Haploid selection, sex ratio bias, and transitions between sex-determining systems

Sex chromosome turnover and biodiversity in fishes

The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology. Fishes are the largest group of vertebrates, and they exhibit unparalleled sexual plasticity, as well as diverse sex-determining (SD) genes, sex chromosomes, and sex determination mechanisms. This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes. Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes, their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown. We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence. We revisit Haldane's rule and the large X-effect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization. By integrating recent findings on the turnover of SD genes, sex chromosomes, and sex determination systems in fish species, this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes.

Beyond Haldane's rule: Sex-biased hybrid dysfunction for all modes of sex determination

Haldane's rule occupies a special place in biology as one of the few 'rules' of speciation, with empirical support from hundreds of species. And yet, its classic purview is restricted taxonomically to the subset of organisms with heteromorphic sex chromosomes. I propose explicit acknowledgement of generalized hypotheses about Haldane's rule that frame sex bias in hybrid dysfunction broadly and irrespective of the sexual system. The consensus view of classic Haldane's rule holds that sex-biased hybrid dysfunction across taxa is a composite phenomenon that requires explanations from multiple causes. Testing of the multiple alternative hypotheses for Haldane's rule is, in many cases, applicable to taxa with homomorphic sex chromosomes, environmental sex determination, haplodiploidy, and hermaphroditism. Integration of a variety of biological phenomena about hybrids across diverse sexual systems, beyond classic Haldane's rule, will help to derive a more general understanding of the contributing forces and mechanisms that lead to predictable sex biases in evolutionary divergence and speciation.

Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here, we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii. We show that weeping willow arose from crosses between a female ancestor from the Salix-clade, which has XY sex chromosomes on chromosome 7, and a male ancestor from the Vetrix-clade, which has ancestral XY sex chromosomes on chromosome 15. We find that weeping willow has one pair of sex chromosomes, ZW on chromosome 15, that derived from the ancestral XY sex chromosomes in the male ancestor of the Vetrix-clade. Moreover, the ancestral 7X chromosomes from the female ancestor of the Salix-clade have reverted to autosomal inheritance. Duplicated intact ARR17-like genes on the four homologous chromosomes 19 likely have contributed to the maintenance of dioecy during polyploidization and sex chromosome turnover. Taken together, our results suggest the rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow.

Synthetic gene drives as an anthropogenic evolutionary force

Genetic drive represents a fundamental evolutionary force that can exact profound change to the genetic composition of populations by biasing allele transmission. Herein I propose that the use of synthetic homing gene drives, the human-mediated analog of endogenous genetic drives, warrants the designation of 'genetic welding' as an anthropogenic evolutionary force. Conceptually, this distinction parallels that of artificial and natural selection. Genetic welding is capable of imposing complex and rapid heritable phenotypic change on entire populations, whether motivated by biodiversity conservation or public health. Unanticipated possible long-term evolutionary outcomes, however, demand further investigation and bioethical consideration. The emerging importance of genetic welding also compels our explicit recognition of genetic drive as an addition to the other four fundamental forces of evolution.

The male-heterogametic sex determination system on chromosome 15 of Salix triandra and Salix arbutifolia reveals ancestral male heterogamety and subsequent turnover events in the genus Salix

Dioecious Salix evolved more than 45 million years ago, but have homomorphic sex chromosomes, suggesting that turnover event(s) prevented major differentiation. Sex chromosome turnover events have been inferred in the sister genus Populus. The genus Salix includes two main clades, Salix and Vetrix, with several previously studied Vetrix clade species having female-heterogametic (ZW) or male-heterogametic (XY) sex-determining systems (SDSs) on chromosome 15, while three Salix clade species have XY SDSs on chromosome 7. We here studied two basal taxa of the Vetrix clade, S. arbutifolia and S. triandra using S. purpurea as the reference genome. Analyses of whole genome resequencing data for genome-wide associations (GWAS) with the sexes and genetic differentiation between the sexes (FST values) showed that both species have male heterogamety with a sex-determining locus on chromosome 15, suggesting an early turnover event within the Vetrix clade, perhaps promoted by sexually antagonistic or (and) sex-ratio selection. Changepoint analysis based on FST values identified small sex-linked regions of ~3.33 Mb and ~2.80 Mb in S. arbutifolia and S. triandra, respectively. The SDS of S. arbutifolia was consistent with recent results that used its own genome as reference. Ancestral state reconstruction of SDS suggests that at least two turnover events occurred in Salix.

