Genetic structure of wild and cultivated olives in the central Mediterranean basin

BACKGROUND AND AIMS: Olive cultivars and their wild relatives (oleasters) represent two botanical varieties of Olea europaea subsp. europaea (respectively europaea and sylvestris). Olive cultivars have undergone human selection and their area of diffusion overlaps that of oleasters. Populations of genuine wild olives seem restricted to isolated areas of Mediterranean forests, while most other wild-looking forms of olive may include feral forms that escaped cultivation. METHODS: The genetic structure of wild and cultivated olive tree populations was evaluated by amplified fragment length polymorphism (AFLP) markers at a microscale level in one continental and two insular Italian regions. KEY RESULTS: The observed patterns of genetic variation were able to distinguish wild from cultivated populations and continental from insular regions. Island oleasters were highly similar to each other and were clearly distinguishable from those of continental regions. Ancient cultivated material from one island clustered with the wild plants, while the old plants from the continental region clustered with the cultivated group. CONCLUSIONS: On the basis of these results, we can assume that olive trees have undergone a different selection/domestication process in the insular and mainland regions. The degree of differentiation between oleasters and cultivated trees on the islands suggests that all cultivars have been introduced into these regions from the outside, while the Umbrian cultivars have originated either by selection from local oleasters or by direct introduction from other regions.     

Mitochondrial DNA variation and RAPD mark oleasters,olive and feral olive from Western and Eastern Mediterranean

The study of genetic diversity within the olive-tree (cultivated and wild forms) may be useful to reveal agronomic traits in the wild germplasm and to try to understand the history of the olive-tree domestication. In this way, a study of nuclear and mitochondrial DNAs of cultivated and wild olives from two Corsican and Sardinian Mediterranean islands was performed using RAPD and RFLP markers. Our results show that most of the varieties and most of the oleasters were separated using the UPGMA dendrogram based on the Nei and Li similarity index. Most of oleasters carried either the MOM or MCK mitotype, characteristic of olives in the Western Mediterranean, whereas most of the varieties carried the ME1 mitotype, characteristic of olives in the East Mediterranean. The results indicate that the combination of mitotype and RAPD markers can be used as a powerful tool for differentiating two groups in the wild forms: the Western true oleasters and the feral forms. The true oleasters are characterized by a Western mitotype and a Western RAPD pattern. Feral forms originate either from varieties or from hybridisation between a variety and an oleaster. Consequently, as expected, some of them aggregated with the varieties from which they were derived. The other feral forms are clustered with the oleasters and were detected only by their mitotype determination. This study has also permitted us to differentiate two populations of cultivated olives in Corsica: one with close relationships with Italian varieties (influenced by the East) and one selected from local oleasters probably due to a better local adaptation than foreign varieties.     

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.     

Genetic diversity and relationships of wild and cultivated olives in Turkey

In the present study, we proposed to determine the genetic diversity and relationships between local cultivars and wild olive trees from three important olive-growing regions, i.e., Marmara, Aegean, and Mediterranean, of Turkey. This is the first known large-scale molecular study to investigate the relationships between local cultivars and wild olives from the eastern Mediterranean basin. Two hundred and four oleaster trees and 27 cultivars were sampled to represent molecular diversity. We used 11 simple sequence repeat and 13 sequence-related amplified polymorphism markers to assess genetic variations and inter-relationships among the samples. The results of the analysis showed differences in the levels of allelic composition and heterozygosity between cultivated and wild olive trees. The observation of a high proportion of a certain wild-type genetic background in the cultivars may indicate the former use of local wild trees in olive domestication in Turkey, a possible autochthonal origin of cultivars. “Gemlik” was found to be the most common olive cultivar in the Marmara region and most of the wild olive samples from this region may be feral forms derived from cultivar seed spreading. The information obtained from this study can help to assist the management of an olive collection and sheds some light on the origin of Turkish olive cultivars.     

