Detecting adaptive trait introgression between Iris fulva and I. brevicaulis in highly selective field conditions

The idea that natural hybridization has served as an important force in evolutionary and adaptive diversification has gained considerable momentum in recent years. By combining genome analyses with a highly selective field experiment, we provide evidence for adaptive trait introgression between two naturally hybridizing Louisiana Iris species, flood-tolerant Iris fulva and dry-adapted I. brevicaulis. We planted reciprocal backcross (BC1) hybrids along with pure-species plants into natural settings that, due to a flooding event, favored I. fulva. As expected, I. fulva plants survived at much higher rates than I. brevicaulis plants. Backcross hybrids toward I. fulva (BCIF) also survived at significantly higher rates than the reciprocal backcross toward I. brevicaulis (BCIB). Survivorship of BCIB hybrids was strongly influenced by the presence of a number of introgressed I. fulva alleles located throughout the genome, while survivorship in the reciprocal BCIF hybrids was heavily influenced by two epistatically acting QTL of opposite effects. These results demonstrate the potential for adaptive trait introgression between these two species and may help to explain patterns of genetic variation observed in naturally occurring hybrid zones.     

The genetic architecture of reproductive isolation in Louisiana irises: flowering phenology

Despite the potential importance of divergent reproductive phenologies as a barrier to gene flow, we know less about the genetics of this factor than we do about any other isolating barrier. Here, we report on the genetic architecture of divergent flowering phenologies that result in substantial reproductive isolation between the naturally hybridizing plant species Iris fulva and I. brevicaulis. I. fulva initiates and terminates flowering significantly earlier than I. brevicaulis. We examined line crosses of reciprocal F1 and backcross (BC1) hybrids and determined that flowering time was polygenic in nature. We further defined quantitative trait loci (QTL) that affect the initiation of flowering in each of these species. QTL analyses were performed separately for two different growing seasons in the greenhouse, as well as in two field plots where experimental plants were placed into nature. For BCIF hybrids (BC1 toward I. fulva), 14 of 17 detected QTL caused flowering to occur later in the season when I. brevicaulis alleles were present, while the remaining 3 caused flowering to occur earlier. In BCIB hybrids (BC1 toward I. brevicaulis), 11 of 15 detected QTL caused flowering to occur earlier in the season when introgressed I. fulva alleles were present, while the remaining 4 caused flowering to occur later. These ratios are consistent with expectations of selection (as opposed to drift) promoting flowering divergence in the evolutionary history of these species. Furthermore, epistatic interactions among the QTL also reflected the same trends, with the majority of epistatic effects causing later flowering than expected in BCIF hybrids and earlier flowering in BCIB hybrids. Overlapping QTL that influenced flowering time across all four habitat/treatment types were not detected, indicating that increasing the sample size of genotyped plants would likely increase the number of significant QTL found in this study.     

The genetic architecture of reproductive isolation in Louisiana irises: pollination syndromes and pollinator preferences

In animal-pollinated plants, pollinator preferences for divergent floral forms can lead to partial reproductive isolation. We describe regions of plant genomes that affect pollinator preferences for two species of Louisiana Irises, Iris brevicaulis and Iris fulva, and their artificial hybrids. Iris brevicaulis and I. fulva possess bee and bird-pollination syndromes, respectively. Hummingbirds preferred I. fulva and under-visited both I. brevicaulis and backcrosses toward this species. Lepidopterans preferred I. fulva and backcrosses toward I. fulva, but also under-visited I. brevicaulis and I. brevicaulis backcrosses. Bumblebees preferred I. brevicaulis and F1 hybrids and rarely visited I. fulva. Although all three pollen vectors preferred one or the other species, these preferences did not prevent visitation to other hybrid/parental classes. Quantitative trait locus (QTL) mapping, in reciprocal BC1 mapping populations, defined the genetic architecture of loci that affected pollinator behavior. We detected six and nine QTLs that affected pollinator visitation rates in the BCIb and BCIf mapping populations, respectively, with as many as three QTLs detected for each trait. Overall, this study reflects the possible role of quantitative genetic factors in determining (1) reproductive isolation, (2) the pattern of pollinator-mediated genetic exchange, and thus (3) hybrid zone evolution.     