Sex-limited chromosomes and non-reproductive traits

Sex chromosomes are typically viewed as having originated from a pair of autosomes, and differentiated as the sex-limited chromosome (e.g. Y) has degenerated by losing most genes through cessation of recombination. While often thought that degenerated sex-limited chromosomes primarily affect traits involved in sex determination and sex cell production, accumulating evidence suggests they also influence traits not sex-limited or directly involved in reproduction. Here, we provide an overview of the effects of sex-limited chromosomes on non-reproductive traits in XY, ZW or UV sex determination systems, and discuss evolutionary processes maintaining variation at sex-limited chromosomes and molecular mechanisms affecting non-reproductive traits.

Are plant and animal sex chromosomes really all that different?

Sex chromosomes in plants have often been contrasted with those in animals with the goal of identifying key differences that can be used to elucidate fundamental evolutionary properties. For example, the often homomorphic sex chromosomes in plants have been compared to the highly divergent systems in some animal model systems, such as birds, Drosophila and therian mammals, with many hypotheses offered to explain the apparent dissimilarities, including the younger age of plant sex chromosomes, the lesser prevalence of sexual dimorphism, or the greater extent of haploid selection. Furthermore, many plant sex chromosomes lack complete sex chromosome dosage compensation observed in some animals, including therian mammals, Drosophila, some poeciliids, and Anolis, and plant dosage compensation, where it exists, appears to be incomplete. Even the canonical theoretical models of sex chromosome formation differ somewhat between plants and animals. However, the highly divergent sex chromosomes observed in some animal groups are actually the exception, not the norm, and many animal clades are far more similar to plants in their sex chromosome patterns. This begs the question of how different are plant and animal sex chromosomes, and which of the many unique properties of plants would be expected to affect sex chromosome evolution differently than animals? In fact, plant and animal sex chromosomes exhibit more similarities than differences, and it is not at all clear that they differ in terms of sexual conflict, dosage compensation, or even degree of divergence. Overall, the largest difference between these two groups is the greater potential for haploid selection in plants compared to animals. This may act to accelerate the expansion of the non-recombining region at the same time that it maintains gene function within it. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Sex determination and sex chromosome evolution in land plants

Linnaeus's very first opus, written when he was 22 years old, dealt with the analogy that exists between plants and animals in how they 'propagate their species', and a revised version with a plate depicting the union of male and female Mercurialis annua plants became a foundational text on the sexuality of plants. The question how systems with separate males and females have evolved in sedentary organisms that appear ancestrally bisexual has fascinated biologists ever since. The phenomenon, termed dioecy, has important consequences for plant reproductive success and is of commercial interest since it affects seed quality and fruit production. This theme issue presents a series of articles that synthesize and challenge the current understanding of how plants achieve dioecy. The articles deal with a broad set of taxa, including Coccinia, Ginkgo, Mercurialis, Populus, Rumex and Silene, as well as overarching topics, such as the field's terminology, analogies with animal sex determination systems, evolutionary pathways to dioecy, dosage compensation, and the longevity of the two sexes. In this introduction, we focus on four topics, each addressed by several articles from different angles and with different conclusions. Our highlighting of unclear or controversial issues may help future studies to build on the current understanding and to ask new questions that will expand our knowledge of plant sexual systems. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Some sexual consequences of being a plant

Plants have characteristic features that affect the expression of sexual function, notably the existence of a haploid organism in the life cycle, and in their development, which is modular, iterative and environmentally reactive. For instance, primary selection (the first filtering of the products of meiosis) is via gametes in diplontic animals, but via gametophyte organisms in plants. Intragametophytic selfing produces double haploid sporophytes which is in effect a form of clonal reproduction mediated by sexual mechanisms. In homosporous plants, the diploid sporophyte is sexless, sex being only expressed in the haploid gametophyte. However, in seed plants, the timing and location of gamete production is determined by the sporophyte, which therefore has a sexual role, and in dioecious plants has genetic sex, while the seed plant gametophyte has lost genetic sex. This evolutionary transition is one that E.J.H. Corner called 'the transference of sexuality'. The iterative development characteristic of plants can lead to a wide variety of patterns in the distribution of sexual function, and in dioecious plants poor canalization of reproductive development can lead to intrasexual mating and the production of YY supermales or WW superfemales. Finally, plant modes of asexual reproduction (agamospermy/apogamy) are also distinctive by subverting gametophytic processes. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Multiple sex chromosome drivers in a mammal with three sex chromosomes

