Multiple introductions from multiple sources: invasion patterns for an important Eucalyptus leaf pathogen

Many population studies on invasive plant pathogens are undertaken without knowing the center of origin of the pathogen. Most leaf pathogens of Eucalyptus originate in Australia and consequently with indigenous populations available, and it is possible to study the pathways of invasion. Teratosphaeria suttonii is a commonly occurring leaf pathogen of Eucalyptus species, naturally distributed in tropical and subtropical regions of eastern Australia where it is regarded as a minor pathogen infecting older leaves; however, repeated infections, especially in exotic plantations, can result in severe defoliation and tree deaths. Nine polymorphic microsatellite markers were used to assess the genetic structure of 11 populations of T. suttonii of which four where from within its native range in eastern Australia and the remaining seven from exotic Eucalyptus plantations. Indigenous populations exhibited high allele and haplotype diversity, predominantly clonal reproduction, high population differentiation, and low gene flow. The diversity of the invasive populations varied widely, but in general, the younger the plantation industry in a country or region, the lower the diversity of T. suttonii. Historical gene flow was from Australia, and while self‐recruitment was dominant in all populations, there was evidence for contemporary gene flow, with South Africa being the most common source and Uruguay the most common sink population. This points distinctly to human activities underlying long‐distance spread of this pathogen, and it highlights lessons to be learned regarding quarantine.     

Botryosphaeriaceae as potential pathogens of prunus species in South Africa, with descriptions of Diplodia africana and Lasiodiplodia plurivora sp. nov

Botryosphaeriaceae are common dieback and canker pathogens of woody host plants, including stone fruit trees. In the present study the diversity of members of the Botryosphaeriaceae isolated from symptomatic wood of Prunus species (plum, peach, nectarine and apricot) was determined in stone fruit-growing areas in South Africa. Morphological and cultural characteristics as well as DNA sequence data (5.8S rDNA, ITS-1, ITS-2 and EF-1a) were used to identify known members and describe novel members of Botryosphaeriaceae. From the total number of wood samples collected (258) 67 isolates of Botryosphaeriaceae were obtained, from which eight species were identified. All species were associated with wood necrosis. Diplodia seriata (= "Botryosphaeria" obtusa) was dominant, and present on all four Prunus species sampled, followed by Neofusicoccum vitifusiforme and N. australe. First reports from Prunus spp. include N. vitifusiforme, Dothiorella viticola and Diplodia pinea. This is also the first report of D. mutila from South Africa. Two species are newly described, namely Lasiodiplodia plurivora sp. nov. from P. salicina and Diplodia africana sp. nov. from P. persica. All species, except Dothiorella viticola, caused lesions on green nectarine and/or plum shoots in a detached shoot pathogenicity assay.     

Clonality in South African isolates and evidence for a European origin of the root pathogen Thielaviopsis basicola

Thielaviopsis basicola is a soil-borne fungal pathogen with a wide host range and a cosmopolitan distribution. It causes disease on many agricultural crops, and in South Africa is the causal agent of black pod rot of groundnuts and black root rot on chicory. Knowledge of the population diversity of T. basicola could provide valuable information regarding management strategies, the possible movement, origin, and reproductive strategies of the fungus. The objective of this study was to determine the population diversity of T. basicola isolates from groundnuts and chicory in South Africa using co-dominant polymorphic markers. These markers were also used to compare isolates from South Africa with those from other hosts and geographic regions. Seven loci revealed nine alleles and two genotypes, one on groundnut and one on chicory, differing at only two loci. T. basicola isolates from eight different countries and ten different hosts revealed 17 genotypes across the seven loci with 39 different alleles. The lack of diversity for the two South African host-related populations of isolates suggests that T. basicola was introduced into South Africa. Some evidence is provided for a European origin of the pathogen, possibly linked to trade in root crops.     

Genetic variation in the wattle wilt pathogenCeratocystis albofundus

Ceratocystis albofundus is an important wilt pathogen on exoticAcacia mearnsii trees in South Africa. It is known only from this country and has also been reported from nativeProtea spp., but it is not clear if the pathogen is native or introduced to South Africa. This study was conduced to determine the nuclear and mitochondrial gene diversity in a population ofC. albofundus and to compare this diversity with that of otherCeratocystis species. Isolates were collected from a number of geographic regions in South Africa. Total genomic, DNA was extracted from each isolate, digested withPstl and probed with the radioactively labelled oligonucleotide marker (CAT)₅ to determine nulear DNA diversity. For the determination of mitochondrial DNA diversity, the RFLPs ofHaeIII digests were scored directly without probing. Nei’s gene diversity (H) was determined and a distance matrix was developed for each set of markers and analyzed using UPGMA. TheC. albofundus population was found to have a high level of both nuclear and mitochondrial gene diversity when compared with published data of populations of otherCeratocystis spp. This further supports the hypothesis thatC. albofundus is native to South Africa.     