Intimately linked or hardly speaking? The relationship between genotype and environmental gradients in a Louisiana Iris hybrid population

Several models of hybrid zone evolution predict the same spatial patterns of genotypic distribution whether or not structuring is due to environment-dependent or -independent selection. In this study, we tested for evidence of environment-dependent selection in an Iris fulva x Iris brevicaulis hybrid population by examining the distribution of genotypes in relation to environmental gradients. We selected 201 Louisiana Iris plants from within a known hybrid population (80 m x 80 m) and placed them in four different genotypic classes (I. fulva, I. fulva-like hybrid, I. brevicaulis-like hybrid and I. brevicaulis) based on seven species-specific random amplified polymorphic DNA (RAPD) markers and two chloroplast DNA haplotypes. Environmental variables were then measured. These variables included percentage cover by tree canopy, elevation from the high water mark, soil pH and percentage soil organic matter. Each variable was sampled for all 201 plants. Canonical discriminant analysis (CDA) was used to infer the environmental factors most strongly associated with the different genotypic groups. Slight differences in elevation (-0.5 m to +0.4 m) were important for distinguishing habitat distributions described by CDA, even though there were no statistical differences between mean elevations alone. I. brevicaulis occurred in a broad range of habitats, while I. fulva had a narrower distribution. Of all the possible combinations, I. fulva-like hybrids and I. brevicaulis-like hybrids occurred in the most distinct habitat types relative to one another. Each hybrid class was not significantly different from its closest parent with regard to habitat occupied, but was statistically unique from its more distant parental species. Within the hybrid genotypes, most, but not all, RAPD loci were individually correlated with environmental variables. This study suggests that, at a very fine spatial scale, environment-dependent selection contributed to the genetic structuring of this hybrid zone.     

Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers

Genetic mapping studies provide insight into the pattern and extent of genetic incompatibilities affecting hybridization between closely related species. Genetic maps of two species of Louisiana Irises, Iris fulva and I. brevicaulis, were constructed from transposon-based molecular markers segregating in reciprocal backcross (BC1) interspecific hybrids and used to investigate genomic patterns of species barriers inhibiting introgression. Linkage mapping analyses indicated very little genetic incompatibility between I. fulva and I. brevicaulis in the form of map regions exhibiting transmission ratio distortion, and this was confirmed using a Bayesian multipoint mapping analysis. These results demonstrate the utility of transposon-based marker systems for genetic mapping studies of wild plant species and indicate that the genomes of I. fulva and I. brevicaulis are highly permeable to gene flow and introgression from one another via backcrossing.     

Environment-dependent performance and fitness of Iris brevicaulis, I. fulva (Iridaceae), and hybrids

We tested the relative fitness of two Louisiana Iris species (Iris brevicaulis and I. fulva) and their first-generation backcross hybrids in three experimental watering treatments: dry, field capacity, and flooded. Leaf area expansion rate, gas exchange (A(max), g(s), c(i)), and biomass at final harvest were measured for each species and hybrid class in all three environmental treatments. Fitness (based on total biomass) of the four genotypic classes differed significantly with environment. All genotypic classes performed most poorly in the dry treatment. The fitness ranking of genotypic class also changed across environments (significant genotypic class by treatment interaction) with hybrid genotype fitness shifting relative to parental genotypes. Integrating over all treatments, backcrosses to I. fulva showed the lowest fitness, whereas backcrosses to I. brevicaulis outperformed I. fulva. The differences in fitness were apparently achieved by a combination of differences in photosynthesis and allocation. In this system, hybrids are not necessarily less fit than their parents, and the relationship between hybrid and parental fitness is influenced by environmental conditions, lending support to the Hybrid Novelty model of hybrid zone evolution.     

