Re-creating ancient hybrid species' complex phenotypes from early-generation synthetic hybrids: three examples using wild sunflowers

Can the complex phenotypes that characterize naturally occurring hybrid species be re-created in early-generation artificial hybrids? We address this question with three homoploid hybrid species (Helianthus anomalus, Helianthus deserticola, Helianthus paradoxus) and their ancestral parents (Helianthus annuus, Helianthus petiolaris) that are phenotypically distinct and ecologically differentiated. These species, and two synthetic hybrid populations of the ancestral parents, were characterized for morphological, physiological, and life-history traits in greenhouse studies. Among the synthetic hybrids, discriminant analysis identified a few individuals with the multitrait phenotype of the natural hybrid species: 0.7%-1.1% were H. anomalus-like, 0.5%-13% were H. deserticola-like, and only 0.4% were H. paradoxus-like. These relative frequencies mirror previous findings that genetic correlations are favorable for generating the hybrid species' phenotypes, and they correspond well with phylogeographic evidence that demonstrates multiple natural origins of H. deserticola and H. anomalus but a single origin for H. paradoxus. Even though synthetic hybrids with hybrid species phenotypes are rare, their phenotypic correlation matrices share most of the same principal components (eigenvectors), setting the stage for predictable recovery of hybrid species' phenotypes from different hybrid populations. Our results demonstrate past hybridization could have generated hybrid species-like multitrait phenotypes suitable for persistence in their respective environments in just three generations after initial hybridization.     

Hybridization and genome size evolution: timing and magnitude of nuclear DNA content increases in Helianthus homoploid hybrid species

Hybridization and polyploidy can induce rapid genomic changes, including the gain or loss of DNA, but the magnitude and timing of such changes are not well understood. The homoploid hybrid system in Helianthus (three hybrid-derived species and their two parents) provides an opportunity to examine the link between hybridization and genome size changes in a replicated fashion. Flow cytometry was used to estimate the nuclear DNA content in multiple populations of three homoploid hybrid Helianthus species (Helianthus anomalus, Helianthus deserticola, and Helianthus paradoxus), the parental species (Helianthus annuus and Helianthus petiolaris), synthetic hybrids, and natural hybrid-zone populations. Results confirm that hybrid-derived species have 50% more nuclear DNA than the parental species. Despite multiple origins, hybrid species were largely consistent in their DNA content across populations, although H. deserticola showed significant interpopulation differences. First- and sixth-generation synthetic hybrids and hybrid-zone plants did not show an increase from parental DNA content. First-generation hybrids differed in DNA content according to the maternal parent. In summary, hybridization by itself does not lead to increased nuclear DNA content in Helianthus, and the evolutionary forces responsible for the repeated increases in DNA content seen in the hybrid-derived species remain mysterious.     

Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data

Background  

Long terminal repeat (LTR) retrotransposons are a class of mobile genetic element capable of autonomous transposition via an RNA intermediate. Their large size and proliferative ability make them important contributors to genome size evolution, especially in plants, where they can reach exceptionally high copy numbers and contribute substantially to variation in genome size even among closely related taxa. Using a phylogenetic approach, we characterize dynamics of proliferation events of Ty3/gypsy-like LTR retrotransposons that led to massive genomic expansion in three Helianthus (sunflower) species of ancient hybrid origin. The three hybrid species are independently derived from the same two parental species, offering a unique opportunity to explore patterns of retrotransposon proliferation in light of reticulate evolutionary events in this species group.     

Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species

New species may arise via hybridization and without a change in ploidy. This process, termed homoploid hybrid speciation, is theoretically difficult because it requires the development of reproductive barriers in sympatry or parapatry. Theory suggests that isolation may arise through rapid karyotypic evolution and/or ecological divergence of hybrid neospecies. Here, we investigate the role of karyotypic change in homoploid hybrid speciation by generating detailed genetic linkage maps for three hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus, and comparing these maps to those previously generated for the parental species, H. annuus and H. petiolaris. We also conduct a quantitative trait locus (QTL) analysis of pollen fertility in a BC2 population between the parental species and assess levels of pollen and seed fertility in all cross-combinations of the hybrid and parental species. The three hybrid species are massively divergent from their parental species in karyotype; gene order differences were observed for between 9 and 11 linkage groups (of 17 total), depending on the comparison. About one-third of the karyoypic differences arose through the sorting of chromosomal rearrangements that differentiate the parental species, but the remainder appear to have arisen de novo (six breakages/six fusions in H. anomalus, four breakages/three fusions in H. deserticola, and five breakages/five fusions in H. paradoxus). QTL analyses indicate that the karyotypic differences contribute to reproductive isolation. Nine of 11 pollen viability QTL occur on rearranged chromosomes and all but one map close to a rearrangement breakpoint. Finally, pollen and seed fertility estimates for F1's between the hybrid and parental species fall below 11%, which is sufficient for evolutionary independence of the hybrid neospecies.     

The ecological genetics of homoploid hybrid speciation

Our understanding of homoploid hybrid speciation has advanced substantially since this mechanism of species formation was codified 50 years ago. Early theory and research focused almost exclusively on the importance of chromosomal rearrangements, but it later became evident that natural selection, specifically ecological selection, might play a major role as well. In light of this recent shift, we present an evaluation of ecology's role in homoploid hybrid speciation, with an emphasis on the genetics underlying ecological components of the speciation process. We briefly review new theoretical developments related to the ecology of homoploid hybrid speciation; propose a set of explicit, testable questions that must be answered to verify the role of ecological selection in homoploid hybrid speciation; discuss published work with reference to these questions; and also report new data supporting the importance of ecological selection in the origin of the homoploid hybrid sunflower species Helianthus deserticola. Overall, theory and empirical evidence gathered to date suggest that ecological selection is a major factor promoting homoploid hybrid speciation, with the strongest evidence coming from genetic studies.     

