A study based on AFLP markers was conducted to characterise the present population genetic struct... more A study based on AFLP markers was conducted to characterise the present population genetic structure of Carpinus betulus in Europe and to formulate guidelines for the use of this species in plantations on a local scale in Flanders. High within-population diversity and little (but significant) genetic differentiation were detected at both Flemish and European scales. However, there was a pattern of isolation by distance only at the European scale. Within-population gene diversity, a new rarefaction-based measure of number of genotypes ('band richness') and percentage of polymorphic loci are lower north of major mountain chains, suggesting that the mountain ranges formed a second bottleneck for the hornbeam during postglacial recolonisation. In Flanders, despite lower gene diversity, there were more polymorphic loci than in other European populations, a pattern that might have been caused by the mixing of material through planting, e.g. in hedges. In view of these findings, it is advised to create a single Flemish seed zone and to use preferentially reproductive material from this seed zone for new plantations in Flanders.
Several species of pines (Pinus spp.; Pinaceae) are highly invasive in parts of the Southern Hemi... more Several species of pines (Pinus spp.; Pinaceae) are highly invasive in parts of the Southern Hemisphere, where pines are widely planted in commercial forestry plantations. Problems associated with the spread of pines from plantations have increased substantially over the past few decades. We review the current extent of the problem and the research that has been undertaken to explain different facets of these invasions, including the factors contributing to species invasiveness and the susceptibility of ecosystems to invasion. Recent interest in producing transgenic pines for wood production raises important issues when considering future scenarios for pine invasions and for sustainable commercial forestry. This chapter considers the genetic diversity in introduced versus native pine populations and then examines the potential for transgene escape from pine plantations in the Southern Hemisphere. Propagule pressure appears to play a major role in these invasions. Commercial plantations have typically introduced a large share of the species' existing genetic diversity, resulting in rapid adaptation to local conditions and favoring the spread of feral pine populations. The extent to which inherent invasiveness of transgenic pines will differ from non-transgenic pines will depend on the properties conferred by the transgenes, but differences could be substantial. Even subtle changes in species-environment interactions could affect the dynamics of pine invasions. Genetic engineering for reproductive sterility could potentially reduce invasiveness, but criteria for forest certification current prohibit the use of any genetically-modified planting, thus blocking a potentially useful avenue of intervention. Integrated programs for managing pine invasions in the Southern Hemisphere will need to give serious attention to transgenic plantation forestry.
Interactions involving forest trees may be particularly vulnerable due to evolutionary rate limit... more Interactions involving forest trees may be particularly vulnerable due to evolutionary rate limitations imposed by long generation times. One mitigation strategy for such impacts is Climate matching -the augmentation of local native tree populations by input from non-local populations currently experiencing predicted future climates. This strategy is controversial because of potential cascading impacts on locally adapted animal communities. We explored these impacts using abundance data for local native gallwasp herbivores sampled from 20 provenances of sessile oak (Quercus petraea) planted in a common garden trial. We hypothesised that non-native provenances would show (i) declining growth performance with increasing distance between provenance origin and trial site, and (ii) phenological differences to local oaks that increased with latitudinal differences between origin and trial site. Under a local adaptation hypothesis, we predicted declining gallwasp abundance with increasing phenological mismatch between native and climate-matched trees. Both hypotheses for oaks were supported. Provenance explained significant variation in gallwasp abundance, but no gall type showed the relationship between abundance and phenological mismatch predicted
... Technical and conceptual developments in genetics will continue to propel paleoecology forwar... more ... Technical and conceptual developments in genetics will continue to propel paleoecology forward. ... data on past and future species distributions has potential to play a key role in conservation ... Such comparisons allow us to anticipate the potential loss of evolutionary heritage in ...
Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an ext... more Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an extensive sample of 389 populations distributed throughout the species range. Special emphasis was given to the analysis of the pattern of geographic variation on the basis of two contrasting measures of genetic diversity, gene diversity (H) and allelic richness, and to their relationship. Measures of allelic richness were corrected for variation in sample size by using the rarefaction method. As expected, maximum allelic richness was found in the southeastern part of the range (southern Italy and the Balkans), where beech was confined during the last ice age. Surprisingly, H was lower in refugia than in recently colonized regions, resulting in a negative correlation between the two diversity measures. The decrease of allelic richness and the simultaneous increase of H during postglacial recolonization was attributed to several processes that differentially affect the two diversity paramete...
Extensive hybridisation between the two sympatric species Quercus petraea and Q.robur is suggeste... more Extensive hybridisation between the two sympatric species Quercus petraea and Q.robur is suggested by the near lack of genetic differentiation between the two species and supported by controlled crosses and mating system analysis in mixed stands. Further ecological and genetic evidence suggest that hybridisation does not impede the ecological specialisation of the two species, raising the issue of its evolutionary
An extension of Nei's analysis of diversity in a subdivided population is proposed for a haploid ... more An extension of Nei's analysis of diversity in a subdivided population is proposed for a haploid locus. The differentiation Gsr becomes a natural extension of Wright's Fsr and generalizes Weir and Cockerham's parameter of co-ancestry by relaxing the assumption of identical correlation for all the alleles. Inter-and intrapopulation variances of the estimated diversities and differentiation are derived. Finally, the optimal sampling strategy for measuring Gsr when a fixed number of individuals can be analysed is considered. It is shown that, at a given locus, there is a unique sample size per population which yields the smallest variance of Gsr, regardless of the number of populations studied. These theoretical developments are illustrated with an analysis of chloroplast DNA diversity in a forest tree. The results emphasize the necessity of sampling many populations, rather than many individuals per population, for an accurate measurement of the subdivision of gene diversity at a single locus.
Proceedings of the Royal Society B: Biological Sciences, 2002
The importance of wood for human societies can hardly be understated. If dry wood were amenable t... more The importance of wood for human societies can hardly be understated. If dry wood were amenable to molecular genetic investigations, this could lead to major applications in wood forensics, certification, archaeology and palaeobotany. To evaluate the potential of wood for molecular genetic investigations, we have attempted to isolate and amplify, by PCR, DNA fragments of increasing size corresponding to all three plant genomes from different regions of 10 oak logs. Stringent procedures to avoid contamination with external DNA were used in order to demonstrate the authenticity of the fragments amplified. This authenticity was further confirmed by demonstrating genetic uniformity within each log using both nuclear and chloroplast microsatellites. For most wood samples DNA was degraded, and the sequences that gave the best results were those of small size and present in high copy number (chloroplast, mitochondrial, or repeated nuclear sequences). Both storage conditions and storage duration play a role in DNA conservation. Overall, this work demonstrates that molecular markers from all three plant genomes can be used for genetic analysis on dry oak wood, but outlines some limitations and the need for further evaluation of the potential of wood for DNA analysis.
Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the h... more Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random-mating populations, Panchal and Beaumont find a high frequency of false-positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other allencompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.
Using two-dimensional polyacrylamide gel electrophoresis, the genetic variation of proteins was e... more Using two-dimensional polyacrylamide gel electrophoresis, the genetic variation of proteins was examined in three organs (needle, bud, and pollen) from 18 trees of maritime pine. Three types of variation were noted: presence/absence, staining intensity, and position variation of the spots. Of the 902 polypeptides scored in the three organs, 245 (27.2%) were polymorphic. Moreover, among these variable spots, 117 were found in a single organ, demonstrating an increased polymorphism of the organ-specific polypeptides (56.0% vs 18.4% for the organ-unspecific polypeptides). Finally, a positive correlation was found between variability level and subunit molecular weight for spots showing position variation but not for spots showing presence/absence or staining intensity variations. Possible explanations for this observation are discussed.
