Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene

Genetic Isolation among Four Lineages of Silene nutans

Speciation is the process leading to the emergence of new species. While being usually progressive, it can sometimes be fast with rapid emergence of reproductive barriers leading to high level of reproductive isolation. Some reproductive barriers might leave signatures in the genome, through elevated level of genetic differentiation at specific loci. Similar signatures might also be the results of linked selection acting in low recombination regions. Nottingham catchfly (Silene nutans) is a Caryophyllaceae species composed of four genetically differentiated lineages for which strong and asymmetric levels of reproductive isolation have been identified. Using population transcriptomic data from several individuals of the four lineages, we inferred the best evo-demographic scenario leading to the current reproductive isolation of these four lineages. We also tested whether loci exhibiting high level of genetic differentiation represented barrier loci or were located in low recombination regions, evolving under strong influence of linked selection. Overall, the four lineages of S. nutans have diverged in strict isolation, likely during the different glacial period, through migration in distinct glacial refugia. Speciation between these four lineages appeared to be particularly fast, likely due to fast evolving plastid genome accelerating plastid-nuclear co-evolution and the probability of plastid-nuclear incompatibilities in inter-lineage hybrids.

Prickly Problems: Cylindropuntia's Low Genetic Diversity Despite Inbreeding Avoidance

Dioecy, the separation of sexes, is found in 6% of flowering plants. One widely known hypothesis suggests that it is an adaptation to mitigate inbreeding. A contrary hypothesis suggests that dioecy is an evolutionary dead end. However, contrasting patterns emerged from population genetic studies that compared the genetic diversity between dioecy versus hermaphroditic species. Specifically, in Silene, it was shown that dioecious species possess higher genetic diversity than hermaphroditic species, challenging the dead end hypothesis. To evaluate whether dioecy is indeed advantageous, further studies are needed in systems with diverse sexual systems such as the genus Cylindropuntia (Cactaceae). It encompasses species with sexual separation observed solely in polyploids. Notably, these polyploids (C. wolfii and C. chuckwallensis) share similar ploidy, flower colors, and geographic proximity, raising speculation about their shared ancestry. Moreover, C. wolfii has been reported to have a low seed production, highlighting the need to assess the reproductive strategies of the species. Our first goal was to compare the genetic diversity patterns among species with different sexual systems within the genus Cylindropuntia (Cactaceae). Our second goal was to investigate genetic shared ancestry among the polyploid species. As C. wolfii is struggling to sexually reproduce, our third objective was to investigate whether it is dominated by clonal reproduction, diversity parameters, and population structure. The clonality of C. wolfii was assessed using a combination of field survey and genetic analysis. The pattern of genetic diversity in species with diverse sexual systems did not support the dead end hypothesis. The field survey of C. wolfii revealed no seed recruitment, but the genetic analysis on the current adult plants showed low signs of clonality, suggesting that this species has recently shifted to clonal reproduction. Results showed that overall, this genus had low genetic diversity and high differentiation, implying that it is vulnerable to environmental threats.

The dynamic regulatory network of stamens and pistils in papaya

BACKGROUND

Papaya exhibits three sex types: female (XX), male (XY), and hermaphrodite (XYh), making it an unusual trioecious model for studying sex determination. A critical aspect of papaya sex determination is the pistil abortion in male flowers. However, the regulatory networks that control the development of pistils and stamens in papaya remain incompletely understood.

RESULTS

In this study, we identified three organ-specific clusters involved in papaya pistils and stamens development. We found that pistil development is primarily characterized by the significant expression of auxin-related genes, while the pistil abortion genes in males is mainly associated with cytokinin, gibberellin, and auxin pathways. Additionally, we constructed expression regulatory networks for the development of female pistils, aborted pistils and stamens in male flowers, revealing key regulatory genes and signaling pathways involved in papaya organ development. Furthermore, we systematically identified 65 members of the MADS-box gene family and 10 ABCDE subfamily MADS-box genes in papaya. By constructing a phylogenetic tree of the ABCDE subfamily, we uncovered gene contraction and expansion in papaya, providing an improved understanding of the developmental mechanisms and evolutionary history of papaya floral organs.

