Sign inversion in selection on ploidy

Ploidy - the number of homologous chromosome sets in a cell - is remarkably variable across the natural world, yet the evolutionary processes that have resulted in such diversity remain poorly understood. Here we use stochastic agent-based simulations to model ploidy evolution under the influence of indirect selection, i.e., selection mediated solely by statistical associations with fitness-affecting mutations. We find that in non-equilibrium asexual populations, the sign of selection on ploidy can change with population size - a phenomenon we have previously termed sign inversion. In large populations, ploidy dynamics are dominated by indirect effects of selection on beneficial mutations, which favors haploids over diploids. However, as population size declines, selection for beneficial mutations is neutralized by random genetic drift before drift can overwhelm selection against the cost of the deleterious mutational load. As a result, in small populations indirect selection is dominated by the cost of the deleterious load, which favors diploids over haploids. Our work adds to the growing body of evidence challenging established evolutionary theory that population size can affect only the efficiency, but not the sign, of natural selection.

A new tribe, two new genera and three new species of Cypridopsinae (Crustacea, Ostracoda, Cyprididae) from Brazil

We describe one new tribe, two new genera and three new species of the subfamily Cypridopsinae Kaufmann, 1900 from Brazilian floodplains. Brasilodopsis gen. nov. belongs in the nominal tribe Cypridopsini, and both new species in this new genus were found in both sexual and asexual populations. Brasilodopsis baiabonita gen. et sp. nov. has a wide distribution and was found in three of the four major Brazilian floodplains. Brasilodopsis amazonica gen. et sp. nov. was recorded only from the Amazon floodplain. Brasilodopsis baiabonita gen. et sp. nov. has a subtriangular shape in lateral view, whereas Brasilodopsis amazonica gen. et sp. nov. is more elongated and has more rounded dorsal margins in both valves, as well as more pronounced external valve ornamentation, consisting of rimmed pores in shallow pits. Paranadopsis reducta gen. et sp. nov. was found in asexual populations in the Upper Paraná River floodplain only and differs from other Cypridopsinae in the more elongated carapace, an A1 with strongly reduced chaetotaxy (hence the specific name) and the total absence of caudal rami in females. Because of these strong reductions in valve and limb morphology, Paranadopsini trib. nov. is created within the Cypridopsinae for this intriguing new genus and species.

Removal of beneficial insertion effects prevent the long-term persistence of transposable elements within simulated asexual populations

Background Transposable elements are significant components of most organism’s genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even in the absence of traditional molecular evolutionary explanations, transposon proliferation may occur through a process known as ‘transposon engineering’. However, their model used a fixed beneficial transposon insertion frequency of 20%, which we believe to be unrealistically high. Results Reducing this beneficial insertion frequency, while keeping all other parameters identical, prevented transposon proliferation. Conclusions We conclude that the author’s original findings are better explained through the action of positive selection rather than ‘transposon engineering’, with beneficial insertion effects remaining important during transposon proliferation events.

On two new species of Cypricercus Sars, 1895 (Crustacea, Ostracoda) from Brazil with a discussion on the taxonomy of the genus

We describe two new species of Cypricercus, Cypricercus alfredo sp. nov. and Cypricercus tiao sp. nov., and briefly redescribe the female of Cypricercus centrurus (Klie, 1940) from Brazilian floodplains. Both new species have the elongated carapace which is characteristic of the genus. Cypricercus alfredo sp. nov. was found as both sexual and asexual populations and has a posterior spine on the right valve and differs from the Brazilian C. centrurus by the position and the size of spine and the size and shape of the carapace. Cypricercus tiao sp. nov. was found as one asexual population only and lacks a posterior spine on the right valve. Cypricercus populations in Brazil mostly consist exclusively of asexual females, but some sexual populations and populations with mixed reproduction can also be found. This genus occurs primarily in the Southern Hemisphere, but some species can also be found in the southern part of North America and in India. We also present a re-appraisal of all species presently allocated to the genus, primarily based on original descriptions.

Simulating Evolution in Asexual Populations with Epistasis

I show how to use OncoSimulR, software for forward-time genetic simulations, to simulate evolution of asexual populations in the presence of epistatic interactions. This chapter emphasizes the specification of fitness and epistasis, both directly (i.e., specifying the effects of individual mutations and their epistatic interactions) and indirectly (using models for random fitness landscapes).

Molecular signatures of resource competition: clonal interference drives the emergence of ecotypes

Microbial ecosystems harbor an astonishing diversity that can persist for long times. To understand how such diversity is generated and maintained, ecological and evolutionary processes need to be integrated at similar timescales, but this remains a difficult challenge. Here, we extend an ecological model of resource competition to allow for evolution via de novo mutation, focusing on large and rapidly adapting asexual populations. Through numerical and analytical approaches, we characterize adaptation and diversity at different levels and show how clonal interference – the interaction between simultaneously emerging lineages – shapes the eco-evolutionary dynamics. We find that large mutational inputs can foster diversification under sympatry, increasing the probability that phenotypically and genetically distinct clusters arise and stably coexist, constituting an initial form of community. Our findings have implications beyond microbial populations, providing novel insights about the interplay between ecology and evolution in clonal populations.

Mutation bias can shape adaptation in large asexual populations experiencing clonal interference

The extended evolutionary synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behaviour of two simultaneously adapting traits, one with larger mutation rate U , the other with larger selection coefficient s , using asexual travelling wave models. We find that adaptation is dominated by whichever trait has the faster rate of adaptation v in isolation, with the other trait subject to evolutionary stalling. Reviewing empirical claims for mutation-biased adaptation, we find that not all occur in the ‘origin-fixation’ regime of population genetics where v is only twice as sensitive to s as to U . In some cases, differences in U are at least ten to twelve times larger than differences in s , as needed to cause mutation-biased adaptation even in the ‘multiple mutations’ regime. Surprisingly, when U > s in the ‘diffusive-mutation’ regime, the required sensitivity ratio is also only two, despite pervasive clonal interference. Given two traits with identical v , the benefit of having higher s is surprisingly small, occurring largely when one trait is at the boundary between the origin-fixation and multiple mutations regimes.