Contributions of human cultures to biodiversity and ecosystem conservation

The expansion of globalized industrial societies is causing global warming, ecosystem degradation, and species and language extinctions worldwide. Mainstream conservation efforts still focus on nature protection strategies to revert this crisis, often overlooking the essential roles of Indigenous Peoples and Local Communities (IP&LC) in protecting biodiversity and ecosystems globally. Here we assess the scientific literature to identify relationships between biodiversity (including ecosystem diversity) and cultural diversity, and investigate how these connections may affect conservation outcomes in tropical lowland South America. Our assessment reveals a network of interactions and feedbacks between biodiversity and diverse IP&LC, suggesting interconnectedness and interdependencies from which multiple benefits to nature and societies emerge. We illustrate our findings with five case studies of successful conservation models, described as consolidated or promising 'social-ecological hope spots', that show how engagement with IP&LC of various cultures may be the best hope for biodiversity and ecosystem conservation, particularly when aligned with science and technology. In light of these five inspiring cases, we argue that conservation science and policies need to recognize that protecting and promoting both biological and cultural diversities can provide additional co-benefits and solutions to maintain ecosystems resilient in the face of global changes.

One sixth of Amazonian tree diversity is dependent on river floodplains

Amazonia's floodplain system is the largest and most biodiverse on Earth. Although forests are crucial to the ecological integrity of floodplains, our understanding of their species composition and how this may differ from surrounding forest types is still far too limited, particularly as changing inundation regimes begin to reshape floodplain tree communities and the critical ecosystem functions they underpin. Here we address this gap by taking a spatially explicit look at Amazonia-wide patterns of tree-species turnover and ecological specialization of the region's floodplain forests. We show that the majority of Amazonian tree species can inhabit floodplains, and about a sixth of Amazonian tree diversity is ecologically specialized on floodplains. The degree of specialization in floodplain communities is driven by regional flood patterns, with the most compositionally differentiated floodplain forests located centrally within the fluvial network and contingent on the most extraordinary flood magnitudes regionally. Our results provide a spatially explicit view of ecological specialization of floodplain forest communities and expose the need for whole-basin hydrological integrity to protect the Amazon's tree diversity and its function.

Critical transitions in the Amazon forest system

The possibility that the Amazon forest system could soon reach a tipping point, inducing large-scale collapse, has raised global concern1-3. For 65 million years, Amazonian forests remained relatively resilient to climatic variability. Now, the region is increasingly exposed to unprecedented stress from warming temperatures, extreme droughts, deforestation and fires, even in central and remote parts of the system1. Long existing feedbacks between the forest and environmental conditions are being replaced by novel feedbacks that modify ecosystem resilience, increasing the risk of critical transition. Here we analyse existing evidence for five major drivers of water stress on Amazonian forests, as well as potential critical thresholds of those drivers that, if crossed, could trigger local, regional or even biome-wide forest collapse. By combining spatial information on various disturbances, we estimate that by 2050, 10% to 47% of Amazonian forests will be exposed to compounding disturbances that may trigger unexpected ecosystem transitions and potentially exacerbate regional climate change. Using examples of disturbed forests across the Amazon, we identify the three most plausible ecosystem trajectories, involving different feedbacks and environmental conditions. We discuss how the inherent complexity of the Amazon adds uncertainty about future dynamics, but also reveals opportunities for action. Keeping the Amazon forest resilient in the Anthropocene will depend on a combination of local efforts to end deforestation and degradation and to expand restoration, with global efforts to stop greenhouse gas emissions.

Mapping density, diversity and species-richness of the Amazon tree flora

Using 2.046 botanically-inventoried tree plots across the largest tropical forest on Earth, we mapped tree species-diversity and tree species-richness at 0.1-degree resolution, and investigated drivers for diversity and richness. Using only location, stratified by forest type, as predictor, our spatial model, to the best of our knowledge, provides the most accurate map of tree diversity in Amazonia to date, explaining approximately 70% of the tree diversity and species-richness. Large soil-forest combinations determine a significant percentage of the variation in tree species-richness and tree alpha-diversity in Amazonian forest-plots. We suggest that the size and fragmentation of these systems drive their large-scale diversity patterns and hence local diversity. A model not using location but cumulative water deficit, tree density, and temperature seasonality explains 47% of the tree species-richness in the terra-firme forest in Amazonia. Over large areas across Amazonia, residuals of this relationship are small and poorly spatially structured, suggesting that much of the residual variation may be local. The Guyana Shield area has consistently negative residuals, showing that this area has lower tree species-richness than expected by our models. We provide extensive plot meta-data, including tree density, tree alpha-diversity and tree species-richness results and gridded maps at 0.1-degree resolution.

