The Relative Power of Structural Genomic Variation versus SNPs in Explaining the Quantitative Trait Growth in the Marine Teleost Chrysophrys auratus.

BACKGROUND: Genetic diversity provides the basic substrate for evolution. Genetic variation consists of changes ranging from single base pairs (single-nucleotide polymorphisms, or SNPs) to larger-scale structural variants, such as inversions, deletions, and duplications. SNPs have long been used as the general currency for investigations into how genetic diversity fuels evolution. However, structural variants can affect more base pairs in the genome than SNPs and can be responsible for adaptive phenotypes due to their impact on linkage and recombination. In this study, we investigate the first steps needed to explore the genetic basis of an economically important growth trait in the marine teleost finfish Chrysophrys auratus using both SNP and structural variant data. Specifically, we use feature selection methods in machine learning to explore the relative predictive power of both types of genetic variants in explaining growth and discuss the feature selection results of the evaluated methods. METHODS: SNP and structural variant callers were used to generate catalogues of variant data from 32 individual fish at ages 1 and 3 years. Three feature selection algorithms (ReliefF, Chi-square, and a mutual-information-based method) were used to reduce the dataset by selecting the most informative features. Following this selection process, the subset of variants was used as features to classify fish into small, medium, or large size categories using KNN, naïve Bayes, random forest, and logistic regression. The top-scoring features in each feature selection method were subsequently mapped to annotated genomic regions in the zebrafish genome, and a permutation test was conducted to see if the number of mapped regions was greater than when random sampling was applied. RESULTS: Without feature selection, the prediction accuracies ranged from 0 to 0.5 for both structural variants and SNPs. Following feature selection, the prediction accuracy increased only slightly to between 0 and 0.65 for structural variants and between 0 and 0.75 for SNPs. The highest prediction accuracy for the logistic regression was achieved for age 3 fish using SNPs, although generally predictions for age 1 and 3 fish were very similar (ranging from 0-0.65 for both SNPs and structural variants). The Chi-square feature selection of SNP data was the only method that had a significantly higher number of matches to annotated genomic regions of zebrafish than would be explained by chance alone. CONCLUSIONS: Predicting a complex polygenic trait such as growth using data collected from a low number of individuals remains challenging. While we demonstrate that both SNPs and structural variants provide important information to help understand the genetic basis of phenotypic traits such as fish growth, the full complexities that exist within a genome cannot be easily captured by classical machine learning techniques. When using high-dimensional data, feature selection shows some increase in the prediction accuracy of classification models and provides the potential to identify unknown genomic correlates with growth. Our results show that both SNPs and structural variants significantly impact growth, and we therefore recommend that researchers interested in the genotype-phenotype map should strive to go beyond SNPs and incorporate structural variants in their studies as well. We discuss how our machine learning models can be further expanded to serve as a test bed to inform evolutionary studies and the applied management of species.

Orchard layout and plant traits influence fruit yield more strongly than pollinator behaviour and density in a dioecious crop.

Mutualistic plant-pollinator interactions are critical for the functioning of both non-managed and agricultural systems. Mathematical models of plant-pollinator interactions can help understand key determinants in pollination success. However, most previous models have not addressed pollinator behavior and plant biology combined. Information generated from such a model can inform optimal design of crop orchards and effective utilization of managed pollinators like western honey bees (Apis mellifera), and help generate hypotheses about the effects of management practices and cultivar selection. We expect that the number of honey bees per flower and male to female flower ratio will influence fruit yield. To test the relative importance of these effects, both singly and simultaneously, we utilized a delay differential equation model combined with Latin hypercube sampling for sensitivity analysis. Empirical data obtained from historical records and collected in kiwifruit (Actinidia chinensis) orchards in New Zealand were used to parameterize the model. We found that, at realistic bee densities, the optimal orchard had 65-75% female flowers, and the most benefit was gained from the first 6-8 bees/1000 flowers, with diminishing returns thereafter. While bee density significantly impacted fruit production, plant-based parameters-flower density and male:female flower ratio-were the most influential. The predictive model provides strategies for improving crop management, such as choosing cultivars which have their peak bloom on the same day, increasing the number of flowers with approximately 70% female flowers in the orchard, and placing enough hives to maintain more than 6 bees per 1000 flowers to optimize yield.

Historical human activities reshape evolutionary trajectories across both native and introduced ranges.

