Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex).

Powerful and accurate detection of first-generation (F1) hybrids and backcrosses in nature is needed to achieve a better understanding of the function and dynamics of introgression. To document the frequency of ongoing interspecific gene exchange between two Mediterranean evergreen oaks, the cork oak (Quercus suber) and the holm oak (Q. ilex), we analyzed 1487 individuals originating from across the range of the two species using eight microsatellite loci and two Bayesian clustering approaches (implemented in the programs STRUCTURE and NEWHYBRIDS). Simulated data were used to assess the differences between the two clustering methods and to back up the choice of the threshold value for the posterior probability to discriminate admixed from pure individuals. We found that the use of STRUCTURE resulted in the highest power to detect hybrids, whereas NEWHYBRIDS provided the highest accuracy. Irrespective of the approach, the two species were clearly distinguished as independent genetic entities without any prior information. In contrast with previous reports, we found no evidence for unidirectional introgression. The overall hybridization rate was very low (<2% of introgressed individuals). Only two individuals were identified as F1 hybrids and five as early backcrosses. This work shows that the combined application of the two complementary Bayesian approaches and their systematic validation with simulations, fit for the case at hand, helps gain resolution in the identification of admixed individuals.

Contrasting nuclear and cytoplasmic exchanges between phylogenetically distant oak species (Quercus suber L. and Q. ilex L.) in Southern France: inferring crosses and dynamics.

Gene flow is particularly frequent in the genus Quercus (oaks), especially between closely related species. We focus here on Quercus ilex and the cork-producing Quercus suber, which occasionally hybridize although they are phylogenetically markedly separated. Morphological observations were combined with both allozymic and chloroplastic diagnostic markers to characterize hybridization and introgression and to infer their dynamics in two French regions (French Catalonia and Provence), which are separated by several hundred kilometres. Some hybrids were found in both regions, indicating recent hybridization events. As expected from previous studies, most hybrids resulted from female symbol Q. ilex x male symbol Q. suber crosses, but our data showed that the reciprocal cross is also possible. Partial independence between nuclear and chloroplastic introgression was observed in the two species. Nuclear introgression was limited in both species and both regions, with no preferred direction. In Provence, chloroplastic introgression was very rare in both species. Conversely, all Q. suber individuals from French Catalonia were introgressed by Q. ilex chlorotypes. This might be explained by introgression in the Iberian Peninsula antedating the first occurrence of the two species in French Catalonia. We also observed a new chlorotype that was created locally, and was exchanged between the two species. However, the two species still remain genetically differentiated. The dynamics and complexity of exchanges and the factors determining them (including human management of Q. suber) are discussed.

Flowering characteristics and fertility of interploidy progeny from normal and 2n gametes in Dactylis glomerata L.

We performed an extensive experiment to compare male fertility, flowering period, seed set and germination rate between triploid and tetraploid cross-progeny of Dactylis glomerata L. originating from reciprocal diploid (2x) × tetraploid (4x) crosses. Four hundred and forty-five triploid and tetraploid individuals, constituting the cross progeny of 2x-4x reciprocal crosses between diploids from nine distinct subspecies, and tetraploids from five subspecies, were tested for male fertility and phenology under homogeneous conditions. A significant negative correlation was observed between the parental genetic distance and the frequency of sterile panicles (ST) in 3x progeny, suggesting that selection may occur against fertility in triploid progeny from interploid crosses involving closely related subspecies. Genetic distance between the parental subspecies was not significantly correlated with the frequency of fertile panicles (FT), non-spreading panicles (NT, non-dehiscent anthers with pollen inside), and ST panicles in the 4x progeny, nor with the frequency of FT and NT panicles in the 3x progeny. Among the 4x progeny individuals that produced panicles, more than 60% were fully fertile, but 24% possessed only sterile panicles. In the triploids, 63% of the reproductive plants were male-sterile, but 31% had variable proportions of fertile panicles and 6% possessed only fertile panicles. Male fertility in the progeny was significantly affected by individual ploidy level, parental diploid subspecies identity, and by the interaction between these 2 factors in the case of the fertile progeny plants. The frequency of vegetative plants was higher in 4x progeny than in 3x progeny, more particularly when the seed parent was tetraploid. However, when the seed parent was diploid, the frequencies of vegetative plants were similar in 3x and 4x progeny. Pollen viability was significantly higher in anthers from fertile panicles than in anthers from non-spreading panicles; viability of pollen from non-spreading panicles was, in turn, significantly higher than in sterile panicles. Also, seed set was higher in panicles with fertile anthers than in the two other types. However, seeds from plants with fertile, non-spreading and sterile anthers showed no differences in germination rate. Therefore, in Dactylis glomerata, tetraploid cross progeny arising from 2n gametes possess higher fertility, on average, than triploid cross progeny involving normal gametes. In addition to lower male fertility (non-spreading or atrophied anthers), the triploids also showed significantly lower pollen fertility in anthers and lower seed set in open pollinating conditions, probably because disturbance in meiosis, due to odd chromosome associations, also occurs in eggs. Moreover, triploids were observed to reproduce preferentially with individuals possessing the same ploidy levels as their seed parent. These results suggest that the production of 4x individuals, derived from 2n gametes in interploid crosses, is likely to be the main effective means of direct gene transfer in contact areas of populations or subspecies possessing distinct ploidy levels.