Genetic diversity and gene flow between the wild olive (oleaster, Olea europaea L.) and the olive: several Plio-Pleistocene refuge zones in the Mediterranean basin suggested by simple sequence repeats analysis

Aim The oleaster is believed to have originated in the eastern Mediterranean, implying that those in the western Mediterranean basin could be feral. Several studies with different molecular markers (isozymes, random amplified polymorphic DNA, amplified fragment length polymorphism) have shown a cline between the eastern and the western populations, which supports this hypothesis. To reconstruct the post‐glacial colonization history and establish a relationship between olive and oleaster populations in the Mediterranean basin, analyses were carried out on the genetic variation of chloroplast DNA (chlorotype) and at 12 unlinked simple sequence repeat (SSR) loci, sampling a total of 20 oleaster groves. Location This is the first known large‐scale molecular study of SSR loci based on samples of both oleasters and cultivars from the entire Mediterranean basin. Methods Samples were taken from 166 oleasters in 20 groves of modern populations, and 40 cultivars to represent molecular diversity in the cultivated olive. The Bayesian method and admixture analysis were used to construct the ancestral populations (RPOP; reconstructed panmictic oleaster populations) and to estimate the proportion of each RPOP in each tree. If one tree can be assigned to two or more RPOPs, it can be regarded as a product of hybridization between trees from different populations (i.e. admix origin). Results On this first examination of the SSR genetic diversity in the olive and oleaster, it was found to be structured in seven RPOPs in both eastern and western populations. Based on different population genetic methods, it was shown that: (1) oleasters are equally present in the eastern and the western Mediterranean, (2) are native, and (3) are not derived from cultivars. Chlorotypes (one and three in the eastern and western Mediterranean, respectively) revealed fruit displacement for the oleasters. Main conclusions Oleaster genetic diversity is divided into seven regions that could overlay glacial refuges. The gradient, or cline, of genetic diversity revealed by chloroplast and SSR molecular markers was explained by oleaster recolonization of the Mediterranean basin from refuges after the last glacial event, located in both eastern and western regions. It is likely that gene flow has occurred in oleasters mediated by cultivars spread by human migration or through trade. Animals may have helped spread oleasters locally, but humans have probably transported olives but not oleaster fruits over long distances. We found that cultivars may have originated in several RPOPs, and thus, some may have a more complex origin than expected initially.     

Centennial olive trees as a reservoir of genetic diversity

Background and Aims

Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin.

Methods

The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars.

Key Results

Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives.

Conclusions

This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.     

Genetic diversity and population structure of wild olives from the North-Western Mediterranean assessed by SSR markers

BACKGROUND AND AIMS: This study examines the pattern of genetic variability and genetic relationships of wild olive (Olea europaea subsp. europaea var. sylvestris) populations in the north-western Mediterranean. Recent bottleneck events are also assessed and an investigation is made of the underlying population structure of the wild olive populations. METHODS: The genetic variation within and between 11 wild olive populations (171 individuals) was analysed with eight microsatellite markers. Conventional and Bayesian-based analyses were applied to infer genetic structure and define the number of gene pools in wild olive populations. KEY RESULTS: Bayesian model-based clustering identified four gene pools, which was in overall concordance with the Factorial Correspondence Analysis and Fitch-Margoliash tree. Two gene pools were predominantly found in southern Spain and Italian islands, respectively, in samples gathered from undisturbed forests of the typical Mediterranean climate. The other two gene pools were mostly detected in the north-eastern regions of Spain and in continental Italy and belong to the transition region between the temperate and Mediterranean climate zones. CONCLUSIONS: On the basis of these results, it can be assumed that the population structure of wild olives from the north-western Mediterranean partially reflects the evolutionary history of these populations, although hybridization between true oleasters and cultivated varieties in areas of close contact between the two forms must be assumed as well. The study indicates a degree of admixture in all the populations, and suggests some caution regarding genetic differentiation at the population level, making it difficult to identify clear-cut genetic boundaries between candidate areas containing either genuinely wild or feral germplasm.     

Chloroplast-DNA variation in cultivated and wild olive (Olea europaea L.)

