The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin

Aim Edaphic heterogeneity may be an important driver of population differentiation in the Amazon but remains to be investigated in trees. We compared the phylogeographic structure across the geographic distribution of two Protium (Burseraceae) species with different degrees of edaphic specialization: Protium alvarezianum, an edaphic specialist of white‐sand habitat islands; and Protium subserratum, an edaphic generalist found in white sand as well as in more widespread soil types. We predicted that in the edaphic specialist, geographic distance would structure populations more strongly than in the edaphic generalist, and that soil type would not structure populations in the edaphic generalist unless habitat acts as a barrier promoting population differentiation. Location Tropical rain forests of the Peruvian and Brazilian Amazon, Guyana and French Guiana. Methods We sequenced 1209–1211 bp of non‐coding nuclear ribosomal DNA (internal transcribed spacer and external transcribed spacer) and a neutral low‐copy nuclear gene (phytochrome C) from P. subserratum (n = 65, 10 populations) and P. alvarezianum (n = 19, three populations). We conducted a Bayesian phylogenetic analysis, constructed maximum parsimony haplotype networks and assessed population differentiation among groups (soil type or geographic locality) using analysis of molecular variance and spatial analysis of molecular variance. Results The edaphic specialist exhibited considerable genetic differentiation among geographically distant populations. The edaphic generalist showed significant genetic differentiation between the Guianan and Amazon Basin populations. Within Peru, soil type and not geographic distance explained most of the variation among populations. Non‐white‐sand populations in Peru exhibited lower haplotype/nucleotide diversity than white‐sand populations, were each other’s close relatives, and formed an unresolved clade derived from within the white‐sand populations. Main conclusions Geographic distance is a stronger driver of population differentiation in the edaphic specialist than in the generalist. However, this difference did not appear to be related to edaphic generalism per se as adjacent populations from both soil types in the edaphic generalist did not share many haplotypes. Populations of the edaphic generalist in white‐sand habitats exhibited high haplotype diversity and shared haplotypes with distant white‐sand habitat islands, indicating that they have either efficient long‐distance dispersal and/or larger ancestral effective population sizes and thus retain ancestral polymorphisms. These results highlight the importance of edaphic heterogeneity in promoting population differentiation in tropical trees.     

Pteridophyte species diversity in the central Peruvian Amazon: Importance of edaphic specialization

Sixty-one species of pteridophytes were found growing in a two-hectare study area that contained two major soil types. Approximately one-third of that species richness was due to the presence of edaphic variation, because 19 species were only found on the sandy loam soil and 24 were restricted to the clay soil. In the Amazon basin, within a particular climatic zone, diversity of soil type and topographic position can result in a habitat mosaic where both edaphic specialists and generalists can be found growing in one area. Sesentaiún especies de pteridófitos se hallaron en el área de estudio de dos hectáreas, el cual contenía dos tipos resaltantes de suelos. Aproximadamente un tercio de la riqueza de especies se debió a la diferencia edáfica, así 19 de ellas se hallaron en el suelo arenoso y 24 sólo en el arcilloso. En la Amazonía, dentro de una determinada zona climática, la diversidad en tipos de suelos y la posición topográfica pueden dar lugar a un habitat en mosaico, donde tanto especialistas edáficos como generalistas pueden crecer en una sola área.     

The effect of spatial heterogeneity and parasites on the evolution of host diversity

Both spatial heterogeneity and exploiters (parasites and predators) have been implicated as key ecological factors driving population diversification. However, it is unclear how these factors interact. We addressed this question using the common plant-colonizing bacterium Pseudomonas fluorescens, which has been shown to diversify rapidly into spatial niche-specialist genotypes when propagated in laboratory microcosms. Replicate populations were evolved in spatially homogeneous and heterogeneous environments (shaken and static microcosms, respectively) with and without viral parasites (bacteriophage) for approximately 60 bacterial generations. Consistent with previous findings, exploiters reduced diversity in heterogeneous environments by relaxing the intensity of resource competition. By contrast, exploiters increased diversity in homogeneous environments where there was little diversification through resource competition. Competition experiments revealed this increase in diversity to be the result of fitness trade-offs between exploiter resistance and competitive ability. In both environments, exploiters increased allopatric diversity, presumably as a result of divergent selection for resistance between populations. Phage increased total diversity in homogeneous environments, but had no net effect in heterogeneous environments. Such interactions between key ecological variables need to be considered when addressing diversification and coexistence in future studies.     