More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia

Indigenous societies are known to have occupied the Amazon basin for more than 12,000 years, but the scale of their influence on Amazonian forests remains uncertain. We report the discovery, using LIDAR (light detection and ranging) information from across the basin, of 24 previously undetected pre-Columbian earthworks beneath the forest canopy. Modeled distribution and abundance of large-scale archaeological sites across Amazonia suggest that between 10,272 and 23,648 sites remain to be discovered and that most will be found in the southwest. We also identified 53 domesticated tree species significantly associated with earthwork occurrence probability, likely suggesting past management practices. Closed-canopy forests across Amazonia are likely to contain thousands of undiscovered archaeological sites around which pre-Columbian societies actively modified forests, a discovery that opens opportunities for better understanding the magnitude of ancient human influence on Amazonia and its current state.

Eighty-four per cent of all Amazonian arboreal plant individuals are useful to humans

Plants have been used in Amazonian forests for millennia and some of these plants are disproportionally abundant (hyperdominant). At local scales, people generally use the most abundant plants, which may be abundant as the result of management of indigenous peoples and local communities. However, it is unknown whether plant use is also associated with abundance at larger scales. We used the population sizes of 4,454 arboreal species (trees and palms) estimated from 1946 forest plots and compiled information about uses from 29 Amazonian ethnobotany books and articles published between 1926 and 2013 to investigate the relationship between species usefulness and their population sizes, and how this relationship is influenced by the degree of domestication of arboreal species across Amazonia. We found that half of the arboreal species (2,253) are useful to humans, which represents 84% of the estimated individuals in Amazonian forests. Useful species have mean populations sizes six times larger than non-useful species, and their abundance is related with the probability of usefulness. Incipiently domesticated species are the most abundant. Population size was weakly related to specific uses, but strongly related with the multiplicity of uses. This study highlights the enormous usefulness of Amazonian arboreal species for local peoples. Our findings support the hypothesis that the most abundant plant species have a greater chance to be useful at both local and larger scales, and suggest that although people use the most abundant plants, indigenous people and local communities have contributed to plant abundance through long-term management.

Pre-colonial Amerindian legacies in forest composition of southern Brazil

Past human societies have left persistent marks on forests worldwide. However, the degree to which pre-colonial Amerindian societies have affected forest structure is still not fully understood, especially in southern Brazil. This study investigated the influence of two distinct Amerindian groups (Southern-Jê and Guarani) over tree composition of forest fragments in the State of Santa Catarina. Vegetation data was obtained from the Santa Catarina Forest and Floristic Inventory (SCFFI): a statewide systematic vegetation sampling project. Archaeological data was collated from literature reviews as well as existing databases for archaeological sites occupied by Guarani and Southern-Jê groups. Using these sites of known Amerindian occupation, and corresponding environmental variables, ecological niche models were developed for each Amerindian group, predicting potential archaeological sites occupied by these groups across southern Brazil. Maps of these potential occupation sites of pre-colonial Amerindian groups were compared with 417 corresponding floristic inventory plots. Redundancy analysis (RDA) was used to identify floristic composition patterns linked to areas with a high probability of Southern-Jê or Guarani presence. Southern-Jê and Guarani pre-colonial occupations overlapped near main rivers; however, Southern-Jê groups generally occupied elevated areas whereas Guarani occupied mostly coastal areas. We observed differences in forest composition associated with the predicted occurrence of these pre-colonial Amerindian groups. Based on these results, we argue there is a relationship between tree species distribution and pre-colonial human occupation by these two Amerindian groups.