Retrotransposon-related DNA sequences in the centromeres of grass chromosomes.

Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-related DNA sequences are not specific to the centromeric regions. However, the Ty3/gypsy-related sequences were present exclusively in the centromeres of all sorghum chromosomes. FISH and gel-blot hybridization showed that these sequences are also conserved in the centromeric regions of all species within Gramineae. Thus, we report a new retrotransposon that is conserved in specific chromosomal regions of distantly related eukaryotic species. We propose that the Ty3/gypsy-like retrotransposons in the grass centromeres may be ancient insertions and are likely to have been amplified during centromere evolution. The possible role of centromeric retrotransposons in plant centromere function is discussed.     

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.     

Patterns of genetic variation suggest a single,ancient origin for the diploid hybrid species Helianthus paradoxus

Abstract.— Experimental and comparative evidence implies that homoploid hybrid speciation is a reproducible process, mediated in part by ecological selection. Here, molecular data from the chloroplast genome and 17 nuclear microsatellite loci were employed to determine whether a well-documented homoploid hybrid species, Helianthus paradoxus , has arisen multiple times. Helianthus paradoxus is ecologically divergent from its parental species, and has a disjunct geographic distribution consistent with multiple origins. The molecular data, however, strongly support a single hybrid origin. First, all sampled populations of H. paradoxus are fixed for a single chloroplast DNA (cpDNA) haplotype, whereas local populations of both parental species, H. annuus and H. petiolaris , have multiple cpDNA haplotypes. Second, H. paradoxus populations form a single, well-supported clade (99.8% bootstrap support) in a neighbor-joining tree based on microsatellite allele frequencies. The microsatellite data also tentatively place the origin of H. paradoxus between 75,000 years and 208,000 years before present, indicating that anthropogenic disturbance likely did not play a role in the formation of this species. Finally, the genetic structure of this species is not consistent with passive riparian dispersal, which has been suggested for other wetland plant species, but may be explained by dispersal mechanisms implicated for H. annuus , such as large migratory mammals.     

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.     

Habitat divergence between a homoploid hybrid sunflower species, Helianthus paradoxus (Asteraceae), and its progenitors

The diploid hybrid species Helianthus paradoxus is restricted to salt marshes with sodium concentrations that exceed those found in the habitats of its progenitors, H. annuus and H. petiolaris. The observed association with saline habitats has led to the hypothesis that H. paradoxus is more salt tolerant than its progenitors. This hypothesis was tested by growing all three species in three NaCl treatments (0 mmol/L, 100 mmol/L, and 200 mmol/L). Helianthus paradoxus treated with NaCl was found to be more than five times as fit, in terms of biomass and survivorship, than its progenitors. Selection for salt tolerance in early generation hybrids may have contributed to the formation of H. paradoxus because theory predicts that homoploid hybrid speciation is feasible even when selection favoring hybrid genotypes is much weaker. Additionally, we show that H. paradoxus is significantly different from its parental species for several traits that often distinguish salt-tolerant species and suggest a mechanistic basis for the elevated salt tolerance expressed by H. paradoxus.     

CASE STUDIES AND MATHEMATICAL MODELS OF ECOLOGICAL SPECIATION. 4. HYBRID SPECIATION IN BUTTERFLIES IN A JUNGLE

We build a spatial individual-based multilocus model of homoploid hybrid speciation tailored for a tentative case of hybrid origin of Heliconius heurippa from H. melpomene and H. cydno in South America. Our model attempts to account for empirical patterns and data on genetic incompatibility, mating preferences and selection by predation (both based on coloration patterns), habitat preference, and local adaptation for all three Heliconius species. Using this model, we study the likelihood of recombinational speciation and identify the effects of various ecological and genetic parameters on the dynamics, patterns, and consequences of hybrid ecological speciation. Overall, our model supports the possibility of hybrid origin of H. heurippa under certain conditions. The most plausible scenario would include hybridization between H. melpomene and H. cydno in an area geographically isolated from the rest of both parental species with subsequent long-lasting geographic isolation of the new hybrid species, followed by changes in the species ranges, the secondary contact, and disappearance of H. melpomene -type ecomorph in the hybrid species. However, much more work (both empirical and theoretical) is necessary to be able to make more definite conclusions on the importance of homoploid hybrid speciation in animals.     

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.     

The Role of Interelement Selection in Saccharomyces cerevisiae Ty Element Evolution

Retrotransposons are mobile genetic elements that are ubiquitous components of eukaryotic genomes. The evolutionary success of retrotransposons is explained by their ability to replicate faster than the host genomes in which they reside. Elements with higher rates of genomic replication possess a selective advantage over less active elements. Retrotransposon populations, therefore, are shaped largely by selective forces acting at the genomic level between elements. To evaluate rigorously the effects of selective forces acting on retrotransposons, detailed information on the patterns of molecular variation within and between retrotransposon families is needed. The sequencing of the Saccharomyces cerevisiae genome, which includes the entire genomic complement of yeast retrotransposons, provides an unprecedented opportunity to access and analyze such data. In this study, we analyzed in detail the patterns of nucleotide variation within the open reading frames of two parental (Ty1 and Ty2) and one hybrid (Ty1/2) family of yeast retrotransposons. The pattern and distribution of nucleotide changes on the phylogenetic reconstructions of the three families of Ty elements reveal evidence of negative selection on both internal and external branches of the Ty phylogenies. These results indicate that most, if not all, Ty elements examined represent active or recently active retrotransposon lineages. We discuss the relevance of these findings with respect to the coevolutionary dynamic operating between genomic element populations and the host organisms in which they reside. Received: 5 November 1998 / Accepted: 17 March 1999