Competition between diploid and derivative autotetraploid Dactylis glomerata L. from Galicia. Implications for the establishment of novel polyploid populations.

The competitive ability of a tetraploid, and its morphologically indistinguishable progenitor diploid Dactylis glomerata L., from Galicia (Spain), was tested in a two-year study, using isolated plants and the same individuals grown at two densities (16 and 36 plants per pot, respectively). Inverse linear regression equations were used to quantify the response of the different ploidy levels (hereafter cytotypes) to density. For the diploids, inter-cytotype competition coefficients were significantly higher than intra-cytotype coefficients. The substitution rate increased from 1. in the first year to 3.9 in the second year, when most of the diploids failed to flower and some died. The competitive superiority of the tetraploids was associated with higher mean tiller weight, particularly in the mixed cultures. The tetraploids also had heavier seeds and faster leaf production in early spring, and they flowered earlier than the diploids. Several of these differences between cytotypes appear to be due to differences in ploidy level and may play a major role in the establishment of the tetraploids in Galician pastures, where competition is high.

Chloroplast DNA variation in dactylis glomerata L. taxa endemic to the macaronesian islands

In the Dactylis glomerata infraspecific polyploid grass complex, restriction fragment length polymorphisms (RFLPs) of chloroplast DNA (cpDNA) were studied in diploid and tetraploid populations of several taxa endemic to Macaronesia (Madeira and the Canary islands) and in populations from the African and European continental areas closest to Macaronesia. Two chlorotypes, which differed by a single 290-bp length mutation, were observed in the Macaronesian and the continental populations. Chlorotype I, which is predominant in the whole D. glomerata complex, was found in the majority of continental populations. It was also observed in the most western Macaronesian islands, in the two diploid taxa endemic to the lowland scrub and the high elevation heath of Tenerife, respectively, and in tetraploids endemic to Madeira and La Palma. These island populations were growing under the influence of humid trade winds. Chlorotype II was found in the eastern part of the Archipelago (closer to Africa), which experienced subarid Mediterranean climate conditions, and in very few diploid and tetraploid Mediterranean populations growing at high elevation on the continent. This geographical and climatic distribution of chlorotype variation in Macaronesia is consistent with that reported previously for morphological, allozyme and phenolic variation in the same plant material. Chlorotype II was, however, also observed in tetraploid populations from La Gomera island and in one of the seven tetraploid populations analysed from Madeira, which all showed clearly subtropical characters for morphology, allozymes and phenolic compounds. This result suggests that cpDNA introgression has occurred more than once from the Mediterranean material into the subtropical one and may indicate that colonization between the mainland and islands, or among the islands, probably played a major role in the geographical pattern observed for that marker.

Polyploidy and habitat differentiation in Dactylis glomerata L. from Galicia (Spain).

The microdistribution of diploid and tetraploid plants of Dactylis glomerata L. was examined and related to their immediate environment in several sites in central Galicia, where morphologically indistinguishable individuals of both ploidies grow in sympatry. The two related cytotypes differed in habitat preference. Diploids were mainly confined to the low-density forest-floor habitat in woodlands of mostly ancient origin, whereas tetraploids were widespread in varied habitats but clearly predominant in open areas, particularly in disturbed anthropic sites. The in situ comparison of plant performance showed that where plants of each ploidy were more common they produced more tillers, panicles and seeds. This habitat preference closely reflected differences in life-history characteristics. The tetraploids had an early and short flowering time almost always completed before the aestival drought, whereas the diploids began to flower several weeks later and flowered throughout the drought. Comparisons along artificial gradients of soil water availability and light transmittance indicated that the cytotypes had distinct physiological requirements which probably originated in metabolic and more general genetic differentiation and could be directly attributable to ploidy. Habitat differentiation increases the species' colonizing ability. It also amplifies divergence in reproductive strategy between diploids and tetraploids, which reduces ineffective crossing between cytotypes and thereby permits them to coexist in sympatry. The effect of hybridization at the polyploid level on the differentiation between cytotypes was assessed from the recent introduction of a foreign tetraploid entity into the study area. Hybridization between the two distinct tetraploids was found to increase habitat differentiation between the diploids and the tetraploids, but the major part of this differentiation is probably attributable to ploidy itself.