Eukaryotes with separate males and females display a great diversity in the way they determine sex, but it is still unclear what evolutionary forces cause transitions between sex-determining systems. Rather that the lack of hypotheses, the problem is the scarcity of adequate biological systems to test them. Here, we take advantage of the recent evolution of a feminizing X chromosome (called X^∗) in the African pygmy mouse Mus minutoides to investigate one of the evolutionary forces hypothesized to cause such transitions, namely sex chromosome drive (i.e., biased transmission of sex chromosomes to the next generation). Through extensive molecular sexing of pups at weaning, we reveal the existence of a remarkable male sex chromosome drive system in this species, whereby direction and strength of drive are conditional upon the genotype of males' partners: males transmit their Y at a rate close to 80% when mating with XX or XX^∗ females and only 36% when mating with X^∗Y females. Using mathematical modeling, we explore the joint evolution of these unusual sex-determining and drive systems, revealing that different sequences of events could have led to the evolution of this bizarre system and that the "conditional" nature of sex chromosome drive plays a crucial role in the short- and long-term maintenance of the three sex chromosomes.

OUP accepted manuscript

Many species have separate haploid and diploid phases. Theory predicts that each phase should experience the effects of evolutionary forces (like selection) differently. In the haploid phase, all fitness-affecting alleles are exposed to selection, whereas in the diploid phase, those same alleles can be masked by homologous alleles. This predicts that selection acting on genes expressed in haploids should be more effective than diploid-biased genes. Unfortunately, in arrhenotokous species, this prediction can be confounded with the effects of sex-specific expression, as haploids are usually reproductive males. Theory posits that, when accounting for ploidal- and sex-specific expression, selection should be equally efficient on haploid- and diploid-biased genes relative to constitutive genes. Here, we used a multiomic approach in honey bees to quantify the evolutionary rates of haploid-biased genes and test the relative effects of sexual- and haploid-expression on molecular evolution. We found that 16% of the honey bee’s protein-coding genome is highly expressed in haploid tissue. When accounting for ploidy and sex, haploid- and diploid-biased genes evolve at a lower rate than expected, indicating that they experience strong negative selection. However, the rate of molecular evolution of haploid-biased genes was higher than diploid-based genes. Genes associated with sperm storage are a clear exception to this trend with evidence of strong positive selection. Our results provide an important empirical test of theory outlining how selection acts on genes expressed in arrhenotokous species. We propose the haploid life history stage affects genome-wide patterns of diversity and divergence because of both sexual and haploid selection.

Unusual Mammalian Sex Determination Systems: A Cabinet of Curiosities

Therian mammals have among the oldest and most conserved sex-determining systems known to date. Any deviation from the standard XX/XY mammalian sex chromosome constitution usually leads to sterility or poor fertility, due to the high differentiation and specialization of the X and Y chromosomes. Nevertheless, a handful of rodents harbor so-called unusual sex-determining systems. While in some species, fertile XY females are found, some others have completely lost their Y chromosome. These atypical species have fascinated researchers for over 60 years, and constitute unique natural models for the study of fundamental processes involved in sex determination in mammals and vertebrates. In this article, we review current knowledge of these species, discuss their similarities and differences, and attempt to expose how the study of their exceptional sex-determining systems can further our understanding of general processes involved in sex chromosome and sex determination evolution.

