Réjane Streiff

Within-population genetic structure in Quercus robur L. and Quercus petraea (Matt.) Liebl. assessed with isozymes and microsatellites

The spatial distribution of alleles is described in a forest stand of natural origin of 5 ha comprising 355 mature Quercus petraea and Q. robur trees. Each tree was genotyped for six microsatellite loci. Previous studies on the same population based on isozymes allowed a comparison of different markers for the detection of spatial genetic structure. Different statistics were used: differentiation measures at different spatial scales, and spatial autocorrelation analysis based on Moran’s index I. For microsatellites, differentiation and autocorrelation were calculated with unordered alleles (identity in state) and with alleles ordered according to their size. Results showed the same tendency of a significant, but low, spatial genetic structure for markers and different statistics. Some differences could, however, be detected. First, microsatellites interpreted as unordered alleles exhibit stronger spatial structure than isozymes or microsatellite interpreted as ordered alleles. Second, differentiation and autocorrelation values were higher in Q. petraea than in Q. robur. These differences were attributed to species differences in gene flow via pollen or seed.

Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis

This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1–0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.

IDENTIFICATION AND CHARACTERIZATION OF (GA/CT)N- MICROSATELLITE LOCI FROM QUERCUS PETRAEA

In this study a size selected genomic library from Quercus petraea was screened for (GA/CT)n-microsatellite sequences. The resulting loci were analysed by PCR for their usefulness as molecular markers in Q. petraea and Q. robur. 17 out of 52 tested primer pairs resulted in the amplification of a polymorphic single-locus pattern. The number of alleles found per locus varied from 6 to 16. Combining the genetic variation observed for the characterized loci provides a unique genotype for all the individuals tested. Using intraspecific controlled crosses of Q. robur trees Mendelian inheritance could be shown for five loci.

A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 5S rDNA markers

Abstract A genetic map of Pedunculate oak (Quercus robur) was constructed based on one 5S rDNA, 271 RAPD, ten SCAR, 18 microsatellite, one minisatellite, and six isozyme markers. A total of 94 individuals from a full-sib family was genotyped. Two maps, including 307 markers, were constructed according to the “two-way pseudo-testcross” mapping strategy. Testcross markers segregating in the 1 : 1 ratio were first used to establish separate maternal (893.2 cM, 12 linkage groups) and paternal (921.7 cM, 12 linkage groups) maps. Both maps provided 85–90% genome coverage. Homologies between the male and female linkage groups were then identified based on 74 intercross markers segregating in the 3 : 1, 1 : 2 : 1 and 1 : 1 : 1 : 1 ratios (RAPDs, SCARs, SSRs, 5S rDNA and isozymes) in the hybrid progeny. In each map, approximately 18% of the studied markers showed segregation distortion. More than 60% of the skewed markers were due to an excess of heterozygote genotypes. This map will be used for: (1) studying the molecular organisation of genomic regions involved in inter- and intraspecific differentiation in oaks and (2) identification of QTLs for adaptive traits.

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine‐scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation‐based approach, we investigated how comparative and single‐point methods, traditionally used in a Wright–Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex ‘quartet’ of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.

Comparative study of genetic variation and differentiation of two pedunculate oak (Quercus robur) stands using microsatellite and allozyme loci

In a comparative study four codominant microsatellite loci and seven allozyme gene loci have been used to investigate the genetic variation and differentiation of two pedunculate oak stands in North Germany. Both number and effective number of alleles were five to six times higher and the observed heterozygosity was three times higher for the microsatellite than for the allozyme loci. One stand showed an overall excess of homozygotes. In general the microsatellites were closer to Hardy–Weinberg expectation. The genetic distances between the two stands were distinctly higher for microsatellites. For most parameters microsatellites exhibited smaller interlocus variation than the allozymes. The different impact of population genetic processes on the genetic structure as assessed by microsatellites or allozymes is discussed.

Genetic structure and gene flow in French populations of two Ostrinia taxa: host races or sibling species?

