Paper List

Papers to discuss Spring 2017

Edit: this Spring’s series has been canceled, but I’m leaving the article list up for the record. For this Spring, the students will need to chose 3 of these 4 series of articles to discuss: Evo-Devo genomics: Lin et al 2016 The seahorse genome and the evolution of its specialized morphology. Nature 540: 395–399 Van Belleghem et al 2017 Complex modular architecture around a simple toolkit of wing pattern genes. Nature Ecology & Evolution 1: 0052 Human populations: Pagani et al 2016 Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538: 238–242 Mallick et al. 2016 The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538: 201–206 Malaspinas et al 2016 A genomic history of Aboriginal Australia. Nature 538: 207–214 Convergent evolution: Yeaman et al 2016 Convergent local adaptation to climate in distantly related conifers. Science 353: 1431-1433 Fukushima et al 2016 Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecology & Evolution 1: 0059 Reid et al 2017 The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science 354: 1305-1308 Speciation: de Manuel et al 2016 Chimpanzee genomic diversity reveals ancient admixture …

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Evolution

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals

Gene duplications are main contributors of genome evolution, but most of the duplicates are redundant and go through pseudogenization. There are several mechanisms proposed to explain how young duplicates survive long-term and escape from being degraded. Among these, dosage-balance model likely to explain the importance of shared expression levels of young duplicate genes. An alternative model indicates sub-functionalization (new copies shares the initial functions) or neo-functionalization (new copy gains new function) as the main mechanisms of the survival of new duplicate. However, it is largely unknown the survival of gene duplication in mammals. In this current study, by using RNA-seq profiles of different human and mouse tissues, authors show that sub-functionalization is a slowly evolving and rare event. Most of the young duplicates are shown to have decreased level of expression, thereby providing initial survival and long-term preservation in the genome. Figure 1 Expression profiles of duplicate genes. Examples of Sub-or Neofunctionalization (A) and asymmetrically expressed gene pairs (B) are shown. In sub-functionalized example, SLC4A2 was shown to be expressed in Lung, Kidney, Liver and Testis, whereas SLC4A3 is expressed in Cortex, Heart and Testis. In asymmetrically expressed gene example, CRB1 is shown to be expressed higher in all tissues …

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Evolution

Peppered moth melanism mutation is a transposable element

One of the most known examples of natural selection in action is the evolution of the peppered moth (Biston betularia), the rapid replacement of the light-colored form of the moth (typica) by a dark-colored form (carbonaria) (Fig. 1) during 1800s in Britain. The first live specimen of the carbonaria form was found in 1848 and its frequency had increased drastically until late 1800s. In 1895, 98% of the moth population in Manchester was the carbonaria form (reviewed in Clarke et al., 1985). Such a phenomenon 36 years after the publication of Darwin’s On the Origin of Species, attracted biologists’ attention. J.W. Tutt first proposed “Differential bird predation hypothesis” in 1896, which is confirmed by a series of experiments by Kettlewell during mid 1950s (reviewed in Cook and Saccheri, 2013). The hypothesis states that the industrial revolution in Britain resulted in blackened trees by soot, so that birds can easily spot light-colored moths on soot-darkened trees while dark-colored moths are camouflaged. However, genetic events giving rise to carbonaria phenotype remained elusive until recently. Researchers from University of Liverpool and Wellcome Trust Sanger Institute now reported in Nature that the mutation causing the peppered moth industrial melanism is the insertion of a …

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Tutorial

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

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 …

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Evolution / Genomics / Human

ExAC presents a catalogue of human protein-coding genetic variation

Exploration of variability of human genomes represents a key step in the holy grail of human genetics – to link genotypes with phenotypes, it also provides insights to human evolution and history. For this purpose Exome Aggregation Consortium (ExAC) have been founded; to capture variability of human exomes using next-generation sequencing. The first ExAC dataset of 63,358 individuals was released 20th of October 2014. Recently, a paper describing updated version of the dataset was published : Analysis of protein-coding genetic variation in 60,706 humans. Authors made a great work on the reproductibility of the downstream analyses they have performed and generally on the availability of data. All the code is well documented in blogpost and available in GitHub repository. All figures in this blogpost I plotted by my own! Dataset ExAC is composed of almost ten fold more individuals and previous dataset of the similar kind Fig 1a. 91,000 individuals were sequenced, of which 60,706 have been kept after quality filtering. Finnish population was excluded from European due to bottleneck they have gone though. ExAC was targeting individuals with various genetic background. Principal component analysis have shown very strong geographical pattern in the dataset (Fig 1b). I expected a continuum …

