Cancer genomes exhibit surprisingly weak signatures of negative selection. This may be because tumors evolve under weak selective pressures (weak selection) or because genome-wide linkage in cancer prevents most deleterious mutations from being removed due to Hill-Robertson interference3 (inefficient selection). The weak selection model argues that most genes are only important for multicellular function and that selection acts only on a subset of essential genes. In contrast, the inefficient selection...
Sun Aug 23, 2020 03:00
Resurrection studies are a useful tool to measure how phenotypic traits have changed in populations and they allow testing whether these traits modifications are a response to selection caused by an environmental change. Selfing, through its reduction of effective size, could challenge the ability of a population to adapt to environmental changes. Here, we used a resurrection study to test for adaptation in a selfing population of Medicago truncatula, by comparing the genetic composition and flowering...
Sun Aug 23, 2020 03:00
Target enrichment is becoming increasingly popular for phylogenomic studies. Although baits for enrichment are typically designed to target single-copy genes, paralogs are often recovered with increased sequencing depth, sometimes from a significant proportion of loci. Common approaches for processing paralogs in target enrichment datasets include removal, random selection, and manual pruning of loci that show evidence of paralogy. These approaches can introduce errors in orthology inference, and...
Sun Aug 23, 2020 03:00
Background: Orthologs diverge after speciation events and paralogs after gene duplications. It is thus expected that orthologs would tend to keep their functions, while paralogs could be a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS) as proxy for functional divergence. We used four working definitions of orthology, including reciprocal best...
Sun Aug 23, 2020 03:00
Recent results comparing the temporal program of genome replication of different yeast species support the scenario that the evolution of replication timing program could be mainly driven by correlated acquisition and loss events of active replication origins. Using these results as a benchmark, we develop an evolutionary model defined as birth-death process for replication origins, and use it to identify the selective pressures that shape the replication timing profiles. Comparing different evolutionary...
Sun Aug 23, 2020 03:00
Competition within and between species can have large effects on fitness and may therefore drive local adaptation. However, these effects are rarely tested systematically, or considered when predicting species responses to environmental change. We used a field transplant experiment to test the effects of intra and interspecific competition on fitness across the ecological niches of two rainforest Drosophila species that replace each other along an elevation gradient. For the species with the broader...
Sun Aug 23, 2020 03:00
Infamously, the presence of honest communication in a signaling environment may be difficult to reconcile with small (relative) signaling costs or a low degree of common interest between sender (beneficiary) and receiver (donor). This paper posits that one mechanism through which such communication can arise is through inattention on the part of the receiver, which allows for honest communication in settings where--should the receiver be fully attentive--honest communication would be impossible....
Sun Aug 23, 2020 03:00
A detailed derivation of the f-statistics formalism is made from a geometrical framework. It is shown that the f-statistics appear when a genetic distance matrix is constrained to describe a four population phylogenetic tree. The choice of genetic metric is crucial and plays an outstanding role as regards the tree-like-ness criterion. The case of lack of treeness is interpreted in the formalism as presence of population admixture. In this respect, four formulas are given to estimate the admixture...
Sun Aug 23, 2020 03:00
During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European sub-species Arabidopsis lyrata ssp petraea, which expanded its Northern range after the last glaciation. We document a sharp decline in effective population size in the range-edge population and observe that non-synonymous...
Sun Aug 23, 2020 03:00
Understanding how genomic and expression variation is linked to adaptation of plants to local environments is fundamental to the fields of evolutionary biology and species conservation. Using locally adapted Arabidopsis thaliana Italy and Sweden populations, we examine how variation in gene expression under control and cold acclimation conditions, is linked to allele frequency differentiation (AFD); linkage disequilibrium (LD); selective constraint at nonsynonymous sites; and genetic-tradeoff quantitative...
