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1.  The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant 
The location and timing of domestication of the olive tree, a key crop in Early Mediterranean societies, remain hotly debated. Here, we unravel the history of wild olives (oleasters), and then infer the primary origins of the domesticated olive. Phylogeography and Bayesian molecular dating analyses based on plastid genome profiling of 1263 oleasters and 534 cultivated genotypes reveal three main lineages of pre-Quaternary origin. Regional hotspots of plastid diversity, species distribution modelling and macrofossils support the existence of three long-term refugia; namely the Near East (including Cyprus), the Aegean area and the Strait of Gibraltar. These ancestral wild gene pools have provided the essential foundations for cultivated olive breeding. Comparison of the geographical pattern of plastid diversity between wild and cultivated olives indicates the cradle of first domestication in the northern Levant followed by dispersals across the Mediterranean basin in parallel with the expansion of civilizations and human exchanges in this part of the world.
PMCID: PMC3574375  PMID: 23390107
coalescent-based molecular dating; crop genetic resources; long-term refugia; Mediterranean climate; plant domestication; species distribution modelling
2.  Measuring the fate of plant diversity: towards a foundation for future monitoring and opportunities for urgent action 
Vascular plants are often considered to be among the better known large groups of organisms, but gaps in the available baseline data are extensive, and recent estimates of total known (described) seed plant species range from 200 000 to 422 000. Of these, global assessments of conservation status using International Union for the Conservation of Nature (IUCN) categories and criteria are available for only approximately 10 000 species. In response to recommendations from the Conference of the Parties to the Convention on Biological Diversity to develop biodiversity indicators based on changes in the status of threatened species, and trends in the abundance and distribution of selected species, we examine how existing data, in combination with limited new data collection, can be used to maximum effect. We argue that future work should produce Red List Indices based on a representative subset of plant species so that the limited resources currently available are directed towards redressing taxonomic and geographical biases apparent in existing datasets. Sampling the data held in the world's major herbaria, in combination with Geographical Information Systems techniques, can produce preliminary conservation assessments and help to direct selective survey work using existing field networks to verify distributions and gather population data. Such data can also be used to backcast threats and potential distributions through time. We outline an approach that could result in: (i) preliminary assessments of the conservation status of tens of thousands of species not previously assessed, (ii) significant enhancements in the coverage and representation of plant species on the IUCN Red List, and (iii) repeat and/or retrospective assessments for a significant proportion of these. This would result in more robust Sampled Red List Indices that can be defended as more representative of plant diversity as a whole; and eventually, comprehensive assessments at species level for one or more major families of angiosperms. The combined results would allow scientifically defensible generalizations about the current status of plant diversity by 2010 as well as tentative comments on trends. Together with other efforts already underway, this approach would establish a firmer basis for ongoing monitoring of the status of plant diversity beyond 2010 and a basis for comparison with the trend data available for vertebrates.
PMCID: PMC1569457  PMID: 15814350
global biodiversity; species richness; conservation assessments; extinction risk; IUCN Red List; Living Planet Index
3.  Femoral shaft medialisation and neck-shaft angle in unstable pertrochanteric femoral fractures 
International Orthopaedics  2004;28(6):347-353.
We analysed the time-dependent mean changes in the femoral neck length, neck-shaft angle and hip offset in a randomised study comprising 48 patients who were treated with the dynamic hip screw (DHS) or the proximal femoral nail (PFN) for an unstable intertrochanteric femoral fracture. As a consequence of fracture compression, the mean post-operative neck length was significantly shorter in patients treated with the DHS. During the first 6 weeks after the operation, a mean decrease of 4.6° was observed in the neck-shaft angle, but there was not a significant difference between the treatment groups. The radiographic measures remained virtually unaffected during the interval from 6 weeks to 4 months in both groups. When the operated hip was compared to the opposite hip, patients who had received the DHS showed significantly greater medialisation of the femoral shaft at 4 months than those treated with the PFN. We thus recommend that unstable intertrochanteric fractures should be initially reduced in a slight valgus position in order to achieve an outcome after healing that is as normal as possible. As a result of differences in operative technique and implant stability, the PFN may be superior to the DHS in retaining the anatomical relations in the hip region in unstable intertrochanteric fractures.
