

Crates used to transport live poultry can be contaminated with Campylobacter, despite periodic sanitization, and are potential vectors for transmission between flocks. We investigated the microbial contamination of standard and silver ion containing crates in normal use and the genetic structure of associated Campylobacter populations. Bacteria from crates were enumerated by appropriate culture techniques, and multilocus sequence typing (MLST) was used to determine the genetic structure of Campylobacters isolated from standard and silver ion containing crates. Compared to standard crates, counts of bacteria, including Campylobacter, were consistently lower on silver ion containing crates throughout the decontamination process. In total, 16 different sequence types were identified from 89 Campylobacter jejuni isolates from crates. These were attributed to putative source population (chicken, cattle, sheep, the environment, wild bird) using the population genetic model, structure. Most (89%) were attributed to chicken, with 22% attribution to live chicken and 78% to retail poultry meat. MLST revealed a progressive shift in allele frequencies through the crate decontamination process. Campylobacter on crates survived for at least 3 h after sanitization, a period of time equivalent to the journey from the processing plant to the majority of farms in the catchment, showing the potential for involvement of crates in transmission. Inclusion of a silver ion biocide in poultry transportation crates to levels demonstrating acceptable antibacterial activity in vitro reduces the level of bacterial contamination during normal crate use compared to standard crates. Molecular analysis of Campylobacter isolates indicated a change in genetic structure of the population with respect to the poultry-processing plant sanitization practice. The application of a sustainable antimicrobial to components of poultry processing may contribute to reducing the levels of Campylobacter circulating in poultry.

Selection for Reduced Fusarium Ear Rot and Fumonisin Content in Advanced Backcross Maize Lines and Their Topcross Hybrids

Backcross breeding is an important method to improve elite cultivars for traits controlled by a small number of loci but has been used less frequently to improve quantitatively controlled traits. Resistances to Fusarium ear rot [caused by Fusarium verticillioides (Sacc.) Nirenberg (teleomorph Gibberella moniliformis Wineland)] and contamination by the associated mycotoxin fumonisin in maize (Zea mays L.) are quantitatively inherited. We backcrossed the more resistant but unadapted inbred GE440 for four generations to the susceptible but agronomically elite commercial inbred FR1064. A selected set of 19 BC4F1:3 lines had greater resistance to ear rot and fumonisin content than their recurrent parent FR1064. Topcrosses of the selected lines had greater resistance to Fusarium ear rot and similar grain yield compared to the topcross of the recurrent parent FR1064. We also genotyped selected lines at DNA markers linked to ear rot and fumonisin resistance quantitative trait loci (QTL) identified in the BC1 generation of this cross to determine which QTL demonstrated allele frequency shifts due to selection. Markers linked to QTL on chromosomes 1 and 4 inherited the GE440 allele significantly more often than expected by random chance.

Adaptations to new environments in humans: the role of subtle allele frequency shifts.

Humans show tremendous phenotypic diversity across geographically distributed populations, and much of this diversity undoubtedly results from genetic adaptations to different environmental pressures. The availability of genome-wide genetic variation data from densely sampled populations offers unprecedented opportunities for identifying the loci responsible for these adaptations and for elucidating the genetic architecture of human adaptive traits. Several approaches have been used to detect signals of selection in human populations, and these approaches differ in the assumptions they make about the underlying mode of selection. We contrast the results of approaches based on haplotype structure and differentiation of allele frequencies to those from a method for identifying single nucleotide polymorphisms strongly correlated with environmental variables. Although the first group of approaches tends to detect new beneficial alleles that were driven to high frequencies by selection, the environmental correlation approach has power to identify alleles that experienced small shifts in frequency owing to selection. We suggest that the first group of approaches tends to identify only variants with relatively strong phenotypic effects, whereas the environmental correlation methods can detect variants that make smaller contributions to an adaptive trait.