Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species

The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long‐lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions.     

Contrasting relationships between species diversity and genetic diversity in natural and disturbed forest tree communities

? This study aimed to reveal species-genetic diversity correlations (SGDCs) and their underlying mechanisms in natural and disturbed forests. ? A community survey and molecular analyses were carried out to compare species diversity (SD), the genetic diversity of the dominant tree species Euptelea pleiospermum (GD), the altitudinal patterns of SD and GD, SGDC, genetic differentiation (F(ST) ), community divergence (F(ST) -C), effective population size (N(e) ), and recent migration rate between mountain riparian forests along the Yandu (natural) and Nan (disturbed) rivers. ? In natural forests, both SD and GD showed a unimodal altitudinal pattern and GD was positively correlated with SD, whereas a unimodal pattern and positive SGDC were not found in the disturbed forests. SD and F(ST) at the natural sites were higher than those at the disturbed sites. However, there were no significant differences in GD, F(ST) -C, N(e) or recent migration rate between the natural and disturbed sites. ? A correlation between the patterns of SD and GD along a geographical gradient (e.g. altitude) is an important driver of positive SGDC. The absence of positive SGDC in the disturbed forests may result from reduced SD but unaffected GD, indicating nonparallel changes in SD and GD. This study furthermore cautions against generalizations about changes in SD and GD following disturbance.     

Range shift and loss of genetic diversity under climate change in Caryocar brasiliense, a Neotropical tree species

Many species have suffered reduction in habitable area due to recent climate change, but few studies evaluated how these range collapses will impact genetic diversity. Here, we modeled shifts in the species’ geographical range to evaluate how genetic diversity of Caryocar brasiliense will change as a consequence of predicted climate change in the next 50 years. A total of 135 records of species occurrence were obtained to model species’ distribution based on the current environment using MAXENT and forecasting future distribution using a combination of three coupled atmospheric–oceanic global circulation models. Genetic parameters were estimated based on the polymorphism at ten microsatellite loci for 466 individuals. Our results show that climatic suitable areas for C. brasiliense will be restricted to the southernmost distribution of savanna vegetation. Genetic diversity and the number of alleles may decrease slowly if populations persist in regions up to 0.5 of environmental suitability estimated by MAXENT, but will sharply decrease above this level. Nevertheless, deviation from mutation–drift equilibrium is significant even if a small amount of local populations is lost. More climatic suitable areas in the future will be in the most disturbed regions in Brazil, and populations that will persist there are those with higher levels of inbreeding at present. This may impose several threats to the species, including the limited capacity to cope with ongoing climatic changes by adaptation and constraints to dispersal.     

Isolation of primers for candidate genes for mechano-sensing in five Neotropical tree species

Mechanical signals have an impact on plant development. Tropical rainforest trees display large variability for life–history traits related to biomechanics and therefore are a unique study system to better understand biomechanical trait variability from an evolutionary perspective. From sequences and gene expression data available in model species, we developed specific primers for six candidate genes for mechano-sensing in five tropical species. Most of the gene sequences were polymorphic in most species.     

Unexpectedly high genetic diversity and divergence among populations of the apomictic Neotropical tree Miconia albicans

• Since tropical trees often have long generation times and relatively small reproductive populations, breeding systems and genetic variation are important for population viability and have consequences for conservation. Miconia albicans is an obligate, diplosporous, apomictic species widespread in the Brazilian Cerrado, the savanna areas in central Brazil and elsewhere in the Neotropics. The genetic variability would be, theoretically, low within these male‐sterile and possibly clonal populations, although some variation would be expected due to recombination during restitutional meiosis.
• We used ISSR markers to assess genetic diversity of M. albicans and to compare with other tropical trees, including invasive species of Melastomataceae. A total of 120 individuals from six populations were analysed using ten ISSR primers, which produced 153 fully reproducible fragments.
• The populations of M. albicans presented mean Shannon's information index (I) of 0.244 and expected heterozygosity (H_e) of 0.168. Only two pairs of apparently clonal trees were identified, and genetic diversity was relatively high. A hierarchical amova for all ISSR datasets showed that 74% of the variance was found among populations, while only 26% of the variance was found within populations of this species. Multivariate and Bayesian analyses indicated marked separation between the studied populations.
• The genetic diversity generated by restitutional meiosis, polyploidy and possibly other genome changes may explain the morpho‐physiological plasticity and the ability of these plants to differentiate and occupy such a wide territory and different environmental conditions. Producing enormous amounts of bird‐dispersed fruits, M. albicans possess weedy potential that may rival other Melastomataceae alien invaders.

