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 …

Read More
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 …

Read More
Tutorial

Patterns of population epigenomic diversity

In my point of vue, this paper is interesting because it’s in my domain of interest but very difficult to understand because they put lot of technical word without definition and they say very often see references, as it’s described in this paper making this paper very difficult to understand. Also in this paper, the aim is not very clear and also there is no conclusion. I have the feeling that they don’t know what they can conclure. But I will try to explain in few words the paper… About the introduction. It is well know that natural epigenetic variation provides a source for the generation of phenotypic diversity but it remains unclear how this epigenetic variation contributes to this diversity and the relationship between genetic variation and epigenetic mechanisms. Epigenetic is defined by heritable modification of genes expression. This modification can be heritate during the meiosis and/or mitosis but does not affect a changing in DNA sequences. Epigenetic modifications are mainly defined by cytosine methylation in a DNA level or histone methylation, histone acetylation. In plant including Arabidopsis thaliana model, basically there are 3 different patterns of methylation: methylation in a cytosine in a CG context, on a CHG …

Read More
Evolution / Genomics / Human

Great ape genetic diversity and population history

Humans and chimpanzees share about 95% of their DNA. Having this in mind the recently published paper of Prado-Martinez et al. 2013, focusing at identifying great-ape genetic variation and resolving great-ape population history (based on historical-effective population sizes) reflects a comprehensive catalogue of great-ape genetic diversity to which the human genome can be compared to. On the other hand, the paper provides a framework of genetically resources between and within species/populations that can be used to improve conservation-management and breeding programs for captive and wild great-ape populations, which suffer dramatic reductions in suitable habitat and are highly endangered. 79 wild and captive born individuals were sequenced, including all six great ape species and seven subspecies. Nine human genomes, three african and six non-african individuals complemented the study. Variant-calls were performed using GATK. Totally, they discovered 84 million fixed substitutions and 88.8 million SNPs. In general they provide very good genomic data, using several quality filters and having less than 2% contamination between samples. To test the quality of SNV-calls they applied three independent validation experiments leading to a concordance of 86-99%. A difference compared to previous discussed papers, in the GEE-tutorial, is that in this article they didn’t look at …

Read More
Evolution / Genomics / Tutorial

Towards discovering the evolutionary history of dogs and dog domestication process

In the times in which publishing a paper is not always totally related with the new knowledge´s contribution but leaded by how the researchers sell this new knowledge, it is quite refreshing to find a paper that outstands because deals with a relevant topic, combines several methods, and shows coherence and consistency. The aim of this study was to underlie dog domestication and reconstructing the early evolutionary history of dogs. To accomplish this aim, the authors built a demographic model. As you might know a demographic model involves variables such as the effective population size, bottlenecks, migration and gene flow. Within the main findings, the authors determined some bottlenecks in dogs and wolves. These bottlenecks were stronger in dogs than in wolves, and it showed that the strength of the bottlenecks in previous studies was underestimated. In addition, it was also shown that dogs and wolves had a common ancestral lineage and the tree shows that the dog form a distinct clade than the wolves, none of the wolf lineages from the hypothesized domestication centers is supported as the source lineage for dogs. Moreover, disregarding from where exactly the dogs come from, the dogs diverged from the wolf population in …

Read More
Adaptation / Evolution / Genomics

Genome-wide signatures of convergent evolution in echolocating mammals (Parker et al., 2013)

Phenotype convergence is a fascinating topic in evolution. Usually species evolve by divergence, starting from a common ancestor and then developing different genomic changes that lead to different phenotypes. which are then selected by the environment. Nevertheless, it has been observed in several examples that two or more different species, even very far-related in the phylogenetic tree, appear to have developed, after their divergence, similar phenotypic traits in order to adapt to the environment, therefore leading to an apparent convergence of their branches. The aim of this work is to investigate the hypothesis according to which convergent phenotypes are not just a lucky coincidence produced by different point-mutations occurred in different species, but rather that a convergent phenotype is associated with the same mutation in all the species involved, and that these mutations are not happen by chance but are pushed by adaptation to the environment. In order to do it, this group analysed sequence identities in the genomes of species that developed independently echolocation, certainly a very complex feature that it’s hard to believe it has developed in different species just by chance. The first step was building the gene set to work on. Therefore, they sequenced the genome …

