Long-term forest-savannah dynamics in the Bolivian Amazon: implications for conservation

The aim of this paper is to evaluate the respective roles of past changes in climate, geomorphology and human activities in shaping the present-day forest-savannah mosaic of the Bolivian Amazon, and consider how this palaeoecological perspective may help inform conservation strategies for the future. To this end, we review a suite of palaeoecological and archaeological data from two distinct forest-savannah environments in lowland Bolivia: Noel Kempff Mercado National Park (NKMNP) on the Precambrian Shield and the 'Llanos de Moxos' in the Beni basin. We show that they contain markedly contrasting legacies of past climatic, geomorphic and anthropogenic influences between the last glacial period and the Spanish Conquest. In NKMNP, increasing precipitation caused evergreen rainforest expansion, at the expense of semi-deciduous dry forest and savannahs, over the last three millennia. In contrast, pre-Hispanic indigenous cultures were instrumental in facilitating recent forest expansion in the Llanos de Moxos by building a vast network of earthworks. Insights from Mid-Holocene palaeodata, together with ecological observations and modelling studies, suggest that there will be progressive replacement of rainforest by dry forest and savannah in NKMNP over the twenty-first century in response to the increased drought predicted by general circulation models. Protection of the latitudinal landscape corridors may be needed to facilitate these future species reassortments. However, devising appropriate conservation strategies for the Llanos de Moxos will be more difficult due to its complex legacy of Palaeo-Indian impact. Without fully understanding the degree to which its current biota has been influenced by past native cultures, the type and intensity of human land use appropriate for this landscape in the future will be difficult to ascertain.     

Endemism and conservation of Amazon palms

Endemicity is important for the delimitation of conservation areas. Endemic areas are those that contain two or more taxa with their distribution restricted to the area. The aim of this study was to detect endemic areas for palms in the Amazon region and to determine whether the species that define these endemic areas are protected within conservation units. Records of occurrence were extracted from the global biodiversity information facility (GBIF). The final dataset consisted of 17,310 records, for 177 species of Amazonian palms. For analysis we used parsimony analysis of endemicity (PAE) and NDM-VNDM program, and grid square size of 1° and 3° as operational geographic units (OGUs). The distribution of endemic species was superimposed on occurrence of the conservation units (CUs). PAE did not show endemic areas in grid squares of 1°, but found 10 palm endemic areas in grid squares of 3° in the western Amazon and Andean sub-region. However, the NDM-VNDM program identified an endemic area in grid squares of 1° located at the eastern Guiana with endemicity score = 2.9, and in grid squares of 3° it identified seven consensus areas with endemicity score > 6.0, all in the western Amazon. The combination of PAE and NDM-VNDM analyses resulted in eight endemic palm areas in the combined western Amazon and Andean sub-region. Of the species that define the endemic areas, five are threatened with extinction in one of three IUCN categories (EN, VU, NT), and they are not protected in any conservation units. The western Amazon, besides having high palm richness, also has palm endemic areas, especially, near the Andean sub-region and the Peruvian Amazon.     

Seasonal forcing on the dynamics ofClethrionomys rufocanus: Modeling geographic gradients in population dynamics

We interpret gradients in population dynamics of the gray-sided vole from the southwestern part of the island of Hokkaido to its northeastern part within the framework of a phenomenological model involving the relative length of summer and winter. In Hokkaido, as in other northern regions, both spring and fall is considered as short transition periods between the two main seasons — summer (the primary breeding season) and winter (the non-reproductive or secondary breeding season). We show that the geographic transition in dynamics may be understood as the combined consequence of different patterns of density-dependence during summer and winter, and geographically varying season lengths. Differences are shown to exist between summer and winter with respect to strength of density-dependence. Direct density-dependence, in particular, is stronger during winter than during summer. A model is presented to show how relative lengths of seasons can induce both stable and periodically fluctuating population dynamics. The results are compared and contrasted with what is otherwise known about the gradient in rodent dynamics in Fennoscandia.     