The same vectors that introduce species to new ranges could move them among native populations, but how human-mediated dispersal impacts native ranges has been difficult to address because human-mediated dispersal and natural dispersal can simultaneously shape patterns of gene flow. Here, we disentangle human-mediated dispersal from natural dispersal by exploiting a system where the primary vector was once extensive but has since ceased. From 10th to 19th Centuries, ships in the North Atlantic exchanged sediments dredged from the intertidal for ballast, which ended when seawater ballast tanks were adopted. We investigate genetic patterns from RADseq-derived SNPs in the amphipod Corophium volutator (n = 121; 4,870 SNPs) and the annelid Hediste diversicolor (n = 78; 3,820 SNPs), which were introduced from Europe to North America, have limited natural dispersal capabilities, are abundant in intertidal sediments, but not commonly found in modern water ballast tanks. We detect similar levels of genetic subdivision among introduced North American populations and among native European populations. Phylogenetic networks and clustering analyses reveal population structure between sites, a high degree of phylogenetic reticulation within ranges, and phylogenetic splits between European and North American populations. These patterns are inconsistent with phylogeographic structure expected to arise from natural dispersal alone, suggesting human activity eroded ancestral phylogeographic structure between native populations, but was insufficient to overcome divergent processes between naturalized populations and their sources. Our results suggest human activity may alter species' evolutionary trajectories on a broad geographic scale via regional homogenization and global diversification, in some cases precluding historical inference from genetic data.

Evaluating the taxa that provide shared pollination services across multiple crops and regions.

Many pollinator species visit multiple crops in multiple regions, yet we know little about their pollination service provisioning at local and regional scales. We investigated the floral visitors (n = 13,200), their effectiveness (n = 1718 single visits) and response to landscape composition across three crops avocado, mango and macadamia within a single growing region (1 year), a single crop (3 years) and across different growing regions in multiple years. In total, eight wild visitor groups were shared across all three crops. The network was dominated by three pollinators, two bees (Apis mellifera and Tetragonula spp.) and a fly, Stomorhina discolor. The visitation network for the three crops was relatively generalised but with the addition of pollen deposition data, specialisation increased. Sixteen managed and wild taxa were consistently present across three years in avocado, yet their contribution to annual network structure varied. Node specialisation (d') analyses indicated many individual orchard sites across each of the networks were significantly more specialised compared to that predicted by null models, suggesting the presence of site-specific factors driving these patterns. Identifying the taxa shared across multiple crops, regions and years will facilitate the development of specific pollinator management strategies to optimize crop pollination services in horticultural systems.

Hybridization is associated with changes in sexual system in the bryophyte genus Atrichum.

PREMISE OF THE STUDY: Over 50% of bryophytes have separate sexes, and numerous transitions have occurred between combined and separate sexes. Polyploidy and hybridization is one proximate mechanism hypothesized to cause evolutionary transitions to hermaphroditism in bryophytes because sex is expressed at the haploid stage and in nonpolyploid dioecious species males have a single V chromosome and females a U. Hermaphroditism can arise if gametophytes of allopolyploids have both U and V chromosomes. We examined the association between polyploidy and hermaphroditism in the bryophyte genus Atrichum, which has species where gametophytes can be haploid, diploid, or triploid, and some species have hermaphroditic individuals. METHODS: We generated phylogenies of Atrichum from sequences of three plastid regions (rbcL, rps4, and trnL-trnF) and the second intron for the nuclear gene Leafy/Floricaula to further understand the relationships among haploid, diploid, and triploid species, and those with combined or separate sexes. KEY RESULTS: The existence of multiple sequences of Leafy/Floricaula in diploid and triploid, but not haploid, individuals is consistent with independent allopolyploid origins of the diploid and triploid species. Allopolyploidy was associated with a likely gain in hermaphroditism in triploid Atrichum undulatum and possibly diploid A. altecristatum, but not in the allopolyploid A. crispulum (diploid at the gametophyte level). CONCLUSIONS: These results highlight a role for hybridization and polyploidy in sexual system evolution, but the presence of diploid (allopolyploid) dioecious species suggest that other factors may influence the maintenance of sexual systems after an evolutionary transition.

Polyploidy influences sexual system and mating patterns in the moss Atrichum undulatum sensu lato.