Read More
Tutorial

Articles to discuss in Genomics, Ecology and Evolution spring 2014

The student votes are in (see previous post), and here is the schedule of our 8 papers to discuss this semester in our tutorial Genomes, Ecology, Evolution, etc. Feb 21: Parker et al. 2013 Genome-wide signatures of convergent evolution in echolocating mammals Feb 28: Freedman et al 2014 Genome Sequencing Highlights the Dynamic Early History of Dogs Mar 14: Amborella Genome Project 2013 The Amborella Genome and the Evolution of Flowering Plants Mar 21: Prado-Martinez et al. 2013 Great ape genetic diversity and population history Mar 28: Long et al. 2013 Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden May 2: Linnen et al. 2013 Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene May 9: Schmizt et al. 2013 Patterns of population epigenomic diversity May 16: Corbett-Detig et al. 2013 Genetic incompatibilities are widespread within species (correction: exchange of dates Prado-Martinez / Corbett-Detig)

Read More
Tutorial

Suggested paper list for Spring 2014

A new semester of our tutorial Genomes, Ecology, Evolution, etc. is starting, and this time we’ll ask the students to chose 8 papers among the following 12. Because there are so many interesting recent papers that we couldn’t chose just 8, and especially because we want to hear what the students prefer. Here is the list of suggested papers, in no special order: Freedman et al 2014 Genome Sequencing Highlights the Dynamic Early History of Dogs Amborella Genome Project 2013 The Amborella Genome and the Evolution of Flowering Plants Corbett-Detig et al. 2013 Genetic incompatibilities are widespread within species Moreno-Estrada et al. 2013 Reconstructing the Population Genetic History of the Caribbean Parker et al. 2013 Genome-wide signatures of convergent evolution in echolocating mammals Prado-Martinez et al. 2013 Great ape genetic diversity and population history Orlando et al. 2013 Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse Long et al. 2013 Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden McTavish et al. 2013 New World cattle show ancestry from multiple independent domestication events Linnen et al. 2013 Adaptive Evolution of Multiple Traits Through Multiple Mutations at a Single Gene Schmizt et al. …

Read More
Adaptation / Evolution / Genomics / Human

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

“ Hunting and gathering was humanity’s first and most successful adaptation, occupying at least 90 percent of human history. Until 12,000 years ago, all humans lived this way. ” [The Cambridge Encyclopedia of Hunters and Gatherers. Richard B. Lee and Richard Daly, 1999] Despite of playing a central role in human evolution, African populations remain one of the most understudied groups in human genomics. Furthermore, African human populations preserve the most genetic diversity in the world, and the study of this genetic diversity among the multitude of diverse African ethnic groups is crucial for reconstructing modern human origins. The succession of African hunter-gatherer societies is the longest and one of the most varied known, and African hunter-gatherer populations have some of the deepest divergence time of our species. In this work the genomes of 15 African hunter-gatherers were sequenced at high coverage, expanding the catalog of human genetic variation and increasing the few number of high coverage African genomes that have been analyzed to date. Samples and population features The 15 sequenced genomes were of male individuals coming from three different hunter-gatherer populations: 5 Pygmies from Cameroon, 5 Hadza and 5 Sandawe from Tanzania (Fig. 1). The Hadza and Sandawe …

Read More
Evolution / Genomics / Selective Sweep

Analyses of pig genomes provide insight into porcine demography and evolution

Pig domestication has started over 10 000 years ago and has had important consequences on human life, changing our agricultural and medical practices. Much has been argued on whether pig was domesticated independently across multiple locations or it was adopted by humans only once and then transported elsewhere. Originally, pig (Sus scrofa) has emerged in the South East Asia during the early Pliocene (~5.3–3.5 Myr ago) and then spread across most of the Eurasian continent. Yet, unraveling the true story of the pig domestication has become possible only recently, with a publication of a near complete pig genome by Groenen et al. featuring the Nature front cover in the November issue 7424, 2012.  Genome assembly The research team (RT hereafter) made impressive efforts on genome sequencing and assembly. The genome was sequenced with both BAC and NGS technologies. For NGS the RT used 44bp paired-end Illumina library, which was likely the headliner technology from Illumina at the time of the initiation of the porcine genome project. In total, the RT obtained 2.60 Gb of sequencing data and thanks to BAC could assign scaffolds (2.5 Gb) quite precisely to 20 (18+X and Y) chromosomes, leaving only 212 Mb of unplaced scaffolds. …

Read More