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 …

Read More
Adaptation / Genomics / Human

The African Genome Variation Project shapes medical genetics in Africa.

  Despite being the world’s most genetically diverse continent, only a handful of studies attempted to understand the genetic risks for diseases of the African populations. This study shines light not only on the genetic diversity to help learn more about the variants that are associated with malaria and hypertension, but also on the population history across sub-Saharan African populations. Beside the comprehensive map of the African variants obtained from genotypes of 1,481 individuals and whole-genome sequences of 320 individuals, authors offered a design of the array suitable to capturing variants of African populations. Summary and comments of the paper Population structure in SSA. Comparing ~2.2 million variants of 18 ethno-linguistic groups from sub-Saharan Africa (SSA), authors found modest differentiation among SSA populations (mean pairwise Fst = 0.019) and among Niger-Congo language groups (mean pairwise Fst = 0.009). In the article, authors suggested that the modest differentiation among Niger-Congo language group showed evidence for ‘Bantu expansion’. However, the Fig1.a shows sample distribution mostly next to the Western, East and South African coasts, rather then inside of continent where the Bantu expansion occurred, therefore indicating the sampling bias. Furthermore, the authors found a high proportion of unshared and novel variants in …

Read More
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 …

Read More
Paper List

Tutorial program Spring 2015: Genomics, ecology, evolution, etc

So here are the papers chosen for our tutorial this Spring (from the list here), in the ordre in wich they will be discussed: Zhan et al 2014 The genetics of monarch butterfly migration and warning colouration Nature 514: 317–321 Foote et al 2015 Convergent evolution of the genomes of marine mammals Nature Genetics doi:10.1038/ng.3198 Artieri and Fraser 2014 Evolution at two levels of gene expression in yeast Genome Res 24: 411-421 Gurdasani et al 2015 The African Genome Variation Project shapes medical genetics in Africa Nature 517: 327–332 Brawnd et al 2014 The genomic substrate for adaptive radiation in African cichlid fish Nature 513: 375–381 Arbeithuber et al 2015 Crossovers are associated with mutation and biased gene conversion at recombination hotspots PNAS 112: 2109–2114 Poelstra et al 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410-1414 Lamichhaney et al 2015 Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature 518: 371–375 An exiting semester in perspective, full of genomes, ecology and evolution.

Read More
Paper List

Suggested paper list for Spring 2015

Like last Spring, we are offering the students following our tutorial Genomes, Ecology, Evolution, etc. the opportunity to chose the 8 papers which we will discuss. Here is the list of papers which we propose: Lamichhaney et al 2015 Evolution of Darwin’s finches and their beaks revealed by genome sequencing Nature 518: 371–375 Poelstra et al 2014 The genomic landscape underlying phenotypic integrity in the face of gene flow in crows Science 344: 1410-1414 Zhan et al 2013 Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle Nature Genetics 45: 563–566 Foote et al 2015 Convergent evolution of the genomes of marine mammals Nature Genetics doi:10.1038/ng.3198 Arbeithuber et al 2015 Crossovers are associated with mutation and biased gene conversion at recombination hotspots PNAS 112: 2109–2114 Zhan et al 2014 The genetics of monarch butterfly migration and warning colouration Nature 514: 317–321 Villar et al 2015 Enhancer Evolution across 20 Mammalian Species Cell 160: 554–566 Artieri and Fraser 2014 Evolution at two levels of gene expression in yeast Genome Res 24: 411-421 Brawnd et al 2014 The genomic substrate for adaptive radiation in African cichlid fish Nature 513: 375–381 Gurdasani et al 2015 The African Genome …

Read More
Adaptation

Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation

Parallel evolution provides evidence for evolution by natural selection and can cause repeated divergence at specific genes. The parallel evolution of phenotypic traits under similar environmental pressures was estimated to cover almost half of same genomic regions. However, the genomic footprints of parallel evolution on parallel speciation is not clearly known yet. In a recent study, Víctor Soria-Carrasco et al. investigated the natural selection’s role in parallel speciation with stick insect populations. Herbivorous stick insect (Timema cristinae) is an endemic species to California and adapted to different host plants, Adenostoma fasciculatum and Ceanothus spinosus. Researchers investigated the whole genome divergence by parallel speciation in a nice experimental set up with this species. T.cristinae individuals were sampled from four replicate population pairs where 3 of them were adjacent and one was 6.4 km far away. They annotated the reference genome for the species and resequenced 160 individuals sampled from field transplant experiment. In the first part of the study, the data obtained was used to analyse the effects of adaptation on genomic divergence in different scales and aspects. The results showed that the divergence between ecotype pairs varied geographically. Principal components analysis and phylogenomic trees clustered the individuals by geography, not …

