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Divergent evolution of genetic sex determination mechanisms along environmental gradients

View ORCID ProfileMartijn A. Schenkel, View ORCID ProfileJean-Christophe Billeter, View ORCID ProfileLeo W. Beukeboom, View ORCID ProfileIdo Pen
doi: https://doi.org/10.1101/2022.05.23.493175
Martijn A. Schenkel
Groningen Institute for Evolutionary Life Sciences; University of Groningen; P. O. Box 11103, 9700 CC Groningen, The Netherlands
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  • For correspondence: maschenkel@gmail.com i.r.pen@rug.nl
Jean-Christophe Billeter
Groningen Institute for Evolutionary Life Sciences; University of Groningen; P. O. Box 11103, 9700 CC Groningen, The Netherlands
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Leo W. Beukeboom
Groningen Institute for Evolutionary Life Sciences; University of Groningen; P. O. Box 11103, 9700 CC Groningen, The Netherlands
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Ido Pen
Groningen Institute for Evolutionary Life Sciences; University of Groningen; P. O. Box 11103, 9700 CC Groningen, The Netherlands
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Abstract

Sex determination (SD) is a crucial developmental process, but its molecular underpinnings are very diverse, both between and within species. SD mechanisms have traditionally been categorized as either genetic (GSD) or environmental (ESD), depending on the type of cue that triggers sexual differentiation. However, mixed systems, with both genetic and environmental components, are more prevalent than previously thought. Here, we show theoretically that environmental effects on expression levels of genes within SD regulatory mechanisms can easily trigger within-species evolutionary divergence of SD mechanisms. This may lead to the stable coexistence of multiple SD mechanisms and to spatial variation in the occurrence of different SD mechanisms along environmental gradients. We applied the model to the SD system of the housefly, a global species with world-wide latitudinal clines in the frequencies of different SD systems, and found that it correctly predicted these clines if specific genes in the housefly SD system were assumed to have temperature-dependent expression levels. We conclude that environmental sensitivity of gene regulatory networks may play an important role in diversification of SD mechanisms.

Introduction

Sex determination (SD) is a crucial aspect of the development of sexually-reproducing organisms, yet the regulatory mechanisms underlying SD are very diverse and prone to evolutionary change1,2. SD mechanisms have traditionally been classified as either environmental (ESD) or genetic (GSD) depending on the type of signal that initiates the determination of an individual’s sex. Under ESD, such signal include temperature, salinity, and acidity during a sensitive period in embryonic development (reviewed in 3,4). Under GSD, the signal is a specific gene (or set of genes) present in zygotes, leading to either male or female development, such as the male-determining Sex-determining Region Y (SRY) gene in mammals or transformer (tra) in many insects5–9. Diversification of SD mechanisms occurs via the evolution of novel SD mechanisms that replace their predecessors, a process called SD transition. SD transitions are prevalent in some taxa but not in others1,2, indicating variable evolvability of SD systems. What enhances the evolvability of some SD systems but not others and what causes SD transitions is still poorly understood.

One often-overlooked aspect of the evolution of SD is how environmental and genetic factors may simultaneously affect SD. Rather than being mutually exclusive, ESD and GSD could instead be considered as two extremes of a continuum2,10,11, with mixed systems occurring in several organismal groups, such as amphibians, fish and insects4,10,12–15. In such mixed systems, SD may reflect a delicate balance between genetic effects that bias the process of SD towards male or female development, counteracted by environmental effects that push the system in the opposite direction16,17. GSD has repeatedly evolved in species which previously had ESD (e.g., 18), and several theoretical models have been developed to predict when such turnovers should occur10,19,20. However, such models typically do not explicitly consider the underlying molecular mechanisms of sex determination. Although sex is determined by genes in species with GSD, environmental conditions can affect SD by modifying the expression levels of these genes21,22. Despite clear evidence that such environmental effects may perturb the action of GSD mechanisms (e.g., 4), their effect on the evolution of GSD systems is still unknown.

In many species, SD involves hierarchical gene regulation23–25, where an initial signal targets a small number of regulatory genes that in turn regulate downstream targets. Evolutionary transitions between GSD systems are thought to occur primarily by the displacement of the initial signal gene by another gene with a similar function, or by the recruitment of a new regulatory gene on top of the ancestral SD regulatory pathway23,24,26. Genes downstream of the top regulatory genes are considered to be more constrained in terms of evolutionary change, as mutations in such genes may interfere with their pre-existing function in regulating SD. Nonetheless, they are not fully prohibited from undergoing further evolution, and some changes may still occur27.

A new evolutionary framework needs to integrate the views that (1) SD is not solely environmentally or genetically determined but is to varying degrees affected by both types of cues; and (2) changes in SD cascades do not only occur at the top but may also occur via changes in the underlying genetic network. Here, we formalize this framework by developing a theoretical model of the evolution of SD systems in the presence of spatial environmental variation that affects expression of SD genes. The model is inspired by the polymorphic SD system of the housefly Musca domestica. In this system, temperature is likely to act as an environmental cue because (1) variation in SD systems is correlated with variation in temperature between natural populations, and (2) temperature affects SD in several M. domestica strains harbouring mutant SD genes (see also Box 1). Like in M. domestica SD, the model features two types of SD genes: an environmentally-sensitive gene F induces femaleness when active, and one or more M-genes that induce maleness by inhibiting F (Figure 1A, see details below). We investigate here how the (co-)evolution of F and M can yield novel SD systems under the influence of environmental sensitivity of F. We then use the model to explain how the multifactorial SD system of houseflies has evolved (Box 1).