We have recently proposed new estimators of the parameters of genetic diversity and differentiati... more We have recently proposed new estimators of the parameters of genetic diversity and differentiation and of their variances for a haploid locus in a population subdivided into a large number of subpopulations, with a two-stage sampling of populations and individuals. Here they are compared with bootstrap estimators. Several resampling methods are evaluated: sampling of populations only, individuals within populations only, or both. Theoretical results and a numerical example show that the most appropriate bootstrap variance estimators are obtained by resampling the populations alone and not both populations and individuals. However, some bias is apparent in the bootstrap methods, and the direct estimators proposed previously should therefore be preferred.
Background: In heterogeneous environments, sex-biased dispersal could lead to environmental adapt... more Background: In heterogeneous environments, sex-biased dispersal could lead to environmental adaptive parental effects, with offspring selected to perform in the same way as the parent dispersing least, because this parent is more likely to be locally adapted. We investigate this hypothesis by simulating varying levels of sex-biased dispersal in a patchy environment. The relative advantage of a strategy involving pure maternal (or paternal) inheritance is then compared with a strategy involving classical biparental inheritance in plants and in animals. Results: We find that the advantage of the uniparental strategy over the biparental strategy is maximal when dispersal is more strongly sex-biased and when dispersal distances of the least mobile sex are much lower than the size of the environmental patches. In plants, only maternal effects can be selected for, in contrast to animals where the evolution of either paternal or maternal effects can be favoured. Moreover, the conditions for environmental adaptive maternal effects to be selected for are more easily fulfilled in plants than in animals.
The effect of species and ecological conditions on oak volatile extractive content was investigat... more The effect of species and ecological conditions on oak volatile extractive content was investigated in an evenaged (100 years) stand located in western France. The sample included a total of 286 trees (118 sessile, 158 pedunculate and 10 oaks with an intermediate morphology) growing in contrasted environments (plateau, intermediate slope, small valley). The main factor influencing oak extractives level is species. The effect of the local environment appears negligible. No correlation between ring width and volatile extractive content was found. Q. petraea is significantly richer than Q. robur in eugenol and whisky-lactone (10.8 vs. 0.6 µg/g). However, two groups of sessile oaks could be identified, one poor and one rich in whisky-lactone. Among the latter, either the cis or the trans stereoisomer was predominant, suggesting that their production is not independent. A strong spatial structure was detected for whisky-lactone (cis-, trans-and total whisky-lactone, for the two species combined but also for Q. petraea alone in the case of the cis isomer).
Evolutionary relationships within Actinidia, a genus known for the contrasting mode of inheritanc... more Evolutionary relationships within Actinidia, a genus known for the contrasting mode of inheritance of its plastids and mitochondria, were studied. The phylogenetic analysis is based on chloroplast (cp) and mitochondrial (mt) restriction site and sequence data (matK, psbC-trnS, rbcL, and trnL-trnF for cpDNA; nad1-2/3 and nad4-1/2 for mtDNA). The analysis of cp sequence data confirms the hypothesis that the four currently recognized sections are not monophyletic. The detection of incongruences among phylogenies (mtDNA vs. cpDNA tree) coupled with the detection of intraspecific polymorphisms confirms some of the reticulations previously emphasized, diagnoses new hybridization/introgression events, and provides evidence for multiple origin of at least two polyploid taxa. A number of hybridization/introgression events at the diploid, tetraploid, and possibly hexaploid levels are documented. The extensive reticulate evolution undergone by Actinidia could account for the lack of clear morphological discontinuities at the species level.