Growth rings of Brazil nut trees (Bertholletia excelsa) as a living record of historical human disturbance in Central Amazonia

The Brazil nut tree (Bertholletia excelsa) is an iconic and economically valuable species that dominates vast swathes of the Amazon Basin. This species seems to have been an important part of human subsistence strategies in the region from at least the Early Holocene, and its current distribution may be a legacy of past human settlement. Because B. excelsa is a long-lived pioneer tree it requires natural or human disturbances to increase light availability in the understory for a successful establishment. However, it remains unclear how the long-term population dynamics of this species have been shaped by pre-colonial and post-colonial human practices. Here, we use tree-ring analyses to look at changes in growing conditions over the past 400 years in a Brazil nut tree population in Central Amazonia. We identify changes in tree recruitment and growth rates associated not only with regional climatic variability, but also major political and socio-economic activities recorded by historical documents in the vicinity of Manaus. We demonstrate that the expansion of a post-colonial political center (Manaus) from the middle of the 18th century onwards coincided with a reduction in recruitment of B. excelsa. We argue that this hiatus suggests the interruption of indigenous management practices, probably due to the collapse of pre-Columbian societies. A second recruitment pulse, and unprecedented cycles of growth release and suppression, aligns with a shift to modern exploitation of the forest into the 20th century. Our findings shed light on how past histories of human-forest interactions can be revealed by the growth rings of trees in Amazonia. Future interdisciplinary analysis of these trees should enable more detailed investigation of how human forest management has changed in this part of the world, through pre-colonial, colonial, and industrial periods of human activity, with potential implications for conservation.

The legacy of 4,500 years of polyculture agroforestry in the eastern Amazon

The legacy of pre-Columbian land use in the Amazonian rainforest is one of the most controversial topics in the social1-10 and natural sciences11,12. Until now, the debate has been limited to discipline-specific studies, based purely on archaeological data8, modern vegetation13, modern ethnographic data3 or a limited integration of archaeological and palaeoecological data12. The lack of integrated studies to connect past land use with modern vegetation has left questions about the legacy of pre-Columbian land use on the modern vegetation composition in the Amazon, unanswered11. Here, we show that persistent anthropogenic landscapes for the past 4,500 years have had an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. We found an abrupt enrichment of edible plant species in fossil lake and terrestrial records associated with pre-Columbian occupation. Our results demonstrate that, through closed-canopy forest enrichment, limited clearing for crop cultivation and low-severity fire management, long-term food security was attained despite climate and social changes. Our results suggest that, in the eastern Amazon, the subsistence basis for the development of complex societies began ~4,500 years ago with the adoption of polyculture agroforestry, combining the cultivation of multiple annual crops with the progressive enrichment of edible forest species and the exploitation of aquatic resources. This subsistence strategy intensified with the later development of Amazonian dark earths, enabling the expansion of maize cultivation to the Belterra Plateau, providing a food production system that sustained growing human populations in the eastern Amazon. Furthermore, these millennial-scale polyculture agroforestry systems have an enduring legacy on the hyperdominance of edible plants in modern forests in the eastern Amazon. Together, our data provide a long-term example of past anthropogenic land use that can inform management and conservation efforts in modern Amazonian ecosystems.

Species Distribution Modelling: Contrasting presence-only models with plot abundance data

Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species’ area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.

Response to Comment on "Persistent effects of pre-Columbian plant domestication on Amazonian forest composition"

McMichael et al state that we overlooked the effects of post-Columbian human activities in shaping current floristic patterns in Amazonian forests. We formally show that post-Columbian human influences on Amazonian forests are indeed important, but they have played a smaller role when compared to the persistent effects of pre-Columbian human activities on current forest composition.

Estimating the global conservation status of more than 15,000 Amazonian tree species

Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world's >40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.

Markedly divergent estimates of Amazon forest carbon density from ground plots and satellites

AIM

The accurate mapping of forest carbon stocks is essential for understanding the global carbon cycle, for assessing emissions from deforestation, and for rational land-use planning. Remote sensing (RS) is currently the key tool for this purpose, but RS does not estimate vegetation biomass directly, and thus may miss significant spatial variations in forest structure. We test the stated accuracy of pantropical carbon maps using a large independent field dataset.