Figure 1:
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Figure 1:

Model overview. (A) Sex is determined based on the net total active F product. Active F is produced by the F locus, and degraded by M, produced by MY and/or MA. Higher temperature increases expression levels of F. If the net total active F product exceeds a threshold θF, individuals become females, whereas below the threshold θM individuals become males; otherwise, individuals develop into infertile intersexes. (B) Demes 1 through N are arranged along a linear gradient where T increases from Tmin to Tmax Each deme contains a variable number of females, males, and intersexes. Reproduction occurs by mating between males and females within the same deme; intersexes do not reproduce. Dispersal occurs at a rate d to neighbouring demes (indicated by arrows). Every individual has three gene loci F, MY, and MA that jointly determine sex.

Model summary

Here we briefly describe the model; a more detailed description of the model and simulation techniques is in the Methods section below. We developed an individual-based simulation model, where individuals occupy a linear array of subpopulations (demes) arranged along a temperature gradient. The life cycle is as follows: adults reproduce sexually and then die; their offspring undergo sexual development and viability selection; a fraction of the surviving offspring migrates from their natal subpopulation to a neighbouring subpopulation; finally, individuals mature and the next round of reproduction begins.

Motivated by the SD mechanisms of the housefly (Box 1), individual sexual development was modelled to result from interactions between a single feminizing gene F, one or more masculinizing genes M and the local temperature of an individual’s environment. The F gene produces a temperature-dependent amount of product which is partially inhibited or degraded by the products from the M genes; the remaining or net amount of F product, denoted by Embedded Image, determines sex: if Embedded Image exceeds a threshold value θF, the individual develops as female, whereas if Embedded Image is below a second threshold value θM < θF it develops into a male. If Embedded Image is between the two thresholds, Embedded Image, then the individual develops into an infertile intersex.

The value of Embedded Image is obtained by summing up the net expression levels zF of both F alleles in an individual. The quantitative value of zF can vary between F alleles and depends on (1) the temperature-dependent expression level of the allele, (2) the allele’s sensitivity to M product, and (3) the amount of M product. Specifically, normalized temperature varies between T = 0 at one end (the “north”) of the array of subpopulations and T = 1 at the other end (the “south”) and it affects the net amount of F product according to Embedded Image

The first factor on the right, Embedded Image, represents the initial amount of F product, before partial degradation by M product, where Embedded Imageis the F allele’s baseline expression level at T = 0, β ≥ 0 quantifies the linear rate of increase in F expression with temperature, and ε represents random variation in expression levels due to environmental and/or developmental noise. The second factor, Embedded Image, represents the proportion of F product that is not degraded by M product, where Embedded Image is the F allele’s sensitivity to M product and Embedded Image is the cumulative amount of M product produced by the individual’s M alleles.

The baseline expression level Embedded Imageand sensitivity Embedded Image of F alleles are evolvable trait values, as are the expression levels of M alleles. Whenever a gamete is produced, each allelic trait incurs a mutation with a certain probability and its trait value is modified. Most mutations are “regular” mutations that modify traits by adding a small Gaussian amount with mean zero, but a small fraction of mutations are “null mutations” such that the resulting trait values (allelic expression levels or sensitivity to M product) are zero and cannot evolve any further. See Supplementary Table 2 for all model parameters and their default values used in the simulations.

The initial populations all have an XY male heterogametic system: all individuals carry two F alleles on an autosomal F locus and males additionally carry a single M allele (designated MY) on their Y-chromosome. Initially there are no M alleles on autosomes, but we assume that during meiosis sometimes a new M allele (designated MA) is created on an autosomal locus; this is assumed to occur via de novo evolution of a novel M allele, but can also occur via transposition from a Y-chromosomal M allele. Individuals carry at most four M alleles: two on the Y-chromosome (if they have two Y chromosomes) and two on an autosome. In natural systems, many loci may be capable of evolving a male-determining function28, but we consider here only a single autosomal locus for simplicity. Thus, the initial XY population has the potential to evolve into a population with a new system of male heterogamety where an autosomal chromosome with an M allele has replaced the original Y-chromosome. Evolution of populations with female heterogamety is also a potential outcome, if females become heterozygous for an insensitive F allele (i.e., with Embedded Image) with a sufficiently high expression level.

We also allowed for Y-chromosomal fitness effects: (1) individuals homozygous for the Y-chromosome will have reduced viability 0 ≤ sYY ≤ 1, and (2) Y-chromosomes carry sexually antagonistic alleles that are beneficial to males and detrimental in females, with additive effect 1 + sa males and 1 − sa in females (where sa ≥ 0 is the antagonistic effect). The combined effects of Y-homozygosity and sexual antagonism are assumed to be multiplicative, i.e., a male with two Y-chromosomes will have his expected fitness modified by a factor sYY(1 + sa), whereas a female with two Y-chromosomes gets sYY (1 − sa).

Results

Evolution of F insensitivity and establishment of SD system gradients

As an initial exploration of the model, we performed a set of simulations without temperature effects, where we instead varied SD thresholds θF and θM to determine how this affects the evolution of F, M, and the SD system as a whole. The results of this analysis are presented in detail in Appendix 1. Most importantly, we find that F can evolve into a dominant female-determining gene by becoming insensitive to M, provided that a single F allele generates enough F product to induce feminization, i.e., the threshold for feminization θF is sufficiently low relative to F expression zF. We refer to such insensitive dominant feminizing F alleles as FI. Provided that the feminization threshold θF is constant under all conditions, local variation in temperature could then lead to divergent evolution of SD systems as temperature effects on F expression could then allow for local evolution of a female heterogamety system.