Read More
Genomics / Human / Primates

Gibbon genome and the fast karyotype evolution of small apes

All contents refer to the original paper (Carbone et al. Nature. 2014 Sep 11;513(7517):195-201) Summary and personal comments This paper concerns a study of gibbon karyotype in the perspective of their divergent evolution from ancestral primates. Gibbons, small monkeys living in South-East Asia, differ from other primates, such as great apes and Old World monkeys, for a surprising number of chromosomal rearrangements. The authors aimed to study the mechanisms underlying such an important plasticity in gibbon genome gibbon. 1) The authors sequenced and assembled the genome of a white-cheeked gibbon female (Nomascus leucogenys), ordered in 26 chromosomes (against human reference), and analyzed gibbon-human synteny breakpoints (= rupture of synteny=physical co-localization of genetic loci on the same chromosome within gibbon and human). Fig 2a shows Oxford plots for human (axys y) versus other primates chromosomes (axys x), expressed in terms of collinear blocks of > 10 Mb. It is evident from the graphic that, when compared to other primates, gibbons present the highest rate of chromosome rearrangements, graphically visualized as a scattered instead of a linear plot (Fig2a), in particular large-scale reshuffling (as shown in Fig 2b, right part of the graphic). Examples of synteny breakpoints, such as chromosomal inversion, are shown in …

Read More
Tutorial

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits.

All content refers the original paper (Moreno Estrada et al. Science 2014) Summary and personal comments This paper is about genetic diversity among Native Mexico populations Mexico is an interesting region/subject to study human genetic diversity since it has a complex history, with various civilizations contributing at various degree to the present-day population. Identification of different Native Mexican populations and analysis of their genetic relationships. The authors studies 1 million SNPs (single nucleotide polymorphisms) of 511 native Mexico individuals identified from 20 different populations covering most geographical regions of Mexico. 1) They performed a PCA (principal component analysis) and identified different clustering of indigenous populations; each cluster was geographically-well-defined across the country and followed a northwest-southeast axis. Fig S1(A) shows the PCA based on native Mexican individuals, when analyzing ancestry from Native Mexicans, Europeans and Africans (left) or analyzing only native Mexicans after removal of Africans and Europeans (right). You can observe that PC1 differentiates Europeans and Africans ancestry from Native Mexicans (left) and that it separates different Native Mexicans subpopulations (right). (B) shows PCA based on admixed Mexican samples from cosmopolitan individuals from different Mexico states combined with ancestral reference samples (African, European and Native Mexican). You can notice that PC1 …

Read More
Genomics / Human / Science

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

Mexico, hosted many cultures such as the Olmec, the Toltec, the Maya and the Aztec, conquered and colonized by the Spanish Empire in 1521. The country harbors a large source of pre-Columbian diversity and their genetic contributions to today’s population. In a recent paper, Moreno-Estrada et al. 2014 performed a detailed genetic study of Mexican genetic diversity. The results showed the genetic stratification among indigenous populations and an association between subcontinental ancestry and lung function. In the first part of the study, to estimate the genetic diversity, researchers examined autosomal single-nucleotide polymorphisms for more than 500 Native Mexican individuals from all around Mexico. Statistical analysis of genomic data showed that some populations within Mexico are more differentiated than European and East Asian populations. This extreme differentiation thought to be a result of isolation followed by a bottleneck and small effective population sizes. The data was analyzed in various ways (ROH and IBD analysis, PCA etc.) and revealed the population substructure of Mexico. In all of the analysis, the results confirmed that Seri (northernmost) and Lacandon (southernmost) have the highest level of differentiation. Also, the differentiation between Seri and Lacandon was greater than average differentiation between human populations. The relationships between …

Read More
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 …

Read More