LOCATION

Tropical forests of the Amazon basin. The permanent archive of the field plot data can be accessed at: http://dx.doi.org/10.5521/FORESTPLOTS.NET/2014_1.

METHODS

Two recent pantropical RS maps of vegetation carbon are compared to a unique ground-plot dataset, involving tree measurements in 413 large inventory plots located in nine countries. The RS maps were compared directly to field plots, and kriging of the field data was used to allow area-based comparisons.

RESULTS

The two RS carbon maps fail to capture the main gradient in Amazon forest carbon detected using 413 ground plots, from the densely wooded tall forests of the north-east, to the light-wooded, shorter forests of the south-west. The differences between plots and RS maps far exceed the uncertainties given in these studies, with whole regions over- or under-estimated by > 25%, whereas regional uncertainties for the maps were reported to be < 5%.

MAIN CONCLUSIONS

Pantropical biomass maps are widely used by governments and by projects aiming to reduce deforestation using carbon offsets, but may have significant regional biases. Carbon-mapping techniques must be revised to account for the known ecological variation in tree wood density and allometry to create maps suitable for carbon accounting. The use of single relationships between tree canopy height and above-ground biomass inevitably yields large, spatially correlated errors. This presents a significant challenge to both the forest conservation and remote sensing communities, because neither wood density nor species assemblages can be reliably mapped from space.

Hyperdominance in the Amazonian tree flora

The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.

Historical human footprint on modern tree species composition in the Purus-Madeira interfluve, central Amazonia

Background

Native Amazonian populations managed forest resources in numerous ways, often creating oligarchic forests dominated by useful trees. The scale and spatial distribution of forest modification beyond pre-Columbian settlements is still unknown, although recent studies propose that human impact away from rivers was minimal. We tested the hypothesis that past human management of the useful tree community decreases with distance from rivers.

Methodology/Principal Findings

In six sites, we inventoried trees and palms with DBH≥10 cm and collected soil for charcoal analysis; we also mapped archaeological evidence around the sites. To quantify forest manipulation, we measured the relative abundance, richness and basal area of useful trees and palms. We found a strong negative exponential relationship between forest manipulation and distance to large rivers. Plots located from 10 to 20 km from a main river had 20–40% useful arboreal species, plots between 20 and 40 km had 12–23%, plots more than 40 km had less than 15%. Soil charcoal abundance was high in the two sites closest to secondary rivers, suggesting past agricultural practices. The shortest distance between archaeological evidence and plots was found in sites near rivers.

Conclusions/Significance

These results strongly suggest that past forest manipulation was not limited to the pre-Columbian settlements along major rivers, but extended over interfluvial areas considered to be primary forest today. The sustainable use of Amazonian forests will be most effective if it considers the degree of past landscape domestication, as human-modified landscapes concentrate useful plants for human sustainable use and management today.

Significance of Early Diagnosis of Abdominal Compartment Syndrome in Major Burns

Four cases of abdominal compartment syndrome in patients suffering major burns, who were treated at Hamilton General Hospital, Hamilton, Ontario, from January 1998 to June 2003, are reported. The pathophysiological changes, and the high morbidity and mortality associated with this condition are also described. The significance of early diagnosis of this syndrome is discussed. The literature is reviewed and a protocol is suggested for measuring urinary bladder pressure when managing major burns.

Expression profiling of Botrytis cinerea genes identifies three patterns of up-regulation in planta and an FKBP12 protein affecting pathogenicity

The ascomycete Botrytis cinerea is a broad-spectrum plant pathogen. Here, we describe the first macroarray transcriptomic study of the fungus in real-time infection conditions. Infection of Arabidopsis thaliana leaves by B.cinerea was monitored using macroarrays, containing 3032 genes. Variance analysis revealed that 7% of B.cinerea genes are differentially expressed during infection and allowed us to identify 27 genes significantly up-regulated in planta. Among them, two genes have already been associated with fungal pathogenicity, while eight genes have unidentified functions. The 27 genes were separated into three groups according to their expression profile. The first group showed maximal expression at the early stage following fungal penetration, the second one showed maximal expression at the outset of the colonization of plant leaves and the third group showed maximal expression when the colonization of plant leaves was completed. A gene of the last group (BcPIC5), which is homologous to FKBP12 proteins, was disrupted in order to determine its role in pathogenicity. At seven days post-inoculation, the lesions caused by the DeltaBcPIC5 mutant on bean leaves were reduced by 69% and did not further expand compared to the wild-type. These results confirm that transcriptomic analysis under infection conditions can be very valuable for the identification of fungal genes related to pathogenicity.