To test this reasoning, we used simulations in which we varied two parameters: the rate β at which temperature increases F expression (see Equation 1) and the threshold value θF for feminization. Here, we exclude Y-chromosomal fitness effects, but explore their impact on SD evolution in the following section. We found that FI can spread in the entire metapopulation when the feminization threshold θF is sufficiently small (Figure 2A), regardless of how strongly temperature affects F expression. For sufficiently high values of θF, FI was unable to spread in colder demes because it would result in intersexual development (Supplementary Figure 4), but could still spread in warmer demes. Under these conditions, a geographical cline in the frequency of FI evolves (Figure 2B).

Figure 2:
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Figure 2:

Conditions for spread of a dominant female-determining gene FI as a function of the temperature-dependent expression rate 1 + β and the feminization threshold θF. When β = 0, expression is unaffected by temperature. (A) Equilibrium frequencies of FI at edges (first/last deme) of the population range; local temperatures are indicated in brackets (parameter values: θM = 0.2; µD = 0.001). In the northern deme (T = 0), temperature-dependent expression of F is lowest while expression is highest in the southern deme (T = 1). (B) Between these two extremes, the equilibrium frequency of FI increases along the temperature gradient (shown here for θF = 1.20; θM = 0.2; β = 0.76; µD = 0.014; the results depicted were chosen based on whether or not a gradient in FI was observed, with parameter values in each simulation being chosen at random from uniform distributions). Depicted in A and B are the frequency of the FI allele at the maternally-inherited locus in females. White dashed lines in A indicate the parameter values for the simulation results depicted in B (vertical line: 1 + β; horizontal line: θF).

These results underline that the distribution of FI is constrained by the expression level of F, and show that temperature-dependent effects on gene expression can establish gradients when temperature varies. Due to its feminizing effect, an FI allele is transmitted as if it were a female-limited W-chromosome in a ZW system, wherein males have a ZZ genotype, whereas females have a ZW genotype (in contrast to XY systems where females are XX and males are XY). As a result, it occurs only in FI/F females (or non-reproducing intersexes). In the presence of M product, the FI product is not broken down but the product of regular sensitive F alleles is degraded, so that regular F alleles do not contribute to the total F product. This scenario becomes increasingly probable as either MY and/or MA frequency increases, as more FI-bearing individuals will also bear MY and/or MA. Therefore, feminization of developing embryos under these conditions is achieved solely by the activity of the FI allele. Because FI is insensitive to M, the total F activity is determined by its expression (see Equation 1). When no temperature-dependent expression occurs, feminization is only achieved when the baseline genetic expression level exceeds the feminization threshold, but in the presence of temperature effects is less constrained. Therefore, when θF is sufficiently low, FI can spread everywhere independent of temperature (Figure 2A, left panel), whereas otherwise FI frequencies depend on the temperature-dependent expression rate (Figure 2A, right panel) and the local temperature (Figure 2B).

Y-chromosomal fitness effects modulate the conditions under which SD turnover can occur and can enable complex SD polymorphisms

For the simulations discussed above, we assumed that MY is not associated with any fitness effects. Under these conditions, MY was always lost and replaced by MA because MY instead was neither favoured by selection nor recurrently formed through mutation. However, as MY is the ancestral SD gene, it may have induced the chromosome on which it is located to undergo Y-chromosome evolution (reviewed in 29,30). If so, this chromosome is expected to become enriched for sexually antagonistic (SA) genetic variants as well as recessive deleterious mutations. In effect, this would cause MY to be associated with higher fitness in heterozygous +/MY males, but to induce a fitness cost to MY-bearing females (who also carry FI) as well as all homozygous MY/MY individuals. Both sexually antagonistic genetic variation and a cost of homozygosity can in theory strongly affect evolutionary transitions in SD (reviewed in 31). We therefore performed additional simulations where we considered a sexually antagonistic fitness effect of the Y-chromosome (see Supplementary Table 1), causing the Y-chromosome to affect individual fitness during the mating phase or during development (positively in males, negatively in females). In addition, we include costs of MY/MY homozygosity as a form of viability selection during embryogenesis.

When MY is under sexually antagonistic selection, we find that it is maintained over MA (Figure 3). Sexually antagonistic selection on MY can also inhibit invasion of FI if selection is sufficiently strong, so that negative effects of MY in females reduces the fitness of FI/F females relative to non-MY-carrying F/F females. However, when the rate of introduction of novel MA alleles is sufficiently high, FI can always invade even if the selective effects associated with MY are strong. When MA originates more frequently and therefore reaches higher frequencies, a more male-biased sex ratio results (similar to Y-chromosomal meiotic drive32,33) and hence the selective benefit for FI as a female-determining factor increases.

Figure 3:
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Figure 3:

Y-chromosomal fitness effects alter the scope for SD transitions. Shown are the predicted equilibrium frequencies of FI in females (maternally-inherited alleles), MY and MA in males (paternally-inherited alleles); we restrict our analysis to the maternal (FI) c.q. paternal (MY, MA) alleles to account for their (potential) sex-specific transmission. Horizontal labels indicate locus and temperature, vertical labels the MA activation rate µD. Further parameter values used in simulations: θF = 1.2; θM = 0.3; βT = 0.5. Predicted allele frequencies were smoothed with binomial generalized additive models.

