Motivation: Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed. Results: We present FastMulRFS, a polynomial-time method for estimating...
Thu May 07, 2020 03:00
Intra-locus sexual conflict, or sexual antagonism, occurs when alleles have opposing fitness effects in the two sexes. Previous theory suggests that sexual antagonism is a driver of genetic variation by generating balancing selection. However, these studies assume that populations are well-mixed, neglecting the effects of spatial subdivision. Here we use mathematical modelling to show that limited dispersal can fundamentally change evolution at sexually antagonistic autosomal and X-linked loci due...
Thu May 07, 2020 03:00
Mammalian hybrids often show striking asymmetries in their phenotypes both between reciprocal crosses, and between sexes in accordance with Haldane's rule. Hybrid inviability is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted genes is a strong candidate mechanism. However, direct evidence for the involvement of abnormal imprinting and the mechanisms behind this proposed misregulation is limited. We used transcriptome and reduced representation...
Thu May 07, 2020 03:00
Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Post-zygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programmed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. While many high-quality somatic genomes have...
Thu May 07, 2020 03:00
Variation in environmental conditions during development can lead to changes in life-history traits with long-lasting effects. Here, we study environmentally induced variation, i.e. the consequences of potential maternal oviposition choices, in a suite of life-history traits in pre-diapause larvae of the Glanville fritillary butterfly. We focus on offspring survival, early growth rates and relative fat reserves, and pay specific attention to intraspecific variation in the responses (GxExE). Globally,...
Thu May 07, 2020 03:00
Type I and type II keratins are subgroups of intermediate filament proteins that provide toughness to the epidermis and protect it from water loss. In terrestrial vertebrates, the keratin genes form two major clusters, clusters 1 and 2, each of which is dominated by type I and II keratin genes. By contrast, such clusters are not observed in teleost fish. Although the diversification of keratins is believed to have made a substantial contribution to terrestrial adaptation, its evolutionary process...
Thu May 07, 2020 03:00
Intense sexual selection in the form of mate choice can facilitate the evolution of different alternative reproductive strategies. These strategies can be condition-dependent, wherein genetically similar individuals express the strategy based on their condition. Our study shows that baffling, a mate attraction strategy using self-made acoustic amplifiers, employed by male tree crickets, is a classic example of a condition-dependent alternative strategy. We show that less preferred males, who are...
Thu May 07, 2020 03:00
Natural populations can contain multiple types of coexisting individuals. How does natural selection maintain such diversity within and across populations? A popular theoretical basis for the maintenance of diversity is cyclic dominance, illustrated by the rock-paper-scissor game. However, it appears difficult to find cyclic dominance in nature. Why is this case? Focusing on continuously produced novel mutations, we theoretically addressed the rareness of cyclic dominance. We developed a model of...
Thu May 07, 2020 03:00
Estimating species divergence with gene flow has been crucial for characterizing the gray zone of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of divergence times and gene flow often ignores spatial information, for example the formation and shape of hybrid zones. Using population genomic data from the eastern ratsnake complex (Pantherophis obsoletus), we infer phylogeographic groups, gene flow, changes...
Thu May 07, 2020 03:00
Symbiotic relationships affect the fitness and organismal function of virtually all organisms. In many cases, the fitness effects of symbiosis may be beneficial or harmful depending on the environment. The hosts of such symbionts are favored to acquire them only when the symbiont is beneficial. However, it is not clear whether such selection favors vertical or horizontal transmission, both, or neither. To address this question, we model the evolution of transmission mode in a conditional mutualism...
Thu May 07, 2020 03:00
In insect-microbe nutritional symbioses the symbiont supplements the low nutrient diet of the host by producing amino acids and vitamins, and degrading lignin or polysaccharides. In multipartite mutualisms composed of multiple symbionts from different taxonomical orders, it has been suggested that in addition to the genes involved in the nutritional symbiosis the symbionts maintain genes responsible for the production of metabolites putatively playing a role in the maintenance and interaction of...
Thu May 07, 2020 03:00
Elucidating the complex evolutionary armory that mosquitoes deploy against insecticides is crucial to maintain the effectiveness of insecticide-based interventions. Here, we deciphered the role of a 6.5kb structural variation (SV) in driving cytochrome P450-mediated pyrethroid resistance in the malaria vector, Anopheles funestus. Whole genome pooled sequencing detected an intergenic 6.5kb SV between duplicated CYP6P9a/b P450s in pyrethroid resistant mosquitoes through a translocation event. Promoter...
Thu May 07, 2020 03:00
Urbanisation is currently increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment, but the extent to which this adaptation is due to genetic changes is poorly understood. Current evidence for evolution is based on localised studies, and thus lacking replicability. Here, we genotyped great tits (Parus major) from nine cities across Europe, each paired with a rural site, and provide evidence of repeated polygenic responses...
Thu May 07, 2020 03:00
Earth's temperature is increasing due to anthropogenic CO2 emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of an organism's physiology via its influence on metabolic rate and protein structure, therefore genetic adaptation to increased temperature may be much harder to achieve compared to other abiotic stresses. There is still much to be learned about the evolutionary potential for adaptation...
Thu May 07, 2020 03:00
Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of...
Thu May 07, 2020 03:00
Discovering autocatalytic chemistries that can evolve is a major goal in systems chemistry and a critical step towards understanding the origin of life. Autocatalytic networks have been discovered in various chemistries, but we lack a general understanding of how network topology controls the Darwinian properties of variation, differential reproduction, and heredity, which are mediated by the chemical composition. Using barcoded sequencing and droplet microfluidics, we establish a landscape of thousands...
Thu May 07, 2020 03:00
A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris, and seek to understand how these have been influenced by introduction history. We use reduced representation sequencing to determine population structure, and identity Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We...
Thu May 07, 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...
Thu May 07, 2020 03:00
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modelling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate...
Wed May 06, 2020 03:00
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