BACKGROUND AND AIMS: Evolutionary transitions between separate and combined sexes have frequently occurred across various plant lineages. In mosses, which are haploid-dominant, evolutionary transitions from separate to combined sexes are often associated with genome doubling. Polyploidy and hermaphroditism have strong effects on the inbreeding depression of a population, and are subsequently predicted to affect the mating system. METHODS: We tested the association between ploidy (haploid, diploid or triploid gametophytes) and mating system in 21 populations of Atrichum undulatum sensu lato, where sex ratios vary widely. For each population, we measured the sex ratio, estimated selfing rates using allozyme markers and determined the level of ploidy through flow cytometry. KEY RESULTS: Hermaphrodites in A. undulatum were either diploid or triploid. However, many diploid populations were strictly separate-sexed, suggesting that hermaphroditism is not a necessary result of genome doubling. Levels of selfing were strongly supported as being greater than zero in one population with strictly separate-sexed individuals, and one-third of populations with hermaphrodites. CONCLUSIONS: Although hermaphrodites are associated with triploidy, hermaphroditism is not a necessary outcome of genome duplication. Hermaphroditism, but not genome duplication alone, increased estimated selfing rates, probably due to the occurrence of selfing within a gametophyte. Thus, genome duplication can influence the mating system and the associated evolution and maintenance of reproductive traits.

Reproductive investment within inflorescences of Stylidium armeria varies with the strength of early resource commitment.

BACKGROUND AND AIMS: Resource allocation to flowers, fruits and seeds can vary greatly within an inflorescence. For example, distal fruits are often smaller and produce fewer and smaller fruits and seeds than more basal fruits. To assess the causes and functional significance of intra-inflorescence variation, pollen and resources were manipulated to test whether such patterns could be altered within racemes of Stylidum armeria, a perennial Australian herb. METHODS: Pollen and resource levels were manipulated over two flowering seasons. How the number of ovules, fertilized ovules and seeds, the probability of fruit set, and the biomass of floral and fruiting structures varied with their position on the raceme were analysed. KEY RESULTS: Most plants showed a decline in ovule and seed number toward the distal positions on the raceme, but plants differed in their pattern of intra-inflorescence allocation: racemes with greater investment in basal fruits displayed a stronger trade-off with distal investment than did racemes that made smaller initial investments. This trade-off was (a) much stronger for ovule number than for seed number, (b) ameliorated but not erased by resource addition, and (c) exacerbated by resource reduction. There was large and seemingly erratic variation across fruit positions in ovule fertilization and seed set following both natural and supplemental pollination. CONCLUSIONS: In S. armeria, allocation to reproductive traits within the inflorescence is influenced by dynamic trade-offs in resource allocation between early and late fruits, and may also be subject to inherent architectural effects. Large, unpredictable variation among fruits in fertilization success and seed set may influence the evolution of inflorescence size, ovule number and floral dimorphism.

Correlated evolution of sexual system and life-history traits in mosses.

In mosses, separate and combined sexes are evolutionarily labile, yet factors selecting for this variation are unknown. In this study, we investigate phylogenetic correlations between sexual system and five life-history traits (asexual reproduction, chromosome number, gametophore length, spore size, and seta length). We assigned states to species on a large-scale phylogeny of mosses and used maximum likelihood analyses to test for the correlations and investigate the sequence of trait acquisition. Mosses in lineages with separate sexes were significantly more likely to be large, whereas those in lineages with combined sexes had higher chromosome numbers. Moreover, evolutionary transitions to separate sexes were more likely to occur in lineages with small spores. There was no support for a correlation between asexual reproduction and separate sexes. These results suggest that sexual system evolution is influenced by traits affecting mate availability and the dispersal of gametes and spores, and provides evidence for the existence of syndromes of life-history traits in mosses.

A test of simultaneous resource and pollen limitation in Stylidium armeria.

This study tests the Haig-Westoby model, which predicts that seed output will be limited simultaneously by pollen and resources when plants optimally distribute their reproductive investment. The test was conducted over 2 yr using Stylidium armeria in a factorial design that fully crossed three pollination levels (small stigmatic loads, open pollination, and supplementation of natural loads) with three levels of resource availability (reduction through partial defoliation, unmanipulated resource conditions, and supplementation through nitrogen, phosphorus and potassium (NPK) addition). There was no evidence of pollen limitation from supplemental pollination; however, pollen reductions (to about half the normal mean stigmatic loads) sharply reduced seed output. There was no evidence of resource limitation, in that NPK addition did not, by itself, significantly elevate seed output in either year of the study, while resource reduction by defoliation lowered seed output in the second year. Simultaneous addition of both pollen and resources strongly and significantly increased seed production. These results match the direction of effects predicted by the Haig-Westoby model, and suggest that S. armeria plants at our site are at or near an equilibrium of joint limitation of seed production by pollen capture and resource availability.

The biochemistry of Rubisco in Flaveria.