Y-chromosomal fitness effects can also enable maintenance of both MY and MA in the population, albeit in different locations. This occurs when MY is disfavoured through reduced survival of YY homozygotes in subpopulations with FI, in contrast to subpopulations without FI, where MY is favoured over MA via sexually antagonistic selection in +/MY heterozygotes. Such MY versus MA polymorphism is highly similar to the distribution of Y-chromosomal versus autosomal M-factors in the housefly M. domestica. In this species, autosomal M-factors are more prevalent at lower latitudes and coincide with a dominant feminizing allele traD (which is equivalent to FI as described above), resulting in three latitudinal gradients in Y-chromosomal M-factors, autosomal M-factors, and the traD allele. We find that Y-chromosomal fitness effects enable the evolution of this complex system in our model (see Box 1). This provides an adaptive explanation for the evolution of this system in contrast to existing models of SD evolution, which have been unable to predict when stable polymorphisms for tra versus traD along with Y-chromosomal M-factors versus autosomal M-factors may occur in general, and in particular when these coincide along environmental clines as observed under natural conditions.

Discussion

We have presented a model for the evolution of SD systems in a context where sex is determined by genetic factors in combination with environmental effects. In our model, female development is induced when the activity of a feminizing gene F exceeds a certain threshold, whereas male development is achieved when F activity is below a different and lower threshold. This can be caused by inhibition of F activity by the maleness-promoting gene(s) MY and/or MA, or by loss of F expression. We incorporated a positive effect of temperature on the expression of a feminizing locus F. We find that several different SD systems can be realized depending on the activity of an F allele relative to the threshold values for masculinization and feminization. Temperature-dependent effects on F expression may alter the relationships between F activity and SD thresholds, thereby enabling the evolution of different genetic SD systems. A particular prediction is the transition from male heterogamety to female heterogamety, which occurs in our model via the evolution of an insensitive dominant feminizing variant (FI) that induces femaleness even in the presence of MY and/or MA. FI can spread when activity of a single F or FI allele is sufficient to induce feminization; when activity is modulated by temperature, this can lead to local invasions of FI and subsequently differentiation between populations along temperature gradients. Differentiation can also occur for MY and MA, with MY being favoured in absence of FI and MA in presence of FI. This occurs when MY is associated with certain fitness effects such due to linkage with sexually antagonistic variants or recessive deleterious mutations. Altogether, we show that this can lead to the coexistence of multiple gradients in SD genes as found in M. domestica.

Our model can be amended to other SD systems than the M. domestica system on which it is based, provided that they have a basic GSD framework influenced by an environmental effect. Environmental effects on genetic sex determination systems are being reported in an increasing number of species16,34. Although temperature-dependent effects are well-documented, other environmental effects may also influence SD in certain systems such as hormonal imbalance in fish due to pollution4. Other components and assumptions of the model that are based on the housefly system may be represented differently in other species but with similar effects. For example, the impact of MA evolution is not due to a specific mechanism of mutation, but more generally by causing a male-biased sex ratio, thereby promoting the invasion of FI. Male-biased sex ratios occur due to MA overrepresentation in the gene pool via its de novo evolution, but the same effect can be achieved by translocation of a Y-chromosomal male-determining gene or via association with meiotic drivers33,35. Additionally, we see that in absence of an association between MY and fitness effects, MA replaces MY altogether, yet still drives the invasion of FI, showing that our model does not strictly require a third locus. Inversely, it is likely that a more complex genetic basis generates similar evolutionary patterns, such as when various genes can evolve into a male-determining gene28. In this scenario, many genes having a small chance to evolve into a male-determining gene may have the same net effect on sex ratio as a gene that is prone to evolving a masculinizing function. In this light, it will be interesting to test whether genes that have acquired ex-determining function in one species are prone to evolve a similar function in a related species, where it has no sex-determining function.

Previous work has shed light on the evolution of ESD and GSD systems, and when transitions between these two may arise10,20,36. However, our understanding of the evolution of polymorphic SD systems and the potential for environmental heterogeneity to influence this process remains limited. Our results highlight environmental effects on GSD systems, and under which conditions this can lead to within-species polymorphism in GSD systems. Moreover, even in systems that appear to be fully GSD, the role of environmental influences on the SD processes must not be ignored as these may have played an important role in their evolution. In extension of this, changes in environment, e.g., due to global warming, may impose yet unforeseen selective pressures on species with GSD systems.

Box 1: Evolution of the polymorphic housefly system

Our model has been inspired by the common housefly Musca domestica, in which wild populations harbour different SD systems (reviewed in 14). Here, we discuss how our model can explain the evolution of this system.

In houseflies, sex is determined by a linear cascade of genes. First, transformer (tra) induces female development when active in developing embryos37; its activity depends on pre-mRNA splicing, which is sensitive to temperature as well as other stressors38. Second, masculinizing factors (M-factors) such as Mdmd 39 trigger male development by inhibition of the tra loop through splicing of tra pre-mRNA to a male-specific variant. Intriguingly, the M-factors in M. domestica are found on different chromosomes in different populations. There also exists an insensitive variant of tra, traD, that induces female development in all carriers regardless of whether they carry any M-factors. In our model, F represents tra and likewise traD corresponds to the dominant FI as discussed in the main text; MY and MA in our model represent M-factors.