CONCLUSIONS

These findings provide a robust framework for identifying candidate sex-determining genes and constructing the sex determination regulatory network in papaya, providing insights and genomic resources for papaya breeding.

Large range sizes link fast life histories with high species richness across wet tropical tree floras

Understanding how the traits of lineages are related to diversification is key for elucidating the origin of variation in species richness. Here, we test whether traits are related to species richness among lineages of trees from all major biogeographical settings of the lowland wet tropics. We explore whether variation in mortality rate, breeding system and maximum diameter are related to species richness, either directly or via associations with range size, among 463 genera that contain wet tropical forest trees. For Amazonian genera, we also explore whether traits are related to species richness via variation among genera in mean species-level range size. Lineages with higher mortality rates-faster life-history strategies-have larger ranges in all biogeographic settings and have higher mean species-level range sizes in Amazonia. These lineages also have smaller maximum diameters and, in the Americas, contain dioecious species. In turn, lineages with greater overall range size have higher species richness. Our results show that fast life-history strategies influence species richness in all biogeographic settings because lineages with these ecological strategies have greater range sizes. These links suggest that dispersal has been a key process in the evolution of the tropical forest flora.

Physiological Responses of Populus cathayana and Salix babylonica to Combined Stress of Diesel Fuel and Sr2+ Stress in Soil

Diesel spills and nuclides pollution cause global ecosystem and human health problems. The remediation of contaminated soil using woody plants has received considerable attention. Differences in plant species and sex can lead to differences in tolerance to various stressors. We aimed to investigate the response of male and female seedlings of Populus cathayana and Salix babylonica to diesel and Sr2+ stress and to compare the enrichment characteristics of Sr2+ in trees. Male and female seedlings of P. cathayana and S. babylonica were treated with diesel fuel and 0, 10 (low), and 100 (high) mg Kg-1 of Sr2+. Results showed that P. cathayana and S. babylonica had good enrichment characteristics and tolerance. S. babylonica had a more robust tolerance and ability to remediate contaminated soil than P. cathayana. The defense mechanisms of both female seedlings in response to stress were similar, while males showed different defense strategies. Male trees had higher Sr2+ enrichment capacity, antioxidant enzymes, soil enzyme activity, and soluble matter content, indicating that males had higher tolerance capacity than females. Under diesel stress alone, the reduced photosynthetic rate of male seedlings of P. cathayana was mainly limited by stomatal factors, and their photosynthetic system was more tolerant to diesel. POD and APX activities, as well as alkaline phosphatase and urease activities in the soil, were significantly higher in S. babylonica seedlings than in P. cathayana, indicating that S. babylonica seedlings were more resistant to diesel pollution. At low concentrations of the Sr2+ complex, diesel and Sr2+ showed antagonistic effects in reducing the damage caused by stress. As the Sr2+ concentration increased, damage to the plants manifested primarily through synergistic enhancement. The results of this study provide a scientific basis for the remediation of diesel fuel and nuclides contaminated soils using woody plants.

Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives

How and why genetic diversity varies among species is a long-standing question in evolutionary biology. Life history traits have been shown to explain a large part of observed diversity. Among them, mating systems have one of the strongest impacts on genetic diversity, with selfing species usually exhibiting much lower diversity than outcrossing relatives. Theory predicts that a high rate of selfing amplifies selection at linked sites, reducing genetic diversity genome-wide, but frequent bottlenecks and rapid population turn-over could also explain low genetic diversity in selfers. However, how linked selection varies with mating systems and whether it is sufficient to explain the observed difference between selfers and outcrossers has never been tested. Here, we used the Aegilops/Triticum grass species, a group characterized by contrasted mating systems (from obligate outcrossing to high selfing) and marked recombination rate variation across the genome, to quantify the effects of mating system and linked selection on patterns of neutral and selected polymorphism. By analyzing phenotypic and transcriptomic data of 13 species, we show that selfing strongly affects genetic diversity and the efficacy of selection by amplifying the intensity of linked selection genome-wide. In particular, signatures of adaptation were only found in the highly recombining regions in outcrossing species. These results bear implications for the evolution of mating systems and, more generally, for our understanding of the fundamental drivers of genetic diversity.

