The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We examined 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex microsatellite genotyping (SSR) to identify FAM-1 and the mtDNA lineage (Herb-1/ Ia) present in historic samples. FAM-1 was detected in approximately 73% of the historic specimens and was found on 6 continents. The US-1 genotype was found in only 27% of the...
Tue Aug 25, 2020 03:00
Since its inception, the investigation of protein divergence has revolved around a more or less constant rate of sequence information decay that led to the formation of the molecular clock model for sequence evolution. We use here the classical approach of amino acid sequence comparisons to examine the overall divergence of proteins and the possibility of lineage-specific acceleration. By generating and analysing a high-confidence dataset of 13,160 syntenic orthologs from four ape species, including...
Tue Aug 25, 2020 03:00
We investigate the evolutionary rescue of a microbial population in a gradually deteriorating environment, through a combination of analytical calculations and stochastic simulations. We consider a population destined for extinction in the absence of mutants, which can only survive if mutants sufficiently adapted to the new environment arise and fix. We show that mutants that appear later during the environment deterioration have a higher probability to fix. The rescue probability of the population...
Tue Aug 25, 2020 03:00
Apart from discriminative models for classification and object detection tasks, the application of deep convolutional neural networks to basic research utilizing natural imaging data has been somewhat limited; particularly in cases where a set of interpretable features for downstream analysis is needed, a key requirement for many scientific investigations. We present an algorithm and training paradigm designed specifically to address this: decontextualized hierarchical representation learning (DHRL)....
Tue Aug 25, 2020 03:00
The relationship between embryonic development and evolution historically investigated based on embryo morphology, could now be reassessed using mRNA expression endophenotype. Here, we investigated the applicability of von Baer's and Haeckel's arguments at mRNA expression level by comparing the developmental changes among nine evolutionarily distinct species: from oyster to mouse. In agreement with models based on von Baer's postulates, up to 36% of mRNA expression indicated nearly linear conservation...
Tue Aug 25, 2020 03:00
The environment organisms experience during development can have effects which carry over into their adult lives. These developmental environments may not only affect adult traits at a given point in time, but also how these traits change with age. Generally, stressful developmental environments can lead to sub-optimal adult fitness traits and a faster deterioration of these traits with age. But whether these environments affect how performance traits change with age or whether they affect males...
Tue Aug 25, 2020 03:00
Hybridization occurs differentially across the genome in a balancing act between selection and migration. With the unprecedented resolution of contemporary sequencing technologies, selection and migration can now be effectively quantified such that researchers can identify genetic elements involved in introgression. Furthermore, genomic patterns can now be associated with ecologically relevant phenotypes, given availability of annotated reference genomes. We do so in North American box turtles (Terrapene)...
Tue Aug 25, 2020 03:00
Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of...
Mon Aug 24, 2020 03:00
Major Histocompatibility Complex (MHC) genes encode for proteins that recognize foreign protein antigens to initiate T-cell mediated adaptive immune responses. They are often the most polymorphic genes in vertebrate genomes. How evolution maintains this diversity is still an unsettled issue. Three main hypotheses seek to explain the maintenance of MHC diversity by invoking pathogen-mediated selection: heterozygote advantage, frequency-dependent selection, and fluctuating selection across landscapes...
Mon Aug 24, 2020 03:00
How gene expression can evolve depends on the mechanisms driving gene expression. Gene expression is controlled in different ways in different developmental stages; here we ask whether different developmental stages show different patterns of regulatory evolution. To explore the mode of regulatory evolution, we used the early stages of embryonic development controlled by two different genomes, that of the mother and that of the zygote. During embryogenesis in all animals, initial developmental processes...
Mon Aug 24, 2020 03:00
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