A study based on AFLP markers was conducted to characterise the present population genetic struct... more A study based on AFLP markers was conducted to characterise the present population genetic structure of Carpinus betulus in Europe and to formulate guidelines for the use of this species in plantations on a local scale in Flanders. High within-population diversity and little (but significant) genetic differentiation were detected at both Flemish and European scales. However, there was a pattern of isolation by distance only at the European scale. Within-population gene diversity, a new rarefaction-based measure of number of genotypes ('band richness') and percentage of polymorphic loci are lower north of major mountain chains, suggesting that the mountain ranges formed a second bottleneck for the hornbeam during postglacial recolonisation. In Flanders, despite lower gene diversity, there were more polymorphic loci than in other European populations, a pattern that might have been caused by the mixing of material through planting, e.g. in hedges. In view of these findings, it is advised to create a single Flemish seed zone and to use preferentially reproductive material from this seed zone for new plantations in Flanders.
Several species of pines (Pinus spp.; Pinaceae) are highly invasive in parts of the Southern Hemi... more Several species of pines (Pinus spp.; Pinaceae) are highly invasive in parts of the Southern Hemisphere, where pines are widely planted in commercial forestry plantations. Problems associated with the spread of pines from plantations have increased substantially over the past few decades. We review the current extent of the problem and the research that has been undertaken to explain different facets of these invasions, including the factors contributing to species invasiveness and the susceptibility of ecosystems to invasion. Recent interest in producing transgenic pines for wood production raises important issues when considering future scenarios for pine invasions and for sustainable commercial forestry. This chapter considers the genetic diversity in introduced versus native pine populations and then examines the potential for transgene escape from pine plantations in the Southern Hemisphere. Propagule pressure appears to play a major role in these invasions. Commercial plantations have typically introduced a large share of the species' existing genetic diversity, resulting in rapid adaptation to local conditions and favoring the spread of feral pine populations. The extent to which inherent invasiveness of transgenic pines will differ from non-transgenic pines will depend on the properties conferred by the transgenes, but differences could be substantial. Even subtle changes in species-environment interactions could affect the dynamics of pine invasions. Genetic engineering for reproductive sterility could potentially reduce invasiveness, but criteria for forest certification current prohibit the use of any genetically-modified planting, thus blocking a potentially useful avenue of intervention. Integrated programs for managing pine invasions in the Southern Hemisphere will need to give serious attention to transgenic plantation forestry.
Interactions involving forest trees may be particularly vulnerable due to evolutionary rate limit... more Interactions involving forest trees may be particularly vulnerable due to evolutionary rate limitations imposed by long generation times. One mitigation strategy for such impacts is Climate matching -the augmentation of local native tree populations by input from non-local populations currently experiencing predicted future climates. This strategy is controversial because of potential cascading impacts on locally adapted animal communities. We explored these impacts using abundance data for local native gallwasp herbivores sampled from 20 provenances of sessile oak (Quercus petraea) planted in a common garden trial. We hypothesised that non-native provenances would show (i) declining growth performance with increasing distance between provenance origin and trial site, and (ii) phenological differences to local oaks that increased with latitudinal differences between origin and trial site. Under a local adaptation hypothesis, we predicted declining gallwasp abundance with increasing phenological mismatch between native and climate-matched trees. Both hypotheses for oaks were supported. Provenance explained significant variation in gallwasp abundance, but no gall type showed the relationship between abundance and phenological mismatch predicted
... Technical and conceptual developments in genetics will continue to propel paleoecology forwar... more ... Technical and conceptual developments in genetics will continue to propel paleoecology forward. ... data on past and future species distributions has potential to play a key role in conservation ... Such comparisons allow us to anticipate the potential loss of evolutionary heritage in ...
Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an ext... more Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an extensive sample of 389 populations distributed throughout the species range. Special emphasis was given to the analysis of the pattern of geographic variation on the basis of two contrasting measures of genetic diversity, gene diversity (H) and allelic richness, and to their relationship. Measures of allelic richness were corrected for variation in sample size by using the rarefaction method. As expected, maximum allelic richness was found in the southeastern part of the range (southern Italy and the Balkans), where beech was confined during the last ice age. Surprisingly, H was lower in refugia than in recently colonized regions, resulting in a negative correlation between the two diversity measures. The decrease of allelic richness and the simultaneous increase of H during postglacial recolonization was attributed to several processes that differentially affect the two diversity paramete...