High intercontinental migration rates and population admixture in the sapstain fungus Ophiostoma ips

Ophiostoma ips is a common fungal associate of various conifer-infesting bark beetles in their native ranges and has been introduced into non-native pine plantations in the Southern Hemisphere. In this study, we used 10 microsatellite markers to investigate the population biology of O. ips in native (Cuba, France, Morocco and USA) and non-native (Australia, Chile and South Africa) areas to characterize host specificity, reproductive behaviour, and the potential origin as well as patterns of spread of the fungus and its insect vectors. The markers resolved a total of 41 alleles and 75 haplotypes. Higher genetic diversity was found in the native populations than in the introduced populations. Based on the origin of the insect vectors, the populations of O. ips in Australia would be expected to reflect a North American origin, and those in Chile and South Africa to reflect a European origin. However, most alleles observed in the native European population were also found in the native North American population; only the allele frequencies among the populations varied. This admixture made it impossible to confirm the origin of the introduced Southern Hemisphere (SH) populations of O. ips. There was also no evidence for specificity of the fungus to particular bark beetle vectors or hosts. Although O. ips is thought to be mainly self-fertilizing, evidence for recombination was found in the four native populations surveyed. The higher genetic diversity in the North American than in the European population suggests that North America could be the possible source region of O. ips.     

Consequences of frugivore diversity for seed dispersal, seedling establishment and the spatial pattern of seedlings and trees

Many plants depend on frugivorous animals for the dispersal of their seeds. However, it is only poorly known whether regional differences in frugivore diversity have consequences for seed dispersal, seedling establishment, and the spatial distribution of seedlings and trees. This comparative study of seed dispersal investigated the consequences of regional differences in frugivore diversity for two tree species of the genus Commiphora. C. harveyi was studied in South Africa where avian frugivore diversity is high, C. guillaumini was studied in Madagascar where the avian frugivore community is depauperate. At both study sites, the percentages of handled and dispersed seeds in Commiphora trees were quantified by fruit traps, and visitation rates, seed handling rates and dispersal rates were quantified for each animal species for two consecutive years. Seedlings were mapped and the spatial distribution of trees quantified. At both study sites, fruits were mainly eaten by birds. The total percentage of dispersed seeds in South Africa was significantly higher than in Madagascar (70.8% vs. 7.9%) because there was a lack of effective dispersers that swallowed seeds in Madagascar. Seed dispersal benefit, i.e. the increase in the probability of becoming established as a seedling away from parent trees due to dispersal was much higher in Madagascar (80 times higher probability) compared to South Africa (6 times higher). Corresponding with the different dispersal percentages, seedlings in South Africa were found at relatively large distances from the nearest Commiphora tree (median distance=21.0 m), whereas in Madagascar seedlings were found mostly under and close to the nearest Commiphora tree (median distance=0.9 m). Finally, Commiphora trees in the Malagasy study site were clumped, but were more randomly distributed in the South African study site. These results suggest that regional differences in frugivore diversity and behaviour strongly affect seed dispersal of trees, seedling establishment and the spatial distribution of seedlings and trees.     

Microsatellite markers for the Eucalyptus stem canker fungal pathogen Kirramyces gauchensis

Ten microsatellite markers were developed for the fungus Kirramyces gauchensis, which causes an important stem canker disease of Eucalyptus trees in plantations. Primers for 21 microsatellite regions were designed from cloned fragments. Fourteen of the primer pairs provided single amplicons and 10 of these were polymorphic for K. gauchensis. Allelic diversity ranged from 0.21 to 0.76 with a total of 30 alleles. None of the markers was able to amplify in the phylogenetically distinct but morphologically similar species Kirramyces zuluensis. The 10 characterized polymorphic microsatellite regions will be studied to determine the population structure of K. gauchensis in plantations of different countries.     

Is there genetic connectivity among the critically endangered White‐winged Flufftail (Sarothrura ayresi) populations from South Africa and Ethiopia?