Random epigenetic inactivation of the X-chromosomal HaMSter gene causes sex ratio distortion in persimmon

In contrast to the recent progress in the genome sequencing of plant sex chromosomes, the functional contribution of the genes in sex chromosomes remains little known1. They were classically thought to be related to sexual dimorphism, which is beneficial to male or female functions, including segregation ratios. Here we focused on the functional evolution of the sex ratio distortion-related locus Half Male Sterile/Inviable (HaMSter), which is located in the short sex-linked region in diploid persimmon (Diospyros lotus). The expression of HaMSter, encoding a plant1589-like undefined protein, is necessary for production of viable seeds. Notably, only X-allelic HaMSter is substantially expressed and half of the maternal X alleles of HaMSter is randomly inactivated, which results in sex ratio distortion in seeds. Genome-wide DNA methylome analyses revealed endosperm-specific DNA hypermethylation, especially in the X-linked region. The maintenance/release of this hypermethylation is linked to inactivation/activation of HaMSter expression, respectively, which determines the sex ratio distortion pattern.

Sexy ways: approaches to studying plant sex chromosomes

Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the specific genetic and epigenetic mechanisms responsible for shaping distinct sexes in plants. While the fundamental methods of molecular biology and genomics are generally employed for the analysis of sex chromosomes, it is often necessary to modify classical procedures not only to simplify and expedite analyses but sometimes to make them possible at all. In this review, we demonstrate how, at the level of structural and functional genetics, cytogenetics, and bioinformatics, it is essential to adapt established procedures for sex chromosome analysis.

Genetic diversity and population structure of an insect-pollinated and bird-dispersed dioecious tree Magnolia kwangsiensis in a fragmented karst forest landscape

This study combined population genetics and parentage analysis to obtain foundational data for the conservation of Magnolia kwangsiensis. M. kwangsiensis is a Class I tree species that occurs in two disjunct regions in a biodiversity hotspot in southwest China. We assessed the genetic diversity and structure of this species across its distribution range to support its conservation management. Genetic diversity and population structure of 529 individuals sampled from 14 populations were investigated using seven nuclear simple sequence repeat (nSSR) markers and three chloroplast DNA (cpDNA) fragments. Parentage analysis was used to evaluate the pollen and seed dispersal distances. The nSSR marker analysis revealed a high genetic diversity in M. kwangsiensis, with an average observed (Ho) and expected heterozygosities (He) of 0.726 and 0.687, respectively. The mean and maximum pollen and seed dispersal distances were 66.4 and 95.7 m and 535.4 and 553.8 m, respectively. Our data revealed two distinct genetic groups, consistent with the disjunct geographical distribution of the M. kwangsiensis populations. Both pollen and seed dispersal movements help maintain genetic connectivity among M. kwangsiensis populations, contributing to high levels of genetic diversity. Both genetically differentiated groups corresponding to the two disjunct regions should be recognized as separate conservation units.

Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae

Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.