Polymorphism in the lengths of restriction fragments of the whole cpDNA molecule was studied in cultivated olive and in oleaster (wild olive) over the whole Mediterranean Basin. Seventy two olive cultivars, 89 very old trees cultivated locally, and 101 oleasters were scored for ten endonucleases. Moreover, maternal inheritance of cpDNA in olive was shown by analysing the progeny of a controlled cross between two parents which differed in their cpDNA haplotypes. In the whole species, three site- and three length-mutations were observed, corresponding to five distinct chlorotypes. The same chlorotype (I) was predominant in both oleasters and cultivated olive trees, confirming that these are closely related maternally. Three other chlorotypes (II, III and IV) were observed exclusively in oleaster material and were restricted either to isolated forest populations or to a few individuals growing in mixture with olive trees possessing the majority chlorotype. An additional chlorotype (V) was characterised by three mutations located in distinct parts the cpDNA molecule but which were never observed to occur separately. This chlorotype, more widely distributed than the other three, in both cultivated and wild olive, and occurring even in distant populations, was observed exclusively in male-sterile trees showing the same specific pollen anomaly. However, in the present study, no evidence was provided for a direct relationship between the occurrence of the cpDNA mutations and male sterility. It is suggested that the large geographic distribution of chlorotype V may be related to the high fruit production usually observed on male-sterile trees. These may be very attractive for birds which are fond of olive fruit and spread the stones efficiently. Probably for the same reason, people preserved male-sterile oleasters for long periods and, in several places, used male-sterile cultivars over large areas. Received: 25 November 1998 / Accepted: 19 December 1998     

Historical biogeography of olive domestication (Olea europaea L.) as revealed by geometrical morphometry applied to biological and archaeological material

Aim This study intends to improve our understanding of historical biogeography of olive domestication in the Mediterranean Basin, particularly in the north-western area. Location Investigations were performed simultaneously on olive stones from extant wild populations, extant cultivated varieties from various Mediterranean countries, and archaeological assemblages of Spanish, French and Italian settlements. Methods A combination of morphometrics (traditional and geometrical) allowed us to study both the size and shape of endocarp structure. Concerning shape, a size-standardized method coupled with fitted polynomial regression analysis was performed. Results We found morphological criteria for discriminating between wild and cultivated olive cultivars, and established patterns of morphological variation of olive material according to the geographical origin (for extant material) and to the age of the olive forms (for archaeological material). Levels of morphological convergences and divergences between wild olive populations and cultivated varieties are presented as evidence. Main conclusions Morphological changes of endocarps of olive under domestication at both geographical and chronological scales provide new criteria for the identification of olive cultivars. They allow to determine the origins of cultivated forms created and/or introduced in the north-western Mediterranean regions and to understand how human migrations affected the rest of the Western Mediterranean regions. A model of diffusion of olive cultivation is proposed. It shows evidence of an indigenous origin of the domestication process, which is currently recognized in the north-western area since the Bronze Age.     

On the origins and spread of Olea europaea L. (olive) domestication: evidence for shape variation of olive stones at Ugarit,Late Bronze Age,Syria—a window on the Mediterranean Basin and on the westward diffusion of olive varieties

Charred archaeological stones of Olea europaea L. (olive) from Late Bronze Age Ugarit, Syria, were analyzed with geometric morphometry and compared with a morphological differentiation model established on the basis of analyses of modern spontaneous (uncultivated) olive populations and cultivated varieties of various origins within the Mediterranean Basin. The results allow a reinterpretation of the east–west morphological diversity previously observed in wild olives. The archaeobotanical data were compared in detail to the partly geographically structured modern morphological diversity of the cultivated olive. Ancient morphotypes could be distinguished, among which one is dominant in the assemblage. Their diffusion from east to west is shown, and their time of arrival in the northwestern Mediterranean can be evaluated by comparison to archaeological material from that area. Combining morphometric and genetic data, modern reference and archaeological material also guides us in understanding the mechanisms that prevailed in the long-term agrobiodiversity of the olive.     