     

Parallel changes in genetic diversity and species diversity following a natural disturbance

We examined the spatial and temporal variation of species diversity and genetic diversity in a metacommunity comprising 16 species of freshwater gastropods. We monitored species abundance at five localities of the Ain river floodplain in southeastern France, over a period of four years. Using 190 AFLP loci, we monitored the genetic diversity of Radix balthica , one of the most abundant gastropod species of the metacommunity, twice during that period. An exceptionally intense drought occurred during the last two years and differentially affected the study sites. This allowed us to test the effect of natural disturbances on changes in both genetic and species diversity. Overall, local (alpha) diversity declined as reflected by lower values of gene diversity H _S and evenness. In parallel, the among-sites (beta) diversity increased at both the genetic ( F _ST) and species ( F _STC) levels. These results suggest that disturbances can lead to similar changes in genetic and community structure through the combined effects of selective and neutral processes.     

iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Lack of requisite genetic variation in cultivated species has necessitated systematic collection, documentation and evaluation of wild Cicer species for use in chickpea variety improvement programs. Cicer arietinum has very narrow genetic variation, and the use of a wild relative in chickpea breeding could provide a good opportunity for increasing the available genetic variation of cultivated chickpea. Genetic diversity and the relationship of 71 accessions, from the core area of chickpea origin and domestication (Southeastern Turkey), belonging to five wild annual species and one cultivated species (Cicer arietinum) were analysed using iPBS-retrotransposon and ISSR markers. A total of 136 scorable bands were detected using 10 ISSR primers among 71 accessions belonging to 6 species, out of which 135 were polymorphic (99.3 %), with an average of 13.5 polymorphic fragments per primer, whereas iPBS detected 130 bands with 100 % polymorphism with an average of 13.0 bands per primer. C. echinospermum and C. pinnatifidum were the most diverse among species, whereas C. arietinum exhibited lower polymorphism. The average polymorphism information contents (PIC) value for both marker systems was 0.91. The clustering of the accessions and species within groups was almost similar, when iPBS and ISSR NeighborNet (NNet) planar graphs were compared. Further detailed studies are indispensable in order to collect Cicer germplasm, especially C. reticulatum, from southeastern Turkey particularly, from Karacada? Mountain for preservation, management of this species, and to study their genetic diversity at molecular level. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in wild chickpea and in cultivated chickpea.     

Spatial structure and genetic diversity of three tropical tree species with different habitat preferences within a natural forest

Analyses of the spatial distribution pattern, spatial genetic structure and genetic diversity were carried out using a 33-ha plot in a hill dipterocarp forest for three dipterocarps with different habitat preferences, i.e. Shorea curtisii on the ridges, Shorea leprosula in the valleys and Shorea macroptera both on the ridges and in the valleys. The significant spatial aggregation in small-diameter trees of all the three species was explained by limited seed dispersal. At the large-diameter trees, only S. macroptera showed random distribution and this might further prove that S. macroptera is habitat generalist, whilst S. curtisii and S. leprosula are habitat specific. The levels of genetic diversity estimated based on five microsatellite loci were high and comparable in all the three studied species. As the three studied species reproduced mainly through outcrossing, the observed high levels of genetic diversity might support the fact that the plant mating system can be used as guideline to infer the levels of genetic diversity, regardless of whether the species is habitat specific or habitat generalist. The lack of spatial genetic structure but significant aggregation in the small-diameter trees of all the three species might indicate limited seed dispersal but extensive pollen flow. Hence, if seed dispersal is restricted but pollen flow is extensive, significant spatial aggregation but no spatial genetic structure will be observed at the small-diameter trees, regardless of whether the species is habitat specific or habitat generalist. The inferred extensive pollen flow might indicate that energetic pollinators are involved in the pollination of Shorea species in the hill dipterocarp forests.     

Population structure and genetic diversity in four tropical tree species in Costa Rica

Despite intensified interest in conservation of tropical forests, knowledge of the population genetics of tropical forest trees remains limited. We used random amplified polymorphic DNA (RAPD) data to evaluate trends in genetic diversity and differentiation for four tropical tree species, Alchornea latifolia, Dendropanax arboreus, Inga thibaudiana and Protium glabrum . These species occur at contrasting population densities along an elevational gradient and we use RAPD and ecological data to examine natural levels of genetic diversity of each species, trends in genetic variability with population density and structure, genetic differentiation along the elevation gradient, and the relationship between genetic diversity and such factors as seed dispersal and pollination syndrome. At the distances we examined (plot distances ranging from 0.8 to 8.6 km) there was very little genetic structuring at any distance along the gradient. All four species exhibited levels of variation expected for spatial distribution, mating system and pollinator syndrome; greater than 96% of the genetic variation occurred within plots for Inga thibaudiana, Protium glabrum and Dendropanax arboreus. Alchornea latifolia only occurred in a single plot. The results of this study contribute to a growing database of genetic diversity data that can be utilized to make predictions about the effect of disturbance and subsequent reductions in population size on genetic variation and structure in tropical tree species.     