The tetraspanin BcPls1 is required for appressorium-mediated penetration of Botrytis cinerea into host plant leaves

Animal tetraspanins are membrane proteins controlling cell adhesion, morphology and motility. In fungi, the tetraspanin MgPls1 controls an appressorial function required for the penetration of Magnaporthe grisea into host plants. An orthologue of MgPLS1, BcPLS1, was identified in the necrotrophic fungal plant pathogen Botrytis cinerea. We constructed a Bcpls1::bar null mutant by targeted gene replacement. Bcpls1::bar is not pathogenic on intact plant tissues of bean, tomato or rose, but it infects wounded plant tissues. Both wild type and Bcpls1::bar differentiate appressoria on plant and artificial surfaces, a process involving an arrest of polarized growth, apex swelling and its cell wall reinforcement. Although wild-type appressoria allowed the penetration of the fungus into the host plant within 6-12 h, no successful penetration events were observed with Bcpls1::bar, suggesting that its appressoria are not functional. An eGFP transcriptional fusion showed that BcPLS1 was specifically expressed in conidia, germ tubes and appressoria during host penetration. Our results indicate that BcPLS1 is required for the penetration of B. cinerea into intact host plants. The defect in pathogenicity of Bcpls1::bar also demonstrates that functional B. cinerea appressoria are required for a successful penetration process. As Bcpls1::bar and Mgpls1 Delta::hph penetration defects are similar, fungal tetraspanins are likely to be required for an essential appressorial function widespread among fungi.

A new class of tetraspanins in fungi

Tetraspanins are animal proteins involved in membrane complexes that are involved in cell adhesion, differentiation, and motility. The PLS1 gene from rice blast fungus Magnaporthe grisea encodes a protein (Pls1p) structurally related to tetraspanins that is required for pathogenicity. In Botrytis cinerea public sequences, we identified an EST homologous to PLS1. Using degenerated oligonucleotides, we amplified sequences homologous to PLS1 in fungi Colletotrichum lindemuthianum and Neurospora crassa. Analysis of N. crassa and M. grisea genome sequences revealed the presence of a single tetraspanin gene. Thus, fungi differ from animals, which contain between 20 and 37 paralogous tetraspanin genes. Fungal proteins encoded by BcPLS1, ClPLS1, and NcPLS1 display all the structural hallmarks of tetraspanins (predicted topology with four transmembrane domains, extra- and intracellular loops; conserved cysteine-based patterns in second extracellular loop). Phylogenetic analysis suggests that these genes define a new family of orthologous genes encoding fungal-specific tetraspanins.

Nerve dependency in scarless fetal wound healing

The human fetus is capable of healing cutaneous wounds without scar up to the third trimester of development This process of tissue repair is more akin to newt limb regeneration than classic adult scar forming wound repair. Regeneration of the newt limb is dependent on neural input in its early stages. This study was an attempt to determine whether a similar dependence on neural input exists for mammalian fetal wounds to heal without scar. The left hind limb of six fetal lambs was denervated during the early second trimester of development (day 55; term = 145 days). Two weeks after denervation, the animals were again exposed to create bilateral incisional and 6-mm-diameter excisional wounds on their innervated right and denervated left lower extremities. Five days after creation of these defects, the wounds were examined for alterations in repair. Four fetal lambs survived, and three were suitable for evaluation. There were marked alterations in wound healing seen after denervation. Excisional wounds on the innervated side contracted and decreased their surface area by 14 percent. In contrast, the denervated wounds not only failed to contract, but increased in size by 60 percent. Changes in the incisional wounds were equally distinctive. Innervated incisional wounds healed completely without scar and had a wound breaking strength comparable to that of normal skin (Table I). In contrast, two of the three denervated incisional wounds dehisced and failed to heal, even in the regions where the skin was approximated by suture. The third denervated incisional wound did heal but with a significant amount of scar. Electron microscopy confirmed this finding by clearly demonstrating thickened and irregular collagen deposition in the extracellular matrix of all the denervated incisional specimens. In summary, like the regenerating newt limb, scarless fetal skin wound repair requires neural stimulation for tissue regeneration to occur. Therefore, in the mammal, the primary regulator for this unique type of tissue repair may have a central neural, rather than a local, tissue origin.

