Homing endonucleases (HE) are enzymes capable of cutting DNA at highly specific target sequences, the repair of the generated double-strand break resulting in the insertion of the HE-encoding gene ("homing" mechanism). HEs are present in all three domains of life and viruses; in eukaryotes, they are mostly found in the genomes of mitochondria and chloroplasts, as well as nuclear ribosomal RNAs. We here report the case of a HE that accidentally integrated into a telomeric region of the nuclear genome...
Tue May 05, 2020 03:00
Emerging infectious diseases due to coronavirus (CoV) infections have received significant global attention in the past decade and have been linked to bats as the original source. The diversity, distribution, and host associations of bat CoVs were investigated to assess their potential for zoonotic transmission. Phylogenetic, network, and principal coordinate analysis confirmed the classification of betacoronaviruses (BetaCoVs) into five groups (2A to 2E) and a potentially novel group, with further...
Tue May 05, 2020 03:00
We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified fourteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer...
Tue May 05, 2020 03:00
Hybridization and introgression are common processes among numerous plant species that present both challenges and opportunities for studies of species delimitation, phylogenetics, taxonomy, and adaptation. Rhus integrifolia and R. ovata are two ecologically important shrubs native to the southwestern USA and Mexico, and are known to hybridize frequently, but the morphological, genetic, and ecological implications of hybridization in these species are poorly studied on a broad geographic scale. Analyses...
Tue May 05, 2020 03:00
Comparisons of vertebrate brain structure suggest a conserved pattern of scaling between components, but also many examples of lineages diverging dramatically from these general trends. Two competing hypotheses of brain evolution seek to explain these patterns of variation by invoking either external processes, such as selection in driving phenotypic change, or internal processes, like developmental coupling among brain regions. Efforts to reconcile these views remain deadlocked, in part due to empirical...
Tue May 05, 2020 03:00
The effects of partner choice have been documented in a large number of biological systems such as sexual markets, inter-specific mutualisms, or human cooperation. By contrast, this mechanism has never been demonstrated in a large number of intra-specific interactions in non-human animals such as collective hunts, although one would expect it to play a role as well. Here we use individual-based simulations to solve this apparent paradox. We show that the conditions for partner choice to operate are...
Tue May 05, 2020 03:00
Synthetic lethal interactions are of paramount importance both in biology and in medicine, and hence increasing efforts have been devoted to their systematic identification. A recent computational study found that synthetic lethal genes tend to be further away in chromosomes than random (i.e. repulsion), which was shown to provide bacterial genomes with greater robustness to large-scale DNA deletions. To evaluate this observation using published experimental data and to test its generalizability...
Tue May 05, 2020 03:00
Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges...
Tue May 05, 2020 03:00
The growing availability of genetic datasets, in combination with machine learning frameworks, offer great potential to answer long-standing questions in ecology and evolution. One such question has intrigued population geneticists, biogeographers, and conservation biologists: What determines intraspecific genetic diversity? This question is challenging to answer because many factors may influence genetic variation, including life history traits, historical influences, and geography, and the relative...
Tue May 05, 2020 03:00
Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees - whose large and undisturbed populations often span a variety of environmental conditions and local habitats - are particularly good models to study this process. Here, we carried out a genome scan for selection through whole-genome sequencing of pools of populations, sampled according to a replicated sampling design, to...
Tue May 05, 2020 03:00
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