Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene.

Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.

Combined forest and soil management after a catastrophic event.

At the end of October 2018, a storm of unprecedented strength severely damaged the forests of the eastern sector of the Italian Alps. The affected forest area covers 42,500 ha. The president of one of the damaged regions asked for help from the University of Padua. After eight months of discussion, the authors of this article wrote a consensus text. The sometimes asper debate brought to light some crucial aspects: 1) even experienced specialists may have various opinions based on scientific knowledge that lead to conflicting proposals for action. For some of them there is evidence that to restore a destroyed natural environment it is more judicious to do nothing; 2) the soil corresponds to a living structure and every ecosystem's management should be based on it; 3) faced with a catastrophe, people and politicians find themselves unarmed, also because they rarely have the scientific background to understand natural processes. Yet politicians are the only persons who make the key decisions that drive the economy in play and therefore determine the near future of our planet. This article is an attempt to respond directly to a governor with a degree in animal production science, who formally and prudently asked a university department called "Land, Environment, Agriculture and Forestry" for help before taking decisions; 4) the authors also propose an artistic interpretation of facts (uncontrolled storm) and conclusions (listen to the soil). Briefly, the authors identify the soil as an indispensable source for the renewal of the destroyed forest, give indications on how to prepare a map of the soils of the damaged region, and suggest to anchor on this soil map a series of silvicultural and soil management actions that will promote the soil conservation and the faster recovery of the natural dynamic stability and resilience. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary material is available for this article at 10.1007/s11629-019-5890-0 and is accessible for authorized users.

Ecology and Genetics of Natural Populations of North American Vitis Species Used as Rootstocks in European Grapevine Breeding Programs.

Three North American Vitis species (V. riparia, V. berlandieri, V. rupestris) became widely used in rootstock breeding programs following the expansion of North American pests and diseases introduced in vineyards of the world during the 19th century. When they escape, they become feral in the most dynamic parts of Mediterranean floodplains. To better understand this ongoing process, we studied the ecology of Vitis species in their native sympatric range. We analyzed in deep 61 plots of 710 m2 containing Vitaceae species along 216 km of the Buffalo River and adjacent plateaus (Arkansas, United States). We investigated the populations structure and genetics of the Vitis complex (i.e., possible hybrids and the Vitis species) and the sharing of habitats with other Vitaceae (Muscadinia rotundifolia and Parthenocissus quinquefolia). Vitaceae share space according to their life strategies and microhabitat along ecological gradients. The plateau niche seems optimal for V. berlandieri and V. aestivalis. V. berlandieri is also found in alluvial zones. The most erosive parts of the river are colonized by V. rupestris, whereas the first terraces include most of the M. rotundifolia populations. Vitis riparia and Parthenocissus live in the largest range of forest habitats, from plateaus to alluvial forests, and from the forest floor to the canopy, with the highest densities along the river. Interestingly, natural hybridization can occur, but establishment success is rare and limited to alluvial forests. In their native range, these populations are controlled by biotic and abiotic conditions. In Europe, the biotic relations among species are different. Our study shows that V. riparia and its hybrids could be the best candidates for a large scale invasion.

Passive rewilding may (also) restore phylogenetically rich and functionally resilient forest plant communities.

Passive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land-use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.

Correction: Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France.

[This corrects the article DOI: 10.1371/journal.pone.0189278.].

Genetic diversity, genetic structure and diet of ancient and contemporary red deer (Cervus elaphus L.) from north-eastern France.