Two Sibling Species of the Botrytis cinerea Complex, transposa and vacuma, Are Found in Sympatry on Numerous Host Plants

ABSTRACT Strains of Botrytis cinerea (the anamorph of Botryotinia fuckeliana) were collected from 21 different plant species around vineyards in the Champagne region (France). Strains were analyzed using three new polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) markers that were found by SWAPP (sequencing with arbitrary primer pairs), in addition to 15 other markers (PCR-RFLP, transposable elements, and resistance to fungicides). The markers revealed a high degree of genetic diversity and were used to investigate population structure. The two sympatric species transposa and vacuma, previously identified on grapes in these vineyards, were also detected on many of the plant species sampled. A new type of strain was also detected, having only the transposable element Boty. We did not detect any differentiation between strains from different organs or locations, but the prevalences of transposa and vacuma were significantly different on the different host plants. Fungicide resistance frequencies were significantly different in transposa and vacuma species. This study confirms that B. cinerea is a complex of sibling species and shows that the sibling species occur sympatrically on many host plants. However, the two species seemed to have different pathogenic behaviors. These findings contradict the traditional view of B. cinerea as a clonal population without specialization.

The minisatellite MSB1, in the fungus Botrytis cinerea, probably mutates by slippage

A minisatellite was identified in the intron of the ATP synthase of the filamentous fungus Botrytis cinerea, and it was named MSB1. This is the second fungal minisatellite described to date. Its 37-bp repeat unit is AT-rich, and it is found at only one locus in the genome. The introns of 47 isolates of Botrytis species were sequenced. The number of tandem repeats varied only from 5 to 11, but there were many repeat variants. The structure of MSB1 is peculiar: the variants are in the same physical order in all individuals, and this order follows the most parsimonious tree. These original characteristics, together with a total lack of recombination between alleles of the flanking regions, suggest that MSB1 probably mutates by slippage. MSB1 was found in the intron of the ATP synthase of all of the Botrytis species analyzed, but the repeat unit was not found in any other genus examined, including Sclerotinia, which is the genus closest to Botrytis.

Telomeric DNA of Botrytis cinerea: a useful tool for strain identification

Telomeric DNA was isolated from the phytopathogenic fungus Botrytis cinerea by PCR using only the oligonucleotide primer (CCCTAA)4. As with other filamentous fungi, B. cinerea has a short TTAGGG telomeric repeat. Telomere-linked restriction fragment length polymorphism (RFLP) was found in strains of B. cinerea isolated from different host plants collected from different regions at different periods. Almost every strain had a specific RFLP pattern, including those collected from the same plant one month apart. Thus, this marker appears to be an excellent tool to show the great polymorphism of B. cinerea strains by fingerprinting. The Southern blots of some strains of B. cinerea showed one band which was much more intense than the others, suggesting that the majority of telomere-associated sequences have the same sequence.

RFLP markers show genetic recombination in Botryotinia fuckeliana (Botrytis cinerea) and transposable elements reveal two sympatric species

Molecular markers revealed that Botryotinia fuckeliana (the teleomorph of Botrytis cinerea), a haploid, filamentous, heterothallic ascomycete, contained a large amount of intrapopulation genetic variation. The markers were used to determine the mode of reproduction and the population structure of this fungus. We did not detect any differentiation between isolates from different organs, collection dates, varieties of grape, or locations in the Champagne region of France, but two unexpected sympatric populations were identified. One group of isolates (transposa) contained the transposable elements Boty and Flipper; the other (vacuma) did not. These groups differed from one another for all the other markers. RFLP markers showed that there was genetic recombination in both groups of isolates. We conclude that there are two sympatric populations of B. fuckeliana in Champagne. One species (transposa) seems to be local and well adapted, while the other one (vacuma) is presumably a heterogeneous migrant population.

