On the importance of balancing selection in plants

Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance

Adaptive mechanisms in bacteria, which are widely assumed to be haploid or partially diploid, are thought to rely on the emergence of spontaneous mutations or lateral gene transfer from a reservoir of pre-existing variants within the surrounding environment. These variants then become fixed in the population upon exposure to selective pressures. Here, we show that multiple distinct wild-type (WT) substrains of the highly polyploid cyanobacterium Synechocystis sp. PCC 6803 can adapt rapidly to the potent herbicide methyl viologen (MV). Genome sequencing revealed that the mutations responsible for adaptation to MV were already present prior to selection in the genomes of the unadapted parental strains at low allelic frequencies. This indicates that chromosomal polyploidy in bacteria can provide cells with a reservoir of conditionally beneficial mutations that can become rapidly enriched and fixed upon selection. MV-resistant strains performed oxygenic photosynthesis less efficiently than WTs when MV was absent, suggesting trade-offs in cellular fitness associated with the evolution of MV resistance and a possible role for balancing selection in the maintenance of these alleles under ecologically relevant growth conditions. Resistance was associated with reduced intracellular accumulation of MV. Our results indicate that genome polyploidy plays a role in the rapid adaptation of some bacteria to stressful conditions, which may include xenobiotics, nutrient limitation, environmental stresses, and seasonal changes.

Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA

Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.

The consequences of flower colour polymorphism on the reproductive success of a neotropical deceptive orchid

Deceptive plants often exhibit elevated levels of polymorphism. The basis of the association between flower polymorphism and deceptive strategies, however, remains unclear. Epidendrum fulgens, a Neotropical deceptive orchid pollinated by butterflies, has an unexplored intrapopulation flower colour polymorphism. Here, we investigate the consequences of this polymorphism on its reproductive success. We performed field and common garden experiments, aiming to detect pollinator-mediated selection strength and direction over time, and test whether the presence of multiple colour morphs increases species' reproductive success. In the field, we monitored plant reproductive success and floral morphology on two populations over two flowering seasons and performed selection gradient analyses. In the common garden, we assembled plots of cultivated plants with same and different flower colour individuals (i.e., mono- and polymorphic plots), exposed them to pollinators and monitored their reproductive success. In both sites we also monitored the local pollinator community. In the field, colour morphs performed equally, but we found coherences between morphological differentiation and the direction of selection, which was very dynamic. In the common garden, mono- and polymorphic plots also performed equally, with highly variable reproductive success over time. We also found a highly diverse pollinator community. Our results suggest that flower polymorphism in E. fulgens is maintained by a combination of factors, including varying pollinator-mediated selection, assortative mating due to differential pollinator preferences and different phenotype heritability. Natural selection varied across time and space, indicating a dynamic interplay between pollinators and flower morphs.

Pollinators do not avoid or prefer a locally rare pollen colour morph in Erythronium americanum (Liliaceae)

The red-yellow pollen colour polymorphism that occurs in populations of Erythronium americanum provides an excellent opportunity to investigate the conditions leading to maintenance of phenotypic variation. Using arrays of cut E. americanum flowers with red- or yellow-pollen set in a naturally monomorphic red-pollen population, we tested whether pollinators exhibit frequency-dependent behaviours . As was previously observed when pollinator preference was tested in a pollen-colour polymorphic population, pollinators accustomed to the monomorphic red-pollen population in this study exhibited no pollen colour preference among flowers cut from a polymorphic population. The lack of pollinator colour preference against either a polymorphic or red-monomorphic background suggests that pollinators do not impose frequency-dependent selection. It is possible, however, that results would differ against a monomorphic yellow-pollen background.

Fluctuating reproductive isolation and stable ancestry structure in a fine-scaled mosaic of hybridizing Mimulus monkeyflowers

Hybridization among taxa impacts a variety of evolutionary processes from adaptation to extinction. We seek to understand both patterns of hybridization across taxa and the evolutionary and ecological forces driving those patterns. To this end, we use whole-genome low-coverage sequencing of 458 wild-grown and 1565 offspring individuals to characterize the structure, stability, and mating dynamics of admixed populations of Mimulus guttatus and Mimulus nasutus across a decade of sampling. In three streams, admixed genomes are common and a M. nasutus organellar haplotype is fixed in M. guttatus, but new hybridization events are rare. Admixture is strongly unidirectional, but each stream has a unique distribution of ancestry proportions. In one stream, three distinct cohorts of admixed ancestry are spatially structured at ~20-50m resolution and stable across years. Mating system provides almost complete isolation of M. nasutus from both M. guttatus and admixed cohorts, and is a partial barrier between admixed and M. guttatus cohorts. Isolation due to phenology is near-complete between M. guttatus and M. nasutus. Phenological isolation is a strong barrier in some years between admixed and M. guttatus cohorts, but a much weaker barrier in other years, providing a potential bridge for gene flow. These fluctuations are associated with differences in water availability across years, supporting a role for climate in mediating the strength of reproductive isolation. Together, mating system and phenology accurately predict fluctuations in assortative mating across years, which we estimate directly using paired maternal and offspring genotypes. Climate-driven fluctuations in reproductive isolation may promote the longer-term stability of a complex mosaic of hybrid ancestry, preventing either complete isolation or complete collapse of species barriers.

Genome-wide identification and evolution-profiling analysis of tps gene family in Camphora longepaniculata and screening of key TPS genes

Camphora longepaniculata is an important economic crop renowned for its rich volatile terpene compounds. Terpene synthases (TPS) are key enzymes in the biosynthesis of these compounds, playing significant roles in plant growth, development, and secondary metabolism. In this study, a total of 86 TPS genes were identified in Camphora longepaniculata, which were classified into five groups based on their evolutionary relationships. Analysis of cis-regulatory elements revealed associations between TPS genes and processes related to plant growth, development, and environmental stress responses. Gene Ontology (GO) enrichment analysis indicated that these TPS genes are predominantly linked to various enzymatic activities. Furthermore, analysis of duplication events revealed that tandem duplications (TD) and whole genome duplications (WGD) are major driving forces in the evolution of the TPS gene family. Notably, 18 TPS genes were found to be upregulated in high essential oil content varieties of Camphora longepaniculata. RT-qPCR validation further confirmed that TPS26, TPS28, and TPS47 exhibit upregulated expression during leaf development, highlighting their potential involvement in terpene biosynthesis during this crucial developmental stage. These findings lay a solid foundation for further exploration of the functions of TPS genes in Camphora longepaniculata.

