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.     

High hunting pressure selects for earlier birth date: wild boar as a case study

Exploitation by humans affects the size and structure of populations. This has evolutionary and demographic consequences that have typically being studied independent of one another. We here applied a framework recently developed applying quantitative tools from population ecology and selection gradient analysis to quantify the selection on a quantitative trait-birth date-through its association with multiple fitness components. From the long-term monitoring (22 years) of a wild boar (Sus scrofa scrofa) population subject to markedly increasing hunting pressure, we found that birth dates have advanced by up to 12 days throughout the study period. During the period of low hunting pressure, there was no detectable selection. However, during the period of high hunting pressure, the selection gradient linking breeding probability in the first year of life to birth date was negative, supporting current life-history theory predicting selection for early births to reproduce within the first year of life with increasing adult mortality.     

Density dependence in Golden Eagle Aquila chrysaetos fecundity better explained by individual adjustment than territory heterogeneity

Density-dependence effects acting on fecundity can be explained by two competing hypotheses. The individual adjustment hypothesis (IAH) states that, as population density increases, interference among individuals negatively affects their breeding performance. The second hypothesis, the habitat heterogeneity hypothesis (HHH), proposes that, as more individuals occupy the space available, lower quality habitats are increasingly used, causing average population fecundity to decline. In territorial species, it is often predicted that interference mechanisms (IAH) should be of less importance than spatial heterogeneity (HHH). Here, we test this prediction in Golden Eagles, using 35 years of reproduction monitoring data from a population that has been recolonizing the grounds of a French National Park (Ecrins) in the Alps. During the study period, the Eagle population increased from c. 11 to 41 territorial pairs, providing a good opportunity to explicitly assess fecundity across a gradient of densities. Under the IAH, we expect the fecundity of all territories to diminish as density rises. Under strict HHH, older territories should maintain higher fecundity across time, and a positive relationship between fecundity and the seniority of a territory should be observed. A density-dependent pattern was clearly detected at the population level. At the territory level, the decrease of fecundity was strongly related to population size but not to territory seniority. Fecundity decreased similarly in all territories, suggesting that the IAH better explains the observed pattern. Two alternative mechanisms, related to the IAH, could be at play in this population: (1) negative interference by neighbours and non-territorial Eagles and (2) the contraction of individual territories over time. Our results provide new insights into density dependence in territorial raptors, suggesting that, in addition to habitat heterogeneity, interference mechanisms might actually also play an important role.     

Foraging niche shift maintains breeding parameters of a colonial waterbird during range expansion

Relating the effects of foraging niche variation to reproductive dynamics is critical to understand species response to environmental change. We examined foraging niche variations of the slender‐billed gull (Chroicocephalus genei), a nomadic colonial waterbird species during its range expansion along the French Mediterranean coast over a 16‐year period (1998–2013). We investigated whether range expansion was associated with a change in chick diet, breeding success, and chicks body condition. We also examined whether breeding success and chicks body condition were explained by diet and colonial characteristics (number of pairs, laying phenology, habitat, and locality). Diet was characterized using dual‐stable isotopic proxies (δ¹³C and δ¹⁵N) of feather keratin from 331 individuals subsampled from a total of 4,154 chicks ringed and measured at 18 different colonies. δ¹³C decreased and δ¹⁵N increased significantly during range expansion suggesting that chicks were fed from preys of increasing trophic level found in the less salty habitat colonized by the end of the study period. Niche shift occurred without significant change of niche width which did not vary among periods, habitats, or localities either. Breeding success and chick body condition showed no consistent trends over years. Breeding success tended to increase with decreasing δ¹³C at the colony level while there was no relationship between stable isotope signatures and chick body condition. Overall, our results suggest that even if range expansion is associated with foraging niche shift toward the colonization of less salty and more brackish habitats, the shift had marginal effect on the breeding parameters of the Slender‐billed gull. Niche width appears as an asset of this species, which likely explains its ability to rapidly colonize new locations.     

Involvement of DNA polymerase mu in the repair of a specific subset of DNA double-strand breaks in mammalian cells

The repair of DNA double-strand breaks (DSB) requires processing of the broken ends to complete the ligation process. Recently, it has been shown that DNA polymerase μ (polμ) and DNA polymerase λ (polλ) are both involved in such processing during non-homologous end joining in vitro. However, no phenotype was observed in animal models defective for either polμ and/or polλ. Such observations could result from a functional redundancy shared by the X family of DNA polymerases. To avoid such redundancy and to clarify the role of polμ in the end joining process, we generated cells over-expressing the wild type as well as an inactive form of polμ (polμD). We observed that cell sensitivity to ionizing radiation (IR) was increased when either polμ or polμD was over-expressed. However, the genetic instability in response to IR increased only in cells expressing polμD. Moreover, analysis of intrachromosomal repair of the I-SceI-induced DNA DSB, did not reveal any effect of either polμ or polμD expression on the efficiency of ligation of both cohesive and partially complementary ends. Finally, the sequences of the repaired ends were specifically affected when polμ or polμD was over-expressed, supporting the hypothesis that polμ could be involved in the repair of a DSB subset when resolution of junctions requires some gap filling.     

