Tutorial Genomics, Ecology, Evolution, etc

The recent formation and habitat diversity of the Galápagos archipelago, in conjunction with its relative isolation from the mainland, has helped the islands become rich in endemic species that have much to offer for the study of evolutionary biology. As a result of their volcanic origin and fluctuating climates, the islands of the Galápagos archipelago vary in age, size, topography and vegetation. In conjunction with their isolation from the mainland, this diversity of relatively new environments, both within and between islands, are perfect breeding grounds for speciation. The finches of the Galápagos archipelago and Cocos Island are the product of a fascinating adaptive radiation that started only about 1.5 million years ago, following the arrival of a common ancestor from South America. These finches are most notable for their diversity in beak morphology, which reflect the differences in their respective adaptations to exploiting various food resources. Charles Darwin’s observations of this diversity in beak morphology played an important role in the development of his theory of natural selection. “Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had …

Introduction Convergent evolution is the independent evolution of similar features in species of different lineages. Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment is a very classic example of convergent evolution. Although there are potentially several genomic routes to reach the same phenotypic outcome, it has been suggested that the genomic changes underlying convergent evolution may to some extent be reproducible and that convergent phenotypic traits may commonly arise from the same genetic changes. To investigate convergent evolution at the genomic level, the authors present high-coverage whole-genome sequences for four marine mammal species: the walrus (Odobenus rosmarus), the bottlenose dolphin (Tursiops truncatus), the killer whale (Orcinus orca) and the West Indian manatee (Trichechus manatus latirostris)(figure 1). Here are some interesting results of this paper. Detecting positively selected protein-coding genes In order to study the molecular mechanism of convergence evolution, firstly, they focused on detecting positive selected protein-coding genes in all three orders; Branch-site likelihood ratio test is a powerful polygenetic method to detect relatively ancient selection. This test is useful for identifying positive selection along prespecified lineages that affects only a few sites in the protein. Applying branch-site likelihood ratio method, they totally tested a series of four different …

In this paper authors returned to the question about the role of interspecific gene flow for the evolution and species diversification. Authors studied hybrid zone between two bird classes of the all-black carrion crows (Corvus corone) and the gray-coated hooded crows (C. cornix). Their morphological hybrid zone in Europe gives the possibility to study the effects of introgression on evolution during early species divergence. Authors identified genome-wide introgression and showed the divergence in the expression levels of genes, implicated in plumage coloration in both species, and genes, involved in visual perception, that could be important for maintaining phenotypic differences and responsible for heterogeneity in introgression landscapes. Principal results Firstly, authors assembled a high-quality reference genome of one hooded crow male which was aligned to chicken and zebra finch genomes and, then, annotated through mRNA sequencing. Consequently, a set of 20.794 protein coding genes containing open reading frames of more than 100 amino acids was found. RNA seq data was used to validate identified in silico genes. Then, authors resequenced 60 genomes of unrelated birds from four populations of carrion and of hooded crows and found 8.44 million single-nucleotide polymorphisms (SNPs) segregated across all investigated populations. Interestingly, carrion and hooded crows …

Evolutionary diversification among species attracts the attention of scientist during long time. Adaptive radiation underlies evolution and comprises the rapid adaptation of a single lineage to its changed environment which provides new resources and opens new environmental niches. Among all biological groups which have undergone evolutionary adaptive radiation the cichlids have been more studied by biologists. In this paper, authors investigated the molecular mechanisms and genomic substrates triggering rapid evolutionary diversification in African cichlid fish through comparative analysis of genomes of five different African cichlid lineages, together with an examination of the genetic changes responsible for divergence in six closely related species from Lake Victoria. They found some differences in all investigated East African lineages compared to ancestral, including increasing gene duplication, an excess of non-coding elements, accelerated evolution of coding sequence and divergence in the expression levels connected with transposons insertions. They also discovered novel microRNAs that alter gene expression in cichlids and genome-wide diversifying selection in coding and regulatory elements. Thus, authors have concluded that multiple molecular mechanisms together with relaxed purifying selection can promote evolutionary diversification in African cichlid fish. Principle results and discussion Authors selected and sequenced the genome of five lineages of African cichlids: four …