High-latitude M. domestica populations have a male heterogamety (XY) system in which the Y-chromosomal Mdmd gene induces maleness, and all individuals carry two regularly-sensitive tra alleles. At lower latitudes, however, females usually carry the insensitive traD allele, and both sexes can be homozygous for an autosomal copy of Mdmd; hence, these populations have a female heterogamety (ZW) system (Figure 4; 14,40). The geographical transition between these two SD systems is gradual, so that clines exist in the frequencies of Y-chromosomal Mdmd (decreasing towards lower latitudes), autosomal Mdmd and traD (both increasing towards lower latitudes). Temperature likely plays a causal role in maintaining these gradients by affecting the SD process41–44. Temperature effects on housefly SD have been reported in the form of biased sex ratios produced in wildtype crosses42 as well as in females carrying the masculinizer (man) mutation, another variant of tra21,37. The man mutation represents a maternal-effect male-determining gene, where man-carrying females can produce all-male progeny even if the progeny do not carry an M-factor. However, this effect is incomplete and temperature-sensitive21, with offspring sex ratios more male-biased at higher temperatures. Altogether, temperature seems to have an important influence on SD in M. domestica, but the underlying mechanisms are not yet fully understood.

Figure 4:
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Figure 4:

Model predictions vs. the observed latitudinal frequency gradient of a female-determining gene in the housefly Musca domestica. (A) The frequency of tra/tra (light orange) and traD//tra (purple) females in Europe. Adapted from 40. (B) Observed (black) and predicted (yellow) frequencies of traD-bearing females (deme position adjusted to match observed latitude range). Dashed lines indicate fitted binomial GLMs for allele frequency with latitude as the sole predictor variable. Parameter values used: β = 0.5; θF = 1.15; µD = 0.005; sa = 0.05; sYY = 0.9; d = 0.1.

The housefly with its different SD systems is represented in our model by gradients in the frequencies of MY (decreasing with temperature), MA, and FI (both increasing with temperature). Presumably, traD is limited to warmer localities for similar reasons as FI in our model, i.e., because a single traD allele may not be sufficient to induce feminization at low temperatures. Y-chromosomal Mdmd and autosomal Mdmd may follow similar dynamics as MY and MA. Y-chromosomal fitness effects can yield gradients in MY and MA, but may also prevent the spread of FI, particularly when novel MA alleles enter the population at a low rate. The evolution of a housefly-like polymorphic SD system therefore depends on a balance between the Y-chromosomal fitness effects and the rate at which new autosomal Mdmd arises. In our model, we find that a housefly-like system can evolve under various rates of MA de novo evolution (Figure 5). Higher rates of MA evolution require stronger SA effects for MY to be maintained in low-temperature demes. Costs of YY homozygosity do not appear essential for MY to be lost in the presence of FI, although they may increase the likelihood of MY being lost in favour of MA in the presence of FI by reducing the fitness of YY homozygotes. Possibly, costs of MY in females due to sexually antagonistic selection may suffice to promote the loss of MY. Our model therefore can explain the evolution of complex SD systems such as those found in houseflies. Thus, we propose a novel hypothesis for the evolution of the housefly system in which the sex determination cascade is shaped by a combination of environmental influences on tra, recurrent evolution of autosomal Mdmd, and fitness effects associated with the Y-chromosomal copy of Mdmd (Figure 6).

Figure 5:
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Figure 5:

Evolution of a housefly-like SD system. A housefly-like SD system is defined by MY being the major allele at T = 0 but the minor allele at T = 1 (in males, paternally-inherited allele), and vice versa for MA (in males, paternally-inherited alleles) and FI (in females, maternally-inherited alleles). Frequency denotes the predicted frequency of observing a housefly-like system at equilibrium in the model. Parameter values: θF = 1.2; θM = 0.3; β = 0.5. Simulations were scored as exhibiting a housefly-like system as described above (10000 simulations in total). To obtain these predicted scores, we fitted a binomial generalized additive model.

Figure 6:
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Figure 6:

A novel hypothesis for the evolution of the housefly polymorphic sex determination mechanism. (A) Evolution of MA (here represented by transposition of MY) results in an excess of M factors in the population and a male-biased sex ratio. (B) At low temperatures, the M-insensitive FI allele (equivalent to traD in M. domestica) cannot evolve, and both MY and MA persist in a heterozygous state. (C) Because MY is associated with a fitness benefit in males, MY-bearing males outcompete MA-bearing males, resulting in a return to the ancestral state with MY as the sole male-determining allele in a XY system. (D) In contrast, at high temperatures, the FD allele can evolve, and has a fitness benefit as a result of sex ratio selection. (E) As FD spreads, M alleles can be transmitted by females resulting in the formation of homozygous MY//MY and MA//MA individuals. (F) Because MY homozygosity is associated with a viability cost, these individuals have lower fitness than MA/MA individuals. This results in a loss of the MY allele and fixation of the MA allele in its place as a co-factor for male development. In effect, a transition has occurred from XY male heterogamety to ZW female heterogamety as the sex-determining role has been taken over by FD.

Data availability

Source code and analysis scripts for all simulations are freely available via GitHub (https://github.com/MartijnSchenkel/Environmental_GSD_evolution).

Methods

An overview of all parameters and their default values are provided in Supplementary Table 2.

