Bruno Fady

GENETICALLY DEPAUPERATE BUT WIDESPREAD: THE CASE OF AN EMBLEMATIC MEDITERRANEAN PINE

Abstract Genetic variation is generally considered a prerequisite for adaptation to new environmental conditions. Thus the discovery of genetically depauperate but geographically widespread species is unexpected. We used 12 paternally inherited chloroplast microsatellites to estimate population genetic variation across the full range of an emblematic circum-Mediterranean conifer, stone pine (Pinus pinea L.). The same chloroplast DNA haplotype is fixed in nearly all of the 34 investigated populations. Such a low level of variation is consistent with a previous report of very low levels of diversity at nuclear loci in this species. Stone pine appears to have passed through a severe and prolonged demographic bottleneck, followed by subsequent natural- and human-mediated dispersal across the Mediterranean Basin. No other abundant and widespread plant species has as little genetic diversity as P. pinea at both chloroplast and nuclear markers. However, the species harbors a nonnegligible amount of variation at adaptive traits. Thus a causal relationship between genetic diversity, as measured by marker loci, and the evolutionary precariousness of a species, cannot be taken for granted.

Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (FST) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysis.

Large‐scale longitudinal gradients of genetic diversity: a meta‐analysis across six phyla in the Mediterranean basin

Biodiversity is the diversity of life at all scales, from genes to ecosystems. Predicting its patterns of variation across the globe is a fundamental issue in ecology and evolution. Diversity within species, that is, genetic diversity, is of prime importance for understanding past and present evolutionary patterns, and highlighting areas where conservation might be a priority. Using published data on the genetic diversity of species whose populations occur in the Mediterranean basin, we calculated a coefficient of correlation between within-population genetic diversity indices and longitude. Using a meta-analysis framework, we estimated the role of biological, ecological, biogeographic, and marker type factors on the strength and magnitude of this correlation in six phylla. Overall, genetic diversity increases from west to east in the Mediterranean basin. This correlation is significant for both animals and plants, but is not uniformly expressed for all groups. It is stronger in the southern than in the northern Mediterranean, in true Mediterranean plants than in plants found at higher elevations, in trees than in other plants, and in bi-parentally and paternally than in maternally inherited DNA makers. Overall, this correlation between genetic diversity and longitude, and its patterns across biological and ecological traits, suggests the role of two non-mutually exclusive major processes that shaped the genetic diversity in the Mediterranean during and after the cold periods of the Pleistocene: east-west recolonization during the Holocene and population size contraction under local Last Glacial Maximum climate in resident western and low elevation Mediterranean populations.

Geographical diversity and genetic relationships among Cedrus species estimated by AFLP

Genetic diversity was described in 17 cedar populations covering the geographical range of the four species of the genus Cedrus. The study was conducted using amplified fragment length polymorphism (AFLP) on haploid tissues (megagametophytes). Eleven selective AFLP primer pairs generated a total of 107 polymorphic amplification products. Correspondence and genetic distance analyses indicated that Cedrus deodara constitutes a separate gene pool from the Mediterranean cedars. Within Mediterranean cedars, we distinguished two groups: the first one is made of Cedrus atlantica, while the second one is made of Cedrus libani and Cedrus brevifolia, these latter two species being genetically similar despite important divergence previously observed for morphological and physiological traits. The lowest intrapopulation variability was found in the two C. deodara populations analyzed. Surprisingly, C. brevifolia, the endemic taxon from the island of Cyprus that is found in small and fragmented populations, showed one of the highest levels of diversity. This unexpected pattern of diversity and differentiation observed for C. brevifolia suggests a recent divergence rather than a relictual, declining population. Patterns of diversity within- and among-populations were used to test divergence and fragmentation hypotheses and to draw conclusions for the conservation of Cedrus gene pools.