Allozyme characterisation of four Mediterranean evergreen oak species.

Polymorphism at 11 enzyme loci was used to compare the four evergreen oak species of the Mediterranean Basin and to establish their taxonomical relationships. As a comparison, two evergreen oak species from Tibet, located in the primary distribution area of evergreen oaks, were analysed at the same loci. Cladistic analyses led to the separation of a cluster of four species, namely the three Mediterranean Q. ilex, Q. coccifera and Q. alnifolia and the Tibetan Q. aquifolioides. The other Tibetan species, Q. semicarpifolia, and Q. suber, from the Western Mediterranean Basin, were very distinct genetically from the four other species. These results were not consistent with previous taxonomical treatment, based on morphology alone, which classified Q. ilex and Q. coccifera in "ilex group" (=subgenus Sclerophyllodrys O. Schwartz), and the other four species in "cerris group" (subgenus Cerris, according to Schwartz). Allozyme variation has thus provided useful information to clarify the taxonomy of evergreen oaks.

Endemic North African Quercus afares Pomel originates from hybridisation between two genetically very distant oak species (Q. suber L. and Q. canariensis Willd.): evidence from nuclear and cytoplasmic markers.

Hybridisation is a potent force in plant evolution, although there are few reported examples of stabilised species that have been created through homoploid hybridisation. We focus here on Quercus afares, an endemic North African species that combines morphological, physiological and ecological traits of both Q. suber and Q. canariensis, two phylogenetically distant species. These two species are sympatric with Q. afares over most of its distribution. We studied two Q. afares populations (one from Algeria and one from Tunisia), as well as several populations of both Q. suber and Q. canariensis sampled both within and outside areas where these species overlap with Q. afares. A genetic analysis was conducted using both nuclear (allozymes) and chloroplastic markers, which shows that Q. afares originates from a Q. suber x Q. canariensis hybridisation. At most loci, Q. afares predominantly possesses alleles from Q. suber, suggesting that the initial cross between Q. suber and Q. canariensis was followed by backcrossing with Q. suber. Other hypotheses that can account for this result, including genetic drift, gene silencing, gene conversion and selection, are discussed. A single Q. suber chlorotype was detected, and all Q. afares individuals displayed this chlorotype, indicating that Q. suber was the maternal parent. Q. afares is genetically, morphologically and ecologically differentiated from its parental species, and can therefore be considered as a stabilised hybrid species.

Plant genetics. Ancient wild olives in Mediterranean forests.

Early domestication and extensive cultivation have meant that staple Mediterranean fruit crops such as olives, grapes and dates exist in wild-looking forms that are secondary derivatives produced by sexual reproduction among cultivated plants (cultivars), which were initially propagated vegetatively. By using genetic markers associated with characters that render plants unsuitable for domestication, we show here that genuinely wild olive trees, which cannot be distinguished morphologically from feral forms, still survive in a few Mediterranean forests. These wild stocks are genetically distinct and more variable than either the crop strains or their derived feral forms, a finding that has important implications for the conservation of these ancient lineages.

The evolutionary dynamics of polyploid plants: origins, establishment and persistence.

The role of polyploidy in the origin of evolutionary novelty and the maintenance of diversity in plant populations has come to be recognized as an integral component of the ecological and evolutionary dynamics of plant species populations. Recent attempts to examine the evolutionary significance of polyploidy have focused on the processes responsible for the origin of polyploid plants and the conditions that favour their establishment and persistence. The importance of these issues is not simply limited to the evolutionary dynamics of polyploidy but is, in fact, central to our understanding of the population biology processes that act on the establishment of new 'types' and the maintenance of biotic diversity at both the inter- and intraspecific levels.

Phylogeographical variation of chloroplast DNA in holm oak (Quercus ilex L.).

Variation in the lengths of restriction fragments (RFLPs) of the whole chloroplast DNA molecule was studied in 174 populations of Quercus ilex L. sampled over the entire distribution of this evergreen and mainly Mediterranean oak species. By using five endonucleases, 323 distinct fragments were obtained. From the 29 and 17 cpDNA changes identified as site and length mutations, respectively, 25 distinct chlorotypes were distinguished, mapped and treated cladistically with a parsimony analysis, using as an outgroup Q. alnifolia Poech, a closely related evergreen oak species endemic to Cyprus where Q. ilex does not grow. The predominant role of Q. ilex as maternal parent in hybridization with other species was reflected by the occurrence of a single very specific lineage of related chlorotypes, the most ancestral and recent ones being located in the southeastern and in the northwestern parts of the species' geographical distribution, respectively. The lineage was constituted of two clusters of chlorotypes observed in the 'ilex' morphotyped populations of the Balkan and Italian Peninsulas (including the contiguous French Riviera), respectively. A third cluster was divided into two subclusters identified in the 'rotundifolia' morphotyped populations of North Africa, and of Iberia and the adjacent French regions, respectively. Postglacial colonization probably started from three distinct southerly refugia located in each of the three European peninsulas, and a contact area between the Italian and the Iberian migration routes was identified in the Rhône valley (France). Chlorotypes identical or related to those of the Iberian cluster were identified in the populations from Catalonia and the French Languedoc region, which showed intermediate morphotypes, and in the French Atlantic populations which possessed the 'ilex' morphotype, suggesting the occurrence of adaptive morphological changes in the northern part of the species' distribution.