Among- and within-population variation in germination response shapes ecological resilience in the Mediterranean cliff species Brassica incana

BACKGROUND AND AIMS

Understanding how plant species respond to extreme conditions is crucial for predicting their ecological resilience under climate change. Here, we aimed to forecast the ecological resilience of the Mediterranean cliff species Brassica incana (Brassicaceae) by estimating population variation in germination response under novel extreme environmental conditions.

METHODS

We investigated the thermal germination responses in 14 populations of B. incana by exposing seeds to temperatures within and outside conditions experienced in their local environment. Then, we quantified among- and within-population variation in germination response to extreme temperatures, estimated genotype-by-environment interactions (G × E) and tested if population performance at extreme temperatures is explained by local climate.

KEY RESULTS

We found significant among-population differences in germination response, a different level of within-population variability and different mechanisms underlying G × E patterns. Also, populations experiencing higher temperatures in their local environment showed a better performance at both cold and hot extremes while populations experiencing lower temperatures showed a limited ability to germinate under extreme conditions.

CONCLUSIONS

Our results suggest that populations experiencing higher temperatures in their local environment have a greater potential to face future thermal extreme conditions and their role is thus crucial to promote species ecological resilience.

Environmental Stress and Resource Availability Affect the Maintenance of Genetic Variation in a Dominant Marsh Plant (Spartina alterniflora)

Changes in genetic variation, and particularly documented declines in genetic diversity, influence not only evolutionary potential but also current ecological function. Given this context, it is essential to understand what abiotic and biotic factors promote or disrupt the maintenance of genetic variation in natural populations. To address this knowledge gap in the context of salt marsh plants, we established a three-year field experiment, testing the independent and interactive effects of nutrient availability and physical stress on the maintenance of plant (Spartina alterniflora) genotypic diversity. We found that in environments with high physical stress (i.e., low marsh elevations), diversity declined over time. However, the addition of nutrients promoted the maintenance of Spartina genotypic diversity across the physical stress gradient. We also observed changes in genotypic composition and genetic divergence across environmental stress treatments, indicating variation among Spartina genotypes in their response to these factors. Our results suggest that tidal inundation acts a selective gradient within coastal marshes, altering genotypic diversity and composition across the landscape. Moreover, our work highlights that the effects of increasing inundation due to continued sea-level rise on the maintenance of diversity may be modulated by concomitant changes in nutrient inputs, with cascading effects on marsh structure and function.

Breaking the Hybrid Myth of Paphiopedilum wenshanense: Double Bifurcated Divergence Followed by Adaptive Introgression Formed a Morphological Intermediate

Species with intermediate phenotypes are usually hypothesised to have originated from hybrid speciation. However, other mechanisms, such as double bifurcated speciation with introgression may create the same phenotypes. Clarifying the underlying process generating the observed intermediate morphology is important for conservation efforts, as it provides insights into the species' evolutionary background and adaptability. Here, we utilised genome-wide single nucleotide polymorphism data to test evolutionary history models for Paphiopedilum wenshanense Z. J. Liu & J. Yong Zhang, an orchid species that is widely considered to be a hybrid with intermediate morphology of other two closely related species, P. concolor Pfitzer and P. bellatulum Pfitzer, distributed in Indochina. Our results rejected the hybrid speciation hypothesis and ascribed the intermediate floral phenotypes of P. wenshanese to introgression from P. concolor after it diverged from P. bellatulum during the last glacial maximum. Excluding the geographic covariate, the current genetic mixing rate of P. wenshanense from P. concolor is stronger in the south part of its range and is associated with precipitation in the early summer, indicating that population divergence in P. wenshanense is being driven by adaptive introgression. These genetic patterns also correspond to the observed floral variation across P. wenshaense populations. The introgression from P. concolor, along with the intermediate and varying floral morphologies, may expand the ecological opportunities for P. wenshanense, providing an explanation for why high genetic diversity has been maintained despite a high level of inbreeding and small census population size. Our study provides a framework for future research to investigate the characteristics and underlying mechanisms of intermediate morphologies in general.

High Resolution Class I HLA -A, -B, and -C Diversity in Eastern and Southern African Populations

Africa remains significantly underrepresented in high-resolution Human Leukocyte Antigen (HLA) data, despite being one of the most genetically diverse regions in the world. This critical gap in genetic information poses a substantial barrier to HLA-based research on the continent. In this study, Class I HLA data from Eastern and Southern African populations were analysed to assess genetic diversity across the region. We examined allele and haplotype frequency distributions, deviations from Hardy-Weinberg Equilibrium (HWE), linkage disequilibrium (LD), and conducted neutrality tests of homozygosity across various populations. Additionally, the African HLA data were compared to those of Caucasian and African American populations using the Jaccard index and multidimensional scaling (MDS) methods. The study revealed that South African populations exhibited 50.4% more genetic diversity within the Class I HLA region compared to other African populations. Zambia showed an estimated 36.5% genetic diversity, with Kenya, Rwanda and Uganda showing 35.7%, 34.2%, and 31.1%, respectively. Furthermore, an analysis of in-country diversity among different tribes indicated an average Class I HLA diversity of 25.7% in Kenya, 17% in Rwanda, 2.8% in South Africa, 13.6% in Uganda, and 6.5% in Zambia. The study also highlighted the genetic distinctness of Caucasian and African American populations compared to African populations. Notably, the differential frequencies of disease-promoting and disease-preventing HLA alleles across these populations emphasize the urgent need to generate high-quality HLA data for all regions of Africa and its major ethnic groups. Such efforts will be crucial in enhancing healthcare outcomes across the continent.

A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide

The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila , antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales multiple alleles are maintained in populations. In this study, we focus on the Drosophila antimicrobial peptide Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri . Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum . In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A . To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab reared and wild caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri , but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.