Nectar Production in Louisiana Iris Hybrids

Nectar is an important attractant for pollinators, and a plant's success in sexual reproduction can be influenced by the amount and concentration of nectar produced by its flowers. We studied nectar production over flower lifetime in Iris fulva, Iris brevicaulis, and four classes of hybrids-reciprocal F1's and backcrosses-between these species. Iris fulva produced less concentrated nectar than did I. brevicaulis, whereas I. brevicaulis flowers had a shorter life span. Hybrids were not intermediate, but they had the high nectar concentration of I. brevicaulis combined with the long life span of I. fulva flowers. Nectar production and concentration declined after the first day in all classes, but flowers continued to produce nectar until they were completely wilted. Backcrosses did not show a shift in mean or increased variation for the characters that distinguished the parental species; backcrosses toward I. fulva retained the high nectar concentration of I. brevicaulis, and backcrosses toward I. brevicaulis did not have a reduced flower life span. Overall, F1 hybrid flowers produced the highest amounts of nectar and nectar sugar over their life spans. These results, together with previously obtained data on pollinator choice in mixed arrays of the same flower classes, show that F1 hybrids between these species do not suffer from reduced attractiveness to pollinators. F1 individuals produced more nectar and nectar sugar than did their parents, and thus, they are possibly even more attractive to pollinators that forage for nectar.     

QTL mapping reveals the genetic architecture of loci affecting pre- and post-zygotic isolating barriers in Louisiana Iris

ABSTRACT: BACKGROUND: Hybridization among Louisiana Irises has been well established and the genetic architecture of reproductive isolation is known to affect the potential for and the directionality of introgression between taxa. Here we use co-dominant markers to identify regions where QTL are located both within and between backcross maps to compare the genetic architecture of reproductive isolation and fitness traits across treatments and years. RESULTS: QTL mapping was used to elucidate the genetic architecture of reproductive isolation between Iris fulva and Iris brevicaulis. Homologous co-dominant EST-SSR markers scored in two backcross populations between I. fulva and I. brevicaulis were used to generate genetic linkage maps. These were used as the framework for mapping QTL associated with variation in 11 phenotypic traits likely responsible for reproductive isolation and fitness. QTL were dispersed throughout the genome, with the exception of one region of a single linkage group (LG) where QTL for flowering time, sterility, and fruit production clustered. In most cases, homologous QTL were not identified in both backcross populations, however, homologous QTL for flowering time, number of growth points per rhizome, number of nodes per inflorescence, and number of flowers per node were identified on several linkage groups. CONCLUSION: Two different traits affecting reproductive isolation, flowering time and sterility, exhibit different genetic architectures, with numerous QTL across the Iris genome controlling flowering time and fewer, less distributed QTL affecting sterility. QTL for traits affecting fitness are largely distributed across the genome with occasional overlap, especially on LG 4, where several QTL increasing fitness and decreasing sterility cluster. Given the distribution and effect direction of QTL affecting reproductive isolation and fitness, we have predicted genomic regions where introgression may be more likely to occur (those regions associated with an increase in fitness and unlinked to loci controlling reproductive isolation) and those that are less likely to exhibit introgression (those regions linked to traits decreasing fitness and reproductive isolation).     

Genetic architecture of leaf ecophysiological traits in Helianthus

We investigated quantitative trait loci (QTLs) for several leaf chemistry traits in early-generation hybrids between Helianthus annuus and Helianthus petiolaris, the parental species of the ancient diploid hybrid sunflower species Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus. We grew individuals of a second-generation backcross (BC(2)) toward H. petiolaris under optimum conditions in a glass house experiment. Trait values were measured once for each individual. In addition, genotypic data previously determined for each individual were employed for composite interval mapping of QTLs. We detected QTLs for leaf carbon concentration, leaf nitrogen concentration, leaf nitrogen per unit area, and photosynthetic nitrogen use efficiency. Leaf carbon isotope discrimination (delta(13)C) and leaf nitrogen isotopic composition (delta(15)N) were analyzed, but no significant QTLs were found for these traits. Interestingly, two neighboring loci explained a relatively large percentage of the variation in leaf nitrogen per unit area. This was notable because leaf nitrogen has been shown to strongly affect the fitness of early-generation sunflower hybrids in the H. anomalus habitat, and QTLs of large effect are expected to respond relatively quickly to selection. We speculate that the genetic architecture underlying leaf nitrogen may have facilitated the colonization of active desert sand dunes by H. anomalus.     