The White‐winged Flufftail (Sarothrura ayresi) is known to occur in the highland marshes of Ethiopia, as well as almost 4000 km in South Africa. The White‐winged Flufftail is listed globally as Critically Endangered. In South Africa the population is estimated to be <50 birds. These birds are severely threatened by habitat destruction. Thus far, no genetic studies have been conducted on S. ayresi to confirm genetic connectivity between the South African and Ethiopian populations. In this study, analysis of mitochondrial and nuclear markers was conducted for White‐winged Flufftail samples from South African and Ethiopian birds, as well as Red‐chested Flufftail (Sarothrura rufa) for species comparison. Analyses of the DNA regions identified three variations between the two populations, supporting the hypothesis that these two populations are not different species or subspecies but are rather one migrating population with different seasonal occupied ranges. However, these results do not exclude the possibility of additional breeding and nonbreeding sites. Low genetic diversity in the populations of White‐winged Flufftails was observed, which needs to be further elucidated with fast evolving co‐dominant markers such as microsatellites, as this low diversity may ultimately contribute to the extinction of the species.     

What is the genetic origin of teak (<Emphasis Type="Italic">Tectona grandis</Emphasis> L.) introduced in Africa and in Indonesia?

The first introduction of Tectona grandis in Indonesia took place between the fourteenth and sixteenth centuries and in Africa in the nineteenth century. A total of 1.1 and 0.3 million ha, respectively were planted in the two areas. The extension of teak plantations often started from these first introductions. Unfortunately, the documentation concerning dates, planting stocks and the sources of origin of the teak imported into the different countries was very inaccurate. In this study, the use of 15 microsatellite molecular markers enabled us to compare 22 exotic teak provenances with 17 provenances of the natural range. Results of the analysis showed that the provenances from South India were not related to the provenances that were first introduced in either Africa or Indonesia. Nearly 95% of teak landraces in Benin, Cameroon, Côte d’Ivoire, Tanzania, Togo and Senegal came from North India, and 96% of Indonesian and Ghanaian teak appeared to be very closely linked to Central Laos. The genetic origin of introduced teak was confirmed by the main traits of interest of provenances observed in international trials. Thus, trees from North India had very bad stem forms compared to Laotian and Thai provenances, which generally had good stem forms but low vigour. This genetic knowledge is essential for programmes to develop varieties and to improve the quality of plantations, particularly in Africa.     

Temporal and spatial variation of Botryosphaeriaceae associated with Acacia karroo in South Africa

The Botryosphaeriaceae are common and diverse members of fungal communities infecting woody plants. They are also increasingly being used as model organisms to understand patterns in the global movement of latent pathogens. The aim of this study was to consider the species richness of the Botryosphaeriaceae associated with the native Acacia (Vachellia) karroo across South Africa, and the variation of species at specific local sites over time. The diversity of these fungi associated with different tissues of this host plant was also considered. These questions were addressed by sampling healthy A. karroo from 23 sites in South Africa and by more intensive hierarchical sampling conducted at 40 sites in one area over 3 yr. In total, 13 species of the Botryosphaeriaceae were identified, including seven that were isolated only from the more intensively sampled area. There was a clear geographical influence, with some species occurring only in some parts of the country. Significant variation in the species richness over time for the intensively sampled area was found and there was no evidence of tissue specificity for this group of fungi in leaves, branches and branchlets. Results of pathogenicity trials showed highly variable lesion sizes for the isolated species in comparison to the control, with Sphaeropsis variabilis, Lasiodiplodia theobromae and Neofusicoccum australe being the most pathogenic. The overall results revealed a rich diversity of Botryosphaeriaceae on this native host, which varied significantly both geographically and on individual trees, even in the absence of obvious disease.     

Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations

Afforestation is a common and widespread management practice throughout the world, yet its implications for the genetic diversity of native populations are still poorly understood. We examined the effect of Aleppo pine (Pinus halepensis) plantations on the genetic composition of nearby conspecific native populations. We focused on two native populations in Israel with different levels of isolation from the surrounding plantations and compared the genetic diversity of naturally established young trees within the native populations with that of local native adults, using nine nuclear microsatellite markers. We found that the genetic composition of the recruits was significantly different from that of local adults in both populations, with allelic frequency changes between generations that could not be ascribed to random drift, but rather to substantial gene flow from the surrounding planted Aleppo pine populations. The more isolated population experienced a lower gene-flow level (22%) than the less isolated population (49%). The genetic divergence between native populations at the adult-tree stage (F(st) = 0.32) was more than twice as high as that of the young trees naturally established around native adults (F(st) = 0.15). Our findings provide evidence for a rapid genetic homogenization process of native populations following the massive planting efforts in the last decades. These findings have important implications for forest management and nature conservation and constitute a warning sign for the risk of translocation of biota for local biodiversity.     

