Mangrove forests in a peri-urban setting: the case of Mombasa (Kenya)

The structure and regeneration patterns of the peri-urban mangrove vegetation of Mombasa at Tudor creek were studied along belt transects at two forest sites of Kombeni and Tsalu. Based on the species importance values, the dominant mangrove species were Rhizophora mucronata Lam. (Rhizophoraceae) and Avicennia marina (Forssk.) Vierh. (Avicenniaceae). Lumnitzera racemosa Willd., reported in an earlier floristic survey, was not encountered. Tree density varied from 1,264 trees ha^–1 at Kombeni to 1,301 trees ha^–1 at Tsalu and mean tree height was higher at the former site compared to the latter. The size-class structure at both localities showed the numerical dominance of small trees over larger trees. The spatial distribution pattern of adults and juveniles varied greatly between sites and showed a close to uniform pattern (Morisita’s Index I _δ ≪ 1) for adult trees, but a tendency to clustered distribution (I _δ ≫ 1) for juveniles. The present paper shows that unmanaged but exploited peri-urban mangroves are structurally stressed, having enlarged canopy gaps that are characterised by spatial and temporal site heterogeneity that influences regeneration, implying longer periods for canopy closure. Diversifying uses of mangrove products and establishing reserves as no cut zones with regulated harvesting will minimise canopy gap sizes, and promote conservation practices. The proposed management strategy shall boost the ecosystem resilience to both anthropogenic and natural stressors expected in the peri-urban setting in the long run.     

Effects of Treefall Gap Disturbances on Ant Assemblages in a Tropical Montane Cloud Forest

The study of gap dynamics and the effects of gaps on diversity has been at the center of tropical ecology for decades. While most studies have focused on the responses of plant species and communities to gap formation, in this study, we consider the effects of treefall gap disturbances on leaf litter ant assemblages in a Neotropical montane cloud forest. We sampled leaf litter ant assemblages and estimated a suite of abiotic parameters in 12 large (>80‐m²) treefall gaps across a chronosequence and in 12 paired adjacent intact forest sites in the Monteverde Cloud Forest Preserve in Costa Rica. No species were more common in gaps than in intact forests, and in fact, species that were common in gaps were also among the most common in forests. The Chao2 estimate of species richness, however, was higher in gap sites than in intact forest sites. In addition, ant assemblages in gap sites did not become more similar to those in adjacent intact sites as gaps aged. In contrast to other studies, our work demonstrates that ant assemblages in the Monteverde Cloud Forest Preserve are weakly affected by the formation of treefall gaps. Together, these results indicate that treefall gap dynamics probably play little role in promoting ant diversity at more regional scales, or coexistence among species at more local scales.     

Which plant traits promote growth in the low-light regimes of vegetation gaps?

Nine temperate grass species were screened for their potential to grow in the low-light conditions typical of gaps in dense vegetation. To this end, photosynthetic photon flux densities (PFD) were simulated in a growth chamber (PFD 100, 50 or 25 μmol photons m⁻² s⁻¹). Relative and absolute growth rates (RGR and AGR, respectively) of the species were regressed on ten different ecophysiological and morphogenetic plant attributes. No significant relationships were found between plant attributes and relative growth rate, while six attributes explained a significant proportion of the interspecific variance in absolute biomass growth: net photosynthetic rate at growth PFD (P _net ) (75.5%), leaf apparent quantum yield of CO₂ fixation (62.5%), leaf dark respiration rate (65.2%), leaf compensation PFD (71.0%), root: shoot ratio (66.4%) and plant nitrogen content on a mass basis (42.0%). Only species with extremely low allocation to roots and very high (relatively speaking) net photosynthetic rates were able to grow fast in low light. Specific leaf area (SLA), instantaneous photosynthetic nitrogen use efficiency (PNUE) and leaf nitrogen content on a mass basis as well as on an area basis were not significantly related to growth. The absence of effects of plant traits on RGR, unlike for AGR, could arise from a relationship that we observed between AGR and a fitted start value of the biomass-time course (i.e. seed mass or germination time). This suggests that interspecific differences in the very early growth stages of the plants were responsible for differences in successful development under low light, rather than differences in RGR. Based on its high explanatory power, its relative constancy with plant age and the lack of effect of growth PFD, P _net would be the best candidate for characterizing potentially shade-tolerant species that are likely to establish in dense vegetation in the field.     