The quantitative genetics of gene expression in Mimulus guttatus

Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR < 0.05). cis eQTLs are usually allelic series with three or more functionally distinct alleles. The cis locus explains about two thirds of the standing genetic variance (on average) but varies among genes and tends to be greatest when there is high indel variation in the upstream regulatory region and high nucleotide diversity in the coding sequence. Despite mapping over 10,000 trans eQTL / affected gene pairs, most of the genetic variance generated by trans acting loci remains unexplained. This implies a large reservoir of trans acting genes with subtle or diffuse effects. Mapped trans eQTLs show lower allelic diversity but much higher genetic dominance than cis eQTLs. Several analyses also indicate that trans eQTLs make a substantial contribution to the genetic correlations in expression among different genes. They may thus be essential determinants of "gene expression modules," which has important implications for the evolution of gene expression and how it is studied by geneticists.

Absence of long-term balancing selection on variation in EuMYB3, an R2R3-MYB gene responsible for the anther-color polymorphism in Erythronium umbilicatum

Balancing selection has been shown to be common in plants for several different types of traits, such as self-incompatibility and heterostyly. Generally, for these traits balancing selection is generated by interactions among individuals or between individuals and other species (e.g., pathogens or pollinators). However, there are phenotypic polymorphisms in plants that do not obviously involve types of interactions that generate balancing selection. Little is known about the extent to which balancing selection also acts to preserve these polymorphisms. Here we ask whether balancing selection preserves an anther-color polymorphism in Erythronium umbilicatum (Liliaceae). We identified a major gene underlying this polymorphism. We then attempted to detect signatures of balancing selection on that gene by developing a new coalescence test for balancing selection. We found that variation in anther color is in large part caused by variation in a paralog of EuMYB3, an anthocyanin-regulating R2R3-MYB transcription factor. However, we found little evidence for balancing selection having acted historically on EuMYB3. Our results thus suggest that plant polymorphisms, especially those not involved in interactions that are likely to generate negative frequency-dependent selection, may reflect a transient state in which one morph will eventually be fixed by either genetic drift or directional selection. Our results also suggest that regulation of the anthocyanin pathway is more evolutionarily labile than is generally believed.

Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking

Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. We generated high-frequency, genome-wide allele frequency data from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December, a period of ∼12 generations. Adaptation throughout the fundamental ecological phases of population expansion, peak density, and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of allele frequency change to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal fitness-relevance of standing variation that is likely to be masked by inference approaches based on static population sampling, or insufficiently resolved time-series data. We propose such fine-scaled temporally fluctuating selection may be an important force maintaining functional genetic variation in natural populations and an important stochastic force affecting levels of standing genetic variation genome-wide.

Mapping yield and yield-related traits using diverse common bean germplasm

Common bean (bean) is one of the most important legume crops, and mapping genes for yield and yield-related traits is essential for its improvement. However, yield is a complex trait that is typically controlled by many loci in crop genomes. The objective of this research was to identify regions in the bean genome associated with yield and a number of yield-related traits using a collection of 121 diverse bean genotypes with different yields. The beans were evaluated in replicated trials at two locations, over two years. Significant variation among genotypes was identified for all traits analyzed in the four environments. The collection was genotyped with the BARCBean6K_3 chip (5,398 SNPs), two yield/antiyield gene-based markers, and seven markers previously associated with resistance to common bacterial blight (CBB), including a Niemann-Pick polymorphism (NPP) gene-based marker. Over 90% of the single-nucleotide polymorphisms (SNPs) were polymorphic and separated the panel into two main groups of small-seeded and large-seeded beans, reflecting their Mesoamerican and Andean origins. Thirty-nine significant marker-trait associations (MTAs) were identified between 31 SNPs and 15 analyzed traits on all 11 bean chromosomes. Some of these MTAs confirmed genome regions previously associated with the yield and yield-related traits in bean, but a number of associations were not reported previously, especially those with derived traits. Over 600 candidate genes with different functional annotations were identified for the analyzed traits in the 200-Kb region centered on significant SNPs. Fourteen SNPs were identified within the gene model sequences, and five additional SNPs significantly associated with five different traits were located at less than 0.6 Kb from the candidate genes. The work confirmed associations between two yield/antiyield gene-based markers (AYD1m and AYD2m) on chromosome Pv09 with yield and identified their association with a number of yield-related traits, including seed weight. The results also confirmed the usefulness of the NPP marker in screening for CBB resistance. Since disease resistance and yield measurements are environmentally dependent and labor-intensive, the three gene-based markers (CBB- and two yield-related) and quantitative trait loci (QTL) that were validated in this work may be useful tools for simplifying and accelerating the selection of high-yielding and CBB-resistant bean cultivars.

The quantitative genetics of gene expression in Mimulus guttatus

Gene expression can be influenced by genetic variants that are closely linked to the expressed gene (cis eQTLs) and variants in other parts of the genome (trans eQTLs). We created a multiparental mapping population by sampling genotypes from a single natural population of Mimulus guttatus and scored gene expression in the leaves of 1,588 plants. We find that nearly every measured gene exhibits cis regulatory variation (91% have FDR < 0.05) and that cis eQTLs are usually allelic series with three or more functionally distinct alleles. The cis locus explains about two thirds of the standing genetic variance (on average) but varies among genes and tends to be greatest when there is high indel variation in the upstream regulatory region and high nucleotide diversity in the coding sequence. Despite mapping over 10,000 trans eQTL / affected gene pairs, most of the genetic variance generated by trans acting loci remains unexplained. This implies a large reservoir of trans acting genes with subtle or diffuse effects. Mapped trans eQTLs show lower allelic diversity but much higher genetic dominance than cis eQTLs. Several analyses also indicate that trans eQTL make a substantial contribution to the genetic correlations in expression among different genes. They may thus be essential determinants of "gene expression modules", which has important implications for the evolution of gene expression and also how it is studied by geneticists.

Chasing the mechanisms of ecologically adaptive salinity tolerance

Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.

