The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish

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 …

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The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish.

Introduction Environmental pollution is a widespread problem that living organisms have to contend with on a global scale. In contaminated sites especially, wild populations undergo intense selective pressure that may result in phenotypic adaptations to pollutants (Hendry et al., 2008). The scientific article (Reid et al., 2016) discussed in this blogpost explores the genetic mechanisms that have allowed the rapid adaptation to industrial pollutants in wild Atlantic killifish populations. Results The genomic landscape of the killifish populations Atlantic killifish (Fundulus heteroclitus) are non-migratory fish that are abundant along the US east coastline (Fig. 1A). Some killifish populations show inherited resistance to lethal levels of industrial pollutants in sites that have been contaminated for decades. For instance, the authors show that the percentage of larva that survive in increasing concentrations of a highly toxic pollutant called PCB 126, is higher in tolerant populations compared to the sensitive populations (Fig. 1B). To understand the genetic adaptations underlying the rapid adaptation to polluted sites in killifish populations, the authors sequenced the complete genomes from eight populations. Four tolerant populations that reside in highly polluted sites were sampled. Each one was paired with a sensitive population from a nearby site (Fig. 1A). The authors combined …

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How the Galapagos cormorant lost its ability to fly

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 …

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Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

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, …

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The parallel evolution in amniotes seen through the eye of functional nodal mutations

Introduction In this article the authors describe an evolutionary convergence in mammals, birds, and reptiles, based on genomic data from NCBI. The evolution of different species and lineages is due to mutations that can appear and accumulate in organisms over time. Those mutations need a high functional potential and have to be conserved in time in order to form new species. The conservation of mutations can occur via selection pressure, mutational compensation, and/or by the separation of members from the same species by geological and environmental events. In this comprehensive study, the authors describe, a genomic landscape of the parallel evolution by analysing functional nodal mutations (fNMs) by using different types of DNA (mitochondrial and nucleic), the thermostability of mtDNA encoding RNA genes, and the structural proximity of proteins, using the available 3D structures from PDB database. Functional nodal mutations (fNMs) can be separated in single nodal (fSNMs), recurrent nodal mutations (fRNMs), occured independently in unrelated lineages and recurrent combinations of nodal mutations (fRCNMs) recurred independently along with other nodal mutations in combinations in more than a single lineage. The recurrent ones can be taken in consideration the most when we are talking about the convergent adaptive responses, that means …

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Reconstructing prehistoric African population structure

INTRODUCTION The highest genetic diversity in humans is found in Africa, in line with Africa being the cradle of humanity. While the three articles we discussed previously during this tutorial (1,2,3) mainly focused on determining the most parsimonious “out-of-Africa” scenarios based on genetic diversity data, this article (Skoglund et al. 2017 4) investigates the population structure of Africa prior to the expansion of food producers (i.e. herders and farmers). In order to reconstruct the prehistoric population structure, the authors analyzed the genomes from 16 ancient African individuals who lived up to 8100 years ago (including 15 newly sequenced genomes), as well as SNP genotypes from 584 present-day Africans, and 300 high coverage genomes from 142 worldwide populations. This is the first study to gather and analyze such a high number of ancient genomes, thereby providing an unpreceded insight into the prehistoric human population structure. RESULTS An ancient cline of southern and eastern African hunter-gatherers The authors used principal component analysis (PCA) and automated clustering in order to relate the 16 ancient individuals to present-day sub-Saharan Africans. This reveals that while the two ancient South African individuals share ancestry with present-day South Africans (Khoe-San), 11 of the 12 ancient individuals living …

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A genomic history of Aboriginal Australia;

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 …

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A journey through the The Simons Genome Diversity Project: more genomes sequenced, more diverse populations

Introduction Since the first genome of Bacteriophage MS21 was completely sequenced, in 1976, until 2001 when the first draft of human genome2 was released, a lot of work was done to improve and to make accessible different methods to get inside of the genetics of various organisms. For human genome, this step was a very important one and the Human Genome Project was declared complete in 20033. During the last years, more and more projects are involved in deciphering the human wanderlust. To all of previous studies, we can add The Simons Genome Diversity Project, that brought us more information by sequencing 300 new genomes from 142 diverse populations. One of the aim was to chose populations that differ in genetics, language and culture. The study shows that some of the populations separated 100000 years ago and reveals more information about the ancestors of Australian, New Guinean and Andamanese people. Results One of the most important thing in discovering the real human peopling of the Earth is to sequence as many as possible genomes, but from individuals coming from diverse populations, that could differ in many aspects. In this study, the 300 samples were prepared by using PCR-free library, through …

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Genomic analyses inform on migration events during the peopling of Eurasia

Introduction In the past two decades, considerable research effort has been made to sequence the human genome and subsequently trying to unveil the demographic history underlying the genetic patterns of diversity we observe today across the globe. Here we discuss a recent research article by Pagani et al. 1 that addresses genomic diversity and historic migration patterns of human populations in Eurasia. The first human genome was sequenced in 2003 by the Human Genome Project2 and larger projects rapidly followed, such as HAPMAP3 and the 1000 Genomes Project4, largely due to the considerable technological improvement of sequencing technologies. Despite being extremely useful tools for a number of studies, these genome databases have some important sampling caveats that limit their use to address some particular topics. Indeed, HAPMAP sampled a reduced number of populations whereas the 1000 Genomes sampled a large number of populations but did not attempt to sample individuals of “pure” ancestry. For instance, the sampling in North America focused considerably on city-based individuals that were found to have a very diverse recent ancestry thus blurring the signal of ancient colonisation history. Importantly, in the studied paper, a considerable effort was made on sampling a broad panel of 447 …

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Papers to discuss Autumn 2017: Human demography and Convergent evolution

This Autumn, we will discuss two series of papers: Series 1: Human demography News & Views: Tucci & Akey 2016 Population genetics: A map of human wanderlust.  Nature 538: 179–180 6 Oct 2017: Pagani et al 2016 Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538: 238–242 2 7 Oct 2017: Mallick et al. 2016 The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538: 201–206 3 Nov 2017: Malaspinas et al 2016 A genomic history of Aboriginal Australia. Nature 538: 207–214 10 Nov 2017: Skoglund et al 2017 Reconstructing Prehistoric African Population Structure. Cell 171: 59–71.e21 Series 2: Convergent evolution 17 Nov 2017: Levin & Mishmar 2017 The genomic landscape of evolutionary convergence in mammals, birds and reptiles. Nature Ecology & Evolution 1: 0041 24 Nov 2017: Burga et al 2017 A genetic signature of the evolution of loss of flight in the Galapagos cormorant. Science 356: eaal3345 (also see preprint comment by Berger and Bejerano) 8 Dec 2017: Reid et al 2017 The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354: 1305-1308 15 Dec 2017: Huang et al 2016 Convergent evolution of caffeine in …

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