Structure of Genetic diversity in Abies alba Mill. from southwestern Alps: multivariate analysis of adaptive and non-adaptive traits for conservation in France

Abstract Abies alba is one of the major European mountain forest species for which a gene resource conservation network exists in France. However, scattered populations from southwestern Alps (southeastern France) are poorly represented in this network. Using a sample of 16 populations, two of which are already included in the network, the structural pattern of genetic diversity was investigated to help decide whether additional populations should be included in the conservation network. Traits were analyzed using both seeds and progenies of selected trees from natural stands (19–43 per stand) grown 4 years in nursery. The southwestern Alpine regional resource was structured into three ecological groups: Sub-Mediterranean Alps, Intermediate Alps and Ligurian Alps. Multivariate analyses were used to compare phytoecological distribution and variability of adaptive and non-adaptive traits. The following traits were analyzed: (i) isozyme diversity of open-pollinated seeds harvested from the stands (seven variables), (ii) mean monoterpene composition of original stands using nursery test progenies (seven variables) and (iii) growth, bud phenology and drought resistance traits using nursery test progenies (nine variables). The 3-group ecological diversity can be relatively well-explained by terpene data but not by isozyme or adaptive trait data. Synthetic variables generated from grouped original data concur with the ecological pattern. Most adaptive trait variability was found within populations, which indicates that selective forces operate at the micro-geographical level. This study suggests a lack of representative populations for the Abies alba genetic conservation network both in Ligurian and Sub-Mediterranean Alpine ecological group. It also suggests that due to isolation, the scattered Sub-Mediterranean ecological group has less non-adaptive genetic diversity and may require additional conservation focus.

Considering evolutionary processes in adaptive forestry

ContextManaging forests under climate change requires adaptation. The adaptive capacity of forest tree populations is huge but not limitless. Integrating evolutionary considerations into adaptive forestry practice will enhance the capacity of managed forests to respond to climate-driven changes.AimsFocusing on natural regeneration systems, we propose a general framework that can be used in various and complex local situations by forest managers, in combination with their own expertise, to integrate evolutionary considerations into decision making for the emergence of an evolution-oriented forestry.MethodsWe develop a simple process-based analytical grid, using few processes and parameters, to analyse the impact of forestry practice on the evolution and evolvability of tree populations.ResultsWe review qualitative and, whenever possible, quantitative expectations on the intensity of evolutionary drivers in forest trees. Then, we review the effects of actual and potential forestry practice on the evolutionary processes. We illustrate the complexity of interactions in two study cases: the evolutionary consequences for forest trees of biotic interactions and of highly heterogeneous environment.ConclusionEvolution-oriented forestry may contribute adapting forests to climate change. It requires combining short-term and long-term objectives. We propose future lines of research and experimentation.

Effects of seed dispersal, adult tree and seedling density on the spatial genetic structure of regeneration at fine temporal and spatial scales

Several demographic factors can produce family structured patches within natural plant populations, particularly limited seed and pollen dispersal and small effective density. In this paper, we used computer simulations to examine how seed dispersal, density, and spatial distribution of adult trees and seedlings can explain the spatial genetic structure (SGS) of natural regeneration after a single reproductive event in a small population. We then illustrated the results of our simulations using genetic (isozymes and chloroplast microsatellites) and demographic experimental data from an Abies alba (silver fir) intensive study plot located in the Southern French Alps (Mont Ventoux). Simulations showed that the structuring effect of limited dispersal on seedling SGS can largely be counterbalanced by high effective density or a clumped spatial distribution of adult trees. In addition, the clumping of natural regeneration far from adult trees, which is common in temperate forest communities where gap dynamics are predominant, further decreases SGS intensity. Contrary to our simulation results, low adult tree density, aggregated spatial distribution of seedlings, and limited seed dispersal did not generate a significant SGS in our A. alba experimental plot. Although some level of long distance pollen and seed flow could explain this lack of SGS, our experimental data confirm the role of spatial aggregation (both in adult trees and in seedlings far from adult trees) in reducing SGS in natural populations.