C(4) plants have been reported to have Rubiscos with higher maximum carboxylation rates (kcat(CO(2))) and Michaelis-Menten constants (K(m)) for CO(2) (K(c)) than the enzyme from C(3) species, but variation in other kinetic parameters between the two photosynthetic pathways has not been extensively examined. The CO(2)/O(2) specificity (S(C/O)), kcat(CO(2)), K(c), and the K(m) for O(2) (K(o)) and RuBP (K(m-RuBP)), were measured at 25 degrees C, in Rubisco purified from 16 species of Flaveria (Asteraceae). Our analysis included two C(3) species of Flaveria, four C(4) species, and ten C(3)-C(4) or C(4)-like species, in addition to other C(4) (Zea mays and Amaranthus edulis) and C(3) (Spinacea oleracea and Chenopodium album) plants. The S(C/O) of the C(4) Flaveria species was about 77 mol mol(-1), which was approximately 5% lower than the corresponding value in the C(3) species. For Rubisco from the C(4) Flaverias kcat(CO(2)) and K(c) were 23% and 45% higher, respectively, than for Rubisco from the C(3) plants. Interestingly, it was found that the K(o) for Rubisco from the C(4) species F. bidentis and F. trinervia were similar to the C(3) Flaveria Rubiscos (approximately 650 microM) while the K(o) for Rubisco in the C(4) species F. kochiana, F. australasica, Z. mays, and A. edulis was reduced more than 2-fold. There were no pathway-related differences in K(m-RuBP). In the C(3)-C(4) species kcat(CO(2)) and K(c) were generally similar to the C(3) Rubiscos, but the K(o) values were more variable. The typical negative relationships were observed between S(C/O) and both kcat(CO(2)) and K(c), and a strongly positive relationship was observed between kcat(CO(2)) and Kc. However, the statistical significance of these relationships was influenced by the phylogenetic relatedness of the species.

Sporophytic inbreeding depression in mosses occurs in a species with separate sexes but not in a species with combined sexes.

Inbreeding depression is a critical factor countering the evolution of inbreeding and thus potentially shaping the evolution of plant sexual systems. Current theory predicts that inbreeding depression could have important evolutionary consequences, even in haploid-dominant organisms. To date, no data have been reported on inbreeding depression in moss species. Here, we present data on the magnitude of inbreeding depression in sporophytic traits of moss species with contrasting breeding systems. In Ceratodon purpureus (Ditrichaceae), a moss species with separate sexes, self-fertilizations between sibling gametophytes (intergametophytic selfing) significantly reduced fitness in two of four traits quantified, with seta length and capsule length having inbreeding coefficients significantly different from zero, resulting in a cumulative inbreeding depression that was also significantly greater than zero (δ = 0.619 ± 0.076). In hermaphroditic Funaria hygrometrica (Funariaceae), there was no evidence of inbreeding depression in seta length, spore number, capsule mass, or capsule length resulting from sporophytes generated by self-fertilization within an individual (intragametophytic selfing), and cumulative inbreeding depression was also not different from zero (δ = 0.038 ± 0.022). These results provide evidence that, despite haploid dominance, inbreeding depression can be expressed at the diploid stage in mosses and may have implications for the evolution and maintenance of combined versus separate sexes in mosses.

A theoretical investigation of the evolution and maintenance of mirror-image flowers.

Enantiostyly is the deflection of the female sex organ either to the left or to the right side of the floral axis, resulting in mirror-image flowers. Two types of enantiostyly occur: in monomorphic enantiostyly, individuals exhibit both flower forms, whereas in dimorphic enantiostyly, the forms occur on separate plants. Monomorphic enantiostyly is known from at least 10 families, whereas dimorphic enantiostyly is reported in only three. Phylogenetic evidence suggests that monomorphic enantiostyly has evolved from a straight-styled ancestor and that dimorphic enantiostyly is derived from monomorphic enantiostyly. Here, we use theoretical models to investigate the role of pollen transfer in influencing these evolutionary transitions. We used numerical calculations to examine the evolution of monomorphic and dimorphic enantiostyly under different conditions of pollen transfer, inbreeding depression, and pollinator visitation. Our results demonstrate that in comparison to a putative straight-styled ancestor, both monomorphic and dimorphic enantiostyly function to reduce geitonogamous pollen transfer with a concomitant increase in pollen export. Our calculations suggest that the first stage in the evolution of monomorphic enantiostyly involves the deflection of the style only, followed by selection for reciprocity in anther position to promote more precise cross-pollination. Constraints associated with the developmental genetics of left-right asymmetries may account for the low number of evolutionary transitions from monomorphic to dimorphic enantiostyly, despite the evolutionary stability of this condition once it arises.

The development of enantiostyly.