Life cycle

We simulate a population consisting of individuals distributed among N demes (K individuals per deme, for a total population size NK) arranged along a linear gradient (Figure 1B); we vary the environmental cue T normalized from 0 in the first deme to 1 in the last deme. T positively affects the expression of a feminizing locus F and may thereby increase the probability of an individual developing as a female. In each deme, we generate a fixed number of K individuals upon initiation. Individuals have a diploid genome consisting of three linkage groups, of which one carries the F locus. The two remaining linkage groups can carry a male-determining M locus, whose product M degrades the F product. We designate one of these linkage groups as being the original sex chromosome pair and accordingly refer to these as XY chromosome pair; we refer to the M-locus on this chromosome pair as MY. The other linkage group is referred to as the autosomal chromosome pair, and we refer to its M-locus as MA. Sex is determined by the total amount of F product available after interacting with M. We assume a male heterogametic system in which females carry two X-chromosomes that lack an active M allele, and males carry one X-chromosome and a Y-chromosome that harbours an active MY allele. All individuals initially lack active MA alleles. Reproduction occurs by random mating between males and females within each deme, during which all linkage groups follow Mendelian segregation. Each allelic trait can mutate with a certain trait-specific probability. Reproduction results in a total of K juveniles within each deme, which may then disperse with a probability d to a random neighbouring deme (or d/2 in the first/last demes). After dispersal, all adults die and are replaced by the juveniles. For all simulations, a “burn-in” period of 20,000 generations is applied during which all demes have a T = 0. After this, we increase T in each deme to its final value (as determined by their position in the gradient) during a warmup period of 10,000 generations. We use a burn-in and warmup phase to ensure that the system can evolve to a stable state prior to incorporating environmental effects and to ensure selection due to environmental effects does not change abruptly. After the warmup phase, we keep conditions stable for 200,000 generations to allow the system to evolve to a new equilibrium. We then analyse the genotypes of all individuals to determine which SD systems have evolved in which demes.

Sex determination

An individual’s sex is determined by the net activity zF of the two alleles at the F locus, based on the initial expression level of each F allele minus the amount of F product that is degraded by M (see Figure 1A). Initially, each allele produces an amount Embedded Image of F product which has a sensitivity Embedded Image to breakdown by M. Environmental effects on SD are included solely with regard to F expression, so that the gross expression Embedded Image (prior to eventual breakdown by M) of an F allele is given by: Embedded Image

Here, β refers to the rate at which F expression increases between T = 0 and T = 1. To model within-deme heterogeneity in T and developmental noise, we add some noise to the expression of F by adding a Gaussian amount ε with µ = 0 and σ = σF. The cumulative amount Embedded Image of M product is determined by summing up the expression levels zM of all M alleles. F breakdown by M is determined per F allele by the expression level and sensitivity of the product, so that the net activity zF of an F allele is given by: Embedded Image

We sum up the net activity of both alleles of F to obtain the net activity of the F locus, Embedded Image, based on which sex is determined: Embedded Image in which i is used to indicate the maternal and paternal allele. Individuals develop into males if Embedded Image or into females if Embedded Image. If Embedded Image individuals develop into infertile intersexes. F expression and sensitivity, as well as M expression, can vary from 0 to 1.

Reproduction and mutation

Reproduction occurs by mating between females and males residing in the same deme; an individual’s probability of being sampled as a mate is proportional to its fitness relative to other same-sex individuals and depends solely on sex chromosome genotype; in absence of Y-chromosomal fitness effects mating effectively occurs between randomly-sampled males and females. Mutations can occur within each gamete, and occur independently for F sensitivity, F expression, and M expression each with a trait-specific probability µ. Mutations may either result in a certain shift in trait value (regular mutations) or in a loss-of-function type mutation where the trait value is set to zero (null mutation). When mutations occur, they have a trait-specific probability µnull of being a null mutation. Regular mutations result in a change in a trait value by summing the current trait value with a value sampled from normal distributions with µ = 0 and standard deviations Embedded Image, and Embedded Image for F sensitivity, F expression, and M expression. Once a trait value equals zero through either regular or null mutations, we consider this to be a loss of function and prevent the trait from undergoing further mutation so that there is no gain of function. New (expressed) MA alleles may arise de novo with a frequency µD. The expression level of newly-evolved MA locus is sampled from a normal distribution with mean µE and standard deviation σE.

Fitness effects of the Y-chromosome

We incorporate two possible fitness effects that are associated with MY. First, we incorporate a sexually antagonistic fitness effect of the Y-chromosome with additive fitness effects −sa and sa in females and males (see Supplementary Table 1). This results in a positive effect in males but a negative effect in females, and resembles a scenario in which the Y-chromosomal M-locus is tightly linked to one or more sexually antagonistic alleles. These fitness effects are effectuated during the mating phase of our model. Second, we incorporate a fully recessive viability cost of MY/MY homozygosity, whereby developing YY individuals survive to the adult stage with a probability sYY ≤ 1. This resembles the effect of mutation accumulation on the Y-chromosome. For both fitness effects, we assume that MY is fully linked to the loci under selection so that no recombination occurs.

