LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

Genetic diversity at nine isozyme loci was surveyed in an endangered tree species, the argan tree, endemic to south-western Morocco. The species is highly diverse (3.6 alleles/locus) with populations strongly differentiated from each other (FST=0.25). This example is used to illustrate a method for standardizing measures of allelic richness in samples of unequal sample sizes, which was developed for the estimation of the number of species and relies on the technique of rarefaction. In addition, it is shown that the measure of subdivision, θST, obtained when allelic richness is used in place ofh (Nei's index of diversity), is much larger than the FST [e.g. θST(40)=0.52, where (40) indicates the specified sample used to estimate the allelic richness]. This suggests that rare alleles (which strongly influence measures of allelic richness) have a more scattered distribution than more frequent ones, a result which raises special conservation issues for the argan tree.

High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco.

A reviewer for the Journal of the Royal Statistical Society of England comments \"This is the first book covering in one volume all important topics in genetical statistics.\" Written to provide basic probability ideas in terms of genetic situations, since the theory of genetics is a probability theory; to give a definitive treatment of applications of these ideas to genetic theory; and to describe statistical methods appropriate to the data models that are developed.

An Introduction to Genetic Statistics

Linear models

What makes the structure and dynamics of coupled natural and human systems difficult to interpret in the Mediterranean is the extreme diversity in space and time of both environments and human societies. The succession of civilizations that waxed and waned in the Mediterranean Basin over several millennia has had great impacts on biota and ecosystems everywhere in the basin. A complex ‘coevolution’ has been claimed to shape the interactions between ecosystem components and human societies. Two opposing schools of thought traditionally have considered the consequences of human pressures on Mediterranean ecosystems. The ‘Ruined Landscape’ or ‘Lost Eden theory’ argues that human action resulted in a cumulative degradation and desertification of Mediterranean landscapes. The second school argues that humans actually contributed to keeping Mediterranean landscapes diverse since the last glacial episode. With this debate in mind, I show the following: (1) One cannot understand the components and dynamics of current biodiversity in the Mediterranean without taking into account the history of human-induced changes; (2) The various systems of land use and resource management that provided a framework for the blossoming of Mediterranean civilizations also had profound consequences on the distribution and dynamics of species, communities, and landscapes; (3) The processes of domestication of plant and animal species, which first occurred in the eastern Mediterranean area some 10,000 years ago, contributed to the increase of certain components of biodiversity at several spatial scales. Positive and negative feedback cycles between cultural practices and natural systems at the local and regional levels have kept ecosystems robust and resilient; (4) Assuming that human action can, to a certain extent, be considered a large-scale surrogate for natural sources of ecosystem disturbance, such patterns give support to the diversity-disturbance hypothesis—specifically, intermediate levels of disturbance have promoted biological diversity; (5) Intraspecific adaptive variation increased as a result of human-induced habitat changes over millennia, resulting in bursts of differentiation during the later Holocene of local ecotypes and gene pools of domesticated and wild plant and animal species, with region-specific characters fitting them to local climate and environmental conditions. High intraspecific adaptive variation also arose from earlier natural processes of the Pleistocene, mainly from a combination of periodic refugia formation and climate dynamics. During the Holocene, the main sources of disturbance came increasingly from humans, specifically from the coupled cultural and natural modifications of community and landscape structure. It is concluded that a high degree of resilience of Mediterranean ecosystems resulted in a dynamic coexistence of human and natural living systems, which in some cases provided stability, while fostering diversity and productivity (Blondel and Aronson, 1999). The word “design” used in the title and elsewhere in this paper metaphorically indicates that the long-lasting influence of human impacts resulted in an unintentional shaping of individual components of landscapes.

The ‘Design’ of Mediterranean Landscapes: A Millennial Story of Humans and Ecological Systems during the Historic Period

One hundred and two olive RAPD profiles were sampled from all around the Mediterranean Basin. Twenty four clusters of RAPD profiles were shown in the dendrogram based on the Ward’s minimum variance algorithm using chi-square distances. Factorial discriminant analyses showed that RAPD profiles were correlated with the use of the fruits and the country or region of origin of the cultivars. This suggests that cultivar selection has occurred in different genetic pools and in different areas. Mitochondrial DNA RFLP analyses were also performed. These mitotypes supported the conclusion also that multilocal olive selection has occurred. This prediction for the use of cultivars will help olive growers to choose new foreign cultivars for testing them before an eventual introduction if they are well adapted to local conditions.

Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars

Chloroplast DNA diversity in the olive (Olea europaea L.) complex was studied using PCR-RFLP and microsatellite markers. Fifteen chlorotypes were distinguished. We constructed a cpDNA phylogenetic tree in which five clades were recognised and located in distinct geographic areas: clade A in Central and Southern Africa, clade C in Asia, clade M in North-West Africa, clade E1 in the Mediterranean Basin and Sahara, and clade E2 in West Mediterranea. Cultivated olive clustered with Mediterranean and Saharan wild forms (clades E1 and E2). Strong genetic differentiation for cpDNA markers was observed between eastern and western Mediterranean olives, suggesting that these areas have represented different glacial refugia. Humans most likely spread one eastern chlorotype, preponderant in cultivars, across the western Mediterranean Basin. Its presence in O. e. subsp. laperrinei from the Sahara suggests a possible Mediterranean olive origin in an African population, which may have overlapped in the Southern Mediterranean during the Quaternary.

