Evolution

Adaptation / Evolution / Genomics

Evolution at two levels of gene expression in yeast

Protein abundances mainly determined by the balance of transcriptional and translational regulation. Because of the limited technology for the translational research, however, gene expression evolution was based almost entirely on studies of transcriptional regulation. With the quickly development of ribosome profiling–isolating and sequencing short fragments of mRNA bound by actively translating ribosomes–now we can study translational regulation conveniently and efficiently. Simultaneous detection of regulatory divergence at two levels In this paper, firstly, in order to assess the relative contributions of regulatory elements evolution to the changes in mRNA abundance and translation rate, the authors applied ribosome profiling and RNAseq to two species of Saccharomyces yeast (S. cerevisiae and  S. paradoxus )and their interspecific hybrid (figure 1). Within hybrids, both alleles share the same trans-acting cellular environment. Therefore, different mRNA abundance or translation efficiency is caused by cis-regulatory divergence. By applied these methods, the authors showed cis-regulatory divergence in both transcription and translation are abundant, almost 35% orthologs have significant divergence in translational efficiency, as compared with 61% with significant divergence in mRNA abundance. Because they identified cis-regulatory elements change at two regulatory levels simultaneously, an interesting question will be asked is whether changes at the two levels could be reinforcing (acting at the same direction) or opposing (acting in opposite directions). Compared …

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Evolution / Genomics

Convergent evolution of the genomes of marine mammals

Convergent evolution is defined by the independent evolution of similar traits in different lineages, in order to adapt to similar environmental conditions. Examples of this phenomenon include adaptations to altitude in humans, independent evolution of flight in birds and bats or the multiple evolution of C4 carbon fixation in plants. Yet, the molecular bases of convergent evolution are often lacking. In this paper, authors shed light on the genomic basis of a classical example of convergent evolution, the adaptation to marine life. Mammals evolved multiple independent times to inhabit the marine environment (Fig 1). Species from three different clades share similar phenotypic adaptations involved in communication, locomotion, thermal regulation, buoyancy… Cetaceans (whales and dolphins) and sirenians (manatees) emerged during the Eocene while pinnipeds (walruses) appeared during Miocene. In this paper, Foote and colleagues investigated the convergent evolution of the genomes of marine mammals at two levels. First, they sought for protein coding genes evolving under positive selection across the three lineages. Second, they studied the convergence of amino acid substitutions within these positively selected genes. Detection of protein coding genes under positive selection The authors performed de novo assembly of the genomes of killer whale, manatee and walrus and completed …

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Conservation / Evolution / Genomics

The genetics of monarch butterfly migration and warning colouration

The monarch butterfly (Danaus plexippus) has a large distribution worldwide. It occurs in North, Central, and South America, Caribbean, and it has recently dispersed to other locations, such as Oceania and Africa. Two traits of this butterfly are incredibly intriguing: their annual migration in North America, and their warning coloration. Among the populations spread out around the globe, only the population of North America has a migrant behavior. Monarchs migrate thousands of kilometers from northern United States and southern Canada to overwinter in Mexico. In Spring, they begin mating and flying back to the North. This long annual migration process happens throughout the life time of more than one generation. Regarding their warning coloration, what is intriguing about it is the occurrence of an intense polymorphism in this trait when compared to other butterflies of the same genus. Monarchs and other Danaus butterflies have by default bright orange wings. This bold coloration warns predators about their toxicity. However, in a monarch population from Hawaii, some butterflies have white instead of orange wings. In this paper, authors investigate, through comparative population genomics, the genetic base for such migration and color polymorphisms of the monarch butterfly. The migration of the monarchs By …

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Evolution / Genomics / Human

