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Introduction The pace of the evolutionary change depends on the existence of genetic variation, population size and intensity of the selection. While environmental change very often exceeds the rate of evolution for many species, killifish (Fundulus heteroclitus), living in U.S Atlantic coast estuaries turn out to be remarkably resilient. They have adapted to survive levels of toxic industrial pollutants, tolerating concentrations up to 8000 times higher than sensitive fish.  In this interesting study, Reid et al. use population genomic and transcriptomic analyses to reveal complex genetic basis of rapid adaptation in killifish to dramatic, human-induced, environmental change. Results Four pairs of sensitive and tolerant populations were compared. Based on comparative trancriptomics and analysis of 384 whole genome sequences few candidate regions are identified to underlay tolerance to complex mixtures of polycyclic and halogenated aromatic hydrocarbons. Interestingly, they are shared among four tolerant populations and are highly ranked. This suggests that the most important targets of selection have evolved in parallel across polluted sites. Within shared outliers are genes involved in aryl hydrocarbon receptor (AHR) signalling pathway. Role of this pathway is to mediate toxicity. Experiments showed that tolerant populations exhibit reduced inducibility of AHR regulated genes while sensitive populations showed …

Introduction Novel traits play a key role in evolution by facilitating the access to new ecological niches. Novelty is often recognized at a phenotypic level and usually related to gain of new function. But can nature innovate through the loss of the function? Wing reduction and loss of flight in birds occurred several times in evolutionary history. It is found among 26 families of birds. However, it is difficult to determine genetic basis underlying this change. In this interesting study Burga et al.  are using flightless Galapagos cormorant (Phalacrocorax harrisi) as an interesting model to study evolution of recent loss of flight. Namely, P.harrisi diverged from its flighted relatives within the past 2 million years and represents the only flightless cormorant among 40 existing species. The entire population (approximately 1500 individuals) is distributed along the coastlines of Isabela and Fernandina islands in the Galapagos archipelago. There are two evolutionary paths that could possibly explain the loss of flight. Flightlessness could be positively selected if it helps birds to develop alternative ability to escape from predators and to survive (like swimming). Alternatively, if flying was not essential for surviving (no need to escape from predators) the mutations that obstruct flight might …

A biochemical story on convergent evolution Introduction Convergent evolution is the process by which similar traits evolve independently in distantly related organisms, such as wings in bats and birds. This can target orthologous or unrelated genes, which gives a different view on the concept of convergent evolution : how much it is constrained to some pathways, or, reversely, how diverse the path to the same function can be. For convergent evolution to arise, different proteins must be assembled into an ordered, functional pathway. Currently, Three hypotheses shed light on the matter. Under the cumulative hypothesis, enzymes catalyzing the earlier reactions of a pathway must evolved first, because, otherwise, enzymes that perform the following steps would have no substrate to react with. Later steps would arise by duplication of the first enzyme. This suppose that intermediates are advantageous. Reversely, under the retrograde hypothesis, enzymes catalazing the later steps of a pathway would evolved first, and then gene duplication would give rise to the enzymes catalysing earlier steps. This suppose that intermediates could be produced non-enzymatically but doesn’t assume anything on their potential effect. Finally, the patchwork hypothesis states that a novel pathway will arise by the recruitment and rerouting of an alternative, …

Blogpost on: Malaspinas et al 2016 A genomic history of Aboriginal Australia. Nature 538: 207–214. Introduction: Prior to the publication of Malaspinas et al. 2016, investigation of Aboriginal Australian genome sequences had been quite limited. In fact, only 3 whole genome sequences from Aboriginals had been analyzed, 2 of these obtained with limited information concerning their place of origin (Rasmussen et al. 2011). Malaspinas et al. 2016 is the first comprehensive study aimed at uncovering how the settlement of Australia occurred. The study combines genomic, linguistic and archeological studies in order to obtain more detailed information on how the settlement of Australia occurred. For the largest part of the past 100000 years, Tasmania, New Guinea and Australia were part of the same continent known as Sahul. This continent was detached from mainland Asia, and its settlement process by human populations still remains poorly understood. Previous archaeological evidence has led to the hypothesis that the settlement of Australia occurred from an African emigration wave, which predates the African emigration wave that settled in Eurasia (Lahr, M. et al. 1994). This has been coined the 2 Out of Africa event hypothesis (2OoA). Yet, other genetic studies support the notion that one major migration …

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons About 450 mya bony vertebrates radiated into Lobe-finned fish, from which tetrapods appeared later, and Ray-finned fish, which include Teleost (Fig.1). Nowadays they make up to 96 percent of all fish in the planet. Among the latter some species such as zebrafish (Dario renio) and medaka (Oryzias latipes) are used as model organisms in biomedical research in order to try to understand which is the genetic basis of certain human diseases. However, the transferability between the models is difficult given the phylogenetic distance between tetrapods (humans) and Ray-finned fish. For this reason, the authors decided to sequence the genome of the Spotted Gar (Lepisosteus oculatos), that can act as a bridge as it split off from the teleosts before the TGN (Teleost Genome Duplication). During vertebrate evolution two other genome duplications happened in the vertebrate linage: VGD1 and VGD2. Fig1: Spotted gar is a ray-finned fish that diverged from teleost fishes before the TGD. Gar connects teleosts to lobe-finned vertebrates, such as coelacanth, and tetrapods, including human, by clarifying evolution after the two earlier rounds of vertebrate genome duplication (VGD1 and VGD2) that occurred before the divergence of ray-finned …

Genetic sex determination, i. e. the determination of sexual phenotypes by the effect of sex-determining genes, is found in the majority of vertebrates. Sex determination genes have evolved multiple times independently and can be located on different chromosomes. Depending on whether the presence of the sex determining region (SDR) determines female or male sex, genetic systems of sex determination are called ZW or XY systems respectively and the sex which is heterozygous for the SDR is called the heterogametic sex. Lower fitness in the heterogametic sex has long been observed in interspecific hybrids in a wide range of animal and even plant species, an observation called Haldane’s rule. In this paper the authors find a similar pattern in (non-hybrid) tetrapod species: by comparing the adult sex ratio in XY and ZW systems in 344 tetrapod species, they find that the ASR is skewed towards the homogametic sex (towards females in an XY system and towards males in a ZW system). This observation is based on a dataset containing known genetic sex determination systems and adult sex ratios (ASRs) of species across the vertebrate phylogeny. Within amphibians and reptiles (in which both XY and ZW systems are found), the authors show …

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 …