PMCID: PMC3456909  PMID: 15597171
4.  Dose dependent but non-linear effects of alcohol on the left and right ventricle 
Heart  2001;86(4):417-423.
OBJECTIVE—To assess how left (LV) and right ventricular (RV) size, wall thickness, and mass depend on daily alcohol consumption. Among alcoholics, most common findings have been LV hypertrophy and mild systolic or diastolic dysfunction, accompanied occasionally by ventricular dilatation resembling dilated cardiomyopathy. Although it is commonly agreed that chronic heavy alcohol use is injurious to the heart, the dose-injury relation remains a matter of dispute.
DESIGN—Prospective series of 700 Finnish men aged 33-70 years who died out of hospital and underwent a medicolegal necropsy.
METHODS AND RESULTS—Data on alcohol use and other risk factors were obtained from the spouse. At necropsy, a transversal slice of the heart was traced on a transparent sheet and analysed later for LV and RV cavity areas and wall thicknesses. Coronary artery stenoses were measured from silicone casts of the arteries. In analyses of all men, daily alcohol dose predicted heart weight (β = 0.17, p < 0.001) and RV cavity area (β = 0.14, p = 0.007) independent of body size, age, coronary artery disease, hypertension, diabetes, and smoking. In the subgroup of men free of significant coronary artery disease, LV area averaged (SEM) 11.0 (1.0) cm2 in men drinking < 12 g/day, 7.7 (0.7) cm2 in those drinking 72-180 g/day, and 10.0 (0.9) cm2 in those drinking > 180 g/day (p = 0.054). Very heavy drinking (> 180 g/day) was associated with an increase in RV cavity area (p = 0.005).
CONCLUSIONS—The effects of alcohol on the heart in middle aged men are dose dependent but partly non-linear. In the absence of coronary artery disease, LV size shows a U shaped reduction with increasing daily alcohol use accompanied by an increase in RV size with very heavy drinking. These findings question the idea of progressive LV dilatation with increasing alcohol consumption among male victims of sudden death.

Keywords: alcohol; cardiomyopathy; remodelling; sudden death
PMCID: PMC1729926  PMID: 11559683
5.  Evolution of the angiosperms: calibrating the family tree. 
Growing evidence of morphological diversity in angiosperm flowers, seeds and pollen from the mid Cretaceous and the presence of derived lineages from increasingly older geological deposits both imply that the timing of early angiosperm cladogenesis is older than fossil-based estimates have indicated. An alternative to fossils for calibrating the phylogeny comes from divergence in DNA sequence data. Here, angiosperm divergence times are estimated using non-parametric rate smoothing and a three-gene dataset covering ca. 75% of all angiosperm families recognized in recent classifications. The results provide an initial hypothesis of angiosperm diversification times. Using an internal calibration point, an independent evaluation of angiosperm and eudicot origins is performed. The origin of the crown group of extant angiosperms is indicated to be Early to Middle Jurassic (179-158 Myr), and the origin of eudicots is resolved as Late Jurassic to mid Cretaceous (147-131 Myr). Both estimates, despite a conservative calibration point, are older than current fossil-based estimates.
PMCID: PMC1088868  PMID: 11674868
6.  Rate of gene sequence evolution and species diversification in flowering plants: a re-evaluation 
Barraclough and co-workers (in a paper published in 1996) observed that there was a significant positive correlation between the rate of evolution of the rbcL chloroplast gene within families of flowering plants and the number of species in those families. We tested three additional data sets of our own (based on both plastid and nuclear genes) and used methods designed specifically for the comparison of sister families (based on random speciation and extinction). We show that, over all sister groups, the correlation between the rate of gene evolution and an increased diversity is not always present. Despite tending towards a positive association, the observation of individual probabilities presents a U-shaped distribution of association (i.e. it can be either significantly positive or negative). We discuss the influence of both phylogenetic sampling and applied taxonomies on the results.
PMCID: PMC1689016

Results 1-6 (6)