Looking for non-hermaphrodite cacti: multidisciplinary studies in Gymnocalycium bruchii endemic to central Argentina

KEY MESSAGE

Through a multidisciplinary study we found that Gymnocalycium bruchii, an endemic cactus from central Argentina, acts as a dioecious species, which is the first record in this genus. Cactaceae species are typically hermaphroditic; however, about 2% have other different reproductive systems. These non-hermaphroditic species may develop sexual dimorphism in flowers or other reproductive, vegetative or ecological traits, besides a specific breeding system and floral ontogeny. Therefore, multidisciplinary research is necessary to fully understand reproduction in those species. For this purpose, we studied Gymnocalicium bruchii, a globose cactus endemic to central Argentina that is presumably dioecious or gynodioecious. We made observations in two natural and two cultivated populations. We made morphological observations of plants and flowers, and performed quantitative analyses to determine the sex ratio, size of plants and flowers, flower production, fruiting, among other variables. We performed hand-pollination, self-fertilization and free-pollination tests to determine the breeding system. Finally, we studied the anatomy and ontogeny of the reproductive organs using permanent histological slides of flower morphs at different stages. Our results confirm that Gymnocalicium bruchii is a dioecious species. Female flowers have atrophied anthers and a functional gynoecium that produces fruits and seeds. Male flowers are bigger and have a functional androecium but a sterile gynoecium. In the cultivated population, the sex ratio was 1/1, whereas the number of male individuals was higher in both natural populations. Pollination tests corroborated dioecy. Ontogenetic studies revealed that in female flowers the anthers collapse before microspore maturation, while in male flowers the gynoecium shows normal development of the ovary, style, stigma, and ovules; however, the latter are never fertilized.

Pericentromeric recombination suppression and the 'large X effect' in plants

X chromosome was reported to be a major contributor to isolation between closely related species-the 'large X' effect (LXE). The causes of LXE are not clear, but the leading theory is that it is caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. However, the LXE was also reported in species with relatively recently evolved sex chromosomes where Y chromosome is not completely degenerate and X-linked genes are not hemizygous, such as the plant Silene latifolia. Recent genome sequencing and detailed genetic mapping in this species revealed a massive (> 330 Mb) non- or rarely-recombining pericentromeric region on the X chromosome (Xpr) that comprises ~ 90% of the chromosome and over 13% of the entire genome. If any of the Xpr genes are involved in species incompatibilities, this would oppose interspecific gene flow for other genes tightly linked in the Xpr. Here we test the hypothesis that the previously reported LXE in S. latifolia is caused by the lack of recombination on most of the X chromosome. Based on genome-wide analysis of DNA polymorphism and gene expression in S. latifolia and its close cross-compatible relative S. dioica, we report that the rarely-recombining regions represent a significant barrier for interspecific gene flow. We found little evidence for any additional factors contributing to the LXE, suggesting that extensive pericentromeric recombination suppression on the X-chromosome is the major if not the only cause of the LXE in S. latifolia and S. dioica.

Between but Not Within-Species Variation in the Distribution of Fitness Effects

New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

Can heterosis and inbreeding depression explain the maintenance of outcrossing in a cleistogamous perennial?

PREMISE

What maintains mixed mating is an evolutionary enigma. Cleistogamy-the production of both potentially outcrossing chasmogamous and obligately selfing cleistogamous flowers on the same individual plant-is an excellent system to study the costs of selfing. Inbreeding depression can prevent the evolution of greater selfing within populations, and heterosis in crosses between populations may further tip the balance in favor of outcrossing. Few empirical estimates of inbreeding depression and heterosis in the same system exist for cleistogamous species.

METHODS

We investigate the potential costs of selfing by quantifying inbreeding depression and heterosis in three populations of the cleistogamous perennial Ruellia humilis Nutt (Acanthaceae). We performed three types of hand-pollinations-self, outcross-within, and outcross-between populations-and measured seed number, germination, total flower production, and estimated cumulative fitness for the resulting progeny in a greenhouse experiment.

RESULTS

We found moderate inbreeding depression for cumulative fitness (<30%) in two populations, but outbreeding depression for crosses within a third population (-26%). For between-population crosses, there was weak to modest heterosis (11-47%) in two of the population combinations, but modest to strong outbreeding depression (-21 to -71%) in the other four combinations.

CONCLUSIONS

Neither inbreeding depression nor heterosis was of sufficient magnitude to explain the continued production of chasmogamous flowers given the relative energetic advantage of cleistogamous flowers previously estimated for these populations. Outbreeding depression either within or between populations makes the maintenance of chasmogamous flowers even harder to explain. More information is needed on the genetic basis of cleistogamy to resolve this conundrum.