Plastid and nuclear DNA polymorphism reveals historical processes of isolation and reticulation in the olive tree complex (Olea europaea)

Aim The olive tree is considered one of the best indicators of the Mediterranean climate. The species’ distribution is associated with geographical and bioclimatic factors, as well as being influenced by a long period of cultivation. Despite concerted efforts of different research groups, the origin of the Mediterranean olive tree still remains elusive. In the present study, relationships between taxa and populations covering the entire range of Olea europaea were investigated using both maternal (plastid genome) and biparental (nuclear genome) markers to disclose evolutionary patterns in the olive complex. Phylogenetic and phylogeographical results of the two‐genome analyses were interpreted in a biogeographical context. Location Mediterranean, temperate and subtropical floristic regions of the Old World. Methods Phylogeographical reconstructions of plastid DNA polymorphism were performed using microsatellites, restriction sites and indels on a wide sample of 185 representative trees across the Old World, including 28 herbarium specimens from remote areas. Additionally, the potential utility of one ITS‐1 pseudogene for phylogenetic analyses was explored using Bayesian and maximum parsimony approaches on a subsample of 38 olive trees. Results Forty plastid haplotypes were recognized and split into two lineages and seven sublineages. The analysis of ITS‐1 sequences also allowed the identification of seven well differentiated groups. Distribution of plastid and ribosomal DNA lineages was congruent, but particular cases of phylogenetic incongruence were disclosed (particularly in the Sahara and Madeira). Lastly, two divergent ITS‐1 copies were isolated from the same sample of four individuals of different subspecies. Main conclusions Phylogenetic congruence of both ITS‐1 and plastid lineages suggested an evolutionary scenario of predominant isolation during the Plio‐Pleistocene in Macaronesia, the Mediterranean, southern Africa, eastern Africa and Asia. The Saharan desert appeared to have played an important role of vicariant barrier between southern and northern African populations in early times. Incongruence of some plastid and nuclear results, as well as intermingled ITS‐1 copies of different lineages in single individuals, was interpreted as a result of recurrent reticulation events in the olive complex. We identified an ancient hybrid zone from the Sahara to north‐eastern African mountains, where divergent plastid and nuclear lineages still co‐exist. Results of this paper, and previous studies, suggest that the cultivated olive originated from a pre‐Quaternary Mediterranean ancestor, with no evidence for a recent hybrid origin. In contrast, a continuous process of olive domestication through local hybridization events of cultivated trees with natural populations may have brought about a remarkably high genomic diversity among cultivated trees across the Mediterranean.     

Genetic structure and core collection of the World Olive Germplasm Bank of Marrakech: towards the optimised management and use of Mediterranean olive genetic resources

The conservation of cultivated plants in ex-situ collections is essential for the optimal management and use of their genetic resources. For the olive tree, two world germplasm banks (OWGB) are presently established, in Córdoba (Spain) and Marrakech (Morocco). This latter was recently founded and includes 561 accessions from 14 Mediterranean countries. Using 12 nuclear microsatellites (SSRs) and three chloroplast DNA markers, this collection was characterised to examine the structure of the genetic diversity and propose a set of olive accessions encompassing the whole Mediterranean allelic diversity range. We identified 505 SSR profiles based on a total of 210 alleles. Based on these markers, the genetic diversity was similar to that of cultivars and wild olives which were previously characterised in another study indicating that OWGB Marrakech is representative of Mediterranean olive germplasm. Using a model-based Bayesian clustering method and principal components analysis, this OWGB was structured into three main gene pools corresponding to eastern, central and western parts of the Mediterranean Basin. We proposed 10 cores of 67 accessions capturing all detected alleles and 10 cores of 58 accessions capturing the 186 alleles observed more than once. In each of the 10 cores, a set of 40 accessions was identical, whereas the remaining accessions were different, indicating the need to include complementary criteria such as phenotypic adaptive and agronomic traits. Our study generated a molecular database for the entire OWGB Marrakech that may be used to optimise a strategy for the management of olive genetic resources and their use for subsequent genetic and genomic olive breeding.     

Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture

Background and Aims

The olive (Olea europaea subsp. europaea) was domesticated in the Mediterranean area but its wild relatives are distributed over three continents, from the Mediterranean basin to South Africa and south-western Asia. Recent studies suggested that this crop originated in the Levant while a secondary diversification occurred in most westward areas. A possible contribution of the Saharan subspecies (subsp. laperrinei) has been highlighted, but the data available were too limited to draw definite conclusions. Here, patterns of genetic differentiation in the Mediterranean and Saharan olives are analysed to test for recent admixture between these taxa.