Olea europaea (Oleaceae) phylogeography based on chloroplast DNA polymorphism.

One hundred and thirteen olive (Olea europaea L.) accessions were characterized using randomly amplified polymorphic DNA (RAPD) markers. Forty-five polymorphic RAPD markers were obtained enabling us to distinguish 102 different RAPD profiles. The approximate estimation of the probability of obtaining the same RAPD profile for two different trees was between 6.75 × 10 -5 and 4.82 × 10 -14 . A dendrogram was constructed using Ward's minimum variance algorithm based on chi-square distances. This led to a more clear-cut classification of profiles than the classical approach of unweighted pair group method with arithmetic average. Twenty-four clusters of RAPD profiles were shown in Ward's dendrogram. Reliability of the dendrogram structure was checked using variance analysis. RAPD data exhibited an acceptable resolving power for cultivar identification. A combination of three primers was proposed for rapid molecular identification of cultivars in collections and in nurseries. Olive (Olea europaea) is of great socioeconomic importance in the Mediterranean basin. Its cultivation is expanding because of increased demand for olive oil. A great number of olive cultivars (presumed clones) are grown throughout the world. Several hundred supposedly clonal accessions are described in the main countries of the Mediterranean basin. In France about 150 cultivars are registered (Andlauer, 1997). During the history of olive cultivation, as for other tree species, different cultivars may have been given the same name, whereas a cultivar may have been named differently in different countries. Therefore, cultivar and denomination (usual or local name) are ambiguous terms. Vegetative propagation of trees of agronomic interest has produced numerous clones (Zohary and Hopf, 1994). Conse- quently, genetic uniformity within a given cultivar, and thus, within a denomination, is expected. Cultivar identification based on phenological and morphological phenotypes from field or nursery observations may not be adequate to assign cultivar identity due to environmental effects on traits. Moreover, the

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Cultivar Identification in Olive Based on RAPD Markers

We assessed the genetic differentiation of the Mediterranean olive from its wild relatives found in different geographic areas (Mediterranean, Asia, Africa) using eighty RAPDs revealed with eight primers. Variance analysis (AMOVA) enabled us to estimate the overall genetic differentiation parameters between wild populations. Oleasters from the Near East and Turkey were discriminated from the other Mediterranean populations. Olea laperrinei, O. maroccana and O. cerasiformis were the taxa the most related to the Mediterranean olive. In contrast, O. africana was shown to be the most genetically distant taxa from the Mediterranean olive. However, we characterised hybrid trees between these two taxa. Significant trends between genetic and geographic distances were met within the subspecies cuspidata and within the Mediterranean olive. A genetic diversity gradient was observed in both subspecies europaea and cuspidata. These results are in agreement with a mechanism of differentiation by distance in the O. europaea complex, but another non-exclusive mechanism could also be gene flow between differentiated taxa. Furthermore, we characterised the discriminating power of each RAPD to recognise the different taxa using intraclass correlation coefficients. Lastly, IGS-RFLPs enabled us to assess rDNA polymorphisms on a sub-sample of individuals. On the basis of these data, a low interspecifc differentiation was found. This suggests a recent genetic divergence between the different taxa of the O. europaea complex or the occurrence of gene flow during favourable periods or because human displacements. All the olive cultivars were genetically related to the oleaster populations supporting that Mediterranean is the olive domestication area.

Genetic differentiation in the olive complex (Olea europaea) revealed by RAPDs and RFLPs in the rRNA genes

Four hundred and four individuals belonging to the species #Olea europaea# were characterised using mitochondrial DNA (mtDNA) RFLPs. Twelve mitotypes were distinguished. The combination of mtDNA information with cpDNA polymorphism (characterised in a previous study) led us to recognise 20 cytoplasmic lineages of which seven were found in the Mediterranean area (oleasters, cultivars and #O. e.# subsp. #maroccana#). In the olive complex, strong cytoplasm genetic differentiation was revealed (Fst = 0.73). Very strong linkage disequilibrium between cpDNA and mtDNA polymorphisms was observed, particularly in the Mediterranean subspecies #europaea#. This high congruence between genetic structure based on cpDNA or mtDNA sustains a low level of recurrent mutation in both organelle DNAs and, thus, the polymorphisms used in this study were pertinent to reconstruct olive phylogeography. In the Mediterranean area, genetic drift due to population regression during Quaternary glaciations, and founder effects associated with the postglacial seed dissemination, have probably contributed to the existence of a high genetic linkage disequilibrium between cpDNA and mtDNA polymorphisms. Thus, four Mediterranean cytoplasmic lineages, clearly distinguished both by cpDNA and mtDNA polymorphisms, most likely reflect four distinct relic populations during Quaternary glaciations. Finally, #O. e.# subsp. #maroccana# from South Morocco, which also displayed specific cytoplasmic lineages, should be considered as another relic Mediterranean population. (Resume d'auteur)

Philippe Baradat

Papers

Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars

Olea europaea (Oleaceae) phylogeography based on chloroplast DNA polymorphism.

Cultivar Identification in Olive Based on RAPD Markers

Genetic differentiation in the olive complex (Olea europaea) revealed by RAPDs and RFLPs in the rRNA genes

Combination of chloroplast and mitochondrial DNA polymorphisms to study cytoplasm genetic differentiation in the olive complex ( Olea europaea L.).