Sun Aug 23, 2020 03:00
Humans rely on sweating to cool off and have the highest eccrine sweat gland density among mammals. We investigated whether altered regulation of the Engrailed 1 (EN1) gene, the levels of which are critical for patterning eccrine glands during development, could underlie the evolution of this defining human trait. First, we identify five EN1 candidate enhancers (ECEs) using comparative genomics and validation of enhancer activity in mouse skin. The human ortholog of one ECE, hECE18, contains multiple...
Sun Aug 23, 2020 03:00
Some multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungus Neurospora crassa has demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of dishonest exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia...
Sat Aug 22, 2020 03:00
Viruses repurpose the host molecular machinery for their own proliferation, block host antiviral factors and recruit host proteins for processes essential for virus propagation. Cross-species transmission requires that the virus can establish crucial interactions in the two different environments of the new and the old hosts. To explore the molecular mechanisms behind host promiscuity, we challenged a lytic phage to propagate in a host in which a protein essential for the assembly of a functional...
Sat Aug 22, 2020 03:00
Diet plays a significant role in maintaining lifelong health. In particular, lowering the dietary protein : carbohydrate ratio can improve lifespan. This has been interpreted as a direct effect of these macronutrients on physiology. Using Drosophila melanogaster, we show that the role of protein and carbohydrate on lifespan is indirect, acting by altering the partitioning of limiting amounts of dietary sterols between reproduction and lifespan. Shorter lifespans in flies fed on high protein : carbohydrate...
Fri Aug 21, 2020 03:00
In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. These lineages and countless others representing a huge diversity of forms and lifestyles all belong to four algal groups: cryptophytes, ochrophytes, haptophytes, and myzozoans. Despite the ecological importance of these groups, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. Over the last years,...
Fri Aug 21, 2020 03:00
Inbreeding depression can be estimated by correlating heterozygosity with fitness components, but such heterozygosity-fitness correlations are typically weak. For over ten years, we studied a population of the self-incompatible plant, Antirrhinum majus, measuring heterozygosity and fitness proxies from 22,353 plants. Using a panel of 91 SNPs, we find that relatedness declines rapidly over short spatial scales. Individual heterozygosity varies more between individuals than expected, reflecting identity...
Fri Aug 21, 2020 03:00
Phenotypic reconstruction of the last universal common ancestor reveals a complex cell [NEW RESULTS]
A fundamental concept in evolutionary theory is the last universal common ancestor (LUCA) from which all living organisms. While some authors have suggested a relatively complex LUCA 1 it is still widely assumed that LUCA must have been a very simple cell and that life has subsequently increased in complexity through time 2,3. However, while current thought does tend towards a general increase in complexity through time in Eukaryotes 4,5, there is increasing evidence that bacteria and archaea have...
Sun Aug 23, 2020 03:00
The uniquely enlarged noses of male proboscis monkeys (Nasalis larvatus) are prominent adornments, and a sexually selected male masculine trait. A recent study showed the significant correlations among nose, body, and testis sizes and the clear association between nose size and the number of females in a male's harem. However, to date, the analyses of other common male traits, i.e., canines, are lacking. Whereas male nose size had a positive correlation with body size, we unexpectedly found a negative...
Fri Aug 21, 2020 03:00
Collective behavior emerges from local interactions between group members, and natural selection can fine-tune these interactions to achieve different collective outcomes. However, at least in principle, collective behavior can also evolve via changes in group-level parameters. Here, we show that army ant mass raiding, an iconic collective behavior in which many thousands of ants spontaneously leave the nest to go hunting, has evolved from group raiding, in which a scout directs a much smaller group...
Thu Aug 20, 2020 03:00
The evolution of mate preferences may depend on natural selection acting on the mating cues and on the underlying genetic architecture. While the evolution of assortative mating with respect to locally adapted traits has been well-characterized, the evolution of disassortative mating is poorly characterized. Here we aim at understanding the evolution of disassortative mating for traits under strong balancing selection, by focusing on polymorphic mimicry as an illustrative example. Positive frequency-dependent...
Sun Aug 23, 2020 03:00
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