Extensive hybridisation between the two sympatric species Quercus petraea and Q.robur is suggeste... more Extensive hybridisation between the two sympatric species Quercus petraea and Q.robur is suggested by the near lack of genetic differentiation between the two species and supported by controlled crosses and mating system analysis in mixed stands. Further ecological and genetic evidence suggest that hybridisation does not impede the ecological specialisation of the two species, raising the issue of its evolutionary
An extension of Nei's analysis of diversity in a subdivided population is proposed for a haploid ... more An extension of Nei's analysis of diversity in a subdivided population is proposed for a haploid locus. The differentiation Gsr becomes a natural extension of Wright's Fsr and generalizes Weir and Cockerham's parameter of co-ancestry by relaxing the assumption of identical correlation for all the alleles. Inter-and intrapopulation variances of the estimated diversities and differentiation are derived. Finally, the optimal sampling strategy for measuring Gsr when a fixed number of individuals can be analysed is considered. It is shown that, at a given locus, there is a unique sample size per population which yields the smallest variance of Gsr, regardless of the number of populations studied. These theoretical developments are illustrated with an analysis of chloroplast DNA diversity in a forest tree. The results emphasize the necessity of sampling many populations, rather than many individuals per population, for an accurate measurement of the subdivision of gene diversity at a single locus.
Proceedings of the Royal Society B: Biological Sciences, 2002
The importance of wood for human societies can hardly be understated. If dry wood were amenable t... more The importance of wood for human societies can hardly be understated. If dry wood were amenable to molecular genetic investigations, this could lead to major applications in wood forensics, certification, archaeology and palaeobotany. To evaluate the potential of wood for molecular genetic investigations, we have attempted to isolate and amplify, by PCR, DNA fragments of increasing size corresponding to all three plant genomes from different regions of 10 oak logs. Stringent procedures to avoid contamination with external DNA were used in order to demonstrate the authenticity of the fragments amplified. This authenticity was further confirmed by demonstrating genetic uniformity within each log using both nuclear and chloroplast microsatellites. For most wood samples DNA was degraded, and the sequences that gave the best results were those of small size and present in high copy number (chloroplast, mitochondrial, or repeated nuclear sequences). Both storage conditions and storage duration play a role in DNA conservation. Overall, this work demonstrates that molecular markers from all three plant genomes can be used for genetic analysis on dry oak wood, but outlines some limitations and the need for further evaluation of the potential of wood for DNA analysis.
Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the h... more Nested clade phylogeographic analysis (NCPA) has become a popular method for reconstructing the history of populations across species ranges. Ever since its invention in 1995, criticisms have been formulated, but the method, which has been regularly updated, continues to attract investigators. finally allows a precise evaluation of the method by developing software that automates the somewhat complicated NCPA procedure. Using simulations of random-mating populations, Panchal and Beaumont find a high frequency of false-positives with their automated NCPA procedure (over 75%). These findings, which echo and amplify earlier warnings, appear serious enough to suggest to researchers to await further evaluation of the method. Although no other allencompassing method such as the NCAP currently exists to evaluate phylogeographic data sets, researchers have many alternative methods to test ever more refined hypotheses.
Using two-dimensional polyacrylamide gel electrophoresis, the genetic variation of proteins was e... more Using two-dimensional polyacrylamide gel electrophoresis, the genetic variation of proteins was examined in three organs (needle, bud, and pollen) from 18 trees of maritime pine. Three types of variation were noted: presence/absence, staining intensity, and position variation of the spots. Of the 902 polypeptides scored in the three organs, 245 (27.2%) were polymorphic. Moreover, among these variable spots, 117 were found in a single organ, demonstrating an increased polymorphism of the organ-specific polypeptides (56.0% vs 18.4% for the organ-unspecific polypeptides). Finally, a positive correlation was found between variability level and subunit molecular weight for spots showing position variation but not for spots showing presence/absence or staining intensity variations. Possible explanations for this observation are discussed.
