The remarkable abilities of the human brain are distinctive features that set us apart from other animals. However, our understanding of how the brain has changed in the human lineage remains incomplete, but i...
Tue Jun 23, 2020 03:00
Small leucine-rich repeat protein (SLRP) family members contain conserved leucine-rich repeat motifs flanked by highly variable N- and C-terminal regions. Most class II and III SLRPs have tyrosine-rich N-termi...
Tue Jun 23, 2020 03:00
Disentangling the drivers of genetic differentiation is one of the cornerstones in evolution. This is because genetic diversity, and the way in which it is partitioned within and among populations across space...
Mon Jun 22, 2020 03:00
Transposable elements (TEs) are a set of mobile elements within a genome. Due to their complexity, an in-depth TE characterization is only available for a handful of model organisms. In the present study, we performed a de novo and homology-based characterization of TEs in the genomes of mosquito species and investigated their mode of inheritance. More than 40% of the genome of Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus is composed of TEs, varying substantially among Anopheles species...
Tue Jun 23, 2020 03:00
Evolution by natural selection occurs when the frequencies of genetic variants change because individuals differ in Darwinian fitness components such as survival or reproductive success. Differential fitness has been demonstrated in field studies of many organisms, but our ability to quantitatively predict allele frequency changes from fitness measurements remains unclear. Here, we characterize natural selection on millions of Single Nucleotide Polymorphisms (SNPs) across the genome of the annual...
Tue Jun 23, 2020 03:00
Long term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the genetic variation underlying plasticity will also be under selection. These processes could create a landscape of differentiation across populations in traits and their plasticity. Here, we studied drought responses in seedlings of a shrub species from the Cape Floristic Region, the...
Tue Jun 23, 2020 03:00
Spatiotemporal bias in genome sequence sampling can severely confound phylogeographic inference based on discrete trait ancestral reconstruction. This has impeded our ability to accurately track the emergence and spread of SARS-CoV-2, which is the virus responsible for the COVID-19 pandemic. Despite the availability of staggering numbers of genomes on a global scale, evolutionary reconstructions of SARS-CoV-2 are hindered by the slow accumulation of sequence divergence over its relatively short transmission...
Tue Jun 23, 2020 03:00
Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability...
Tue Jun 23, 2020 03:00
SARS-CoV-2 is a once-in-a-century pandemic, having emerged suddenly as a highly infectious viral pathogen. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus isolated from bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor binding domain, or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and...
Tue Jun 23, 2020 03:00
Adaptation of species to new environments is governed by natural selection that discriminates among genetic variations and favors survival of the fittest. Here, we propose climate plays an important role in the evolution of SARS CoV-2 and the spread of COVID-19 all over the world which was previously not known. To understand the climatic factors responsible for shaping the molecular determinants of the novel coronavirus, genotyping SARS CoV-2 across different latitudes and Koppen climate is imperative....
Tue Jun 23, 2020 03:00
Many male animals donate nutritive materials during courtship or mating to their female mates. Donation of large-sized gifts, though costly to prepare, can result in increased sperm transfer during mating and delayed remating of the females, resulting in a higher paternity Nuptial gifting sometimes causes severe female-female competition for obtaining gifts (i.e., sex-role reversal in mate competition) and female polyandry, changing the intensity of sperm competition and the resultant paternity gains....
Tue Jun 23, 2020 03:00
Many models of evolution are implicitly causal processes. Features such as causal feedback between evolutionary variables and evolutionary processes acting at multiple levels, though, mean that conventional causal models miss important phenomena. We develop here a general theoretical framework for analyzing evolutionary processes drawing on recent approaches to causal modeling developed in the machine-learning literature, which have extended Pearl's 'do'-calculus to incorporate cyclic causal interactions...
Tue Jun 23, 2020 03:00
Kin recognition plays a fundamental role in social evolution, enabling active inbreeding avoidance, nepotism, and promoting cooperative social organization. Many organisms recognize kin based on phenotypic similarity, a process called phenotype matching, by comparing information associated with their own phenotype against the phenotypes of conspecifics. However, recent theory demonstrates that to accurately judge phenotypic similarity (and hence, relatedness), individuals require estimates of the...
Tue Jun 23, 2020 03:00
Understanding the rate and pattern of germline mutations is of fundamental importance for understanding evolutionary processes. Here we analyzed 19 parent-offspring trios of rhesus macaques (Macaca mulatta) at high sequencing coverage of ca. 76X per individual, and estimated an average rate of 0.73 x 10-8 de novo mutations per site per generation (95 % CI: 0.65 x 10-8 - 0.81 x 10-8). By phasing 50 % of the mutations to parental origins, we found that the mutation rate is positively correlated with...
Tue Jun 23, 2020 03:00
Telomere length measured in blood cells is predictive of subsequent adult health and survival across a range of vertebrate species. However, we currently do not know whether such associations result from among-individual differences in telomere length determined genetically or by environmental factors early in life, or from differences in the rate of telomere attrition over the course of life. Here, we measured relative leukocyte telomere length (RLTL) multiple times across the entire lifespan of...
Tue Jun 23, 2020 03:00
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species...
Tue Jun 23, 2020 03:00
Frequent fluctuations in sulfate availability rendered syntrophic interactions between the sulfate reducing bacterium Desulfovibrio vulgaris (Dv) and the methanogenic archaeon Methanococcus maripaludis (Mm) unsustainable. By contrast, prolonged laboratory evolution in obligate syntrophy conditions improved the productivity of this community but at the expense of erosion of sulfate respiration (SR). Hence, we sought to understand the evolutionary trajectories that could both increase the productivity...
Mon Jun 22, 2020 03:00
Sex and sexual differentiation are ubiquitous across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to...
Mon Jun 22, 2020 03:00
Ongoing antagonistic coevolution with selfish genetic elements (SGEs) can drive the evolution of host genomes. Here, we investigated whether natural variation allows some Saccharomyces cerevisiae strains to suppress 2-micron (2) plasmids, multicopy nuclear parasites that have co-evolved with budding yeasts. To quantitatively measure plasmid stability, we developed a new method, Single-Cell Assay for Measuring Plasmid Retention (SCAMPR) that measures copy number heterogeneity and 2 plasmid loss in...
Mon Jun 22, 2020 03:00
The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to "study replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies...
Mon Jun 22, 2020 03:00
Abstract Pediocin PA-1 is a bacteriocin that shows strongly anti-microbial activity against some Gram-positive pathogens such as Listeria monocytogenes, Staphylococcus aureus, and Enterococcus faecalis. With the broad inhibitory spectrum as well as high-temperature stability, pediocin has a potential application in the food preservation and pharmaceutical industry. Pediocin has been studied to express in many heterologous expression systems such as Escherichia coli, Saccharomyces...
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Endogenous α1‐antitrypsin levels in the perilymphatic fluid correlates with severity of hearing loss
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