Tutorial Genomics, Ecology, Evolution, etc
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Blog of a tutorial of Ecole doctorale de biologie UNIL
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 geneti ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 mode ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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. U ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 a ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 wh ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 archeologic ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 informatio ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 t ..read more
Tutorial Genomics, Ecology, Evolution, etc
3y ago
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 Preh ..read more