Gibbon genome and the fast karyotype evolution of small apes

Gibbons are small apes living in southeast Asia that diverged between Old Monkeys and great apes and whose most distinctive feature is the high rate of evolutionary chromosomal rearrangement. The aim of this study was threefold: First, the authors looked into the mechanisms that could explain the extraordinary rate of chromosomal rearrangement of gibbons. Second, they explored their evolutionary history to shed light into the timing and order of splitting of the gibbon genera. Third, they looked into the functional evolution of genes that might be associated with gibbon-specific adaptations. To do so, they sequenced and assembled the genome of the white-cheeked gibbon (Nomascus leucogenys), showing that the quality and statistics of the assembled genome was comparable to that of other primates (Table 1 and Fig.S1).   Chromosomal rearrangement and LAVA insertions Chromosomal rearrangement was confirmed by comparing the karyotype of the assembled Gibbon genome (Nleu1.0) to that of human. Figure 2A shows the extraordinarily high number of rearrangements compared to other primates. Furthermore these reshuffling events affect long stretches of chromosomes (displayed in Fig.2A are collinear blocks larger than 10Mb), whereas short-scale rearrangement events occur at levels comparable to other primates (Fig.2B). Since the four Gibbon genera of this …

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Adaptation / Evolution / Fish / Genomics / Science

Electrogenic fish – what’s in charge of the charge?

Electric organs – organs that are capable of creating and discharging electricity – have evolved independently in at least six different lineages of fish (Torpediniformes, Rajiformes, Mormyroidea, Euteleostei, Siluriformes, Gymnotiformes) and play an important role in communication, navigation, defense and predation. To investigate whether the convergent evolution of these organs has a common genetic basis, Jason Gallant and his coworkers studied the transcriptome of five species of electrogenic fish in three different lineages: Electrophorus electricus, Sternopygus macrurus, Eigenmannia virescens (Gymnotiforme), Malapterurus electricus (Siluriforme) and Brienomyrus brachyistius (Mormyroidea). Electric organs are comprised of arrays of electrocytes – asymmetric cells that are enriched in cation-specific ion channels on one and sodium pumps on the opposing side. The resulting ion flux slowly charges the electrocyte membrane and upon activation by a neuronal stimulus, the voltage is discharged, generating an electrical pulse from the fish. Although the morphology of electric organs and electrocytes varies substantially amongst these species, they are all muscle-derived tissue and originate developmentally from muscle progenitor cells. Since this evolution of muscular to electrogenic tissue has occurred several times independently, the authors investigated, whether the underlying genetic mechanisms are shared. To address this question, Gallant et al. first sequenced and assembled …

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Evolution / Science

Genomic basis of the convergent evolution of electric organs

Electric organs in fish have evolved independently in six lineages and are an interesting example of convergent evolution. However, the genetic basis underlying the convergence of this trait is poorly understood. By sequencing and assembling the transcriptomes from the electric organ (EO) and skeletal muscle of three of those lineages of electric fish, Galant et al. showed the presence of shared patters of gene expression in pathways related to differentiation from muscle cell, increased cell size, reduced contractility and increased excitability. Paper summary Electric organs allow fish to communicate, navigate and cope with predators and preys. They have evolved rather recently: less than 100 million years ago in the Cenozoic (as shown in Figure 1A). Importantly they have evolved independently in at least six taxonomically diverse lineages, constituting a clear example of convergent evolution. Electrocytes are thought to be developmentally derived from myogenic precursors and are morphologically very different among fish lineages. This is illustrated in Figure 1B, where the authors show micrographs of electrocytes in two lineages of electric fish: gymnotiformes, such as Electrophorus electricus and Sternopygus macrurus, present electrocytes devoid of sarcomere, the contractile unit of muscle cells. In contrast, in mormiroids like Paramormyrops kingsleyae a disorganized and …

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Adaptation / Evolution / Genomics

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

The polar bear (Ursus maritimus) is a carnivorous species which is closely related to the brown bear (Ursus arctos) and is adapted to the severe living conditions of the High Arctic due to the great physiological changes happened during evolutionary speciation. Despite numerous researches it is still unclear when exactly this two species diverged. That’s why, Liu with colleagues in their work tried to determine a reliable divergence time of polar bear and brown bear populations and investigated demographic history as well as selection and adaptation of polar bears. Summary By applying a population genomic framework the authors analyzed 89 complete nuclear genomes of polar bears and brown bears. They showed that two species diverged 479-343 thousand years ago (kya) and found 16 genes under strong positive selection on the polar bear in comparison with the brown bear. They analyzed more precisely nine of these genes that are known to be associated with high risk of cardiomyopathy and vascular diseases in humans. However, in polar bears these genes are responsible for an important reorganization of the cardiovascular system which allowed them to survive in extreme life’s conditions within Arctic Circle (e.g. very low temperatures, high physical activity in cold water, high …