Establishment of a new sex-determining allele driven by sexually antagonistic selection

The turnover of sex-determining loci has repeatedly occurred in a number of species, rather than having a diverged pair of sex chromosomes. We model the turnover process by considering a linked locus under sexually antagonistic selection. The entire process of a turnover may be divided into two phases, which are referred to as the stochastic and deterministic phases. The stochastic phase is when a new sex-determining allele just arises and is still rare and random genetic drift plays an important role. In the deterministic phase, the new allele further increases in frequency by positive selection. The theoretical results currently available are for the deterministic phase, which demonstrated that a turnover of a newly arisen sex-determining locus could benefit from selection at a linked locus under sexually antagonistic selection, by assuming that sexually antagonistic selection works in a form of balancing selection. In this work, we provide a comprehensive theoretical description of the entire process from the stochastic phase to the deterministic phase. In addition to balancing selection, we explore several other modes of selection on the linked locus. Our theory allows us make a quantitative argument on the rate of turnover and the effect of the mode of selection at the linked locus. We also performed simulations to explore the pattern of polymorphism around the new sex-determining locus. We find that the pattern of polymorphism is informative to infer how selection worked through the turnover process.

The Diversity and Dynamics of Sex Determination in Dioecious Plants

The diversity of inflorescences among flowering plants is captivating. Such charm is not only due to the variety of sizes, shapes, colors, and flowers displayed, but also to the range of reproductive systems. For instance, hermaphrodites occur abundantly throughout the plant kingdom with both stamens and carpels within the same flower. Nevertheless, 10% of flowering plants have separate unisexual flowers, either in different locations of the same individual (monoecy) or on different individuals (dioecy). Despite their rarity, dioecious plants provide an excellent opportunity to investigate the mechanisms involved in sex expression and the evolution of sex-determining regions (SDRs) and sex chromosomes. The SDRs and the evolution of dioecy have been studied in many species ranging from Ginkgo to important fruit crops. Some of these studies, for example in asparagus or kiwifruit, identified two sex-determining genes within the non-recombining SDR and may thus be consistent with the classical model for the evolution of dioecy from hermaphroditism via gynodioecy, that predicts two successive mutations, the first one affecting male and the second one female function, becoming linked in a region of suppressed recombination. On the other hand, aided by genome sequencing and gene editing, single factor sex determination has emerged in other species, such as persimmon or poplar. Despite the diversity of sex-determining mechanisms, a tentative comparative analysis of the known sex-determining genes and candidates in different species suggests that similar genes and pathways may be employed repeatedly for the evolution of dioecy. The cytokinin signaling pathway appears important for sex determination in several species regardless of the underlying genetic system. Additionally, tapetum-related genes often seem to act as male-promoting factors when sex is determined via two genes. We present a unified model that synthesizes the genetic networks of sex determination in monoecious and dioecious plants and will support the generation of hypothesis regarding candidate sex determinants in future studies.

Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages

Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10750-021-04560-7.

JC, McFarland K, Goffinet B. Population Genomics and Phylogeography of a Clonal Bryophyte With Spatially Separated Sexes and Extreme Sex Ratios

The southern Appalachian (SA) is one of the most biodiversity-rich areas in North America and has been considered a refugium for many disjunct plant species, from the last glacial period to the present. Our study focuses on the SA clonal hornwort, Nothoceros aenigmaticus J. C. Villarreal & K. D. McFarland. This hornwort was described from North Carolina and is widespread in the SA, growing on rocks near or submerged in streams in six and one watersheds of the Tennessee (TR) and Alabama (AR) Rivers, respectively. Males and female populations occur in different watersheds, except in the Little Tennessee (TN) River where an isolated male population exists ca. 48 km upstream from the female populations. The sex ratio of 1:0 seems extreme in each population. In this study, we use nuclear and organellar microsatellites from 250 individuals from six watersheds (seven populations) in the SA region and two populations from Mexico (23 individuals). We, then, selected 86 individuals from seven populations and used genotyping by sequencing to sample over 600 bi-allelic markers. Our results suggest that the SA N. aenigmaticus and Mexican plants are a nested within a clade of sexual tropical populations. In the US populations, we confirm an extreme sex ratio and only contiguous US watersheds share genotypes. The phylogenetic analysis of SNP data resolves four clusters: Mexican populations, male plants (Little Pigeon and Pigeon river watersheds) and two clusters of female plants; one from the Little Tennessee and Hiwassee Rivers (TR) and the other from the Ocoee (TR) and Coosa (AR) Rivers. All clusters are highly differentiated (Fst values over 0.9). In addition, our individual assignment analyses and PCAs reflect the phylogenetic results grouping the SA samples in three clades and recovering males and female plants with high genetic differentiation (Fst values between 0.5 and 0.9 using microsatellites and bi-allelic markers). Our results point to Pleistocene events shaping the biogeographical pattern seen in US populations. The extreme sex ratio reflects isolation and highlights the high vulnerability of the populations in the SA.