A Foundational Population Genetics Investigation of the Sexual Systems of Solanum (Solanaceae) in the Australian Monsoon Tropics Suggests Dioecious Taxa May Benefit from Increased Genetic Admixture via Obligate Outcrossing

Solanum section Leptostemonum is an ideal lineage to test the theoretical framework regarding proposed evolutionary benefits of outcrossing sexual systems in comparison to cosexuality. Theoretically, non-cosexual taxa should support more genetic diversity within populations, experience less inbreeding, and have less genetic structure due to a restricted ability to self-fertilize. However, many confounding factors present challenges for a confident inference that inherent differences in sexual systems influence observed genetic patterns among populations. This study provides a foundational baseline of the population genetics of several species of different sexual systems with the aim of generating hypotheses of any factor-including sexual system-that influences genetic patterns. Importantly, results indicate that dioecious S. asymmetriphyllum maintains less genetic structure and greater admixture among populations than cosexual S. raphiotes at the same three locations where they co-occur. This suggests that when certain conditions are met, the evolution of dioecy may have proceeded as a means to avoid genetic consequences of self-compatibility and may support hypotheses of benefits gained through differential resource allocation partitioned across sexes. Arguably, the most significant finding of this study is that all taxa are strongly inbred, possibly reflective of a shared response to recent climate shifts, such as the increased frequency and intensity of the region's fire regime.

Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes

BACKGROUND

Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions.

RESULTS

We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination.

CONCLUSIONS

The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.

Macroevolutionary trends and diversification dynamics in Atripliceae (Amaranthaceae s.l., Chenopodioideae): a first approach

BACKGROUND AND AIMS

Atripliceae evolved and diversified by dispersals and radiations across continents in both hemispheres, colonizing similar semi-arid, saline-alkaline environments throughout the world. Meanwhile, its species developed different life forms, photosynthetic pathways, mono- or dioecy, and different morphological features in flowers, fruiting bracteoles and seeds. In this study, we introduce a first approach to the macroevolutionary patterns and diversification dynamics of the Atripliceae to understand how time, traits, speciation, extinction and new habitats influenced the evolution of this lineage.

METHODS

We performed molecular phylogenetic analyses and clade age estimation of Atripliceae to apply time-, trait- and geographic-dependent diversification analyses and ancestral state reconstructions to explore diversification patterns within the tribe.

KEY RESULTS

Opposite diversification dynamics within the two major clades of Atripliceae, the Archiatriplex and Atriplex clades, could explain the unbalanced species richness between them; we found low mean speciation rates in the Archiatriplex clade and one shift to higher speciation rates placed in the branch of the Atriplex core. This acceleration in diversification seems to have started before the transition between C3 and C4 metabolism and before the arrival of Atriplex in the Americas, and matches the Mid-Miocene Climatic Optimum. Besides, the American species of Atriplex exhibit slightly higher net diversification rates than the Australian and Eurasian ones. While time seems not to be associated with diversification, traits such as life form, photosynthetic pathway and plant sex may have played roles as diversification drivers.

CONCLUSIONS

Traits more than time played a key role in Atripliceae diversification, and we could speculate that climate changes could have triggered speciation. The extreme arid or saline environments where Atripliceae species prevail may explain its particular evolutionary trends and trait correlations compared with other angiosperms and highlight the importance of conservation efforts needed to preserve them as genetic resources to deal with climatic changes.