Overcoming the congenitally disadvantageous mutation through adaptation to environmental UV exposure in land snails

Congenital fitness-disadvantageous mutations are not maintained in the population; they are purged from the population through processes such as purifying selection. However, these mutations could persist in the population as polymorphisms when it is advantageous for the individuals carrying them in adapting to a specific external environment. We tested this hypothesis using the dimorphic land snail Euhadra peliomphala simodae in Japan; these snails have dark or bright coloured shells. The survival rate of dark snails at hatching was lower than that of the bright ones, as observed in the F1 progenies produced through crossing. Dark snails have a congenital fitness-disadvantageous mutation; however, they also have protection against ultraviolet radiation. They have a higher survival rate than the bright snails in a UV environment, as observed using the UV exposure experiments and UV transmittance measurements. This is a good example of a congenitally disadvantageous mutation that is advantageous for adapting to the external environment. These results explain the maintenance of polymorphism and highlight the genotypic and phenotypic diversity in the wild population.

Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome

Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill-Robertson interference on the efficiency of protein adaptation in P. abies. Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long-term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.

A persistent major mutation in canonical jasmonate signaling is embedded in an herbivory-elicited gene network

When insect herbivores attack plants, elicitors from oral secretions and regurgitants (OS) enter wounds during feeding, eliciting defense responses. These generally require plant jasmonate (JA) signaling, specifically, a jasmonoyl-L-isoleucine (JA-Ile) burst, for their activation and are well studied in the native tobacco Nicotiana attenuata. We used intraspecific diversity captured in a 26-parent MAGIC population planted in nature and an updated genome assembly to impute natural variation in the OS-elicited JA-Ile burst linked to a mutation in the JA-Ile biosynthetic gene NaJAR4. Experiments revealed that NaJAR4 variants were associated with higher fitness in the absence of herbivores but compromised foliar defenses, with two NaJAR homologues (4 and 6) complementing each other spatially and temporally. From decade-long seed collections of natural populations, we uncovered enzymatically inactive variants occurring at variable frequencies, consistent with a balancing selection regime maintaining variants. Integrative analyses of OS-induced transcriptomes and metabolomes of natural accessions revealed that NaJAR4 is embedded in a nonlinear complex gene coexpression network orchestrating responses to OS, which we tested by silencing four hub genes in two connected coexpressed networks and examining their OS-elicited metabolic responses. Lines silenced in two hub genes (NaGLR and NaFB67) co-occurring in the NaJAR4/6 module showed responses proportional to JA-Ile accumulations; two from an adjacent module (NaERF and NaFB61) had constitutively expressed defenses with high resistance. We infer that mutations with large fitness consequences can persist in natural populations due to compensatory responses from gene networks, which allow for diversification in conserved signaling pathways and are generally consistent with predictions of an omnigene model.

The impact of habitat loss on molecular signatures of coevolution between an iconic butterfly (Alcon blue) and its host plant (Marsh gentian)

Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects of decreasing habitat patch size and connectivity associated with habitat loss on molecular signatures of coevolution in the Alcon blue butterfly (Phengaris alcon) and its most limited host, the marsh gentian (Gentiana pneumonanthe). Because reciprocal coevolution is characterized by negative frequency-dependent selection as a particular type of balancing selection, we investigated how signatures of balancing selection vary along a gradient of patch size and connectivity, using single nucleotide polymorphisms (SNPs). We found that signatures of coevolution were unaffected by patch characteristics in the host plants. On the other hand, more pronounced signatures of coevolution were observed in both spatially isolated and in large Alcon populations, together with pronounced spatial variation in SNPs that are putatively involved in coevolution. These findings suggest that habitat loss can facilitate coevolution in large butterfly populations through limiting swamping of locally beneficial alleles by maladaptive ones. We also found that allelic richness (Ar) of the coevolutionary SNPs is decoupled from neutral Ar in the butterfly, indicating that habitat loss has different effects on coevolutionary as compared with neutral processes. We conclude that this specialized coevolutionary system requires particular conservation interventions aiming at generating a spatial mosaic of both connected and of isolated habitat to maintain coevolutionary dynamics.

Spatially and temporally varying selection influence species boundaries in two sympatric Mimulus

Spatially and temporally varying selection can maintain genetic variation within and between populations, but it is less well known how these forces influence divergence between closely related species. We identify the interaction of temporal and spatial variation in selection and their role in either reinforcing or eroding divergence between two closely related Mimulus species. Using repeated reciprocal transplant experiments with advanced generation hybrids, we compare the strength of selection on quantitative traits involved in adaptation and reproductive isolation in Mimulus guttatus and Mimulus laciniatus between two years with dramatically different water availability. We found strong divergent habitat-mediated selection on traits in the direction of species differences during a drought in 2013, suggesting that spatially varying selection maintains species divergence. However, a relaxation in divergent selection on most traits in an unusually wet year (2019), including flowering time, which is involved in pre-zygotic isolation, suggests that temporal variation in selection may weaken species differences. Therefore, we find evidence that temporally and spatially varying selection may have opposing roles in mediating species boundaries. Given our changing climate, future growing seasons are expected to be more similar to the dry year, suggesting that in this system climate change may actually increase species divergence.

Variation in scent amount but not in composition correlates with pollinator visits within populations of deceptive Arum maculatum L. (Araceae)

Floral scent is vital for pollinator attraction and varies among and within plant species. However, little is known about how inter-individual variation in floral scent affects the abundance and composition of floral visitor assemblages within populations. Moreover, for deceptive plants it is predicted that intra-population variation in scent can be maintained by negative frequency-dependent selection, but empirical evidence is still lacking. To investigate the ecological and evolutionary relations between inter-individual scent variation (i.e., total emission and composition) and floral visitors in deceptive plants, we studied floral scent, visitor assemblages, and fruit set in two populations of fly-pollinated (Psychodidae, Sphaeroceridae; Diptera) and deceptive Arum maculatum from Austria (JOS) and northern Italy (DAO). By correlating individual data on floral scent and visitor assemblages, we show that inter-individual variation in floral scent partly explains variation in visitor assemblages. The quantity of floral scent emitted per individual correlated positively with visitor abundance in both populations but explained visitor composition only in DAO, where strongly scented inflorescences attracted more sphaerocerid flies. However, in each population, the composition of floral scent did not correlate with the composition of floral visitors. There was also no evidence of negative frequency-dependent selection on floral scent. Instead, in JOS, more frequent scent phenotypes attracted more pollinators and were more likely to set an infructescence than rarer ones. Our results show that floral scent, despite being key in pollinator attraction in A. maculatum, only partly explains variation in pollinator abundance and composition. Overall, this study is the first to shed light on the importance of inter-individual variation in floral scent in explaining floral visitor assemblages at the population level in a deceptive plant species.