Methods

Nuclear microsatellite and plastid DNA (ptDNA) data were compiled from previous studies and completed for a sample of 470 cultivars, 390 wild Mediterranean trees and 270 Saharan olives. A network was reconstructed for the ptDNA haplotypes, while a Bayesian clustering method was applied to identify the main gene pools in the data set and then simulate and test for early generations of admixture between Mediterranean and Saharan olives.

Key Results

Four lineages of ptDNA haplotypes are recognized: three from the Mediterranean basin and one from the Sahara. Only one haplotype, primarily distributed in the Sahara, is shared between laperrinei and europaea. This haplotype is detected once in ‘Dhokar’, a cultivar from the Maghreb. Nuclear microsatellites show geographic patterns of genetic differentiation in the Mediterranean olive that reflect the primary origins of cultivars in the Levant, and indicate a high genetic differentiation between europaea and laperrinei. No first-generation hybrid between europaea and laperrinei is detected, but recent, reciprocal admixture between Mediterranean and Saharan subspecies is found in a few accessions, including ‘Dhokar’.

Conclusions

This study reports for the first time admixture between Mediterranean and Saharan olives. Although its contribution remains limited, Laperrine''s olive has been involved in the diversification of cultivated olives.     

Diversity of Olea genotypes and the origin of cultivated olives

Tandem repeats belonging to three DNA sequence families (OeTaq80, OeTaq178, and OeGEM86) were isolated from the nuclear DNA of Olea europaea cv. Carolea and dot-hybridized to the genomic DNA of 14 hypothetically different Olea species, 78 olive cultivars, and 14 wild olives. The copy number per unreplicated haploid genome of OeTaq80- and OeTaq178-related sequences was in the 10⁷-10⁶ range and that of OeGEM86-related sequences was in the 10⁵ range in cultivars, wild olives and some Olea species. A large variation in the frequency of repeats belonging to each sequence family was observed within each group of plants. Positive correlations existed in each genome between the frequencies of repeats belonging to each family, and their overall frequency was positively correlated to the genome size. Duncan grouping showed that the frequency variation of tandem repeats within each group of plants was not continuous. Two main groups and several subgroups of genotypes could be separated within both the olive cultivars and the wild olives. Discrete areas in the Mediterranean Basin could be delimited by the geographic distribution of cultivated olives with different genotypes and the wild plants were associated with the cultivars in these areas according to genotypic similarity. The Olea species could be divided into four genotypic groups. Three of these, comprising accessions from Asia and North Africa, showed similarity with the genotypes of cultivars and wild olives. These results suggest a polyphyletic origin of cultivated olives from different wild Olea forms distributed throughout the Mediterranean Basin.     

Cytoplasmic male sterility in the olive (Olea europaea L.)

The olive tree is usually hermaphrodite but self-incompatible. In the Western Mediterranean some cultivars are totally male-sterile. Three different male-sterile phenotypes have been recognised. To infer the genetic basis of male sterility we studied its inheritance and cytoplasmic diversity in wild (oleaster) and cultivated Mediterranean olive. In the cross Olivière×Arbequina, the male-sterile trait was maternally inherited and affected all progenies. We also checked that both chloroplast and mitochondrial DNAs are maternally inherited. RFLP studies on chloroplast and mitochondrial DNAs revealed several cytotypes: two chlorotypes and four mitotypes in cultivars and oleaster (wild or feral Mediterranean olive). Furthermore, a total linkage desequilibrium between the CCK chlorotype and the MCK mitotype in cultivars and oleaster from different regions supports the fact that paternal leakage of organelles was not observed. The male sterility (ms 2) displayed by Olivière, plus six other cultivars and three oleaster was strictly associated with the CCK chlorotype and the MCK mitotype. These facts suggest that Olivière carries cytoplasmic male sterility. Male-fertile and male-sterile oleasters carrying this cytotype showed the presence of restorer alleles. This CMS might be due to a distant cross between olive taxa. The two other male-sterile phenotypes displayed by Lucques (ms 1) and Tanche (ms 3) were associated with the ME1 mitotype but we have not demonstrated CMS. Received: 26 July 1999 / Accepted: 27 August 1999     

Olive tree varieties cultivated for the great Baetican oil trade between the 1st and the 4th centuries <Emphasis Type="SmallCaps">ad</Emphasis>: morphometric analysis of olive stones from Las Delicias (Ecija,Province of Seville,Spain)