We have recently proposed new estimators of the parameters of genetic diversity and differentiati... more We have recently proposed new estimators of the parameters of genetic diversity and differentiation and of their variances for a haploid locus in a population subdivided into a large number of subpopulations, with a two-stage sampling of populations and individuals. Here they are compared with bootstrap estimators. Several resampling methods are evaluated: sampling of populations only, individuals within populations only, or both. Theoretical results and a numerical example show that the most appropriate bootstrap variance estimators are obtained by resampling the populations alone and not both populations and individuals. However, some bias is apparent in the bootstrap methods, and the direct estimators proposed previously should therefore be preferred.
Background: In heterogeneous environments, sex-biased dispersal could lead to environmental adapt... more Background: In heterogeneous environments, sex-biased dispersal could lead to environmental adaptive parental effects, with offspring selected to perform in the same way as the parent dispersing least, because this parent is more likely to be locally adapted. We investigate this hypothesis by simulating varying levels of sex-biased dispersal in a patchy environment. The relative advantage of a strategy involving pure maternal (or paternal) inheritance is then compared with a strategy involving classical biparental inheritance in plants and in animals. Results: We find that the advantage of the uniparental strategy over the biparental strategy is maximal when dispersal is more strongly sex-biased and when dispersal distances of the least mobile sex are much lower than the size of the environmental patches. In plants, only maternal effects can be selected for, in contrast to animals where the evolution of either paternal or maternal effects can be favoured. Moreover, the conditions for environmental adaptive maternal effects to be selected for are more easily fulfilled in plants than in animals.
The effect of species and ecological conditions on oak volatile extractive content was investigat... more The effect of species and ecological conditions on oak volatile extractive content was investigated in an evenaged (100 years) stand located in western France. The sample included a total of 286 trees (118 sessile, 158 pedunculate and 10 oaks with an intermediate morphology) growing in contrasted environments (plateau, intermediate slope, small valley). The main factor influencing oak extractives level is species. The effect of the local environment appears negligible. No correlation between ring width and volatile extractive content was found. Q. petraea is significantly richer than Q. robur in eugenol and whisky-lactone (10.8 vs. 0.6 µg/g). However, two groups of sessile oaks could be identified, one poor and one rich in whisky-lactone. Among the latter, either the cis or the trans stereoisomer was predominant, suggesting that their production is not independent. A strong spatial structure was detected for whisky-lactone (cis-, trans-and total whisky-lactone, for the two species combined but also for Q. petraea alone in the case of the cis isomer).
Evolutionary relationships within Actinidia, a genus known for the contrasting mode of inheritanc... more Evolutionary relationships within Actinidia, a genus known for the contrasting mode of inheritance of its plastids and mitochondria, were studied. The phylogenetic analysis is based on chloroplast (cp) and mitochondrial (mt) restriction site and sequence data (matK, psbC-trnS, rbcL, and trnL-trnF for cpDNA; nad1-2/3 and nad4-1/2 for mtDNA). The analysis of cp sequence data confirms the hypothesis that the four currently recognized sections are not monophyletic. The detection of incongruences among phylogenies (mtDNA vs. cpDNA tree) coupled with the detection of intraspecific polymorphisms confirms some of the reticulations previously emphasized, diagnoses new hybridization/introgression events, and provides evidence for multiple origin of at least two polyploid taxa. A number of hybridization/introgression events at the diploid, tetraploid, and possibly hexaploid levels are documented. The extensive reticulate evolution undergone by Actinidia could account for the lack of clear morphological discontinuities at the species level.
Here, palaeobotanical and genetic data for common beech ( Fagus sylvatica ) in Europe are used to... more Here, palaeobotanical and genetic data for common beech ( Fagus sylvatica ) in Europe are used to evaluate the genetic consequences of long-term survival in refuge areas and postglacial spread.
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Papers by Rémy Petit