Enantiostyly, the deflection of the style either to the left (left-styled) or right (right-styled) side of the floral axis, has evolved in at least ten angiosperm families. Two types of enantiostyly occur: monomorphic enantiostyly, in which individuals exhibit both stylar orientations, and dimorphic enantiostyly, in which the two stylar orientations occur on separate plants. To evaluate architectural or developmental constraints on the evolution of both forms of enantiostyly, we examined inflorescence structure and floral development among unrelated enantiostylous species. We investigated relations between the position of left- and right-styled flowers and inflorescence architecture in four monomorphic enantiostylous species, and we examined the development of enantiostyly in nine monomorphic and dimorphic enantiostylous species from five unrelated lineages. The location of left- and right-styled flowers within inflorescences ranged from highly predictable (in Solanum rostratum) to random (in Heteranthera mexicana). There were striking differences among taxa in the timing of stylar bending. In Wachendorfia paniculata, Dilatris corymbosa, and Philydrum lanuginosum, the style deflected in the bud, whereas in Heteranthera spp., Monochoria australasica, Cyanella lutea, and Solanum rostratum, stylar bending occurred at the beginning of anthesis. Comparisons of organ initiation and development indicated that asymmetries along the left-right axis were expressed very late in development, despite the early initiation of a dorsiventral asymmetry. We suggest that the evolution of dimorphic enantiostyly from monomorphic enantiostyly may be constrained by a lack of left-right positional information in the bud.

The genetics of mirror-image flowers.

Conspicuous asymmetries in forms that are polymorphic within a species can be genetically or environmentally determined. Here, we present a genetic analysis of the inheritance of dimorphic enantiostyly, a sexual polymorphism in which all flowers on a plant have styles that are consistently deflected either to the left or the right side of the floral axis. Using Heteranthera multiflora (Pontederiaceae), a short-lived herb, we conducted crosses within and between left- and right-styled plants and scored progeny ratios of the style morphs in F(1), F(2) and F(3) generations. Crosses conducted in the parental generation between morphs or right-styled plants resulted in right-styled progeny, whereas crosses between left-styled plants resulted in left-styled progeny. When putative heterozygous F(1) plants were selfed, the resulting F(2) segregation ratios were not significantly different from a 3 : 1 ratio for right- and left-styled plants. Crosses between left- and right-styled plants in the F(2) generation yielded F(3) progeny with either a 1 : 1 ratio of left- and right-styled plants or right-styled progeny. Our results are consistent with a model in which a single Mendelian locus with two alleles, with the right-styled allele (R) dominant to the left-styled allele (r), governs stylar deflection. The simple inheritance of dimorphic enantiostyly has implications for the evolution and maintenance of this unusual sexual polymorphism.

Solving the puzzle of mirror-image flowers.

Enantiostyly is a plant sexual polymorphism in which female sex organs are deflected to the left or right -- resulting in 'mirror-image' flowers -- but, although it occurs in at least a dozen unrelated families of flowering plants, its adaptive significance has been unclear. Here we show that a mendelian locus governs the inheritance of style orientation and that this curious form of sexual asymmetry functions to promote cross-pollination in bee-pollinated plants.

Enantiostyly in Wachendorfia (Haemodoraceae): the influence of reproductive systems on the maintenance of the polymorphism.

Enantiostyly is a form of directional asymmetry in plants in which the style is deflected away from the main axis of the flower, either to the left or right side. In Wachendorfia (Haemodoraceae), a small genus of insect-pollinated geophytes restricted to the Cape Province of South Africa, populations are usually polymorphic for asymmetry. Here we investigate dimorphic enantiostyly in the four species of Wachendorfia to determine whether variation in their reproductive systems influences the maintenance of this genetic polymorphism. Experimental field pollinations of W. paniculata and W. thyrsiflora indicated higher fertility for cross- than for self-pollinations, whereas in W. brachyandra, these types of pollination produced similar levels of fertility. Outcrossing rates were highest in W. paniculata (t = 0.78-0.98), with W. brachyandra (t = 0.39-0.79) and W. thyrsiflora (t = 0.76) exhibiting mixed mating systems. Outcrossing rates in two populations of W. parviflora varied from mixed mating (t = 0.61) to predominant selfing (t = 0.07). Population style-morph ratios ranged from 1 : 1 in outcrossing W. paniculata to monomorphism in selfing W. parviflora and clonal W. thyrsiflora. In W. brachyandra, a species with delayed selfing, morph ratios were usually biased. The maintenance of enantiostyly in Wachendorfia appears to be strongly influenced by levels of disassortative mating and the balance between sexual and clonal recruitment.