The big ecological questions inhibiting effective environmental management in Australia

The need to improve environmental management in Australia is urgent because human health, well‐being and social stability all depend ultimately on maintenance of life‐supporting ecological processes. Ecological science can inform this effort, but when issues are socially and economically complex the inclination is to wait for science to provide answers before acting. Increasingly, managers and policy‐makers will be called on to use the present state of scientific knowledge to supply reasonable inferences for action based on imperfect knowledge. Hence, one challenge is to use existing ecological knowledge more effectively; a second is to tackle the critical unanswered ecological questions. This paper identifies areas of environmental management that are profoundly hindered by an inability of science to answer basic questions, in contrast to those areas where knowledge is not the major barrier to policy development and management. Of the 22 big questions identified herein, more than half are directly related to climate change. Several of the questions concern our limited understanding of the dynamics of marine systems. There is enough information already available to develop effective policy and management to address several significant ecological issues. We urge ecologists to make better use of existing knowledge in dialogue with policy‐makers and land managers. Because the challenges are enormous, ecologists will increasingly be engaging a wide range of other disciplines to help identify pathways towards a sustainable future.     

Distribution of Indel lengths

Protein sequence alignment has become a widely used method in the study of newly sequenced proteins. Most sequence alignment methods use an affine gap penalty to assign scores to insertions and deletions. Although affine gap penalties represent the relative ease of extending a gap compared with initializing a gap, it is still an obvious oversimplification of the real processes that occur during sequence evolution. To improve the efficiency of sequence alignment methods and to obtain a better understanding of the process of sequence evolution, we wanted to find a more accurate model of insertions and deletions in homologous proteins. In this work, we extract the probability of a gap occurrence and the resulting gap length distribution in distantly related proteins (sequence identity < 25%) using alignments based on their common structures. We observe a distribution of gaps that can be fitted with a multiexponential with four distinct components. The results suggest new approaches to modeling insertions and deletions in sequence alignments.     

Overstorey Control of Understorey Species Composition in a Near-natural Temperate Broadleaved Forest in Denmark

Little is known about the importance of the forest overstorey relative to other factors in controlling the spatial variability in understorey species composition in near-natural temperate broadleaved forests. We addressed this question for the 19 ha ancient forest Suserup Skov (55°22′ N, 11°34′ E) in Denmark, one of the few old-growth temperate broadleaved forest remnants in north-western Europe, by inventorying understorey species composition and environmental conditions in 163 100 m² plots. We use unconstrained and constrained ordinations, variation partitioning, and Indicator Species Analysis to provide a quantitative assessment of the importance of the forest overstorey in controlling understorey species composition. Comparison of the gradients extracted by unconstrained and constrained ordinations showed that the main gradients in understorey species composition in our old-growth temperate broadleaved forest remnant are not caused by variability in the forest overstorey, but are related to topography and soil, edge effects, and unknown broad-scale factors. Nevertheless, overstorey-related variables uniquely accounted for 15% of the total explained variation in understorey species composition, with the pure overstorey-related (R_po), topography and soil (R_pt), edge and anthropogenic disturbance effects (R_pa), and spatial (R_ps) variation fractions being of equal magnitude. The forward variable selection showed that among the overstorey-related variables understorey light availability and to a lesser extent vertical forest structure were most important for understorey species composition. No unique influence of overstorey tree species identity could be documented. There were many indicator species for high understorey light levels and canopy gap centres, but none for medium or low light or closed canopy. Hence, no understorey species behaved as obligate shade plants. Our study shows that, the forest overstorey has a weak control of understorey species composition in near-natural broadleaved forest, in contrast to results from natural and managed forests comprising both conifer and broadleaved species. Nevertheless, >20% of the understorey species found were indicators of high light conditions or canopy openings. Hence, variability in canopy structure and understorey light availability is important for maintaining understorey species diversity.     

Genet dynamics of a regenerating dwarf bamboo population across heterogeneous light environments in a temperate forest understorey