Common microgeographical selection patterns revealed in four European conifers

Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computation inferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains within-population diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

Spatio-Temporal Variations in Pollen Limitation and Floral Traits of an Alpine Lousewort (Pedicularis rhinanthoides) in Relation to Pollinator Availability

Populations of the same plant species living in different locations but flowering at different times may vary in pollinator availability and floral traits. However, the spatial and temporal links between floral traits and pollination are rarely included in single studies. In this study, three populations of an alpine lousewort, Pedicularis rhinanthoides Schrenk subsp. tibetica (Bonati) Tsoong, were surveyed to detect the variations in floral traits and pollinator activity. We hypothesized that floral divergence was spatio-temporally correlated with pollen limitation (PL) in relation to pollinators. Sampled plants from each population were divided into three groups, according to flowering stage: early, peak, and late. Pollen-supplementation experiments and investigations into pollinators, reproductive success, and floral traits were conducted on the plants from the different flowering stages and across the populations. Our results showed that the extent of PL varies across populations and among flowering stages. Populations in which more pollinators were recorded displayed a lower extent of PL. Furthermore, the temporal differences in PL showed a similar pattern for the three populations; the plants from the peak flowering stage suffered slighter PL than those from the other two stages. Nevertheless, some of the floral traits displayed similar spatial and temporal patterns to the PL, while the others only varied among the populations spatially. The results indicated that the performance of floral traits in a particular spatial-temporal situation shows they are well adapted to the corresponding pollination environment, which might help plants to optimize their reproductive fitness under different abiotic factors.

Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

Plant hybridization is a pathway for the evolution of adaptive traits. However, hybridization between adapted and nonadapted populations may affect the persistence of combinations of adaptive alleles evolved through natural selection. Seed dormancy is an adaptive trait for weedy rice because it regulates the timing of seed germination and the persistence of the soil seed bank. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. Here, we explored the influence of hybridization on the conservation of adaptive allele combinations by evaluating natural variation and genetic structure in seed dormancy-associated genomic regions. Based on sequence variation in the genomic regions associated with seed dormancy, hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, hybrid-derived weedy rice strains were more dormant than their parental weedy rice strains, and this trait was strongly influenced by the environment. This study suggests that hybridization between weedy rice (adaptive allelic combinations for seed dormancy) and cultivated rice (nonadaptive combinations) generates weedy rice strains expressing deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and nonadapted populations appears to be reinforcing the trajectory towards the evolution of adaptive traits.

The Boechera model system for evolutionary ecology

Model systems in biology expand the research capacity of individuals and the community. Closely related to Arabidopsis, the genus Boechera has emerged as an important ecological model owing to the ability to integrate across molecular, functional, and eco-evolutionary approaches. Boechera species are broadly distributed in relatively undisturbed habitats predominantly in western North America and provide one of the few experimental systems for identification of ecologically important genes through genome-wide association studies and investigations of selection with plants in their native habitats. The ecologically, evolutionarily, and agriculturally important trait of apomixis (asexual reproduction via seeds) is common in the genus, and field experiments suggest that abiotic and biotic environments shape the evolution of sex. To date, population genetic studies have focused on the widespread species B. stricta, detailing population divergence and demographic history. Molecular and ecological studies show that balancing selection maintains genetic variation in ~10% of the genome, and ecological trade-offs contribute to complex trait variation for herbivore resistance, flowering phenology, and drought tolerance. Microbiome analyses have shown that host genotypes influence leaf and root microbiome composition, and the soil microbiome influences flowering phenology and natural selection. Furthermore, Boechera offers numerous opportunities for investigating biological responses to global change. In B. stricta, climate change has induced a shift of >2 weeks in the timing of first flowering since the 1970s, altered patterns of natural selection, generated maladaptation in previously locally-adapted populations, and disrupted life history trade-offs. Here we review resources and results for this eco-evolutionary model system and discuss future research directions.

Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

In white-throated sparrows, two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes such as the mammalian Y, the rearranged version of chromosome two (ZAL2m) is in a near-constant state of heterozygosity, offering opportunities to investigate both degenerative and selective processes during the early evolutionary stages of 'supergenes.' Here, we generated, synthesized, and analyzed extensive genome-scale data to better understand the forces shaping the evolution of the ZAL2 and ZAL2m chromosomes in this species. We found that features of ZAL2m are consistent with substantially reduced recombination and low levels of degeneration. We also found evidence that selective sweeps took place both on ZAL2m and its standard counterpart, ZAL2, after the rearrangement event. Signatures of positive selection were associated with allelic bias in gene expression, suggesting that antagonistic selection has operated on gene regulation. Finally, we discovered a region exhibiting long-range haplotypes inside the rearrangement on ZAL2m. These haplotypes appear to have been maintained by balancing selection, retaining genetic diversity within the supergene. Together, our analyses illuminate mechanisms contributing to the evolution of a young chromosomal polymorphism, revealing complex selective processes acting concurrently with genetic degeneration to drive the evolution of supergenes.

Effects of condensed tannins on behavior and performance of a specialist aphid on aspen

Genes involved in plant defences against herbivores and pathogens are often highly polymorphic. This is a putative sign that balancing selection may have operated reciprocally on the hosts and their herbivores. Spatial and temporal variations (for example, in soil nutrients and the plants' ontogenetic development) may also modulate resistance traits, and thus selection pressures, but have been largely overlooked in theories of plant defences. Important elements of defences in Populus tremula (hereafter aspen) are phenolic compounds, including condensed tannins (CTs). Concentrations of CTs vary considerably with both variations in external factors and time, but they are also believed to provide genotype-dependent resistance, mainly against chewing herbivores and pathogens. However, evidence of their contributions to resistance is sparse. Detailed studies of co-evolved plant-herbivore associations could provide valuable insights into these contributions. Therefore, we examined correlations between CT levels in aspen leaves and both the feeding behavior and reproduction of the specialist aspen leaf aphid (Chaitophorus tremulae) in varied conditions. We found that xylem sap intake and probing difficulties were higher on genotypes with high-CT concentrations. However, aphids engaged in more nonprobing activities on low-CT genotypes, indicating that CTs were not the only defence traits involved. Thus, high-CT genotypes were not necessarily more resistant than low-CT genotypes, but aphid reproduction was generally negatively correlated with local CT accumulation. Genotype-specific resistance ranking also depended on the experimental conditions. These results support the hypothesis that growth conditions may affect selection pressures mediated by aphids in accordance with balancing selection theory.

