Evolution

Evolution / Fish / Genomics

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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Adaptation / Conservation / Evolution / Genomics

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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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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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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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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Adaptation / Conservation / Evolution / Genomics

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

Introduction Darwin’s finches from Galapagos and Cocos Island are classic example of young adaptive radiation, entirely intact because none of the species having become extinct as a result of human activity. They have diversified in beak sizes and shapes, feeding habits and diets in adapting to different food resources. Although traditional taxonomy of Darwin’s is based on morphology and has been largely supported by observations of breeding birds finches, in this paper, authors showed the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin’s finch species inhabiting Galapagos archipelago (Fig. 1a) and two close relatives, trying to analyse patterns of intra-and interspecific genome diversity and phylogenetic relationships among the species. Figure 1a. Sample location of Darwin’s finches Summary and comments of the paper The authors analyzed location and phylogeny of Darwin’s finches and found widespread evidence of interspecific gene flow that may have enhanced evolutionary diversification throughout phylogeny. They also reported discovery of a locus with the major effect on beak shape. They generated 10x sequence coverage per individual bird and using 2×100 base-pair (bp) paired-end reads and found evidence of introgression from three sources: ABBA-BABA tests, discrepancies between phylogenetic trees based on autosomal and sex linked …

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Adaptation / Evolution

The genomic substrate for adaptive radiation in African cichlid fish

In African lakes, cichlid fishes are famous for large, diverse and replicated adaptive radiations. Nearly 1,500 new species of cichlid fish evolved in a few million years when environmentally determined opportunity for sexual selection and ecological niche expansion was met by an evolutionary lineage with unusual potential to adapt, speciate and diversify. The phenotypic diversity encompasses variation in behaviour, body shape, coloration and ecological specialization. The frequent occurrence of convergent evolution of similar ecotypes suggests a primary role of natural selection in shaping cichlid phenotypic diversity. To identify the ecological and molecular basis of divergent evolution in the cichlid system, David et al. [1] sequenced the genomes and transcriptomes of five lineages of African cichlids, Pundamilia nyererei (endemic of Lake Victoria); Neolamprologus brichardi (endemic of Lake Tanganyika); Metriaclima zebra (endemic of Lake Malawi); Oreochromis niloticus (from rivers across northern Africa); Astatotilapia burtoni (from rivers connected to Lake Tanganyika). These five lineages diverged primarily through geographical isolation, and three of them subsequently underwent adaptive radiations in the three largest lakes of Africa. Authors comprehensively investigate the features from these massive genomic data. Here is some interesting finding: Accelerated gene evolution was assessed by non-synonymous/synonymous ratio. Compare with stickleback fish, O. niloticus has significant …

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Evolution / Genomics

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

The role of interspecific gene flow in species diversification has long been debated and is increasingly appreciated. However, the effect of gene introgression on phenotypic divergences and genome heterogeneity remain unclear in case of early speciation. To investigate these questions Poelstra and colleagues studied the hybrid zone between the all-black carrion crows (Corvus corone) and the gray-coated hooded crows (C. cornix). Indeed, the absence of neutral genetic diversity between these two species and successful back-crossing of hybrids strongly contrast with the plumage coloration polymorphism that remained stable in natural populations. Moreover, colour assortative mating has been observed suggesting a prezygotic isolation and ongoing speciation. To investigate the causes of this stable phenotypes the authors first analysed the effect of gene flow on genome heterogeneity and then tried to link the observed gene flow heterogeneity with gene expression and phenotypes. Genetic differentiation between hooded and carrion crows First, they assembled and annotated a high-quality reference genome of one hooded male crow and identified 20’794 protein-coding genes. This reference genome was then used to aligned 60 genomes of unrelated individuals from two populations of carrion and two populations of hooded crows (Fig. 1). They identified 8.44 million of SNPs among which 5.27 …

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Conservation / Evolution

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

Meiosis is an important biological process by which combination of various types of the genes called alleles, are segregated and packed in each germ cell waiting to be transferred and expressed in descendants. This combinations of alleles are products of chromosomal crossovers (COs) during meiotic recombination, which increases the genetic diversity of gametes. Recombination may cause local mutagenic effect at crossover sites with recurrent double strand breaks (DSBs) and thus be the source of sequence variation too. SUMMARY OF THE PAPER By sequencing a large number of single sperm DNA molecules, the authors showed that meiosis is an important source of germline mutations and consequently gene variation. They found more de novo mutations in molecules with COs then in molecules without a recombination event by amplifying single CO products, using allele-specific PCR, at two previously identified recombination hotspots (HSI and HSII) from a pool of sperm. The binding site used by the human recombination machinery contains PRDM9 (PR Domain Containing 9), very polymorphic in humans. In order to investigate why sequence diversity positively correlates with high recombination activity regions, the authors sequenced 5,796 COs in total, including both reciprocal recombination products from 6 Caucasian donors. As a control they screened …

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