Despite the advantage of plant clonality in patchy environments, studies focusing on genet demography in relation to spatially heterogeneous environments remain scarce. Regeneration of bamboos in forest understoreys after synchronous die‐off provides an opportunity for assessing how they come to proliferate across heterogeneous light environments. In a Japanese forest, we examined genet demography of a population of Sasa kurilensis over a 7‐year period starting 10 years after die‐off, shortly after which some genets began spreading horizontally by rhizomes. The aboveground biomass was estimated, and genets were discriminated in 9‐m² plots placed under both canopy gaps and closed canopies. Overall, the results suggest that the survival and spread of more productive genets and the spatial expansion of genets into closed canopies underlie the proliferation of S. kurilensis. Compared to canopy gaps, the recovery rate of biomass was much slower under closed canopies for the first 10 years after the die‐off, but became accelerated during the next 7 years. Genet survival was greater for more productive genets (with greater initial number of culms), and the spaces occupied by genets that died were often colonized afterward by clonal growth of surviving genets. The number of genets decreased under canopy gaps due to greater mortality, but increased under closed canopies where greater number of genets colonized clonally from outside the plots than genets died. The colonizing genets were more productive (having larger culms) than those originally germinated within the plots, and the contribution of colonizing genets to the biomass was greater under closed canopies. Our study emphasizes the importance of investigating genet dynamics over relevant spatiotemporal scales to reveal processes underlying the success of clonal plants in heterogeneous habitats.     

Effect of treefall gaps on the patchiness and species richness of Neotropical ant assemblages

Natural formation of treefall gaps plays an integral role in the ecological and evolutionary dynamics of many tropical forests, affecting the spatiotemporal distribution of plants and the animals that interact with them. This study examines the impact of treefall gaps on the spatial and temporal patchiness of ant assemblages in a moist lowland forest in Panama. Using pitfall traps and honey baits, we compared ant assemblages in five 1 to 2-year-old treefall gaps (ca 100 m²) and five adjacent plots (ca 100 m²) in undisturbed forest understory at three different times of year (late wet season, late dry season, and early wet season). We found little evidence that ant assemblages respond dramatically to the formation of treefall gaps and the differences in habitat qualities they produce. Ant abundance, species richness, species composition, and rates of resource discovery did not differ between gaps and forest understory. However, we did find significant differences in numerical abundance related to forest stratum (ground vs vegetation) and resource type in pitfall traps (oil-cockroach vs honey), and significant differences in ant species richness and rates of resource discovery across seasons. While habitat effects by themselves were never statistically significant, habitat and seasonal differences in species richness interacted significantly to produce complex, season-dependent differences among gap and forest habitats. These results suggest that the formation of natural treefall gaps has less of an effect on Neotropical ant assemblages compared to other groups of organisms (e.g., plants, birds) or other causes of patchiness (e.g., ant mosaics, moisture availability, army ant predation). The results of our study also have important implications for the underlying causes of habitat differences in the distribution of ant-defended plants. Received: 3 February 1998 / Accepted: 7 April 1998     

DEMOGRAPHIC GENETICS OF A PIONEER TROPICAL TREE SPECIES: PATCH DYNAMICS,SEED DISPERSAL,AND SEED BANKS

We consider whether changes in population-genetic structure through the life cycle of Cecropia obtusifolia, a tropical pioneer tree, reflect its gap-dependent demography and the role of evolutionary processes that are important for this species. We asked whether the spatial scale at which population-genetic subdivision occurs corresponds to the scale of habitat patchiness created by gap dynamics; whether patterns of seed dispersal and storage in the soil affect spatial genetic patterns; and whether spatial genetic patterns change through the species life cycle. We estimated Wright's F-statistics for six successive life-history stages for individuals grouped into subpopulations according to occurrence in natural gaps, physical proximity, or occurrence within large quadrats. For each life stage, F_ST-statistics were significantly higher when individuals were grouped by gaps, although concordant patterns across life stages for the three grouping methods were obtained. This supports the hypothesis that patchy recruitment in gaps or among-gap heterogeneity influences the species' genetic structure. F-statistics of seeds collected from females before dispersal (tree seeds), seed-rain seeds, soil seeds, seedlings, juveniles, and adults grouped by gaps, were, respectively: F_IT = 0.004, 0.160, 0.121, 0.091, –0.0002, –0.081; F_IS = –0.032, 0.124, 0.118, 0.029, –0.016, –0.083; and F_ST = 0.035, 0.041, 0.003, 0.063, 0.015, 0.002. Spatial genetic differentiation in rain seeds was not significantly lower than that of tree seeds. The loss of genetic structure in the soil seed bank, relative to that found in the seed rain may be due to sampling artifacts, but alternative explanations, such as microsite selection or temporal Wahlund effect are also discussed. If structure among soil seeds is unbiased, the peak in seedling F_ST may be due to microsite selection. F_IS of seeds in the rain and soil were significantly greater than zero. A Wahlund effect is the most likely cause of these positive F_IS values. Such fine-scale substructuring could be caused by correlated seed deposition by frugivores. The decrease in F_IS from seedlings to adults could result from loss of fine-scale genetic structure during stand thinning or from selection.