Sex-Specific Physiological Responses of Populus cathayana to Uranium Stress

Attention is increasingly being paid to the contamination of soil by the radioactive element uranium (U). Phytoremediation of contaminated soil by economically advantageous and environment-protective plants shows considerable potential for addressing this problem. Populus cathayana is a species with high heavy-metal tolerance, economic value, and notable potential for phytoremediation. Plant-sex-related differences can lead to differences in vegetative growth and tolerance to various stressors. As such, in this study, we designed a pot experiment to analyze the responses of male and female trees of P. cathayana to 50 mg kg−1 U stress in contaminated soil for 3 months. We studied the U uptake and distribution, photosynthesis, chlorophyll fluorescence, active oxygen species, and antioxidant enzymes of P. cathayana. The results showed that the photosynthetic activity and chlorophyll fluorescence of male and female trees were similar, and U stress mainly affected the nonstomatal factors and photosystem II during photosynthesis. Regarding the physiological and biochemical processes, male and female trees showed different defense strategies: male trees had higher peroxidase (POD), H2O2, and soluble sugars, but lower malondialdehyde (MDA), superoxide dismutase (SOD), and soluble proteins. Under U stress, the active oxygen produced by male trees could be cleared by antioxidant enzymes, preventing damage to the cell membrane. Male trees accumulated a higher U concentration in their roots than female trees, whereas the transportation of U from roots to leaves in male trees was lower than that in female trees. Therefore, our results suggested that male trees have a higher tolerance capacity and greater ability to remediate U-polluted soil than female trees. Future phytoremediation studies should consider the differences between plant sexes in the tolerance to U-contaminated land.

Adaptive changes of the autosomal part of the genome in a dioecious clade of Silene

The genus Silene brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in Silene subgenus Silene and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (ca 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy, as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the formation of general conclusions. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.

Genetic Diversity and Population Structure of Doum Palm (Hyphaene compressa) Using Genotyping by Sequencing

Doum palm (Hyphaene compressa) is a perennial economic plant primarily growing in Kenya’s Arid and Semi-Arid Lands (ASALs). It is heavily relied upon for food, animal feed, construction materials and medicine, making it an ideal plant for resource sustainability. However, the limited information on its genetic resources has hindered its breeding and conservation studies. This study used the genotyping by sequencing approach to identify Single Nucleotide Polymorphisms. These SNPs were further used to assess the genetic diversity and population structure of 96 H. compressa accessions from Coastal, Northern and Eastern ASAL regions of Kenya using two approaches; reference-based and de novo-based assemblies. STRUCTURE analysis grouped the sampled accessions into two genetic clusters (Cluster 1 and Cluster 2). Cluster 1 included accessions from the Northern region, whereas Cluster 2 included all accessions from Eastern and Coastal regions. Accessions from Kwale (Coastal) had mixed ancestry from both Cluster 1 and Cluster 2. These STRUCTURE findings were further supported by principal components analysis, discriminant analysis of principal components and phylogenetic analysis. Analysis of molecular variance indicated greater genetic variation within populations (92.7%) than among populations (7.3%). An overall F_ST of 0.074 was observed, signifying moderate genetic differentiation among populations. The results of this study will provide information useful in breeding, marker-assisted selection and conservation management of H. compressa.

What does the distribution of fitness effects of new mutations reflect? Insights from plants

The distribution of fitness effects (DFE) of new mutations plays a central role in molecular evolution. It is therefore crucial to be able to estimate it accurately from genomic data and to understand the factors that shape it. After a rapid overview of available methods to characterize the fitness effects of mutations, we review what is known on the factors affecting them in plants. Available data indicate that life history traits (e.g. mating system and longevity) have a major effect on the DFE. By contrast, the impact of demography within species appears to be more limited. These results remain to be confirmed, and methods to estimate the joint evolution of demography, life history traits, and the DFE need to be developed.

Simulated herbivory enhances leaky sex expression in the dioecious herb Mercurialis annua

BACKGROUND AND AIMS

Plant reproductive traits are widely understood to be responsive to the selective pressures exerted by pollinators, but there is also increasing evidence for an important role for antagonists such as herbivores in shaping these traits. Many dioecious species show leaky sex expression, with males and females occasionally producing flowers of the opposite sex. Here, we asked to what extent leakiness in sex expression in Mercurialis annua (Euphorbiaceae) might also be plastically responsive to simulated herbivory. This is important because enhanced leakiness in dioecious populations could lead to a shift in both the mating system and in the conditions for transitions between combined and separate sexes.