Molecular genetic evidence for interspecific hybridization among endemic Hispaniolan Bursera (Burseraceae)

Historically, genetic introgression among species as well as hybrid origins for species of the diploid tree genus Bursera (Burseraceae) have been proposed based on the supposition that individuals morphologically intermediate between sympatric "parent" species must be derived from hybridization. This study reports the first molecular genetic evidence for both unidirectional and reciprocal interspecific hybridization within Bursera. Phylogenies of hybrids and other species in B. subgenus Bursera are reconstructed based on nuclear and chloroplast sequence data. Compelling evidence supports the hybrid origin of three endemic Hispaniolan species: B. brunea (B. nashii × B. simaruba), B. gracilipes (B. spinescens × B. simaruba), and B. ovata (B. simaruba × B. spinescens). Cloning studies of nuclear markers from B. ovata suggests that this species is an introgressed or later backcross generation hybrid and thus reproduces sexually.     

Microsatellite signature of ecological selection for salt tolerance in a wild sunflower hybrid species, Helianthus paradoxus

The hybrid sunflower species Helianthus paradoxus inhabits sporadic salt marshes in New Mexico and southwest Texas, USA, whereas its parental species, Helianthus annuus and Helianthus petiolaris, are salt sensitive. Previous studies identified three genomic regions - survivorship quantitative trait loci (QTLs) - that were under strong selection in experimental hybrids transplanted into the natural habitat of H. paradoxus. Here we ask whether these same genomic regions experienced significant selection during the origin and evolution of the natural hybrid, H. paradoxus. This was accomplished by comparing the variability of microsatellites linked to the three survivorship QTLs with those from genomic regions that were neutral in the experimental hybrids. As predicted if one or more selective sweeps had occurred in these regions, microsatellites linked to the survivorship QTLs exhibited a significant reduction in diversity in populations of the natural hybrid species. In contrast, no difference in diversity levels was observed between the two microsatellite classes in parental populations.     

QTL mapping with near-isogenic lines in maize

A set of 89 near-isogenic lines (NILs) of maize was created using marker-assisted selection. Nineteen genomic regions, identified by restriction fragment length polymorphism loci and chosen to represent portions of all ten maize chromosomes, were introgressed by backcrossing three generations from donor line Tx303 into the B73 genetic background. NILs were genotyped at an additional 128 simple sequence repeat loci to estimate the size of introgressions and the amount of background introgression. Tx303 introgressions ranged in size from 10 to 150 cM, with an average of 60 cM. Across all NILs, 89% of the Tx303 genome is represented in targeted and background introgressions. The average proportion of background introgression was 2.5% (range 0–15%), significantly lower than the expected value of 9.4% for third backcross generation lines developed without marker-assisted selection. The NILs were grown in replicated field evaluations in two years to map QTLs for flowering time traits. A parallel experiment of testcrosses of each NIL to the unrelated inbred, Mo17, was conducted in the same environments to map QTLs in NIL testcross hybrids. QTLs affecting days to anthesis, days to silking, and anthesis-silk interval were detected in both inbreds and hybrids in both environments. The testing environments differed dramatically for drought stress, and different sets of QTLs were detected across environments. Furthermore, QTLs detected in inbreds were typically different from QTLs detected in hybrids, demonstrating the genetic complexity of flowering time. NILs can serve as a valuable genetic mapping resource for maize breeders and geneticists. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION IN LOUISIANA IRISES: HYBRID FITNESS IN NATURE

