A high resolution genome-wide scan for significant selective sweeps: an application to pooled sequence data in laying chickens

In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a "creeping window" strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value<0.001), including genes known to be associated with eggshell structure and immune system such as CALB1 and GAL cluster, respectively. A substantial proportion of signals was found in poor gene content regions including the most extreme signal on chromosome 1. The observation of multiple signals in a highly selected layer line of chicken is consistent with the hypothesis that egg production is a complex trait controlled by many genes

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

<p>Abstract</p> <p>Background</p> <p>The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.</p> <p>Results</p> <p>One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (<it>p </it>≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including <it>WNT10B </it>and <it>DKK2 </it>in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- <it>BAX </it>and <it>BMPR1B </it>were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (<it>p </it>≤ 0.1 or <it>p </it>≤ 0.05).</p> <p>Conclusions</p> <p>Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of <it>BAX </it>and <it>BMPR1B </it>gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.</p

A spatially explicit data-driven approach to assess the effect of agricultural land occupation on species groups

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Vibrational communication networks: eavesdropping and biotic noise

In nature, communication predominantly occurs in a group of several conspecific and/or heterospecific individuals within signaling and receiving range of each other, i.e., in a network environment. Vibrational communication in the context of sexual behavior has been, in the past, usually considered as a private communication channel, free of potential competitors and eavesdropping predators or parasitoids and consequently only rarely studied outside an emitter–receiver dyad. We provide an overview of work related to vibrational communication in the presence of (a) environmental (abiotic) noise, (b) other conspecific and/or heterospecific signalers (biotic noise), (c) rivals and (d) exploiters (predators and parasitoids) The evidence gathered in the last few years shows that arthropods relying on substrate-borne vibrations communicate within a rich and complex vibrational world and reveals diverse interactions and mechanisms. Considering vibrational communication from a network perspective may allow us in the future to identify sources of selection pressures that cannot be recognized in a communication dya

Vibrational communication networks

In nature, communication predominantly occurs in a group of several conspecific and/or heterospecific individuals within signaling and receiving range of each other, i.e., in a network environment. Vibrational communication in the context of sexual behavior has been, in the past, usually considered as a private communication channel, free of potential competitors and eavesdropping predators or parasitoids and consequently only rarely studied outside an emitter–receiver dyad. We provide an overview of work related to vibrational communication in the presence of (a) environmental (abiotic) noise, (b) other conspecific and/or heterospecific signalers (biotic noise), (c) rivals and (d) exploiters (predators and parasitoids). The evidence gathered in the last few years shows that arthropods relying on substrate-borne vibrations communicate within a rich and complex vibrational world and reveals diverse interactions and mechanisms. Considering vibrational communication from a network perspective may allow us in the future to identify sources of selection pressures that cannot be recognized in a communication dyad