Fifty Generations of Amitosis: Tracing Asymmetric Allele Segregation in Polyploid Cells with Single-Cell DNA Sequencing

Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis have been gleaned by assessing the rate of phenotypic assortment. Though powerful, this experimental approach relies on the availability of phenotypic markers. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dualism and a highly polyploid somatic nucleus, we probe the limits of single-cell whole-genome sequencing to study the consequences of amitosis. To this end, we first evaluate the suitability of single-cell sequencing to study the AT-rich genome of P. tetraurelia, focusing on common sources of genome representation bias. We then asked: can alternative rearrangements of a given locus eventually assort after a number of amitotic divisions? To address this question, we track somatic assortment of developmentally acquired Internal Eliminated Sequences (IESs) up to 50 amitotic divisions post self-fertilization. To further strengthen our observations, we contrast empirical estimates of IES retention levels with in silico predictions obtained through mathematical modeling. In agreement with theoretical expectations, our empirical findings are consistent with a mild increase in variation of IES retention levels across successive amitotic divisions of the macronucleus. The modest levels of somatic assortment in P. tetraurelia suggest that IESs retention levels are largely sculpted at the time of macronuclear development, and remain fairly stable during vegetative growth. In forgoing the requirement for phenotypic assortment, our approach can be applied to a wide variety of amitotic species and could facilitate the identification of environmental and genetic factors affecting amitosis.

Social selection is density dependent but makes little contribution to total selection in New Zealand giraffe weevils

Social selection occurs when traits of interaction partners influence an individual's fitness and can alter total selection strength. However, we have little idea of what factors influence social selection's strength. Further, social selection only contributes to overall selection when there is phenotypic assortment, but simultaneous estimates of social selection and phenotypic assortment are rare. Here, we estimated social selection on body size in a wild population of New Zealand giraffe weevils ( Lasiorhynchus barbicornis ). We measured phenotypic assortment by body size and tested whether social selection varied with sex ratio, density and interacted with the body size of the focal individual. Social selection was limited and unaffected by sex ratio or the size of the focal individual. However, at high densities social selection was negative for both sexes, consistent with size-based competitive interactions for access to mates. Phenotypic assortment was always close to zero, indicating negative social selection at high densities will not impede the evolution of larger body sizes. Despite its predicted importance, social selection may only influence evolutionary change in specific contexts, leaving direct selection to drive evolutionary change.

Fifty generations of amitosis: tracing asymmetric allele segregation in polyploid cells with single-cell DNA sequencing

Amitosis is a widespread form of unbalanced nuclear division whose biomedical and evolutionary significance remain unclear. Traditionally, insights into the genetics of amitosis are acquired by assessing the rate of phenotypic assortment. The phenotypic diversification of heterozygous clones during successive cell divisions reveals the random segregation of alleles to daughter nuclei. Though powerful, this experimental approach relies on the availability of phenotypic markers. Here, we present an approach that overcomes the requirement for phenotypic assortment. Leveraging Paramecium tetraurelia, a unicellular eukaryote with nuclear dimorphism and a highly polyploid somatic nucleus, we use single-cell whole-genome sequencing to track the assortment of developmentally acquired somatic DNA variants. Accounting for genome representation biases, we measure the effect of amitosis on allele segregation across the first ~50 amitotic divisions post self-fertilization and compare our empirical findings with theoretical predictions estimated via mathematical modeling. In line with our simulations, we show that amitosis in P. tetraurelia produces measurable but modest levels of somatic assortment. In forgoing the requirement for phenotypic assortment and employing developmental, environmentally induced somatic variation as molecular markers, our work provides a new powerful approach to investigate the consequences of amitosis in polyploid cells.

Social selection is density dependent but makes little contribution to total selection in New Zealand giraffe weevils

Social selection occurs when traits of interaction partners influence an individual’s fitness and can fundamentally alter total selection strength. Unlike for direct selection, however, we have little idea of what factors influence the strength of social selection. Further, social selection only contributes to overall selection when there is phenotypic assortment, but simultaneous estimates of social selection and phenotypic assortment are rare. Here we estimated social selection on body size in a wild population of New Zealand giraffe weevils (Lasiorhynchus barbicornis). We did this in a range of contexts and measured phenotypic assortment for both sexes. Social selection was mostly absent and not affected by sex ratio or the body size of the focal individual. However, at high densities selection was negative for both sexes, consistent with competitive interactions based on size for access to mates. Phenotypic assortment was also density dependent, flipping from positive at low densities to negative at high densities. However, it was always close to zero, indicating negative social selection at high densities will not greatly impede the evolution of larger body sizes. Despite its predicted importance, social selection may only influence evolutionary change in specific contexts, leaving direct selection as the dominant driver of evolutionary change.

Phenotypic assortment in wild primate networks: implications for the dissemination of information

Individuals' access to social information can depend on their social network. Homophily—a preference to associate with similar phenotypes—may cause assortment within social networks that could preclude information transfer from individuals who generate information to those who would benefit from acquiring it. Thus, understanding phenotypic assortment may lead to a greater understanding of the factors that could limit the transfer of information between individuals. We tested whether there was assortment in wild baboon ( Papio ursinus ) networks, using data collected from two troops over 6 years for six phenotypic traits—boldness, age, dominance rank, sex and the propensity to generate/exploit information—using two methods for defining a connection between individuals—time spent in proximity and grooming. Our analysis indicated that assortment was more common in grooming than proximity networks. In general, there was homophily for boldness, age, rank and the propensity to both generate and exploit information, but heterophily for sex. However, there was considerable variability both between troops and years. The patterns of homophily we observed for these phenotypes may impede information transfer between them. However, the inconsistency in the strength of assortment between troops and years suggests that the limitations to information flow may be quite variable.

Conditional Behaviors and Inclusive Fitness

This chapter examines social behaviors that are expressed conditional on the phenotype of others. David Queller argued that inclusive fitness analyses need to be done on a per-behavior basis, citing as an example the decision over whether to reproduce directly, and whether to aid a reproductive. Queller showed that inclusive fitness predictions are only sensible when one analyzes what an individual should do, given it finds itself in a particular behavioral role. The chapter first provides an overview of implicit and explicit conditionality and presents two classic examples: William D. Hamilton's greenbeard traits and Robert Trivers's theory of reciprocal cooperation. It also introduces an extension of Hamilton's rule to deal with explicitly conditional behaviors; this extension features a measure of phenotypic assortment that appears not to be the classic genetic relatedness of Hamilton's rule.

Variants of Hamilton’s Rule and Evolutionary Explanations

This chapter examines four variants of Hamilton's rule and how they give different evolutionary explanations for certain social behaviors such as greenbeard traits. These variants are: HR1, which extends Hamilton's rule with a synergistic coefficient capturing the deviation from additivity of fitness interactions; HR2, which deals with the conditional expression of phenotype; HR3, which is concerned with fitness as partial regression; and HR4, the geometric view of relatedness. These variants differ in how they treat the three key parameters of the original: “relatedness,” “cost,” and “benefit.” The chapter also considers how the nongenetic explanation of the evolution of altruism can actually be recast in a version with genetic relatedness, and how geometric relatedness underlies phenotypic assortment. Finally, it discusses different viewpoints on conditional behaviors.