Differentiating Groups of Abies Species With a Simple Molecular Marker

Abstract The unambiguous identification of closely related species is useful for many practical purposes in forest tree species. For example, international laws require timber identification and the control of the origin of forest reproductive material. In this paper, we present a mitochondrial DNA marker which can be used to differentiate among groups of fir species (Abies spp.). Eight Mediterranean and one North American fir species (used as reference) were analysed at the fourth intron of the NAD subunit 5 gene. A total of six different haplotypes was identified, one in the American Abies concolor, the other five in Mediterranean species. Two different haplotypes were found each in the widespread A. alba and in A. cephalonica, one haplotype being shared among the two species. A single species specific haplotype was found in the near-eastern A. cilicica. The two southwestern species A. pinsapo and A. numidica shared one haplotype. The fifth haplotype was shared by all remaining eastern Mediterranean firs, A. cephalonica, A. bornmuelleriana, A. equi-troiani, and A. nordmanniana. Differences in haplotype sequences were mainly due to large insertions/deletions. Agarose gel electrophoresis thus provides a fast, cheap and reliable diagnosis method for species or species group identification.

Walnut demonstrates strong genetic variability for adaptive and wood quality traits in a network of juvenile field tests across Europe

Adaptive and wood quality trait data were collected and analyzed on commercially available Juglans regia and J. regia×J. nigra provenances and progenies planted across Europe in a multi-site network. A total of 19 seed sources, replicated 35 times per site, were planted at 13 sites from 5 European countries, encompassing the potential distribution area of timber production plantation sites. The following traits were evaluated: survival, height, diameter at breast height, stem form, apical dominance, vegetative budbreak, along with biotic and abiotic damage. Mean values were significantly different both among provenances/progenies and sites. Most common damage was late spring and early autumn frost. Bud break ranking was significantly correlated with provenance and progeny origin. Although J. regia is fast growing, southern European early budbreak plant material should not be planted under most middle European conditions where late spring frost can be expected, as it has a significant negative impact on architectural (and thus wood quality) traits. Hybrid J. regia×J. nigra progeny performed better than J. regia provenances/progenies for most traits measured. Differences were significantly in favor of hybrids at sites with medium to low fertility, although some locally selected seed sources tended to perform as well as hybrids on high fertility sites.

Geographic variability of terpene composition in Abies cephalonica Loudon and Abies species around the Aegean: hypotheses for their possible phylogeny from the Miocene

SummaryCortical oleoresin composition of lateral shoots (mono- and sesquiterpenes) was analysed by gas chromatography on 18 Mediterranean fir populations grown in experimental fields in southern France: 13 Abies cephalonica Loudon provenances and one A. borisii regis Mattfeld provenance from Greece, 2 A. alba Miller provenances from Romania and Bulgaria, 1 Abies bornmuelleriana Mattfeld provenance and 1 A. equi trojani Ascherson and Sintenis provenances from Turkey. Terpenes with the highest between-provenance variability were limonene, β-pinene, longifolene, δ-cadinene and α-humulene. Both similarity in terpene composition of all the firs studied and paleogeographical data demonstrated the possible existence of a unique Eastern Mediterranean tertiary ancestor for present-day Aegean species. The Pliocene marine transgression of the Aegean basin could have caused this geographical disjunction. According to this hypothesis, A. alba would have appeared in the Northern part of the Aegean and then colonized all of Europe while A. bornmuelleriana would have appeared in its Eastern part. Frequent Pleistocene contacts between the two species could have contributed to the individualization of A. equi trojani and given rise to the particular morphology of the south-eastern ecotypes of A. alba. In the western part of the basin, A. cephalonica populations would have appeared. Southern migrations of A. alba during the Ice Age and contact with A. cephalonica in refugia probably led to the development of A. borisii regis hybrid populations. Evidence for an A. alba gene flow can be found in the southernmost A. cephalonica populations.