European traditional tomatoes galore: a result of farmers' selection of a few diversity-rich loci

A comprehensive collection of 1254 tomato accessions, corresponding to European traditional and modern varieties, early domesticated varieties, and wild relatives, was analyzed by genotyping by sequencing. A continuous genetic gradient between the traditional and modern varieties was observed. European traditional tomatoes displayed very low genetic diversity, with only 298 polymorphic loci (95% threshold) out of 64 943 total variants. European traditional tomatoes could be classified into several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed higher genetic diversity than the remaining varieties, suggesting that these regions might be independent secondary centers of diversity with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a genome-wide association study with fruit morphological traits in the European traditional collection. The corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise a low-diversity population suggests a history of balancing selection, in which tomato farmers likely maintained the morphological variation by inadvertently applying a high selective pressure within different varietal types.

Do Genetic Drift and Gene Flow Affect the Geographic Distribution of Female Plants in Gynodioecious Lobelia siphilitica?

Variation in population sex ratio is particularly pronounced in gynodioecious angiosperms. Extremely high female frequencies in gynodioecious populations cannot be readily explained by selective forces alone. To assess the contributions of drift and gene flow to extreme sex-ratio variation, we documented sex ratio and population size in 92 populations of Lobelia siphilitica across its range and genotyped plants using plastid and nuclear genetic markers. Similarity in spatial patterns of genetic and demographic variables may suggest that drift and/or gene flow have contributed to population sex-ratio variation in L. siphilitica. We found strong spatial structuring of extremely high female frequencies: populations with >50% female plants are restricted to the south−central portion of the range. However, we did not detect any spatial structuring in population size nor metrics of genetic diversity, suggesting that extreme variation in female frequency is not strongly affected by drift or gene flow. Extreme sex-ratio variation is frequently observed in gynodioecious plants, but its causes are difficult to identify. Further investigation into mechanisms that create or maintain the spatial structure of sex ratios in gynodioecious species will provide much needed insight.

Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment

When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within-population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within-population adaptive differentiation. We used a simulation approach to analyze the joint effects of environmental heterogeneity patterns, selection intensity and number of QTL controlling a selected trait on local adaptation in a hierarchical metapopulation design. We show the general effects of within-population environmental heterogeneity: (i) it increases occupancy rate at the margins of distribution ranges, under extreme environments and high levels of selection; (ii) it increases the adaptation lag in all environments; (iii) it impacts the genetic variance in each environment, depending on the ratio of within- to between-populations environmental heterogeneity; (iv) it reduces the selection-induced erosion of adaptive gene diversity. Most often, the smaller the number of QTL involved, the stronger are these effects. We also show that both within- and between-populations phenotypic differentiation (Q_ST ) mainly results from covariance of QTL effects rather than QTL differentiation (F_STq ), that within-population QTL differentiation is negligible, and that stronger divergent selection is required to produce adaptive differentiation within populations than among populations. With a high number of QTL, when the difference between environments within populations exceeds the smallest difference between environments across populations, high levels of within-population differentiation can be reached, reducing differentiation among populations. Our study stresses the need to account for within-population environmental heterogeneity when investigating local adaptation.

Ecological factors influence balancing selection on leaf chemical profiles of a wildflower

Balancing selection is frequently invoked as a mechanism that maintains variation within and across populations. However, there are few examples of balancing selection operating on loci underpinning complex traits, which frequently display high levels of variation. We investigated mechanisms that may maintain variation in a focal polymorphism-leaf chemical profiles of a perennial wildflower (Boechera stricta, Brassicaceae)-explicitly interrogating multiple ecological and genetic processes including spatial variation in selection, antagonistic pleiotropy and frequency-dependent selection. A suite of common garden and greenhouse experiments showed that the alleles underlying variation in chemical profile have contrasting fitness effects across environments, implicating two ecological drivers of selection on chemical profile: herbivory and drought. Phenotype-environment associations and molecular genetic analyses revealed additional evidence of past selection by these drivers. Together, these data are consistent with balancing selection on chemical profile, probably caused by pleiotropic effects of secondary chemical biosynthesis genes on herbivore defence and drought response.

Identification of novel heavy metal detoxification proteins in Solanum tuberosum: Insights to improve food security protection from metal ion stress

With increasingly serious environmental pollution problems, research has focused on identifying functional genes within plants that can help ensure food security and soil governance. In particular, plants seem to have been able to evolve specific functional genes to respond to environmental changes by losing partial gene functions, thereby representing a novel adaptation mechanism. Herein, a new category of functional genes was identified and investigated, providing new directions for understanding heavy metal detoxification mechanisms. Interestingly, this category of proteins appears to exhibit specific complexing functions for heavy metals. Further, a new approach was established to evaluate ATP-binding cassette (ABC) transporter family functions using microRNA targeted inhibition. Moreover, mutant and functional genes were identified for future research targets. Expression profiling under five heavy metal stress treatments provided an important framework to further study defense responses of plants to metal exposure. In conclusion, the new insights identified here provide a theoretical basis and reference to better understand the mechanisms of heavy metal tolerance in potato plants. Further, these new data provide additional directions and foundations for mining gene resources for heavy metal tolerance genes to improve safe, green crop production and plant treatment of heavy metal soil pollution.