Data analysis

We categorize all F alleles based on their sensitivity level and their expression level, where an F allele is considered insensitive if its sensitivity is equal to 0 (and sensitive if it is larger than 0), and is unexpressed when its expression is less than θM/2 (and expressed if otherwise). We classify all alleles that are insensitive and expressed as FI alleles, and all others as F alleles. We categorize all M alleles based on their expression level; we consider an M allele unexpressed when its expression is lower than (2 − θF)/2, and expressed if its expression equals or exceeds (2 − θF)/2. The threshold for F expression is based on the assumption that an expression value below θM/2 is insufficient to prevent maleness when an individual is homozygous. Similarly, an M allele may break down a small amount of F product without preventing female development. Assuming F is fully expressed (and hence a total of 2 F product is generated), breakdown by M can at most be 2 − θF. When both F alleles are fully sensitive, this means that an individual can be homozygous for an M that breaks down at most (2 − θF)/2 and still develop into a female.

Following categorization, for each deme we recorded the frequencies of F and FI as well as unexpressed and expressed M alleles on the maternally-inherited and paternally-inherited alleles. We used the ‘mgcv’ package45 to fit generalized additive models (GAMs) with binomial distributions on the allele frequencies at the two extremes T = 0 and T = 1 for each locus. For the F locus, we did so on the allele frequency of the FI allele on the maternally-inherited copy and for both MY and MA we fit GAMs on the frequency of expressed alleles on the paternally-inherited copies. In each GAM, we included a full tensor product smooth between the parameters of interest.

To assess whether a polymorphic system resembling that found in natural housefly populations had evolved, we determined for each simulation whether (1) FI was the minor allele at T = 0 and the major allele at T = 1; (2) MY was the major allele at T = 0 and the minor allele at T = 1; and (3) MA was the minor allele at T = 0 and the major allele at T = 1. Minor (major) alleles are defined as having a frequency below (over) ½. Simulations that met all three criteria were considered to have evolved a housefly-like SD system. The resulting scores were used to fit a binomially-distributed GAM with a full tensor product smooth between MA de novo rate (µD), sexually-antagonistic fitness effect (sa), and YY survival rates (sYY).

All data analysis was carried out in R (v.4.0.0; 46) and RStudio (v.1.2.5033; 47), using the ‘cowplot’48, ‘maps’49, ‘mapsproj’50, ‘mgcv’45, ‘tidyverse’51, and ‘viridis’52 packages.

Authorship contributions

LWB and IP conceived the study; MAS, J-CB, LWB and IP designed the model; MAS and IP generated the model source code; MAS conducted the simulations, performed the data analysis, wrote the initial draft; MAS, J-CB, LWB and IP contributed to writing the final manuscript.

Supplementary Material

Appendix 1: F activity relative to SD thresholds determines which SD systems are evolutionary stable

As an initial exploration of our model, we performed a set of 10,000 simulations without temperature-dependent overexpression, but for different values for the SD thresholds θM and θF. In addition, for these simulations we did not incorporate fitness effects associated with MY. For each simulation, we determined the most prevalent genotype among females and males at equilibrium, based on the expression and sensitivity levels of their F alleles as well as the number of expressed MY and MA alleles. We categorized simulations according to the activity of a single F allele (zF) relative to θM and θF to determine which SD systems can evolve under different levels of F activity.

We find that under different relationships between the maximum potential activity of a single F allele (zF) and the SD thresholds, different SD systems can evolve (Table 1). When θM < zF < θF, nearly all simulations yield an SD system where both sexes have two sensitive and expressed F alleles, and males are heterozygous for a single M (either MY or MA; females F/F; +/+, males F/F; +/M, with + indicating the absence of an expressed M allele). In contrast, when zF < θM < θF or θM < θF < zF, we additionally encounter systems in which F alleles evolved to become insensitive and/or unexpressed, but the distribution of these alleles over the sexes differs between these two scenarios: when zF < θM < θF, females carry two insensitive F alleles, whereas males carry a single insensitive F and one unexpressed F; here, insensitive F alleles can be regarded as recessive female-determining alleles, whereas the sensitive and expressed F allele (in presence of expressed M) or unexpressed F plays the role of a dominant male-determining allele. In contrast, when θM < θF < zF, females may carry a single insensitive F allele, whereas males carry none, suggesting that insensitive F alleles are dominant female-determining alleles. This is corroborated by the presence of expressed M alleles in both sexes in the simulations, which would otherwise induce maleness in their carriers.

In simulations where insensitive F alleles have evolved, we find that the remaining F alleles have become unexpressed, and in some cases that expressed M alleles are lost as well. In these simulations, insensitive F alleles spread first, along with an increased frequency of expressed M alleles in both sexes (Supplementary Figure 1), the latter being required to achieve an equal sex ratio. Next, we see that sensitive F alleles become unexpressed (and subsequently insensitive due to the constant mutation pressure affecting F sensitivity); the insensitive expressed F allele is retained as it now performs the SD function. Along with the increase in unexpressed F alleles, we similarly find that M alleles lose their expression. Based on these dynamics, we infer that evolution of F insensitivity indirectly renders the loss of expression selectively neutral for sensitive F alleles, which in turn renders the loss of M expression neutral; both genes may therefore decay via mutation accumulation in a stepwise order (Supplementary Figure 3). In addition to the systems identified in our simulations, we speculate some other systems may also be evolutionary stable (Supplementary Figure 2). Their absence from our simulations may be because they only rarely arise through evolution, or because they represent intermediate states between some of the systems that are observed. The latter for example applies to systems where females have one insensitive and one sensitive F allele, males have two sensitive F alleles, and M is fixed in both sexes (females FI/F; M/M, males F/F; M/M in Figure 3). This system is prevalent in some simulations prior to the accumulation of unexpressed F alleles and loss of M (e.g., Supplementary Figure 1). In absence of fitness effects related to MY, recurrent de novo mutation of MA results in MA replacing MY as the male-determining factor; without evolution of F, this represents a transition from one male heterogamety system to another, as MY and MA perform equivalent functions. Male heterogamety systems with MY or MA as the male-determining gene are observed regardless of the activity of F relative to the SD thresholds (Supplementary Table 3). Moreover, male heterogamety with MY or MA as a dominant male-determiner is observed in all simulations when θM < zF < θF.