Ectomycorrhizal fungal diversity and community structure on three co-occurring leguminous canopy tree species in a Neotropical rainforest

? The ectomycorrhizal (ECM) symbiosis was historically considered restricted to the temperate zones, but recent studies have shown the importance of this symbiosis across the tropics. We examined ECM fungal diversity, host plant phylogeny and ECM host preferences in a rainforest dominated by the leguminous host plants Dicymbe corymbosa, Dicymbe altsonii and Aldina insignis. ? Ectomycorrhizal fungi were identified by internal transcribed spacer rDNA sequencing and host species were verified with chloroplast trnL sequencing. To test whether Dicymbe and Aldina represent independent gains of the ECM symbiosis, we constructed a Fabaceae phylogeny using MatK and trnL. We identified four independent ECM lineages within the Fabaceae. ? We detected a diverse community of 118 ECM species dominated by the /clavulina, /russula-lactarius, /boletus, and /tomentella-thelephora lineages. Ectomycorrhizal species in Agaricales, Atheliales and Polyporales may represent previously unrecognized tropical-endemic ECM lineages. Previous studies suggested that ECM fungi did not diversify in the tropics, but the /clavulina lineage appears to have a center of diversity in tropical South America. ? Dicymbe and Aldina represent independent gains of the ECM symbiosis in Fabaceae but their fungal symbionts showed no host preferences. Spatial factors are more important than hosts in structuring the ECM fungal community in this ecosystem.     

Ecology: linking species diversity and genetic diversity

Although there is a great deal of interest in the biological diversity of species and of genes, it is only recently that researchers have begun to investigate the processes that exert parallel influences on these different levels of diversity.     

Disturbance, selective logging and bird diversity: a Neotropical forest study

The composition and structure of bird communities, and the damage to forest structure were surveyed in northern French Guiana (northeastern Amazonia) one year and ten years after selective logging and compared with the situation in a similar undisturbed primary forest. A point-count method was used in which 937 0.25ha sample plots were censused for 20 minutes each, and their vegetation structure was measured. On average, 38% of the forest undergrowth was destroyed, then invaded by dense regrowth, and up to 63% of the canopy was substantially opened as a result of selective logging. Hunting pressure also increased due to access roads opened for logging. Among the 256 species recorded, overall bird species richness and abundance were depressed by 27–34% in the logged areas compared to primary forest. The most vulnerable guilds, which decreased by 37–98% in abundance, were mature forest understorey species, especially terrestrial ones and mixed flocks of insectivores. Hummingbirds, small gaps, vine tangles and canopy species did not decrease, nor increase significantly after logging. Only species naturally associated with dense second growth, forest edges and large gaps actually increased. Habitat specialization was the major determinant of vulnerability to logging, and, to a lesser degree, size (large) and diet (insectivorous), but foraging behaviour and rarity had little effect. Bird sensitivity to changes in logged forest structure may involve physiological intolerance, reduced food categories, increased exposure to predators, too dense understorey for their specific foraging behaviour and/or avoidance of gaps. Suggested improvements of current forest management and logging techniques for the maintenance of a higher proportion of the original biodiversity include minimizing logging damages, long rotations (>50 years) between cuts, and keeping unlogged forest patches within logging concessions.     

Components of water potential estimated from xylem pressure measurements in five tree species

Summary Pressure volume curves were measured with a pressure bomb in leaves collected in the field from Ilex opaca, Acer rubrum, Liquidambar styraciflua, Liriodendron tulipifera and Cornus florida. Water potential components were calculated from the curves. The species differed in the relationships measured. In all species the trends from summer to fall were toward lower (more negative) osmotic potentials, lower matric potentials more rapid loss of turgor with increasing leaf water deficit, and the occurrence of incipient plasmolysis at lower values of leaf water deficit. Initial osmotic potentials ranged from-14.8 to-19.8 bars, similar to values reported in the literature for other mesophytic plants. These values, however, were much higher than those reported for halophytes and xerophytes. The fraction of leaf water which contributes to the osmotic potential ranged from 0.74 to 0.98 in this study. Values reported for other mesophytes and for halophytes and xerophytes all fall well within this range. Patterns of component water potentials are discussed in relation to potential growth rates and water flow in the total plant system.     