Applying AFLPs in Aizoaceae: The Delosperma herbeum complex as a case study

Amplified fragment length polymorphic (AFLP) markers were used to discriminate between populations of Delosperma herbeum as well as other species of Delosperma occurring in Gauteng and adjacent provinces in South Africa. A total of 99 individuals representing 30 populations were examined for 158 polymorphic AFLP markers using the EcoRI and MseI restriction enzymes. Cluster analysis of AFLP marker scores, visualized through Neighbor-Joining and Neighbor-Net trees as well as Principal Coordinate Analysis, provides an effective means of discriminating between different species in the complex. The lack of bootstrap support for Delosperma davyi in the Neighbor-Joining tree and its position in the Principal Coordinate Analysis probably signifies it to be a superfluous name for D. herbeum. The clustering of the other species also suggests that flower colour is not a reliable feature for grouping species in Delosperma. A number of clusters of D. herbeum were correlated to a degree with distribution.     

Linking seed dispersal and genetic structure of trees: a biogeographical approach

Aim Natural and human‐induced differences in frugivore assemblages can influence the seed dispersal distances of trees. An important issue in seed dispersal systems is to understand whether differences in seed dispersal distances also affect the genetic structure of mature trees. One possible approach to test for a relationship between seed dispersal and the genetic structure of mature trees is to compare the genetic structure of two closely related tree species between two biogeographical regions that differ in frugivore assemblages and seed dispersal distances. Previous studies on two Commiphora species revealed that Commiphora guillauminii in Madagascar has a much lower seed dispersal distance than Commiphora harveyi in South Africa. We tested whether the lower seed dispersal distance might have caused decreased gene flow, resulting in a stronger genetic structure in Madagascar than in South Africa. Location Madagascar and South Africa. Methods Using amplified fragment length polymorphism markers we investigated the genetic structure of 134 trees in Madagascar and 158 trees in South Africa at a local and a regional spatial scale. Results In concordance with our hypothesis, kinship analysis suggests that gene flow was restricted mostly to 3 km in Madagascar and to 30 km in South Africa. At the local spatial scale, the genetic differentiation among groups of trees within sample sites was marginally significantly higher in Madagascar (F_ST = 0.069) than in South Africa (F_ST = 0.021). However, at a regional spatial scale genetic differentiation was lower in Madagascar (F_ST = 0.053) than in South Africa (F_ST = 0.163). Main conclusions Our results show that lower seed dispersal distances of trees were linked to higher genetic differentiation of trees only at a local spatial scale. This suggests that seed dispersal affects the genetic population structure of trees at a local, but not at a regional, spatial scale.     

Pollen flow in Eucalyptus grandis determined by paternity analysis using microsatellite markers

Gene flow by pollen dispersal from forestry plantations containing introduced species, provenances or selected elite breeding material may impact on local native forest by changing the genetic diversity, introducing new genes or gene combinations, or causing the extinction of rare genotypes in adjacent native forest areas. Patterns of pollen flow can be used to assess the risk of genetic pollution of native forest areas from nearby plantations. Pollen flow in an artificial population of Eucalyptus grandis was estimated using molecular markers and paternity analysis. Microsatellite genotyping was used to identify pollen parents of progeny arrays from six mother trees. Of 329 progeny analysed, 178 (54%) were assigned to pollen parents within the population. Pollen parents located within the population were between 0–192 m from the respective mother trees, with an average pollination distance of 57.96 m. Pollination of mother trees was outcrossed, not by nearest neighbours, and displayed a preference for inter-provenance matings within the population. Progeny that could not be assigned pollen parents within the population (46%) were assumed to have resulted from pollen immigration from external sources. These pollen flow parameters provide useful information about the dynamics of pollen movement within E. grandis populations and may be used in risk assessment of gene flow from plantations to adjacent areas of native forest.     

Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae)

Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.     

The role of local versus biogeographical processes in influencing diversity and body‐size variation in mammal assemblages

Our objective was to estimate and analyze the body‐size distribution parameters of terrestrial mammal assemblages at different spatial scales, and to determine whether these parameters are controlled by local ecological processes or by larger‐scale ones. Based on 93 local assemblages, plus the complete mammal assemblage from three continents (Africa, North, and South America), we estimated three key distribution parameters (diversity/size slope, skewness, and modal size) and compared the values to those expected if size distributions are mainly controlled by local interactions. Mammal diversity decreased much faster as body size increased than predicted by fractal niche theory, both at continental and at local scales, with continental distributions showing steeper slopes than the localities within them. South America showed a steeper slope (after controlling for species diversity), compared to Africa and North America, at local and continental scales. We also found that skewness and modal body size can show strikingly different correlations with predictor variables, such as species richness and median size, depending on the use of untransformed versus log‐transformed data, due to changes in the distribution density generated by log‐transformation. The main differences in slope, skewness, and modal size between local and continental scales appear to arise from the same biogeographical process, where small‐sized species increase in diversity much faster (due to higher spatial turnover rates) than large‐sized species. This process, which can operate even in the absence of competitive saturation at local scales, generates continental assemblages with steeper slopes, smaller modal sizes, and higher right skewness (toward small‐sized species) compared to local communities. In addition, historical factors can also affect the size distribution slopes, which are significantly steeper, in South American mammal assemblages (probably due to stronger megafauna extinction events in South America) than those in North America and Africa.     