METHODS

We examined the effect of simulated herbivory on the sexual expression of males and females of M. annua in two experiments in which different levels of simulated herbivory led to enhanced leakiness in both sexes.

KEY RESULTS

We showed that leaky sex expression in both males and females of the wind-pollinated dioecious herb M. annua is enhanced in response to simulated herbivory, increasing the probability for and the degree of leakiness in both sexes. We also found that leakiness was greater in larger females but not in larger males.

CONCLUSIONS

We discuss hypotheses for a possible functional link between herbivory and leaky sex expression, and consider what simulated herbivory-induced leakiness might imply for the evolutionary ecology of plant reproductive systems, especially the breakdown of dioecy and the evolution of hermaphroditism.

OUP accepted manuscript

The nearly neutral theory is a common framework to describe natural selection at the molecular level. This theory emphasizes the importance of slightly deleterious mutations by recognizing their ability to segregate and eventually get fixed due to genetic drift in spite of the presence of purifying selection. As genetic drift is stronger in smaller than in larger populations, a correlation between population size and molecular measures of natural selection is expected within the nearly neutral theory. However, this hypothesis was originally formulated under equilibrium conditions. As most natural populations are not in equilibrium, testing the relationship empirically may lead to confounded outcomes. Demographic nonequilibria, for instance following a change in population size, are common scenarios that are expected to push the selection–drift relationship off equilibrium. By explicitly modeling the effects of a change in population size on allele frequency trajectories in the Poisson random field framework, we obtain analytical solutions of the nonstationary allele frequency spectrum. This enables us to derive exact results of measures of natural selection and effective population size in a demographic nonequilibrium. The study of their time-dependent relationship reveals a substantial deviation from the equilibrium selection–drift balance after a change in population size. Moreover, we show that the deviation is sensitive to the combination of different measures. These results therefore constitute relevant tools for empirical studies to choose suitable measures for investigating the selection–drift relationship in natural populations. Additionally, our new modeling approach extends existing population genetics theory and can serve as foundation for methodological developments.

Metabolic Pathways for S-Metolachlor Detoxification Differ Between Tolerant Corn and Multiple-Resistant Waterhemp

Herbicide resistance in weeds can be conferred by target-site and/or non-target-site mechanisms, such as rapid metabolic detoxification. Resistance to the very-long-chain fatty acid-inhibiting herbicide, S-metolachlor, in multiple herbicide-resistant populations (CHR and SIR) of waterhemp (Amaranthus tuberculatus) is conferred by rapid metabolism compared with sensitive populations. However, enzymatic pathways for S-metolachlor metabolism in waterhemp are unknown. Enzyme assays using S-metolachlor were developed to determine the specific activities of glutathione S-transferases (GSTs) and cytochrome P450 monooxygenases (P450s) from CHR and SIR seedlings to compare with tolerant corn and sensitive waterhemp (WUS). GST activities were greater (∼2-fold) in CHR and SIR compared to WUS but much less than corn. In contrast, P450s in microsomal extracts from CHR and SIR formed O-demethylated S-metolachlor, and their NADPH-dependent specific activities were greater (>20-fold) than corn or WUS. Metabolite profiles of S-metolachlor generated via untargeted and targeted liquid chromatography-mass spectrometry from CHR and SIR differed from WUS, with greater relative abundances of O-demethylated S-metolachlor and O-demethylated S-metolachlor-glutathione conjugates formed by CHR and SIR. In summary, our results demonstrate that S-metolachlor metabolism in resistant waterhemp involves Phase I and Phase II metabolic activities acting in concert, but the initial O-demethylation reaction confers resistance.

Detecting sex-linked genes using genotyped individuals sampled in natural populations

We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.

Epigenetics drive the evolution of sex chromosomes in animals and plants

We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila, male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'