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Paper List

Papers to discuss Autumn 2016

This Autumn, we will continue to discuss papers in related series: Series 1: human genome evolution Sulem et al 2015 Identification of a large set of rare complete human knockouts.     Nature Genetics 47: 448–452 Hehn et al 2016 Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. PNAS 113: E440-E449 Lek et al 2016 Analysis of protein-coding genetic variation in 60,706 humans. Nature 536: 285–291 Series 2: moth coloration van’t Hof 2016 The industrial melanism mutation in British peppered moths is a transposable element. Nature 534: 102–105 Nadeau et al 2016 The gene cortex controls mimicry and crypsis in butterflies and moths. Nature 534: 106–110 Series 3: gene and genome duplication Braasch et al 2016 The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics 48: 427–437 Lien et al 2016 The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200–205 Lan and Pritchard 2016 Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science 352: 1009-1013  

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Tutorial

The genetic sex-determination system predicts adult sex ratios in tetrapods

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 …

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Genomics / Human

Identification of a large set of rare complete human knockouts

High throughput genotyping and sequencing has led to the discovery of numerous sequence variants associated to human traits and diseases. An important type of variants involved are Loss of Function (LoF) mutations (frameshift indels, stop-gain and essential sites variants), which are predicted to completely disrupt the function of protein-coding genes. In case of Mendelian recessive diseases, for the condition to occur, the LoF variants must be biallelic, i.e. affecting both copies of a gene. The affected gene is then defined as “knockout”. By studying the Icelandic population, authors aim to identify rare LoF mutations (Minor Allele Frequency, MAF < 2%) present in individuals participating in various disease projects. They then investigate at which frequency in the population these LoF mutations are homozygous (i.e. knockout) in the germline genome. The Icelandic population Iceland is well-suited for genetic studies for three main reasons. The island was colonized by human population around the 9th century by 8-20 thousand settlers. Since then the population grew to around 320’000 inhabitants today. The initial founder effect and rare genetic admixture make the Icelandic population a genetic isolate. In addition to an unusual genetic isolation, Iceland’s population benefits of a genealogical database containing family histories reaching centuries …

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Evolution / Genomics / Tutorial

Supergenes and social organization in a bird species

      Cindy Dupuis, Xinji Li, Casper van der Kooi   The development of new molecular mechanisms and next generation sequencing techniques have advanced our knowledge on the genetic basis underlying phenotypic polymorphism. Over the coarse of recent years, scientific studies have documented large genomic regions with drastic phenotypic effects, the so-called supergenes. A supergene is a set of genes on the same chromosome that exhibit close genetic linkage and thus inherits as one unit. The evolution of a supergene requires that multiple loci with complementary effects become linked (i.e. they are genetically clustered and recombination between the loci is suppressed) and that optimal alleles at the linked loci are combined. Genetic clustering of different loci can occur when, via mutation, an adaptive interaction between two closely placed loci is created. In addition, gene duplications or translocations that generate a series of (novel) complementary genes can give rise to supergenes. The probability of a recombination event occurring in between loci depends on various factors. The chance of a recombination event occurring in between two loci will be small when the loci are located closely together, as the chance of a recombination event in between two loci generally decreases with …

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Genomics / Human / PNAS

Reconstructing human population history : ancestry and admixture

Understanding the evolutionary history of our own species, how migration and mixture of ancestral populations have shaped modern human populations is a key question in evolutionary biology. Here we present three articles related to this topic, the first two dealing with India and the third one focusing on a single Ethiopian group : 1) Moorjani et al 2013 Genetic Evidence for Recent Population Mixture in India AJHG 93,: 422–438 2) Basu et al 2016 Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure PNAS online before print 3) Van Dorp et al 2016 Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference PLOS Genetics 11(8): e1005397 All of them use genome wide data from micro array. After a brief abstract of  each paper, showing their similarities and differences, we discuss their methodological approaches. Ancestral populations of India The aim of the first two articles is to understand the history of the populations of the Indian subcontinent. The first one (Moorjani et al 2013) reports data from 73 groups living in India for more than 570 individuals sampled. …

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