Multiple‐scale assessment of understory herb species diversity in pine plantations after long‐term restoration

Plantations are established for a variety of purposes including wood production, soil and water conservation, and carbon sequestration. However, their implications for species diversity are considerably debated. To assess restoration effect of species diversity in plantations after 50 years’ natural restoration, understory herb species diversity of Chinese pine (Pinus tabulaeformis) plantations were characterized and compared with secondary growth oak (Quercus wutaishanica) forests by additive partitioning across three different nested spatial scales (subplot, plot and site scales) in the middle of the Loess Plateau, northwestern China. Whether these two forest types demonstrate different structuring processes was also examined by quantifying the relative contributions of space and the environment on community composition. Overall, the two forests displayed similar accumulation of species diversity across spatial scales. The contribution of species diversity components increased with the spatial scale, and both forests displayed lower alpha diversity at the subplot scale but higher beta diversity at the plot and site scales. There was no significant difference in alpha or beta diversity between the two forests at any of the three scales, but in species compositions at the subplot and plot scales (p < 0.05). The diversity of both forest types were simultaneously governed by environmental and spatial processes, with the exception of a greater contribution of each component in the secondary growth oak forests, but both forests were dominated by environmental processes. Our study highlight the significant role of spatial scales in assessing the result of biodiversity restoration of plantations. These results suggest that pine plantations function in a similar manner as secondary growth oak forests for understory herb diversity, albeit with different community compositions.     

Genetic diversity in Hemileia vastatrix based on RAPD markers

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs.     

Tree community structure, dynamics, and diversity partitioning in a Bornean tropical forested landscape

Human-modified forested landscapes are prevalent in the tropics, and the role of complex mosaics of diverse vegetation types in biodiversity conservation remains poorly understood. Demographic traits and the spatial pattern of biodiversity are essential information when considering proper forest management and land use strategies. We compared the tree community structure (stem density, basal area, tree diversity, abundance of rare, endemic, and upper-layer trees, and species composition) and the forest dynamics (mortality, recruitment rate, and increments of basal area, and above- and below-ground biomass) of 39–46 plots among five dominant forest types: young and old fallows, rubber plantations, and fragmented and old-growth forests in Sarawak, Malaysia. We also explored how tree diversity was distributed across different spatial scales using additive partitioning of diversity. Swidden cultivation and rubber plantations showed decreased stem density, basal area, tree diversity, abundance of rare, endemic, and upper-layer trees, and increments of above- and below-ground biomass, which affected tree mortality, dominant trees, and species composition. Little distinction in species composition was observed among young and old fallows and rubber plantations, indicating a relatively quick recovery of the tree community in the early stages. The highest diversity was found among forest types, indicating that the whole forested landscape comprises a suitable scale for tree biodiversity conservation in the region. Our results suggest that although fragmented and old-growth forests have an irreplaceable role and a high priority in conserving biodiversity and sustaining the function of the forest ecosystem, secondary forests may also have a reinforcing role in maintaining tree diversity in the region, especially under the current circumstances in which a large portion of the landscape is human-modified and faces an increasing threat from the expansion of oil palm plantations.     

亚高山针叶林人工恢复过程中物种多样性变化

通过样方调查,以空间代替时间的方法,对亚高山人工针叶林恢复过程中,乔木、灌木和草本层物种多样性的变化进行了研究,探讨了不同恢复阶段各层物种的相关系数．结果表明,亚高山人工针叶林恢复过程中物种的丰富度、多样性和均匀性都在波动中逐渐增加,云杉人工林恢复过程中总体上是朝着有利于物种多样性恢复的方向发展．在人工林恢复序列中群落乔木物种的平均相关系数为41．88％。灌木为50．61％,草本为37．22％,说明在70年的人工林恢复过程中,灌木种类具有较高的连续性和稳定性;草本植物则随着人工林环境条件的改变而出现较大的消亡和更新,显示出较大的波动性．乔木层物种的稳定性和连续性介于灌木和草本植物之间．