Analyses of pig genomes provide insight into porcine demography and evolution

DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. This protocol explains how to use DAVID, a high-throughput and integrated data-mining environment, to analyze gene lists derived from high-throughput genomic experiments. The procedure first requires uploading a gene list containing any number of common gene identifiers followed by analysis using one or more text and pathway-mining tools such as gene functional classification, functional annotation chart or clustering and functional annotation table. By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.

The history of human population size is important to understanding human evolution. Various studies 1-5 have found evidence for a founder event (bottleneck) in East Asian and European populations associated with the human dispersal out-of-Africa event around 60 thousand years ago (kya) before present. However, these studies have to assume simplified demographic models with few parameters and do not precisely date the start and stop times of the bottleneck. Here, with fewer assumptions on population size changes, we present a more detailed history of human population sizes between approximately ten thousand to a million years ago, using the pairwise sequentially Markovian coalescent (PSMC) model applied to the complete diploid genome sequences of a Chinese male (YH) 6 , a Korean male (SJK) 7 , three European individuals (Venter 8 , NA12891 and NA12878 9 ) and two Yoruba males (NA18507 10 and NA19239). We infer that European and Chinese populations had very similar population size histories before 10–20kya. Both populations experienced a severe bottleneck between 10–60kya while African populations experienced a milder bottleneck from which they recovered earlier. All three populations have an elevated effective population size between 60–250kya, possibly due to a population structure 11 . We also infer that the differentiation of genetically modern humans may have started as early as 100–120kya 12 , but considerable genetic exchanges may still have occurred until 20–40kya.

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.