Theory in Service of Narratives in Evolution and Ecology

Considering the role of theory in ecology and evolution, we argue that scientific theorizing involves an interplay between narratives and models in which narratives play a key creative and organizing role. Specifically, as scientists, we reason through the use of narratives that explain biological phenomena by envisaging, or mentally simulating, causal paths leading from a plausible initial state to an outcome of interest. Within these narratives, some parts may appear clear, while others may appear puzzling. It is at these tenuous junctions-junctions where reasoning is made challenging by conflicting possible outcomes-that we often build mathematical models to support and extend, or reject and revise, our narratives. Accordingly, models, both analytical and computational, are framed by and interpreted within a narrative. We illustrate these points using case studies from population genetics. This perspective on scientific theorizing helps to clarify the nature of theoretical debates, which often arise from the narratives in which math is embedded, not from the math itself. Finally, this perspective helps place appropriate creative weight on the importance of developing, revising, and challenging narratives in the scientific enterprise.

Haploid Selection in “Diploid” Organisms

Evolutionary rates and strength of selection differ markedly between haploid and diploid genomes. Any genes expressed in a haploid state will be directly exposed to selection, whereas alleles in a diploid state may be partially or fully masked by a homologous allele. This difference may shape key evolutionary processes, including rates of adaptation and inbreeding depression, but also the evolution of sex chromosomes, heterochiasmy, and stable sex ratio biases. All diploid organisms carry haploid genomes, most notably the haploid genomes in gametes produced by every sexually reproducing eukaryote. Furthermore, haploid expression occurs in genes with monoallelic expression, in sex chromosomes, and in organelles, such as mitochondria and plastids. A comparison of evolutionary rates among these haploid genomes reveals striking parallels. Evidence suggests that haploid selection has the potential to shape evolution in predominantly diploid organisms, and taking advantage of the rapidly developing technologies, we are now in the position to quantify the importance of such selection on haploid genomes.

How to identify sex chromosomes and their turnover

Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non-model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.

Young sex chromosomes in plants and animals

A major reason for studying plant sex chromosomes is that they may often be 'young' systems. There is considerable evidence for the independent evolution of separate sexes within plant families or genera, in some cases showing that the maximum possible time during which their sex-determining genes have existed must be much shorter than those of several animal taxa. Consequently, their sex-linked regions could either have evolved soon after genetic sex determination arose or considerably later. Plants, therefore, include species with both young and old systems. I review several questions about the evolution of sex-determining systems and sex chromosomes that require studies of young systems, including: the kinds of mutations involved in the transition to unisexual reproduction from hermaphroditism or monoecy (a form of functional hermaphroditism); the times when they arose; and the extent to which the properties of sex-linked regions of genomes reflect responses to new selective situations created by the presence of a sex-determining locus. I also evaluate which questions are best studied in plants, vs other suitable candidate organisms. Studies of young plant systems can help understand general evolutionary processes that are shared with the sex chromosomes of other organisms.

Evolutionary potential for genomic islands of sexual divergence on recombining sex chromosomes

Differentiated sex chromosomes are thought to develop through the accumulation of polymorphisms at loci subject to opposing selection between males and females, and/or between haploids and diploids. As sex chromosomes differentiate, reduced recombination becomes favored between selected loci and the sex-determining region, strengthening genetic associations between alleles favored in a sex and the corresponding sex chromosome. Here a model is analyzed to explore whether polymorphism at one sexually or ploidally antagonistic locus facilitates the spread of rare alleles at other loci experiencing antagonistic selection, promoting further differentiation of the sex chromosomes. It is found that antagonistic polymorphisms can spread and capture other such loci, building 'genomic islands' of differentiation on sex chromosomes, but the conditions are very restrictive, requiring the loci to be strongly selected, tightly linked and distant from the sex-determining region. Epistatic interactions can facilitate the promotion of polymorphism among selected loci, but only if preferentially favoring heterozygotes. Although these results apply to any taxa, plants provide a fertile ground for testing these and related theories given the recurrent evolutionary transitions to dioecy, which provide multiple opportunities to track the early evolution of sex chromosomes.