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Conservation / Evolution / Genomics

Comparative analysis of regulatory information and circuits across distant species

Development and homeostasis of all organisms is tightly controlled by transcription regulatory factors that are often highly conserved across deep phylogenies. However, it is unclear to what extend the basic components of these networks (e.g. network motifs and structure, binding frequencies, factor interactions) are preserved in distantly related species. Boyle and colleagues try to shed light on this question in a recent study published by nature in August 2014 (doi:10.1038/nature13668). Paper summary The scientists compare genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors in different cellular contexts (developmental stages and tissues) to identify the common properties of their underlying networks (data overview shown in Figure 1, taken from original publication). As already described in smaller-scale studies, they see that DNA binding motifs of orthologous regulatory factors remain similar in distantly related species. Furthermore, these orthologous factors are expressed in similar contexts. However, expression of the orthologous targets is only weakly correlated suggesting an extensive re-wiring of regulatory networks across human, worm and fly. Reconstructions of regulatory networks point to a higher number of master-regulators and upward-flowing edges in human when compared to worm and fly. In all three species, the most abundant network motif …

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Evolution / Genomics / Science / Tutorial

The Amborella Genome and the Evolution of Flowering Plants

Amborella trichopoda, an endemic species to New Caledonia, is the most early-diverging taxa of flowering plants (angiosperms, Figure 1). As such, the sequencing of its genome was of considerable interest for the investigation of the emergence and evolution of this highly diverse lineage presenting at least 350’00 species. In this work, the Amborella genome project (http://www.amborella.org/) reports the draft genome sequence for A. trichopoda. Notably, it was used as reference for the reconstruction of genomic features and architecture of the most recent common ancestor of living angiosperms, the investigation of gene families specific to flowering plants, and the investigation of the Amborella population structure. Genome structure The identification of frequent duplicated collinear genes (Figure 2a) within A. trichopoda genome provides evidence of an a ancient whole genome duplication (WGD). WGD is known to be a pervasive feature in the evolution of plants, with modern plants frequently presenting traces of multiple past duplication events. Thus, a comparison with Vitis vinifera (grape) showed that the genome of A. trichopoda is almost entirely covered by three syntenic grape regions (Figure 2b and 2c). This 1:3 relationship between those two genomes indicates that the WGD detected in A. trichopoda occurred in the common ancestor …

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Adaptation / Evolution / Selective Sweep

Single and independent mutations lead to an adaptive and complex color phenotype in deer mice living on the light-colored soils of the Nebraska Sand Hills

Pleiotropy of genes is often the main solution to explain genetic basis of complex phenotypes (i.e., those composed of multiple traits). But dissection of those genes or loci are rarely studied, and it remains unclear which of single pleiotropic mutations or multiple mutations with independent effects are responsible to elaborate complex phenotypes. Linnen et al. are interested in coloration of the deer mice (Peromyscus maniculatus) present on the light-colored soils of the Nebraska Sand Hills. Adaptation for crypsis is the strongest hypothesis to explain prevalence of the light morph compared to the black morph,  and they wanted to dissect the genetic basis of this adaptation. This study is composed of two main parts : first to understand and to evaluate the complexity of coloration phenotype and then to find the mutations responsible of those variation in traits and on which morph selection is acting on. First of all, they implemented an experimentation with plasticine models to count the number of attacks on each coloration morph. As they expected, statistical test reveals that the dark models are significantly more attacked than light models. Closer inspection reveals multiple pigmentation traits and pattern that differ between the light and the dark morph to compose complex coloration …

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