Negative epistasis in hybrid genomes commonly results in postzygotic isolation between divergent lineages. However, some genomic regions may be selectively neutral or adaptive in hybrids and thus may potentially cross species barriers. We examined postzygotic isolation between ecologically similar species of Louisiana Iris: Iris brevicaulis and I. fulva to determine the potential for adaptive introgression in nature. Line-cross analyses allowed us a general overview of the gene action responsible for fitness-related traits. We then used a QTL mapping approach to detect genomic regions responsible for variation in these traits. Although hybrid classes suffered reduced fitness for many traits, hybrid means were equivalent to at least one of the parental species in overall estimates of maternal and paternal fitness during the two years of the field study. The genetic architecture underlying the fitness-related traits varied across field site and year of the study, thus emphasizing the importance of the environment in determining the degree of postzygotic isolation and potential for introgression across natural hybrid zones.     

Natural selection for salt tolerance quantitative trait loci (QTLs) in wild sunflower hybrids: implications for the origin of Helianthus paradoxus,a diploid hybrid species

For a new diploid or homoploid hybrid species to become established, it must diverge ecologically from parental genotypes. Otherwise the hybrid neospecies will be overcome by gene flow or competition. We initiated a series of experiments designed to understand how the homoploid hybrid species, Helianthus paradoxus, was able to colonize salt marsh habitats, when both of its parental species (H. annuusxH. petiolaris) are salt sensitive. Here, we report on the results of a quantitative trait locus (QTL) analysis of mineral ion uptake traits and survivorship in 172 BC2 hybrids between H. annuus and H. petiolaris that were planted in H. paradoxus salt marsh habitat in New Mexico. A total of 14 QTLs were detected for mineral ion uptake traits and three for survivorship. Several mineral ion QTLs mapped to the same position as the survivorship QTLs, confirming previous studies, which indicated that salt tolerance in Helianthus is achieved through increased Ca uptake, coupled with greater exclusion of Na and related mineral ions. Of greater general significance was the observation that QTLs with effects in opposing directions were found for survivorship and for all mineral ion uptake traits with more than one detected QTL. This genetic architecture provides an ideal substrate for rapid ecological divergence in hybrid neospecies and offers a simple explanation for the colonization of salt marsh habitats by H. paradoxus. Finally, selection coefficients of +0.126, -0.084 and -0.094 for the three survivorship QTLs, respectively, are sufficiently large to account for establishment of new, homoploid hybrid species.     

Genetic basis of hybrid male sterility among three closely related species of Drosophila

The genetic basis of hybrid male sterility among three closely related species, Drosophila bipectinata, D. parabipectinata and D. malerkotliana has been investigated by using backcross analysis methods. The role of Y chromosome, major hybrid sterility (MHS) genes (genetic factors) and cytoplasm (non-genetic factor) have been studied in the hybrids of these three species. In the species pair, bipectinata--parabipectinata, Y chromosome introgression of parabipectinata in the genomic background of bipectinata and the reciprocal Y chromosome introgression were unsuccessful as all males in second backcross generation were sterile. Neither MHS genes nor cytoplasm was found important for sterility. This suggests the involvement of X-Y, X-autosomes or polygenic interactions in hybrid male sterility. In bipectinata--malerkotliana and parabipectinata--malerkotliana species pairs, Y chromosome substitution in reciprocal crosses did not affect male fertility. Backcross analyses also show no involvement of MHS genes or cytoplasm in hybrid male sterility in these two species pairs. Therefore, X- autosome interaction or polygenic interaction is supposed to be involved in hybrid male sterility in these two species pairs. These findings also provide evidence that even in closely related species, genetic interactions underlying hybrid male sterility may vary.     