Supplementary Tables

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Supplementary Table 1:

Sexually antagonistic fitness effects of MY. sa denotes the sexually antagonistic fitness effect of MY in females and males, whereas hF and hM denote the dominance of these fitness effects in +/MY heterozygotes. We assume MY to be deleterious to females but beneficial to males.

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Supplementary Table 2:

Parameters in the model and their default values.

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Supplementary Table 3:

Sex determination systems evolved under different levels of F activity relative to the maleness and femaleness thresholds θM and θF. Shown are the number of simulations in which a certain combination of female and male genotypes for F and M were found to be the most prevalent genotype. For F genotypes, F alleles are indicated by F (expressed and sensitive), FI (expressed and insensitive), and F0 (unexpressed). For M, we indicate the number of expressed M alleles in females and males. Dashes indicate that the system has not been observed under those particular conditions. We performed 10,000 independent simulations under different conditions, of which 9,927 terminated successfully (e.g., did not end with population extinction) and could be categorized.

Supplementary Figures

Supplementary Figure 1:
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Supplementary Figure 1:

Evolutionary dynamics of sex determination genes. The spread of an insensitive F allele enables the fixation of MA in both sexes, followed by the gradual accumulation of unexpressed F and loss of expressed MA. (A) Evolutionary dynamics over 5,000 generations. (B) Detail of the initial 250 generations shown in (A). Parameter values: µD = 0.027; θM = 0.399; θF = 0.789.

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Supplementary Figure 2:

Classification of sex determination systems depending on relative values of thresholds and F activity. Each system is defined by a recurrent pair of female and male genotypes that can only generate those two genotypes (conform 26). Here we define three alleles for locus F: a regular F that is expressed and sensitive to M; a variant FI that is insensitive to M and expressed; and a variant F0 that is unexpressed. For M, we distinguish between active (M) and inactive (0) variants. We use zF to refer to the activity of a single F allele. In systems with both FI and F0, M has no function and may be present or absent; this is indicated by asterisks (*/*).

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Supplementary Figure 3:

Genetic decay of F and M following the evolution of an insensitive feminizing FI allele. Starting from a standard male heterogametic system, a feminizing FI allele can invade resulting in a transition to a female heterogamety system. For this to occur, an M allele must be fixed in both sexes. Fixation of M ensures the regularly-sensitive F product is always degraded and hence these alleles confer no function leaving them susceptible to genetic decay by mutation accumulation. This can eventually lead to loss of functional F in favour of non-expressed F alleles (denoted F0). Loss of F obviates the need for M to be maintained as no regular F product is generated that must be broken down to ensure maleness in non-FI-bearing individuals (genetic males). Similar to F previously, M functionality is no longer necessary and mutations may accumulate by which M becomes unexpressed (denoted 0). Note that FI is depicted here as a dominant feminizing allele (females FI//F, males F/F) but similar scenarios apply for a recessive feminizing FI allele (females FI//FI, males FI//F). The only difference is that the F allele that is susceptible to decay is now only found in males in a heterozygous state rather than in heterozygous females and homozygous males; decay of F and M can occur according to the same principles as when FI is a dominant feminizing allele.

Supplementary Figure 4:
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Supplementary Figure 4:

Constraints on the spread of a dominant feminizing FI allele. (A) When θF < 1, FI can invade in the entire population as a single F allele generates sufficient product to induce female development. (B) When θF > 1, FI cannot spread in absence of temperature-dependent overexpression as it does not generate sufficient product to induce femaleness, and instead intersexual development is induced in FI-bearing individuals. At high temperatures, F overexpression enables a single F allele to be sufficient for feminization, allowing for FI to spread. In all cases, we assume a FI//F; M/M genotype so that regular F product is degraded.

Acknowledgements

We thank the Center for Information Technology of the University of Groningen for providing access to the Peregrine high-performance computing cluster; Pina Brinker, Fangying Chen, and Peter Hoitinga for feedback on an earlier version of the manuscript; and Babak Arani and the Evolutionary Genetics cluster for fruitful discussion. MAS was supported by an Adaptive Life grant awarded to LWB, IP, and J-CB by the University of Groningen.

Footnotes

  • https://github.com/MartijnSchenkel/Environmental_GSD_evolution

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Divergent evolution of genetic sex determination mechanisms along environmental gradients
Martijn A. Schenkel, Jean-Christophe Billeter, Leo W. Beukeboom, Ido Pen
bioRxiv 2022.05.23.493175; doi: https://doi.org/10.1101/2022.05.23.493175
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Divergent evolution of genetic sex determination mechanisms along environmental gradients
Martijn A. Schenkel, Jean-Christophe Billeter, Leo W. Beukeboom, Ido Pen
bioRxiv 2022.05.23.493175; doi: https://doi.org/10.1101/2022.05.23.493175

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