Tutorial Genomics, Ecology, Evolution, etc

Gibbons (Hylobatidae) are small arboreal apes that form a key node in primate evolution. One of the most distinctive phenotype is their high genome plasticity involving large-scale chromosomal rearrangements and karyotype changes. The four gibbon genera (Nomascus, Hylobates, Hoolock, Symphalangus) bear between 38 to 52 chromosomes per diploid cell despite their relative recent differentiation about 5 million years ago. In this study, Carbone et al. used genomic approaches i) to better understand the underlying mechanism for gibbon genome plasticity, ii) to reveal the phylogeny of the four gibbon genera, and iii) to study genes involved in functional adaptation in gibbon evolution. Key findings and personal comments Sequencing and assembly of the Gibbon reference genome reveal a total genome size of about 2.9Gb with a sequence quality comparable to other Sanger-sequence based genomes. Genome alignments of several primate genomes to the human reference genome, the best genome assembly available, show differences in synteny between primates (Fig.2). In general, the more recent the common ancestor, the more synteny is shared. The gibbon-human alignment contains many large-scale rearrangements that are not present in other human-primate alignments. Small-scale rearrangements are comparable among all primates suggesting that the gibbon genome does not possess global genome …

Oryza glaberrima is an African species of rice that is not of the same origin as the Asian rice (Oryza sativa) and was independently domesticated from the progenitor Oryza barthii about 3,000 years ago.In this study recently published by Nature genetics, Wang et al. use a genomic approach to investigate the evolutionary history of O. glaberrima and to identify whether the artificial selection of this species shares common traits with the domestication process that occurred in O. sativa. Main findings and personal comments Sequencing genomic DNA of O. glaberrima revealed that the genome of this species consists of 316 Mb arranged in 12 chromosomes. 33,000 genes were identified with ab initio gene finding, protein homology and tentative consensus transcripts, approaches that nowadays could be efficiently replaced by RNA-seq. To determine the extent of conservation of functional genes, they selected a set of O. sativa genes to search for orthologous in O. glaberrima and found that the 95.5% of these genes were intact and syntenic. However, the 178 genes in the set belong to three very important pathways associated with flowering time and light and stress response; for this reason, I think that the extent of conservation could be overestimated when …

Introduction & Methods The demographic history of the human species has always fascinated us. It is known that the ancestral human lineage appeared in East Africa, and that it subsequently migrated out of Africa towards Eurasia, separating into distinct lineages through time. Although many studies have focused on human demographic history, some aspects remain unknown, partly due to the difficulty in finding ancient samples from wide geographic and temporal scales. Particularly, the specific origins of certain populations at more local scales, remains uncertain. For example, it is known that early European farmers originated at least in part from the Near-East, which was one of the centers of the development of agriculture, and that hunter-gatherers were already present in Europe when early farmers arrived. However, as Lazaridis et al (2014) mention, modeling present-day Europeans as a mixture of only these two ancestral populations does not account for all present genetic diversity. Their main goal was therefore to clarify the prehistory of present-day Europeans. To address this question, the authors sequenced the genomes of nine ancient Europeans: seven from Sweden and one from Luxembourg (hunter-gatherers), as well as one farmer from Stuttgart, Germany, a member of the first widespread farming culture in …

The role and importance of epistasis (non-additive interactions between alleles) in shaping genetic variation, and its effects on fitness have been the focus of much debate. Russell et al. recently investigated the genomic footprint of epistatic fitness effects. Starting from two sets of 8 highly inbred Drosophila melanogaster strains, they created 4 panels of 400 recombinant inbred lines. Then, they investigated non independent allelic segregation of pairs of unlinked loci (i.e. on different chromosomes; figure 1 a and c). Indeed, it is expected that unfavourable allelic combinations will be under-represented in a the population. This deviation from Mendelian proportions was refereed as genotype ratio distortion (GDP). 22 pairs of epistatically interacting alleles could be identified. Many of the incompatible alleles are present in more than one founder strain, suggesting that they were segregating in natural populations. They estimated that any pairwise combination of founder strains has, on average, 1.15 pairs of epistatically interacting alleles . They performed experimental crosses in order to investigate two incompatibilities in more details. They discovered that the negative interaction is caused by the minor alleles at each locus in both cases (Figure 1 b, d). Interestingly, both involved a reduction in male fertility (with respectively …

Epistasis is the phenomenon whereby one polymorphism’s effect on a trait depends on other polymorphisms present in the genome(Hemani et al. 2014). Although it has been proved to shape genetic variation and contribute to differences within and between populations for long time, there is still lack of empirical evidence to show genomic footprint shaped by epistasis. Here, Corbettdetig et al(2013) designed a simple approach to capture the genotype ratio distortion caused by epistasis using a large panel of Drosophila melanogaster. In brief, Corbettdetig and colleagues first create the Drosophila Synthetic Population Resource(DSPR) using strains original from diverse geographic location (Extended Data Fig.1). And the PCA analysis (Extended Data Fig.2) indicate there is no residual population structure. In these DSPR population, the unfavourable allelic combinations will be under-represented if epistasis effect virtually exist. And the authors do found such under-representation which corresponding to genotype ratio distortion (GRD) in 22 pairs of interacting alleles(Fig. 1). These genomic incompatible alleles were confirmed using extra cross experiment which indicate a significant decrease of reproductive fitness. Meanwhile, Corbettdetig and colleagues also screen for GRD in two additional plant species. 7 GRD instances in Arabidopsis and 5 in maize were detected using same method. So it …