Most models of ecological speciation concern phytophagous insects in which speciation is thought to be driven by host shifts and subsequent adaptations of populations. Despite the ever‐increasing number of studies, the current evolutionary status of most models remains incompletely resolved, as estimates of gene flow between taxa remain extremely rare. We studied the population genetics of two taxa of the Ostrinia genus — one feeding mainly on maize and the other on mugwort and hop — occurring in sympatry throughout France. The actual level of divergence of these taxa was unknown because the genetic structure of populations had been investigated over a limited geographical area and the magnitude of gene flow between populations had not been estimated. We used 11 microsatellite markers to investigate the genetic structure of populations throughout France and the extent of gene flow between the two Ostrinia taxa at several sites at which they are sympatric. We observed clear genetic differentiation between most populations collected on the typical respective hosts of each taxon. However, populations displaying intermediate allelic frequencies were found on hop plants in southern France. Individual assignments revealed that this result could be accounted for by the presence of both taxa on the same host. Gene flow, estimated by determining the proportion of hybrids detected, was low: probably < 1% per generation, regardless of site. This indicates that the two Ostrinia taxa have reached a high level of genetic divergence and should be considered sibling species rather than host races.

Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species

It has recently been shown that the European corn borer, a major pest of maize crops, is actually composed of two genetically differentiated and reproductively isolated taxa, which are found in sympatry over a wide geographical range in Eurasia. Each taxon is adapted to specific host plants: Ostrinia nubilalis feeds mainly on maize, while O. scapulalis feeds mainly on hop or mugwort. Here, we present a genome scan approach as a first step towards an integrated molecular analysis of the adaptive genomic divergence between O. nubilalis and O. scapulalis. We analysed 609 AFLP marker loci in replicate samples of sympatric populations of Ostrinia spp. collected on maize, hop and mugwort, in France. Using two genome scan methods based on the analysis of population differentiation, we found a set of 28 outlier loci that departed from the neutral expectation in one or the other method (of which a subset of 14 loci were common to both methods), which showed a significantly increased differentiation between O. nubilalis and O. scapulalis, when compared to the rest of the genome. A subset of 12 outlier loci were sequenced, of which 7 were successfully re‐amplified as target candidate loci. Three of these showed homology with annotated lepidopteran sequences from public nucleotide databases.

‘Becoming a species by becoming a pest’ or how two maize pests of the genus Ostrinia possibly evolved through parallel ecological speciation events

New agricultural pest species attacking introduced crops may evolve from pre‐existing local herbivores by ecological speciation, thereby becoming a species by becoming a pest. We compare the evolutionary pathways by which two maize pests (the Asian and the European corn borers, ACB and ECB) in the genus Ostrinia (Lepidoptera, Crambidae) probably diverged from an ancestral species close to the current Adzuki bean borer (ABB). We typed larval Ostrinia populations collected on maize and dicotyledons across China and eastern Siberia, at microsatellite and mitochondrial loci. We found only two clusters: one on maize (as expected) and a single one on dicotyledons despite differences in male mid‐tibia morphology, suggesting that all individuals from dicotyledons belonged to the ABB. We found evidence for migrants and hybrids on both host plant types. Hybrids suggest that field reproductive isolation is incomplete between ACB and ABB. Interestingly, a few individuals with an ‘ABB‐like’ microsatellite profile collected on dicotyledons had ‘ACB’ mtDNA rather than ‘ABB‐like’ mtDNA, whereas the reverse was never found on maize. This suggests asymmetrical gene flow directed from the ACB towards the ABB. Hybrids and backcrosses in all directions were obtained in no‐choice tests. In laboratory conditions, they survived as well as parental strain individuals. In Xinjiang, we found ACB and ECB in sympatry, but no hybrids. Altogether, our results suggest that reproductive isolation between ACB and ABB is incomplete and mostly prezygotic. This points to ecological speciation as a possible evolutionary scenario, as previously found for ECB and ABB in Europe.

Eleven polymorphic microsatellite markers for Oedaleus decorus (Orthoptera, Acrididae), an endangered grasshopper in Central Europe

We isolated and characterized 11 microsatellite loci in the grasshopper Oedaleus decorus (Orthoptera: Acrididae), an endangered species in Central Europe. Polymorphism was studied from two populations, one out of two populations known from Switzerland (n = 20 individuals) and one site from south of France (n = 20). The number of alleles and the expected heterozygosity ranged from five to 12 and from 0.559 to 0.898, respectively, in the Swiss population, and from 14 to 23 and from 0.895 to 0.974, respectively, in the French population. These microsatellite markers are suitable for further conservation genetic studies of O. decorus.