Genomics – Page 3 – Tutorial Genomics, Ecology, Evolution, etc

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 …

Evolution / Genomics / Science / Tutorial

The Amborella Genome and the Evolution of Flowering Plants

May 14, 2014November 8, 2021

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 …

Evolution / Genomics / Human

Great ape genetic diversity and population history

April 12, 2014November 8, 2021

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 …

Evolution / Genomics / Tutorial

Towards discovering the evolutionary history of dogs and dog domestication process

March 13, 2014November 8, 2021

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 …

Adaptation / Evolution / Genomics

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

February 27, 2014November 8, 2021

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 …

Adaptation / Evolution / Genomics / Human

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

June 19, 2013November 8, 2021

“ 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 …

Evolution / Genomics / Selective Sweep

Analyses of pig genomes provide insight into porcine demography and evolution

May 27, 2013November 8, 2021

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. …

Adaptation / Bears / Conservation / Evolution / Genomics / PNAS / Science

The evolutionary history of polar bears

September 18, 2012November 8, 2021

The study of the Ursus lineage, including brown bear (Ursus arctos), black bear (Ursus americanus) and polar bear (Ursus maritimus), provides the ability of addressing the subject of adaptation to extreme (salty and glacial) environments in mammals. Moreover, in last few decades, polar bears won public and media attention, being one of the most charismatic species endangered by global warming and Arctic ice melting. To trace history of innovations and determine response to environmental changes in populations of polar bears, two articles published in Science and Proceedings of the National Academy of Sciences in April and June 2012 provide new data and insights to resolve this question. The absence of fossil of polar bears dating before the late Pleistocene (circa 126 000 years ago) and mitochondrial data, suggesting that polar bear were very closely related to a group of brown bear living in Admiralty, Baranof and Chichagof (ABC) islands in Alaska, previously led to believe that polar bears recently emerged from brown bears. The consequences of this hypotheses would be : Polar bear underwent a very rapid and recent (less than 200 ky ago) adaptation to extreme environment (previously not seen in mammals) Brown bear is a paraphyletic taxon, as …

Adaptation / Evolution / Genomics / Human / Science / Selective Sweep

Classic Selective Sweeps Were Rare in Recent Human Evolution

November 30, 2011November 8, 2021

With the rise of genomics and the availability of whole genome sequences, geneticists hope to be able to understand the recent adaptations humans underwent. Classic selective sweeps, where a beneficial allele arises in a population and subsequently goes to fixation, leave a specific pattern. Indeed, all variation is erased as the selected allele invades the population, and the neighboring neutral variation is also partially swept, with an intensity depending on the linkage with the selected region. An example of classic selective sweep pattern. As the distance from the selected nucleotide increases, diversity increases. Fig. 2 from Hernandez et al. 2011. The selective sweep pattern was used to find evidence for recent adaptation in humans. Many candidate genes for recent adaptation in humans were found. Nevertheless, the preeminence of classic selective sweeps compared with other modes of adaptation (like background selection or recurrent a.k.a. “soft” sweeps) is still unknown. In this paper, the authors claim that classic selective sweeps are in fact a rare event in human recent evolution. They argue that the overall pattern found in genome scan studies can be explained with only nearly neutral mechanisms (neutral evolution plus some purifying selection), without any positive selection going on. This …

Evolution / Genomics / Stickleback

RAD tagging adaptation

November 7, 2011November 8, 2021

The threespine stickleback, Gasterosteus aculeatus, is a small fish that inhabits marine, estuarine and freshwater habitats in the holarctic. It has been previously inferred that in many regions, freshwater populations derived from oceanic ancestors. As soon as the freshwater populations are in different drainage systems, they can be considered as independent of each other. Those natural replicates are one of the reasons why sticklebacks are a model system to study adaptive evolution. Sticklebacks adapt to freshwater habitats in a recurrent manner by modifying several key phenotypic traits. Many studies focused on identifying those traits and measuring their heritability or fitness properties. At the phenotypic level, there is a striking parallelism between derived freshwater population, but what is unclear is how much this parallelism is underlined by genome-wide patterns of parallel evolution. That is the main question that Hohenlohe et al. tackled in their 2010 paper entitled “Population genomics of parallel adaptation in threespine stickleback using RAD Tags”. They compared the genomes of fish originating from three lakes and two coastal saltwater habitats located along Alaska’s southern coast. The three lakes were chosen in different drainage systems to have three independent instances of adaptation to freshwater (and maybe to have an …