Epigenetically Inherited Mutation Rates Predicted to Maximize Adaptation Rates

The mutation rate is an important determinant of evolutionary dynamics. Because the mutation rate determines the rate of appearance of beneficial and deleterious mutations, it is subject to second-order selection. The mutation rate varies between and within species and populations, increases under stress, and is genetically controlled by mutator alleles. The mutation rate may also vary among genetically identical individuals: empirical evidence from bacteria suggests that the mutation rate may be affected by translation errors and expression noise in various proteins (1). Importantly, this non-genetic variation may be heritable via transgenerational epigenetic inheritance. Here we investigate how the inheritance mode of the mutation rate affects the rate of adaptive evolution on rugged fitness landscapes. We model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. The rate of switching between the mutation rate phenotypes is allowed to span a range of values. Thus, the mutation rate can be interpreted as a genetically inherited trait when the switching rate is low, as an epigenetically inherited trait when the switching rate is intermediate, or as a randomly determined trait when the switching rate is high. We find that epigenetically inherited mutation rates result in the highest rates of adaptation on rugged fitness landscapes for most realistic parameter sets. This is because an intermediate switching rate can maintain the association between a mutator phenotype and pre-existing mutations, which facilitates the crossing of fitness valleys. Our results provide a rationale for the evolution of epigenetic inheritance of the mutation rate, suggesting that it could have been selected because it facilitates adaptive evolution.

Demographic Diversity of the Aromantic/Asexual Spectrum in Japan: Findings from the 2020 Aro/Ace Survey

In Western countries, studies using representative surveys and community surveys have begun to reveal the size and the diversity of the asexual population. On the other hand, in Japan, there are only a few studies using representative surveys, and the detailed realities of the asexual population are yet to be explored. This article analyzed a web survey “Aromantic/Asexual Spectrum Survey 2020,” conducted by the Aro/Ace Survey Executive Committee. Most of the respondents tended to be cisgender women, young people, and residents of the southern Kanto region. Many identified as aromantic and asexual, but some identified as other aro/ace identities. We also conducted an analysis on “nonsexual,” an identity category unique to Japan. While masturbation and sex drives were found in a certain number of asexual respondents, the proportion of those who would like to have sexual contact with others was particularly low among asexual respondents. We conclude that sexual contact with others has important implications for self-identification.

Resampling the pool of genotypic possibilities: an adaptive function of sexual reproduction

Background Natural populations harbor significant levels of genetic variability. Because of this standing genetic variation, the number of possible genotypic combinations is many orders of magnitude greater than the population size. This means that any given population contains only a tiny fraction of all possible genotypic combinations. Results We show that recombination allows a finite population to resample the genotype pool, i.e., the universe of all possible genotypic combinations. Recombination, in combination with natural selection, enables an evolving sexual population to replace existing genotypes with new, higher-fitness genotypic combinations that did not previously exist in the population. This process allows the sexual population to gradually increase its fitness far beyond the range of fitnesses in the initial population. In contrast to this, an asexual population is limited to selection among existing lower fitness genotypes. Conclusions The results provide an explanation for the ubiquity of sexual reproduction in evolving natural populations, especially when natural selection is acting on the standing genetic variation.

Characterization of Phytophthora infestans populations in Cyprus, the southernmost potato-producing European country.

Cyprus is the southernmost island country of Europe located in the Mediterranean and despite its limited area, potato production is considered an integral source of the national agricultural revenue. During 2010-2012, a late blight-epidemic period for the country, the population structure of Phytophthora infestans was analyzed via a sample of 539 isolates collected from all the main potato-cultivating regions of Cyprus. We determined mating type, mefenoxam sensitivity, and genetic polymorphism at 12 simple sequence repeat (SSRs) loci. Although both mating types were detected in the country, a gradual -but dynamic- shift towards A2 dominance was manifested over time. The pathogen population also demonstrated reduced sensitivity to the phenylamide fungicide, since 96.2% of the tested isolates had high (70.3%) and intermediate resistance (25.9%) to mefenoxam, suggesting it should be replaced with other active ingredients in local disease management strategies. The genotypic analysis also revealed the predominance of the highly aggressive, mefenoxam-insensitive EU_13_A2 lineage across the country with a frequency of 79.2%. Other samples comprised an older lineage EU_2_A1 (19.5%), a very low proportion of EU_23_A1 (0.37%), and others that did not match any known lineage (0.92%). SSRs data supported triploid genomes among the dominant lineages and patterns of their asexual population history were also apparent. High sub-clonal variation of the 13_A2 population was detected, suggesting introduction events of this widespread genotype to Cyprus from major tuber exporting countries. Present data indicate the severe impact of inoculum migration to the structure of the local population; thus, current phytosanitary procedures should be reconsidered and possibly attuned. This is the first comprehensive study to elucidate the diversity of P. infestans in Cyprus and could serve as a baseline for future monitoring of this highly adaptive plant pathogen since late blight management strategies should be constantly refined according to the traits of the dominant genotypes of P. infestans.

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.

The adaptive function of sexual reproduction: resampling the pool of genotypic possibilities.