Effects of host heterogeneity on pathogen diversity and evolution

Phenotypic variation is common in most pathogens, yet the mechanisms that maintain this diversity are still poorly understood. We asked whether continuous host variation in susceptibility helps maintain phenotypic variation, using experiments conducted with a baculovirus that infects gypsy moth (Lymantria dispar) larvae. We found that an empirically observed tradeoff between mean transmission rate and variation in transmission, which results from host heterogeneity, promotes long‐term coexistence of two pathogen types in simulations of a population model. This tradeoff introduces an alternative strategy for the pathogen: a low‐transmission, low‐variability type can coexist with the high‐transmission type favoured by classical non‐heterogeneity models. In addition, this tradeoff can help explain the extensive phenotypic variation we observed in field‐collected pathogen isolates, in traits affecting virus fitness including transmission and environmental persistence. Similar heterogeneity tradeoffs might be a general mechanism promoting phenotypic variation in any pathogen for which hosts vary continuously in susceptibility.     

Genetic diversity of chloroquine-resistant Plasmodium vivax parasites from the western Brazilian Amazon

The molecular basis of Plasmodium vivax chloroquine (CQ) resistance is still unknown. Elucidating the molecular background of parasites that are sensitive or resistant to CQ will help to identify and monitor the spread of resistance. By genotyping a panel of molecular markers, we demonstrate a similar genetic variability between in vitro CQ-resistant and sensitive phenotypes of P. vivax parasites. However, our studies identified two loci (MS8 and MSP1-B10) that could be used to discriminate between both CQ-susceptible phenotypes among P. vivax isolates in vitro. These preliminary data suggest that microsatellites may be used to identify and to monitor the spread of P. vivax-resistance around the world.     

The contribution of multiple barriers to reproduction between edaphically divergent lineages in the Amazonian tree Protium subserratum (Burseraceae)

Disentangling the strength and importance of barriers to reproduction that arise between diverging lineages is central to our understanding of species origin and maintenance. To date, the vast majority of studies investigating the importance of different barriers to reproduction in plants have focused on short‐lived temperate taxa while studies of reproductive isolation in trees and tropical taxa are rare. Here, we systematically examine multiple barriers to reproduction in an Amazonian tree, Protium subserratum (Burseraceae) with diverging lineages of soil specialist ecotypes. Using observational, molecular, distributional, and experimental data, we aimed to quantify the contributions of individual prezygotic and postzygotic barriers including ecogeographic isolation, flowering phenology, pollinator assemblage, pollen adhesion, pollen germination, pollen tube growth, seed development, and hybrid fitness to total reproductive isolation between the ecotypes. We were able to identify five potential barriers to reproduction including ecogeographic isolation, phenological differences, differences in pollinator assemblages, differential pollen adhesion, and low levels of hybrid seed development. We demonstrate that ecogeographic isolation is a strong and that a combination of intrinsic and extrinsic prezygotic and postzygotic barriers may be acting to maintain near complete reproductive isolation between edaphically divergent populations of the tropical tree, P. subserratum.     

Sap tension in flooded trees and bushes of the Amazon

The water relations of the inundated forest of the Rio Negro in the Amazon have been investigated. The sap pressure in trees and bushes standing in several meters of water was found to average between −15 and −20 atm in sunshine. and above −10 in overcast. In rainy weather and at night. the pressure would remain close to ambient. Submerged leaves had ambient or sometimes very slightly positive pressure. Pinnate leaves of legumes folded when the pressure rose above a critical level characteristic of the species. Dehydration curves from full turgor to negative turgor showed 3 characteristic phases: A) a steep decline in pressure when the turgor disappeared; B) a linear decline at zero turgor proportional to the increase in osmotic pressure; and C) a steep decline as negative turgor (intracellular packing) developed. The tensions in the drowned forests were similar to those found in inundated plants of temperate lakes. and hence like many plants in a humid forest. However, in the daytime many flooded plants of the Amazon reached zero turgor without any external sign of wilting.     

Diversity of palm uses in the western Amazon

We used palm knowledge to understand the interaction between people and the rainforests and the factors that influence this dynamic process. We interviewed 278 informants in 12 villages in the Pastaza and Madidi areas of the western Amazon basin. Together they used 38 different palm species for 38 different uses in six use-categories (food, construction, utensils, ritual, medicine, commercial). Euterpe precatoria, Iriartea deltoidea, and Oenocarpus bataua were best known and were mentioned as useful by 76–72% of the informants in the 12 villages. There was a great variation in number of uses and in how widespread the uses were and five of the 38 useful palms were mentioned by only one informant. Among the socioeconomic factors analyzed, the residence village influenced the informants’ knowledge of palms and their uses more than any other factor. Length of education, prosperity and for how long the informant had lived in the village were also positively correlated to how many palms and palm uses were known. Gender differences in informants’ knowledge of palm uses were not observed in our data. We suggest, that the high importance of forest products to the livelihood of the villagers, the great variation in the knowledge they possess, and the fact that the differences between villages is so great, are important elements to consider when developing management plans for the sustainable use of the rainforest resources in the western Amazon.     