Speciation along a latitudinal gradient: The origin of the Neotropical cycad sister pair Dioon sonorense-D. vovidesii (Zamiaceae)

Latitude is correlated with environmental components that determine the distribution of biodiversity. In combination with geographic factors, latitude-associated environmental variables are expected to influence speciation, but empirical evidence on how those factors interplay is scarce. We evaluated the genetic and environmental variation among populations in the pair of sister species Dioon sonorense-D. vovidesii, two cycads distributed along a latitudinal environmental gradient in northwestern Mexico, to reveal their demographic histories and the environmental factors involved in their divergence. Using genome-wide loci data, we determined the species delimitation, estimated the gene flow, and compared multiple demographic scenarios of divergence. Also, we estimated the variation of climatic variables among populations and used ecological niche models to test niche overlap between species. The effect of geographic and environmental variables on the genetic variation among populations was evaluated using linear models. Our results suggest the existence of a widespread ancestral population that split into the two species ~829 ky ago. The geographic delimitation along the environmental gradient occurs in the absence of major geographic barriers, near the 28th parallel north, where a zonation of environmental seasonality exists. The northern species, D. vovidesii, occurs in more seasonal environments but retains the same niche of the southern species, D. sonorense. The genetic variation throughout populations cannot be solely explained by stochastic processes; the latitudinal-associated seasonality has been an additive factor that strengthened the species divergence. This study represents an example of how speciation can be achieved by the effect of the latitude-associated factors on the genetic divergence among populations.

An ABA-GA bistable switch can account for natural variation in the variability of Arabidopsis seed germination time

Genetically identical plants growing in the same conditions can display heterogeneous phenotypes. Here we use Arabidopsis seed germination time as a model system to examine phenotypic variability and its underlying mechanisms. We show extensive variation in seed germination time variability between Arabidopsis accessions and use a multiparent recombinant inbred population to identify two genetic loci involved in this trait. Both loci include genes implicated in modulating abscisic acid (ABA) sensitivity. Mutually antagonistic regulation between ABA, which represses germination, and gibberellic acid (GA), which promotes germination, underlies the decision to germinate and can act as a bistable switch. A simple stochastic model of the ABA-GA network shows that modulating ABA sensitivity can generate the range of germination time distributions we observe experimentally. We validate the model by testing its predictions on the effects of exogenous hormone addition. Our work provides a foundation for understanding the mechanism and functional role of phenotypic variability in germination time.

Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

The maintenance of polygenic sex determination depends on the dominance of fitness effects which are predictive of the role of sexual antagonism

In species with polygenic sex determination (PSD), multiple male- and female-determining loci on different proto-sex chromosomes segregate as polymorphisms within populations. The extent to which these polymorphisms are at stable equilibria is not yet resolved. Previous work demonstrated that PSD is most likely to be maintained as a stable polymorphism when the proto-sex chromosomes have opposite (sexually antagonistic) fitness effects in males and females. However, these models usually consider PSD systems with only two proto-sex chromosomes, or they do not broadly consider the dominance of the alleles under selection. To address these shortcomings, I used forward population genetic simulations to identify selection pressures that can maintain PSD under different dominance scenarios in a system with more than two proto-sex chromosomes (modeled after the house fly). I found that overdominant fitness effects of male-determining proto-Y chromosomes are more likely to maintain PSD than dominant, recessive, or additive fitness effects. The overdominant fitness effects that maintain PSD tend to have proto-Y chromosomes with sexually antagonistic effects (male-beneficial and female-detrimental). In contrast, dominant fitness effects that maintain PSD tend to have sexually antagonistic multi-chromosomal genotypes, but the individual proto-sex chromosomes do not have sexually antagonistic effects. These results demonstrate that sexual antagonism can be an emergent property of the multi-chromosome genotype without individual sexually antagonistic chromosomes. My results further illustrate how the dominance of fitness effects has consequences for both the likelihood that PSD will be maintained as well as the role sexually antagonistic selection is expected to play in maintaining the polymorphism.

Balancing selection in self-fertilizing populations

Self-fertilization commonly occurs in hermaphroditic species, either occasionally or as the main reproductive mode. It strongly affects the genetic functioning of a population by increasing homozygosity and genetic drift and reducing the effectiveness of recombination. Balancing selection is a form of selection that maintains polymorphism, which has been extensively studied in outcrossing species. Yet, despite recent developments, the analysis of balancing selection in partially selfing species is limited to specific cases and a general treatment is still lacking. In particular, it is unclear whether selfing globally reduced the efficacy of balancing selection as in the well-known case of overdominance. I provide a unifying framework, quantify how selfing affects the maintenance of polymorphism and the efficacy of the different form of balancing selection, and show that they can be classified into two main categories: overdominance-like selection (including true overdominance, selection variable in space and time, and antagonistic selection), which is strongly affected by selfing, and negative frequency dependent selection, which is barely affected by selfing, even at multiple loci. I also provide simple analytical results for all cases under the assumption of weak selection. This framework provides theoretical background to analyze the genomic signature of balancing selection in partially selfing species. It also sheds new light on the evolution of selfing species, including the evolution of selfing syndrome, the interaction with pathogens, and the evolutionary fate of selfing lineages.

A potential role for overdominance in the maintenance of colour variation in the Neotropical tortoise beetle, Chelymorpha alternans

The presence of persistent polymorphisms within natural populations elicits the question of how such polymorphisms are maintained. All else equal, genetic drift and natural selection should remove genetic variants from populations. Disassortative mating and overdominance are potential mechanisms for maintaining variation within populations. Here, we consider the potential role of these mechanisms in maintaining variation in colour pattern in the tortoise beetle, Chelymorpha alternans. Five colour morphs distinguished by elytral and pronotal coloration are largely determined by a single locus of large effect with four segregating alleles. As many as four morphs co-occur in natural populations. We first assessed whether disassortative mating might maintain this polymorphism. To test for assortative and disassortative mating, we paired females with two males, one with the same colour pattern as the female and one with a different colour pattern and examined the colour patterns of the offspring. We found strong evidence for random mating as a function of colour pattern. We next assessed whether differences in offspring survival among assortative and disassortative male-female pairs maintain colour variation. Crosses involving disassortative pairings had significantly higher offspring survival during development and resulted in more adult progeny. This result is consistent with the effects of overdominance, whereby outcrossed individuals have higher fitness than their homozygous counterparts. Overall, differences in offspring survival appear to play a greater role in maintaining polymorphisms than nonrandom mating in species.

What Maintains Flower Colour Variation within Populations?