In north-eastern France, red deer (Cervus elaphus L.) populations were rebuilt from a few hundred individuals, which have subsisted in remote valleys of the Vosges mountains, and to a lesser extent from individuals escaped from private enclosures; at present times, this species occupies large areas, mainly in the Vosges Mountains. In this study, we examined the population dynamics of red deer in the Vosges Mountains using ancient and contemporary mitochondrial DNA (mtDNA) from 140 samples (23 ancient + 117 modern) spanning the last 7'000 years. In addition, we reconstructed the feeding habits and the habitat of red deer since the beginning of agriculture applying isotopic analyses in order to establish a basis for current environmental management strategies. We show that past and present red deer in the Vosges Mountains belong to mtDNA haplogroup A, suggesting that they originated from the Iberian refugium after the last glacial maximum (LGM). Palaeogenetic analysis of ancient bone material revealed the presence of two distinct haplotypes with different temporal distributions. Individuals belonging to the two haplotype groups apparently occupied two different habitats over at least 7'000 years. AM6 correlates with an ecological type that feeds in densely forested mountain landscapes, while AM235 correlates with feeding in lowland landscapes, composed of a mixture of meadows and riverine, herb-rich woodlands. Our results suggest that red deer of north-eastern France was able to adapt, over the long term, to these different habitat types, possibly due to efficient ethological barriers. Modern haplotype patterns support the historical record that red deer has been exposed to strong anthropogenic influences as a major game species.

Insights into the Vitis complex in the Danube floodplain (Austria).

European grapevine populations quickly disappeared from most of their range, massively killed by the spread of North American grapevine pests and diseases. Nowadays taxonomic pollution represents a new threat. A large Vitis complex involves escaped cultivars, rootstocks, and wild grapevines. The study aimed to provide insight into the Vitis complex in the Danube region through field and genetic analyses. Among the five other major rivers in Europe which still host wild grapevine populations, the Danube floodplain is the only one benefiting from an extensive protected forest area (93 km²) and an relatively active dynamic flood pulse. The Donau-Auen National Park also regroups the largest wild grapevine population in Europe. Ninety-two percent of the individuals collected in the park were true wild grapevines, and 8% were hybrids and introgressed individuals of rootstocks, wild grapevines, and cultivars. These three groups are interfertile acting either as pollen donor or receiver. Hybrids were established within and outside the dykes, mostly in anthropized forest edges. The best-developed individuals imply rootstock genes. They establish in the most erosive parts of the floodplain. 42% of the true wild grapevines lived at the edges of forest/meadow, 33.3% at the edges forest/channels, and 23.9% in forest gaps. DBH (Diameter Breast Height) varied significantly with the occurrence of flooding. Clones were found in both true wild and hybrids/introgressed grapevines. The process of cloning seemed to be prevented in places where flooding dynamics is reduced. The current global distribution of true wild grapevines shows a strong tendency toward clustering, in sites where forestry practices were the most extensive. However, the reduced flooding activity is a danger for long-term sustainability of the natural wild grapevine population.

Wild European apple (Malus sylvestris (L.) Mill.) population dynamics: insight from genetics and ecology in the Rhine Valley. Priorities for a future conservation programme.

The increasing fragmentation of forest habitats and the omnipresence of cultivars potentially threaten the genetic integrity of the European wild apple (Malus sylvestris (L.) Mill). However, the conservation status of this species remains unclear in Europe, other than in Belgium and the Czech Republic, where it has been declared an endangered species. The population density of M. sylvestris is higher in the forests of the upper Rhine Valley (France) than in most European forests, with an unbalanced age-structure, an overrepresentation of adults and a tendency to clump. We characterize here the ecology, age-structure and genetic diversity of wild apple populations in the Rhine Valley. We use these data to highlight links to the history of this species and to propose guidelines for future conservation strategies. In total, 255 individual wild apple trees from six forest stands (five floodplain forests and one forest growing in drier conditions) were analysed in the field, collected and genotyped on the basis of data for 15 microsatellite markers. Genetic analyses showed no escaped cultivars and few hybrids with the cultivated apple. Excluding the hybrids, the genetically "pure" populations displayed high levels of genetic diversity and a weak population structure. Age-structure and ecology studies of wild apple populations identified four categories that were not randomly distributed across the forests, reflecting the history of the Rhine forest over the last century. The Rhine wild apple populations, with their ecological strategies, high genetic diversity, and weak traces of crop-to-wild gene flow associated with the history of these floodplain forests, constitute candidate populations for inclusion in future conservation programmes for European wild apple.