Autopolyploidy in Dactylis glomerata L.: further evidence from studies of chloroplast DNA variation.

Chloroplast DNA variation has been used to examine some of the maternal lineages involved in the evolution of the intraspecific polyploid complex, Dactylis glomerata L. Diploid (2x) and tetraploid (4x) individuals were collected from natural populations of the subspecies glomerata (4x), marina (4x) and lusitanica (2x), as well as from sympatric 2x/4x populations of the Galician type. Digestion of their ctDNA with 11 restriction endonucleases revealed enough variation to characterise three ctDNA variants, designated MBMK, MBmK and mBMK. The distribution of these ctDNA variants reflects different stages in their spread among the populations. The MBMK ctDNA variant predominated at both ploidy levels in subspecies glomerata, lusitanica and marina, and in recent tetraploid Galician/glomerata hybrids. The MBmK variant was detected in a single tetraploid individual and probably results from a relatively recent mutation. Fixation of the mBMK minority variant in the diploid and tetraploid Galician populations adds to the evidence concerning the possible origin of the Galician tetraploids. It means that the Galician diploids were maternal ancestors of the tetraploids. This result complements evidence from earlier studies based on morphology or biochemical markers, and reduces the likelihood that the tetraploids arose by hybridisation between an ancient Galician diploid and an alien tetraploid. It is, however, consistent with a true autopolyploid origin of the tetraploids.

Haplotype variation of cpDNA in the agamic grass complex Pennisetum section Brevivalvula (Poaceae).

The Brevivalvula section of the grass polyploid complex Pennisetum shows various reproductive systems, apomixis being the most widespread. Haplotype variation of chloroplast DNA was studied in the six morphological taxa (species) of this section by using RFLP analysis in 54 plants corresponding to 14 elementary taxa, each characterized on the basis of morphology and ploidy level. Two additional species, Pennisetum glaucum and P. purpureum, which belong to another section of the same genus, were analysed for comparison. In Brevivalvula, chloroplast DNA size was estimated to range between 130 and 133 kb. Thirteen of 15 distinct haplotypes identified in the study were specific to the Brevivalvula section. They were unequally distributed among the morphotypes, the ploidy levels and sampling sites. Within the Brevivalvula section, plants of P. setosum, which are perennial and reproduce vegetatively or by agamospermy, possessed a single specific haplotype. This species differed clearly from the five other morphological species, which are known to be annual, to show either sexual or agamospermic reproduction and which shared most of the 12 other haplotypes observed in the section, suggesting the occurrence of multiple hybridization events between the taxa. Chloroplast DNA variation was highly geographically structured, suggesting low seed dispersal between sites, whereas the substantial haplotype diversity observed in the sites may indicate that agamic reproduction is responsible for the maintenance of distinct genetically isolated clones. Haplotype classification using Wagner's parsimony suggested the occurrence of bidirectional gene flow between the diploids and the polyploids, as reported already in other related apomictic complexes.

Allozyme variation of oleaster populations (wild olive tree) (Olea europaea L.) in the Mediterranean Basin.

As a result of the early domestication and extensive cultivation of the olive tree throughout the Mediterranean Basin, the wild-looking forms of olive (oleasters) presently observed constitute a complex, potentially ranging from wild to feral forms. Allozyme variation was analysed at 10 loci in 31 large and 44 small oleaster populations distributed in various habitats of the Mediterranean Basin and in two populations of the wild subspecies Olea europaea subsp (ssp) guanchica, endemic to the Canary islands and closely related to oleasters. At eight polymorphic loci, 25 alleles were identified. Genetic evidence that nondomesticated oleasters still survive locally was provided by the occurrence of four and one alleles shared exclusively by the eight western and two eastern oleaster populations, respectively, which were collected in forests potentially containing genuinely wild forms according to environmental, historical and demographic criteria. As reported previously from cytoplasmic and RAPDs analysis, substantial genetic differentiation was observed between the eastern oleaster populations genetically close to most olive clones cultivated in the Mediterranean Basin, and the western populations that are related to the wild Canarian populations. In addition, the occurrence of significantly lower heterozygosity in cultivated olive than in oleasters, whatever their origin, suggests that intensive selection involving inbreeding has taken place under cultivation to obtain particular characteristics in the olive cultivars.