Natural selection acts on phenotypic trait variation. Understanding the mechanisms that create and maintain trait variation is fundamental to understanding the breadth of diversity seen on Earth. Flower colour is among the most conspicuous and highly diverse traits in nature. Most flowering plant populations have uniform floral colours, but a minority exhibit within-population colour variation, either discrete (polymorphic) or continuous. Colour variation is commonly maintained by balancing selection through multiple pollinators, opposing selection regimes, or fluctuating selection. Variation can also be maintained by heterozygote advantage or frequency-dependent selection. Neutral processes, or a lack of selection, may maintain variation, although this remains largely untested. We suggest several prospective research directions that may provide insight into the evolutionary drivers of trait variation.

Arabidopsis natural variation in insect egg-induced cell death reveals a role for LECTIN RECEPTOR KINASE-I.1

In Arabidopsis (Arabidopsis thaliana), a hypersensitive-like response (HR-like response) is triggered underneath the eggs of the large white butterfly Pieris brassicae (P. brassicae), and this response is dependent on salicylic acid (SA) accumulation and signaling. Previous reports indicate that the clade I L-type LECTIN RECEPTOR KINASE-I.8 (LecRK-I.8) is involved in early steps of egg recognition. A genome-wide association study was used to better characterize the genetic structure of the HR-like response and discover loci that contribute to this response. We report here the identification of LecRK-I.1, a close homolog of LecRK-I.8, and show that two main haplotypes that explain part of the variation in HR-like response segregate among natural Arabidopsis accessions. Besides, signatures of balancing selection at this locus suggest that it may be ecologically important. Disruption of LecRK-I.1 results in decreased HR-like response and SA signaling, indicating that this protein is important for the observed responses. Furthermore, we provide evidence that LecRK-I.1 functions in the same signaling pathway as LecRK-I.8. Altogether, our results show that the response to eggs of P. brassicae is controlled by multiple LecRKs.

A Comprehensive Approach to Detect Hybridization Sheds Light on the Evolution of Earth's Largest Lizards

Hybridization between species occurs more frequently in vertebrates than traditionally thought but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoensis) from Indonesia and a common ancestor of an Australian group of monitor lizards known colloquially as sand monitors. Our data comprises >300 nuclear loci, mitochondrial genomes, phenotypic data, fossil and contemporary records, and past/present climatic data. We show that the four sand monitor species share more nuclear alleles with V. komodoensis than expected given a bifurcating phylogeny, likely as a result of hybridization between the latter species and a common ancestor of sand monitors. Sand monitors display phenotypes that are intermediate between their closest relatives and V. komodoensis. Biogeographic analyses suggest that V. komodoensis and ancestral sand monitors co-occurred in northern Australia. In agreement with the fossil record, this provides further evidence that the Komodo dragon once inhabited the Australian continent. Our study shows how different sources of evidence can be used to thoroughly characterize evolutionary histories that deviate from a treelike pattern, that hybridization can have long-lasting effects on phenotypes and that detecting hybridization can improve our understanding of evolutionary and biogeographic patterns.

A candidate gene association analysis identifies SNPs potentially involved in drought tolerance in European beech (Fagus sylvatica L.)

Studies of genetic variation underlying traits related to drought tolerance in forest trees are of great importance for understanding their adaptive potential under a climate change scenario. In this study, using a candidate gene approach, associations between SNPs and drought related traits were assessed in saplings of European beech (Fagus sylvatica L.) representing trees growing along steep precipitation gradients. The saplings were subjected to experimentally controlled drought treatments. Response of the saplings was assessed by the evaluation of stem diameter growth (SDG) and the chlorophyll fluorescence parameters FV/FM, PIabs, and PItot. The evaluation showed that saplings from xeric sites were less affected by the drought treatment. Five SNPs (7.14%) in three candidate genes were significantly associated with the evaluated traits; saplings with particular genotypes at these SNPs showed better performance under the drought treatment. The SNPs were located in the cytosolic class I small heat-shock protein, CTR/DRE binding transcription factor, and isocitrate dehydrogenase genes and explained 5.8-13.4% of the phenotypic variance. These findings provide insight into the genetic basis of traits related to drought tolerance in European beech and could support the development of forest conservation management strategies under future climatic conditions.

Does the Rarity of a Flower's Scent Phenotype in a Deceptive Orchid Explain Its Pollination Success?

Floral scent, a key mediator in plant-pollinator interactions, varies not only among plant species, but also within species. In deceptive plants, it is assumed that variation in floral scents and other traits involved in pollinator attraction is maintained by negative frequency-dependent selection, i.e., rare phenotypes are more attractive to pollinators and hence, have a higher fitness than common phenotypes. So far, it is unknown whether the rarity of multivariate and/or continuous floral scent traits influences the pollination success of flowers. Here, we tested in the deceptive orchid Cypripedium calceolus, whether flowers with rarer scent bouquets within a population have a higher chance to getting pollinated than flowers with more common scents. We collected the scent of more than 100 flowers in two populations by dynamic headspace and analyzed the samples by gas chromatography coupled to mass spectrometry (GC/MS). From the same flowers we also recorded whether they set a fruit or not. We introduced rarity measures of uni- and multivariate floral scent traits for single flowers, which allowed us to finally test for frequency-dependent pollination, a prerequisite for negative frequency-dependent selection. Our results do not show rarity has an effect on the likelihood to set fruits in neither of the two populations and in none of the scent characteristics analyzed. Hence, there is no evidence of negative frequency-dependent pollination mediated by the floral scent of C. calceolus. We discuss that our approach to determine rarity of a scent is applicable to any univariate or multivariate (semi)quantitative trait.

Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum

'Living fossils' are testimonies of long-term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience, and persistence in the face of Quaternary climate fluctuations remains unclear. To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum, a widespread East Asian Tertiary relict tree, and resequenced 99 individuals of C. japonicum and its sister species, Cercidiphyllum magnificum (Central Japan). We dated this speciation event to the mid-Miocene, and the intraspecific lineage divergence of C. japonicum (China vs Japan) to the Early Pliocene. Throughout climatic upheavals of the late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by, first, long-term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance, and, second, selective sweeps at stress response and growth-related genes likely involved in local adaptation. Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range; that is, both types of selection could be major factors contributing to the species' survival, resilience, and persistence.