During the excavations of a Roman amphora workshop and oil mill of the 1st–4th century ad in Las Delicias, Genil valley, Ecija, Spain, large quantities of charred olive stones were recovered. The assemblages discovered in the pottery kilns demonstrate the use as fuel of olive residues, which were obtained from the extraction of the oil in the nearby mill. The abundance of material offered the opportunity to study the infra-specific diversity of the olives growing in the province of Baetica, which is known to have been an important oil-producing region during the Roman Empire. In total, 335 intact charred archaeological olive stones were analysed using geometric morphometry (outline analysis) and compared with several current morphotypes. These have been identified within a set of dimensional references of the stones established from the morphometric study of current varieties and wild populations, including genuinely wild and feral forms of olives, from various areas around the Mediterranean. The morphotype mainly found in wild populations was widely represented among the olive stones from Las Delicias. A large proportion of the archaeological stones were however close to various domesticated forms, which reflect the history of the region and of its varied cultural Mediterranean influences, Punic, Greek and Roman. Moreover, intermediate forms between two distinct morphotypes were identified. They suggest that hybrid olive trees derived from crosses among domesticated varieties and also between domesticated and wild forms, were grown in Las Delicias. In the Genil valley, Roman olive cultivation was based on a set of local olives which included wild and domesticated varieties from various origins, and whose diversity arose from breeding for improvement of varieties.     

Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe "domestication bottleneck" during pigeonpea domestication.     

Substantial genetic diversity in cultivated Moroccan olive despite a single major cultivar: a paradoxical situation evidenced by the use of SSR loci

To assess the genetic diversity in Moroccan cultivated olive, Olea europaea L. subsp. europaea, we performed molecular analysis of olive trees sampled in four geographic zones representing all areas of traditional olive culture. The analysis of 215 trees using 15 simple sequence repeat (SSR) loci revealed 105 alleles distributed among 60 SSR profiles. The analysis of chloroplast deoxyribonucleic acid polymorphism for these 60 olive genotypes allowed to identify four chlorotypes: 42 CE1, one CE2, nine COM1 and eight CCK. Among the 60 SSR profiles, 52 corresponded to cultivated olive trees for which neither denomination nor characterisation is available. These local olive genotypes displayed a spatial genetic structuring over the four Moroccan geographic zones (northwest, north centre, Atlas and southwest), as pairwise Fst values ranged from 0.0394 to 0.1383 and varied according to geographic distance. As single alleles detected in local olive were also observed in Moroccan oleaster populations, results suggest that plant material was mainly selected from indigenous populations. The assumption that Picholine marocaine cultivar is a multi-clonal cultivar was not supported by our data because we found a single genotype for 112 olive trees representing 31 to 93% of the olives sampled locally in the 14 different areas. Picholine marocaine and the few other named cultivars do not seem to belong to the same gene pools as the unnamed genotypes cultivated only locally. The situation is paradoxical: a substantial genetic diversity in Moroccan olive germplasm, probably resulting from much local domestication, but a single cultivar is predominant.     

Population structure and colonization history of the olive fly, Bactrocera oleae (Diptera, Tephritidae)

The olive fly, Bactrocera oleae, is the major pest of olives in most commercial olive-growing regions worldwide. The species is abundant in the Mediterranean basin and has been introduced recently into California and Mexico, creating problems for quarantine protection and international trade. Here, we use nuclear microsatellite markers and mitochondrial sequences to examine the history of olive fly range expansion and colonization. Sampled populations span the current distribution of the olive fly worldwide, including South and Central Africa, Pakistan, Mediterranean Europe and Middle East, California, and Mexico. The Pakistani populations appear to be genetically well differentiated from the remaining populations, though rooting the origins of the species is problematic. Genetic similarity and assignment tests cluster the remaining populations into two genetic groups--Africa and a group including the Mediterranean basin and the American region. That Africa, and not the Mediterranean, is the origin of flies infesting cultivated olive is supported by the significantly greater genetic diversity at microsatellite loci in Africa relative to the Mediterranean area. The results also indicate that the recent invasion of olive flies in the American region most likely originated from the Mediterranean area.