Glacial in situ survival in the Western Alps and polytopic autopolyploidy in Biscutella laevigata L. (Brassicaceae)

Past climatic changes and especially the ice ages have had a great impact on both the distribution and the genetic composition of plant populations, but whether they promoted speciation is still controversial. The autopolyploid complex Biscutella laevigata is a classical example of polyploidy linked to glaciations and is an interesting model to explore migration and speciation driven by climate changes in a complex alpine landscape. Diploid taxa survived the last glacial maximum in several never-glaciated areas and autotetraploids are clearly dominant in the central parts of the Alps; however, previous range-wide studies failed to identify their diploid ancestor(s). This study highlights the phylogeographical relationships of maternal lineages in the Western Alps and investigates the polyploidy process using plastid DNA sequences (trnS-trnG and trnK-intron) combined with plastid DNA length polymorphism markers, which were transferable among Brassicaceae species. Twenty-one distinct plastid DNA haplotypes were distinguished in 67 populations densely sampled in the Western Alps and main lineages were identified by a median-joining network. The external Alps harboured high levels of genetic diversity, while the Central Alps contained only a subset of haplotypes due to postglacial recolonization. Several haplotypes were restricted to local peripheral refugia and evidence of in situ survival in central nunataks was detected by the presence of highly differentiated haplotypes swamped by frequent ones. As hierarchical genetic structure pointed to an independent evolution of the species in different biogeographical districts, and since tetraploids displayed haplotypes belonging to different lineages restricted to either the northern or the southern parts of the Alpine chain, polytopic autopolyploidy was also apparent in the Western Alps.     

Sex‐dependent habitat selection in a high‐density Little Bustard Tetrax tetrax population in southern France,and the implications for conservation

Conservation measures often rely on habitat management, so knowledge about a species’ habitat use is a prerequisite for effective conservation planning. The Little Bustard Tetrax tetrax, a medium‐sized bird native to the Palaearctic steppes and today found in extensively farmed habitats, is a threatened species. Its population experienced a 94% decline in farmland habitats in France between 1982 and 1996, and populations all over Europe have suffered equally sharp declines. Due to this steep negative trend, this species has been the subject of a number of habitat selection studies in order to develop relevant conservation measures based on its habitat requirements. In this study, we investigated the habitat selection of a range of habitat types by both sexes and at two nested spatial scales: plot scale and landscape scale. In addition, we analysed intra‐specific social interactions by incorporating conspecific density in the statistical models of habitat use. The study was conducted on a very high‐density population, perhaps the highest ever recorded for this species at around 50 Bustards per 100 ha of suitable habitat. Our methodology combined two field approaches (point counts and quadrat counts). The findings showed rather limited sexual dimorphism in terms of habitat selection at a local scale, with only vegetation height differing between sexes at a micro‐habitat scale, no selection at landscape scale, and a prevailing role of social factors at both scales. The implications for future conservation strategies in relation to population density and landscape composition are discussed.     

Joint estimation of survival and breeding probability in female dolphins and calves with uncertainty in state assignment

While the population growth rate in long‐lived species is highly sensitive to adult survival, reproduction can also significantly drive population dynamics. Reproductive parameters can be challenging to estimate as breeders and nonbreeders may vary in resighting probability and reproductive status may be difficult to assess. We extended capture–recapture (CR) models previously fitted for data on other long‐lived marine mammals to estimate demographic parameters while accounting for detection heterogeneity between individuals and state uncertainty regarding reproductive status. We applied this model to data on 106 adult female bottlenose dolphins observed over 13 years. The detection probability differed depending on breeding status. Concerning state uncertainty, offspring were not always sighted with their mother, and older calves were easier to detect than young‐of‐the‐year (YOY), respectively, 0.79 (95% CI 0.59–0.90) and 0.58 (95% CI 0.46–0.68). This possibly led to inaccurate reproductive status assignment of females. Adult female survival probability was high (0.97 CI 95% 0.96–0.98) and did not differ according to breeding status. Young‐of‐the‐year and 1‐year‐old calves had a significantly higher survival rate than 2‐year‐old (respectively, 0.66 CI 95% 0.50–0.78 and 0.45 CI 95% 0.29–0.61). This reduced survival is probably related to weaning, a period during which young are exposed to more risks since they lose protection and feeding from the mother. The probability of having a new YOY was high for breeding females that had raised a calf to the age of 3 or lost a 2‐year‐old calf (0.71, CI 95% 0.45–0.88). Yet, this probability was much lower for nonbreeding females and breeding females that had lost a YOY or a 1‐year‐old calf (0.33, 95% CI 0.26–0.42). The multievent CR framework we used is highly flexible and could be easily modified for other study questions or taxa (marine or terrestrial) aimed at modeling reproductive parameters.