Transformation of Botrytis cinerea with the nitrate reductase gene (niaD) shows a high frequency of homologous recombination

The nitrate reductase (niaD) gene was isolated from the phytopathogenic ascomycete Botrytis cinerea using a probe obtained by a polymerase chain reaction (PCR) with degenerate oligonucleotides corresponding to domains conserved among three fungal nitrate reductases. The B. cinerea niaD gene encodes a predicted protein of 907 amino acids and contains no intron. Nitrate reductase-deficient mutants of B. cinerea have been isolated. One of them was transformed with the niaD genes of Fusarium oxysporum f.sp. melonis and B. cinerea. The transformation was always ectopic when the donor DNA originated from F. oxysporum, but there was 80% gene replacement when the donor DNA originated from B. cinerea.

Flipper, a mobile Fot1-like transposable element in Botrytis cinerea

A transposable element, Flipper, was isolated from the phytopathogenic fungus Botrytis cinerea. The element was identified as an insertion sequence within the coding region of the nitrate reductase gene. The Flipper sequence is 1842 bp long with perfect inverted terminal repeats (ITRs) of 48 bp and an open reading frame (ORF) of 533 amino acids, potentially encoding for a transposase; the element is flanked by the dinucleotide TA. The encoded protein is very similar to the putative transposases of three elements from other phytopathogenic fungi, Fot1 from Fusarium oxysporum, and Pot2 and MGR586 from Magnaporthe grisea. The number of Flipper elements in strains of B. cinerea varied from 0 to 20 copies per genome. Analysis of the descendants of one cross showed that the segregation ratio of Flipper elements was 2:2 and that the copies were not linked.

The 5' untranslated region of PVY RNA, even located in an internal position, enables initiation of translation

Potato virus Y (PVY) is the type member of the potyvirus group. Potyviruses, like picorna-, como-, and nepoviruses, belong to the picornavirus-like supergroup. All these viral RNAs have a VPg at their 5' end, and for four picornaviruses and one comovirus internal initiation of translation has been reported. To know if such a translational mechanism holds true for potyviral RNAs, the 5' nontranslated region (NTR) of PVY RNA was placed in an internal position, either by adding 91 bases upstream of the PVY 5'NTR or by inserting the PVY 5'NTR into an intercistronic region. The addition of extra bases stimulates translation in a rabbit reticulocyte lysate, and the presence of the PVY 5'NTR in the intercistronic region allows the synthesis of the second cistron. These findings strongly suggest that PVY RNA initiates translation by an internal ribosome-binding mechanism. Furthermore, the use of antisense oligodeoxynucleotides indicates that the entire 5'NTR seems to be involved in such a mechanism.

Effects of antisense oligodeoxynucleotide hybridization on in vitro translation of potato virus Y RNA

Potato virus Y (PVY), a potyvirus, has an RNA genome containing 9704 nucleotides of which 185 belong to the 5' nontranslated region (NTR). Contrary to most eukaryotic mRNAs that have a cap structure, the potyvirus RNA has a genome-linked protein (VPg). In order to understand the mechanisms of PVY RNA translation initiation, hybrid-arrest translation was used to localize sequences involved in binding of proteins and/or ribosomes. The 5' NTR was fused to the beta-glucuronidase (GUS) reporter gene. Six antisense oligodeoxynucleotides were used for hybridization, and the efficiency of the in vitro translation of the hybridized mRNA was modified to different levels depending upon the position of the oligodeoxynucleotide used. The highest inhibition was obtained with an oligodeoxynucleotide hybridized to the 5' end. In addition, translation of GUS mRNA containing the PVY 5' NTR was greatly enhanced when this mRNA was capped. These results differ from those obtained with the tobacco etch virus (TEV) and three picornaviruses, but are similar to those obtained with capped mRNA.