Effects of colonization processes on genetic diversity: differences between annual plants and tree species

Tree species are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than trees. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for trees. This explanation is problematic because it relies on equilibrium hypotheses. Because trees have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest trees, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of trees are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in trees and annual species by much less diversity and much more differentiation than nuclear genes.     

High genetic diversity and contrasting fine-scale spatial genetic structure in four seasonally dry tropical forest tree species

In this study we compared population structure, genetic diversity and fine-scale spatial genetic structure (SGS) in four Bignoniaceae tree species, Handroanthus chrysotrichus, H. impetiginosus, Tabebuia roseoalba and H. serratifolius in a remnant of seasonally dry tropical forest in Central-West Brazil, based on polymorphisms at six microsatellite loci. All species, except T. roseoalba, presented the inverted ‘J’ population structure indicating recruitment of juveniles. Juveniles presented a clumped distribution suggesting limitation in dispersal or patchy distribution of suitable microhabitat for recruitment. All species showed high levels of polymorphism and genetic diversity but without a clear pattern of distribution among life stages. The SGS was significant for all species, except T. roseoalba, but the pattern and strength of the spatial genetic structure differed among species. Handroanthus serratifolius had stronger SGS with significant kinship until 77 m. For H. impetiginosus and H. chrysotrichus, kinship was significant just until 23 and 6 m, respectively. Despite the high genetic diversity, all species showed low number of adults and high fixation indices suggesting that habitat fragmentation and disturbance have been affecting these populations in Central-West Brazil.     

Glacial refugia and modern genetic diversity of 22 western North American tree species

North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r² = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles.     

Fine-scale genetic structure and gene dispersal inferences in 10 neotropical tree species

The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies.     

Adaptation to drought in two wild tomato species: the evolution of the Asr gene family

Wild tomato species are a valuable system in which to study local adaptation to drought: they grow in diverse environments ranging from mesic to extremely arid conditions. Here, we investigate the evolution of members of the Asr (ABA/water stress/ripening induced) gene family, which have been reported to be involved in the water stress response. We analysed molecular variation in the Asr gene family in populations of two closely related species, Solanum chilense and Solanum peruvianum. We concluded that Asr1 has evolved under strong purifying selection. In contrast to previous reports, we did not detect evidence for positive selection at Asr2. However, Asr4 shows patterns consistent with local adaptation in an S. chilense population that lives in an extremely dry environment. We also discovered a new member of the gene family, Asr5. Our results show that the Asr genes constitute a dynamic gene family and provide an excellent example of tandemly arrayed genes that are of importance in adaptation. Taking the potential distribution of the species into account, it appears that S. peruvianum can cope with a great variety of environmental conditions without undergoing local adaptation, whereas S. chilense undergoes local adaptation more frequently.     

Testing for enemy‐mediated density‐dependence in the mortality of seedlings: field experiments with five Neotropical tree species

The coexistence of plant species in species‐rich tropical forests can be promoted by specialised enemies acting in a negatively density‐dependent manner. While survival of tropical tree seedlings is often negatively density‐dependent, the causes have rarely been identified. We tested whether insects and plant pathogens cause density‐dependent seedling recruitment and survival in five forest tree species in Belize, Central America. We manipulated densities of seeds or newly germinated seedlings in small (1 m² or 0.25 m²) plots close to fruiting conspecific trees. Using a factorial design, we excluded enemies from subsets of the plots with fungicides and insecticides. Seed germination (for two species) and early seedling survival (for all species) were monitored at approximately weekly intervals for up to eight weeks, during the period when plants are likely to be most susceptible to natural enemies. In Terminalia amazonia, seed germination was negatively density‐dependent and the proportion of seeds germinating increased when insects were excluded. However, the magnitude of the insecticide effect was independent of density. The only significant density effect for survival of young seedlings was in Acacia polyphylla; counter to expectation, seedling survival was higher at high densities. In a few cases pesticide application had a significant effect on seedling survival, but in only one case (Terminalia amazonia) was a significant pesticide × density interaction detected. Our results caution against generalising from studies conducted on a single species at a single time and place and illustrate the challenges of experimentally testing for enemy‐mediated negative density‐dependence. Experimental outcomes are likely to depend on the spatial scale at which the principal enemies disperse and respond to plant density, and the timescales over which they act. Gathering information on these variables will improve our understanding of the natural histories of tropical forest species and help inform the design of future experiments.