QTL analysis of potato tuberization

Quantitative trait loci (QTLs) affecting tuberization were detected in reciprocal backcrosses between Solanum tuberosum and S. berthaultii. Linkage analyses were performed between traits and RFLP alleles segregating from both the hybrid and the recurrent parent using a set of framework markers from the potato map. Eleven distinct loci on seven chromosomes were associated with variation in tuberization. Most of the loci had small effects, but a QTL explaining 27% of the variance was found on chromosome 5. More QTLs were detected while following alleles segregating from the recurrent S. tuberosum parent used to make the backcross than were detected by following alleles segregating from the hybrid parent. More than half of the alleles favoring tuberization were at least partly dominant. Tuberization was favored by an allele from S. berthaultii at 3 of the 5 QTLs detected by segregation from the hybrid parent. The additive effects of the QTLs for tuberization explained up to 53% of the phenotypic variance, and inclusion of epistatic effects increased this figure to 60%. The most common form of epistasis was that in which presence of an allele at each of 2 loci favoring tuberization was no more effective than the presence of a favorable allele at 1 of the 2 loci. The QTLs detected for tuberization traits are discussed in relationship to those previously detected for trichome-mediated insect resistance derived from the unadapted wild species.Paper number 54 of the Department of Fruit and Vegetable Science, Cornell University     

The Evolutionary History of DROSOPHILA BUZZATII. Xii. the Genetic Basis of Sterility in Hybrids between D. BUZZATII and Its Sibling D. SERIDO from Argentina

The genetic basis of hybrid sterility has been investigated in backcross segmental hybrids between two sibling species, Drosophila buzzatii and D. serido. Asynapsis of homologous bands in hybrid polytene chromosomes has been used to identify the D. serido chromosome segments introgressed into the D. buzzatti genome. All the investigated chromosomes contain male sterility factors. For autosomes, sterility is produced when an introgressed D. serido chromosome segment, or combination of segments, reaches a minimum size. On the other hand, any introgressed X chromosome segment from D. serido, irrespective of its size, produces either male hybrid sterility or inviability.     

The genetic basis of postzygotic reproductive isolation between Drosophila santomea and D. yakuba due to hybrid male sterility

A major unresolved challenge of evolutionary biology is to determine the nature of the allelic variants of "speciation genes": those alleles whose interaction produces inviable or infertile interspecific hybrids but does not reduce fitness in pure species. Here we map quantitative trait loci (QTL) affecting fertility of male hybrids between D. yakuba and its recently discovered sibling species, D. santomea. We mapped three to four X chromosome QTL and two autosomal QTL with large effects on the reduced fertility of D. yakuba and D. santomea backcross males. We observed epistasis between the X-linked QTL and also between the X and autosomal QTL. The X chromosome had a disproportionately large effect on hybrid sterility in both reciprocal backcross hybrids. However, the genetics of hybrid sterility differ between D. yakuba and D. santomea backcross males, both in terms of the magnitude of main effects and in the epistatic interactions. The QTL affecting hybrid fertility did not colocalize with QTL affecting sexual isolation in this species pair, but did colocalize with QTL affecting the marked difference in pigmentation between D. yakuba and D. santomea. These results provide the basis for future high-resolution mapping and ultimately, molecular cloning, of the interacting genes that contribute to hybrid sterility.     

MALADAPTED GENE COMPLEXES WITHIN POPULATIONS OF THE INTERTIDAL COPEPOD TIGRIOPUS CALIFORNICUS?

The prevalence of F2 hybrid breakdown in interpopulation crosses of the marine copepod Tigriopus californicus can be explained by disruption of coadapted gene complexes. This study further dissects the nature of hybrid gene interactions, revealing that parental populations may also harbor maladapted gene complexes. Diagnostic molecular markers (14) were assayed in reciprocal F2 hybrids to test for gene interactions affecting viability. Results showed some evidence of nuclear–nuclear coadaptation. Although there were no significant examples of pairwise linkage disequilibrium between physically unlinked loci, one of the two reciprocal crosses did show an overall excess of parental double homozygotes and an overall dearth of nonparental double homozygotes. In contrast, the nuclear–cytoplasmic data showed a stronger tendency toward maladaptation within the specific inbred lines used in this study. For three out of four loci with significant frequency differences between reciprocal F2, homozygotes were favored on the wrong cytoplasmic background. A separate study of reciprocal backcross hybrids between the same two populations (but different inbred lines) revealed faster development time when the full haploid nuclear genome did not match the cytoplasm. The occurrence of such suboptimal gene complexes may be attributable to effects of genetic drift in small, isolated populations.