BackgroundNatural populations harbor significant levels of genetic variability. Because of this standing genetic variation, the number of possible genotypic combinations is many orders of magnitude greater than the population size. This means that any given population contains only a tiny fraction of all possible genotypic combinations.ResultsWe show that recombination allows a finite population to resample the genotype pool, i.e., the universe of all possible genotypic combinations. Recombination, in combination with natural selection, enables an evolving sexual population to replace existing genotypes with new, higher-fitness genotypic combinations that did not previously exist in the population. Gradually the selected sexual population approaches a state where the optimum genotype is produced by recombination and where it rises to fixation. In contrast to this, an asexual population is limited to selection among existing lower fitness genotypes.ConclusionsThe significance of the result is two-fold. First, it provides an explanation for the ubiquity of sexual reproduction in evolving populations. Secondly, it shows that recombination serves to remove concerns about the cost of natural selection acting on the naturally occurring standing genetic variation. This means that classic population genetics theory is applicable to ecological studies of natural selection acting on standing genetic variation.

Sex, fitness decline and recombination – Muller’s ratchet vs. Ohta’s ratchet

It is generally accepted that the absence of recombination reduces the efficacy of natural selection for, or against, mutations. A special case is Muller’s Ratchet (MR) whereby non-recombining genomes experience irreversible fitness decline due to the accumulation of deleterious mutations. MR has been a main hypothesis for sexual reproduction as well as many other biological phenomena. We now ask whether the fitness decline can indeed be stopped if an asexual population turns sexual to become recombining. The possible fitness decline under recombination is referred to as Ohta’s Ratchet (OR). In comparison, MR is more effective in driving fitness reduction than OR, but only in a restricted parameter space of mutation rate, population size and selection. Outside of this space, the two ratchets are equally effective or, alternatively, neither is sufficiently powerful. Furthermore, beneficial mutations can affect the population fitness, which may diverge between the two ratchets, but only in a small parameter space. Since recombination plays a limited role in driving fitness decline, the operation of MR could be far less common in nature than believed. A companion report (see Supplement) surveying the biological phenomena attributed to MR indeed suggests the alternative explanations to be generally more compelling.

Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum

It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen Phytophthora ramorum NA1 revealed considerable genetic variation in the form of Structural Variants (SVs). To better understand how SVs arise and their significance to the California NA1 population, we studied the evolutionary histories of SVs and the forest conditions associated with their emergence. Ancestral state reconstruction suggests that SVs arose by somatic mutations among multiple independent lineages, rather than by recombination. We asked if this unusual phenomenon of parallel evolution between isolated populations is transmitted to extant lineages and found that SVs persist longer in a population if their genetic background had a lower mutation load. Genetic parallelism was also found in geographically distant demes where forest conditions such as host density, solar radiation, and temperature, were similar. Parallel SVs overlap with genes involved in pathogenicity such as RXLRs and have the potential to change the course of an epidemic. By combining genomics and environmental data, we identified an unexpected pattern of repeated evolution in an asexual population and identified environmental factors potentially driving this phenomenon.

The adaptive function of sexual reproduction: resampling the genotype pool

Recombination allows a finite population to resample the genotype pool, i.e., the universe of all possible genotypic combinations. This is important in populations that contain abundant genetic variation because, in such populations, the number of potential genotypes is much larger than the number of individuals in the population. Here, we show how recombination, in combination with natural selection, enables an evolving sexual population to replace existing genotypes with new, higher-fitness genotypic combinations. In contrast to this, an asexual population is limited to selection among existing genotypes. Since it has been shown that most eukaryotic species are genetically polymorphic, our model can explain the ubiquity of sex among such species. The model also indicates that classic population genetics theory is applicable to ecological studies of natural selection acting on standing genetic variation.

Understanding Sexual Orientation Identity, Sexual/Romantic Attraction, and Sexual Behavior beyond Western Societies: The Case of Japan

As a growing amount of research examines the impact of sexuality on various demographic outcomes, it becomes important to understand the complex intersections of sexual orientation identity, sexual/romantic attraction, and sexual behavior. However, most previous studies use data from Western countries that have particular histories of sexuality, limiting the generalizability of the findings beyond Western societies. We describe dimensions of sexuality in Japan, where there has not been any religious authority condemning same-sex behavior and any law prohibiting same-sex relations except for a decade in the late 19th century. We use data from the “Survey on Diversity of Work and Life, and Coexistence among the Residents of Osaka City,” the first population-based survey with detailed questions about multiple aspects of sexuality in Japan, to conduct descriptive analysis. More women identify as bisexual or asexual than lesbian. Among the respondents who selected “Don’t want to decide, haven’t decided”—a category originally created for queer/questioning respondents—as their sexual orientation, the proportion of those who indicated exclusive heterosexuality is higher than expected, raising the possibility that some heterosexual respondents with no heterosexual identity may have mistakenly chosen this category. The data suggest that the population of heterosexual-identified men who have sex with men is small. The prevalence of the asexual population differs by whether sexual orientation identity or sexual/romantic attraction is used to capture this population. Our analysis extends the demography of sexuality by examining unique non-Western data and putting in context the previous findings observed in Western countries.