Density and species diversity of trees in four tropical forests of the Albertine rift, western Uganda

We assessed tree species density and diversity in 12 1‐ha plots in four forests of the Albertine rift, western Uganda. There were 5747 trees of diameter ≥ 10 cm in 53 families, 159 genera, and 212 species. Density ranged between 344 and 557 trees ha^?1 (average 479 trees ha^?1). Tree species diversity was highest in the Bwindi and Budongo forests. The Euphorbiaceae family was the most species rich (25 species) followed by Rubiaceae and Meliaceae with 16 species each. Canonical Correspondence Analysis (CCA) showed that major gradients in environmental variables influenced tree species distribution. Sample scores on ordination axes 1 and 2 were strongly correlated with pH and altitude, respectively. Correlated with rainfall and other soil factors, pH and altitude are presumed to be among the most important in influencing the distribution of tree species in the Albertine rift forests. Strategies that take account of variations in pH and elevation are required to conserve tree species in forests of the Albertine rift.     

The contribution of slippage-like processes to genome evolution

Simple sequences present in long (>30 kb) sequences representative of the single-copy genome of five species (Homo sapiens, Caenorhabditis elegans Saccharomyces cerevisiae, E. coli, and Mycobacterium leprae) have been analyzed. A close relationship was observed between genome size and the overall level of sequence repetition. This suggested that the incorporation of simple sequences had accompanied increases of genome size during evolution. Densities of simple sequence motifs were higher in noncoding regions than in coding regions in eukaryotes but not in eubacteria. All five genomes showed very biased frequency distributions of simple sequence motifs in all species, particularly in eukaryotes where AAA and TTT predominated. Interspecific comparisons showed that noncoding sequences in eukaryotes showed highly significantly similar frequency distributions of simple sequence motifs but this was not true of coding sequences. ANOVA of the frequency distributions of simple sequence motifs indicated strong contributions from motif base composition and repeat unit length, but much of the variation remained unexplained by these parameters. The sequence composition of simple sequences therefore appears to reflect both underlying sequence biases in slippage-like processes and the action of selection. Frequency distributions of simple sequence motifs in coding sequences correlated weakly or not at all with those in noncoding sequences. Selection on coding sequences to eliminate undesirable sequences may therefore have been strong, particularly in the human lineage.     

The contribution of grazing to plant diversity in alpine grassland and heath

Abstract Grazing on transplants of a grass, a forb and a tree was examined in low-diversity grassland and more diverse heath in Australia's Snowy Mountains. Transplants were surrounded by 2 mm mesh netting. In one grassland plot, grazers (probably soil invertebrates) attacked 40–90% of tree and forb seedlings but no grass seedlings. In heath, which had about half the grass cover of grassland, grazers consumed grasses but not trees or forbs. The results suggest that grazers can depress diversity in grassland by attacking species other than grass. In heath, they may promote diversity by attacking only grass and releasing other species from competition.     

Strategies for genetic conservation of trees in the Peruvian Amazon

Forestry practices and high rates of land clearance for agriculture are causing genetic erosion of valuable tree species in the Peruvian Amazon, thereby endangering the economic sustainability of rural communities and limiting Peru's opportunities for the development of new timber and non-timber forest products. The potential utility and limitations of six low-input interventions to help forestall further genetic erosion in the region are discussed, with a focus on local community involvement. Improved agroforestry systems may help reduce deforestation by increasing farm productivity, although methods to increase the currently low adoption rate of these technologies need to be developed. Use of strategic tree domestication techniques can also improve farm productivity and prevent inadvertent genetic drift and inbreeding associated with traditional domestication practices, although to have a major impact, current programs need to be extended across the region. Woodlot forestry could supplant selective extraction of timber and offers an attractive opportunity for poverty alleviation if appropriate credit and land tenure policies can be developed. However, it may also result in increased deforestation if activities on public land cannot be controlled. The implementation of improved seed collection systems and simple seed transfer guidelines would help to reduce the collection of seed of poor quality and low genetic diversity, and avoid maladapted plantings, although such programs are difficult to monitor and seed costs may increase. Strategic identification and design of in situ conservation areas would help to ensure the viability of conserved populations, but requires the forfeiture of significant revenue from timber concessions.     

Disentangling regional and local tree diversity in the Amazon

We analyzed the most extensive data set of tree inventory plots spread over the complete Amazon basin and Guiana shield. We aimed to separate the regional and local tree alpha-diversity to investigate the drivers of diversity at the relevant scale. Our results are consistent with the partitioning of total tree alpha-diversity into regional and local components, which are controlled by evolutionary- and ecological processes, respectively. Regional diversity is correlated with palaeo-climatic stability (31%), and long-term large-scale ecosystem dynamics (14%), as represented by the age of the geological formation. Both mechanisms contribute to high diversity in the central to western Amazon. Actual rainfall seasonality is correlated with regional tree diversity to a certain extent (19%), but we argue that this is of little consequence for the evolutionary drivers of the regional species pool. Frequency of disturbance is the main process driving local diversity, although its explanatory power is relatively small (17%).