Modeling Daphnia population dynamics and demography under natural conditions

Various approaches to modeling the population dynamics and demography of Daphnia have been published. These methods range from the simple egg-ratio method, to mathematically complex models based on partial differential equations and numerically complex individual-based Daphnia population models. The usefulness of these models in unraveling the population dynamics and demography of Daphnia under natural conditions is discussed. Next to this, an extended version of an existing individual-based Daphnia model is documented (Cladosim) and its application to a typical field data set collected in 1995 in Lake Volkerak is shown. To answer the question which factor was limiting Daphnia numbers during the course of the season food level and temperature in the model were varied and results were compared with those obtained for the observed food level and temperature. These analysis showed that in April temperature was limiting while during May–July and September–October food was limiting. In August neither temperature nor food was limiting. Analysis with a set of size-selective mortality scenarios showed that on average the Daphnia population in Lake Volkerak experienced a mild positive size-selective mortality during the year that was analyzed. Birth rates derived with the detailed individual-based model were compared with those derived with the much simpler egg-ratio method. For the conditions as observed in Lake Volkerak in 1995, both methods gave very comparable results, despite sampling intervals of up to four weeks. The same holds under the environmental scenarios. Using the size-selective mortality scenarios it could be shown, however, that under strong mortality of the smaller daphnids, the egg-ratio method severely underestimates the birth rate. The vices and virtues of the new model and potential extensions are discussed.     

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.     

Strategies for mammal conservation under climate change in the Amazon

Climate change is not only a major threat to biodiversity, it is also a big challenge to the development of conservation strategies. Scientists and practitioners need to select or avoid areas at greatest risk for species protection, i.e., acting in a proactive or a reactive manner. This proactive/reactive dichotomy takes a particular formulation under the likely changes in climate. Selecting for low-risk areas (usually referred to as climate refugia) is supposed to protect more species with a greater guarantee of their long-term persistence. As a consequence, populations at greatest risk are left unprotected and probably committed to extinction. On the other hand, managing species in high-risk areas is more expensive than setting aside areas of climate refugia and encompasses a set of uncertainties, which makes highly-threatened species more costly and difficult to save. Here, we combine ecological niche models and metrics of climate change to develop spatial conservation schemes for mammals in the Brazilian Amazon. These schemes efficiently identify networks of high-risk and refugia priority areas within species current and future distributions, while complementing the protection already achieved by the Amazon’s network of protected areas (PAs). We found that, on average, 25% of mammal distribution is already represented in the established network of PAs. Also, 26% of high-risk and 17% of refugia priority areas overlap with indigenous lands. In addition, species distributions were found mostly in high-risk, compared to in refugia priority areas. We highlight that the strategy to be employed does not necessarily should be binary and a mix of both strategies would guarantee the protection of a larger number of species.     

Long-term tree population dynamics and their implications for the conservation of the Kakamega Forest, Kenya

Long-term studies of tree population dynamics play an important role in identifying the conservation needs of tropical forest ecosystems. We examined changes in tree population structure and composition over an 18-year period (1981–1999) in three plots located at the center of the Isecheno study site in the Kakamega Forest, Kenya, a forest with a history of logging and other anthropogenic disturbance. DBH size class distribution took the shape of an inverse J curve in both 1981 and 1999 and did not differ significantly between the two study periods. Stem density increased significantly during the study with most of the increase occurring in the smallest stem size class (10–14 cm DBH). Nearly all of the most common species in 1981 remained among the most common in 1999, though the density of pioneer species decreased by 21% during the study. Our results suggest that forest in the study plots remained relatively undisturbed and in good condition over the study period. Forest in the plots also appeared still to be recovering from the selective logging of large trees that took place at Isecheno in the 1940s. In addition to our longitudinal study, we compared tree population parameters at three additional Isecheno sites spread over a distance of 1 km that have experienced different histories of disturbance: (i) a lightly human disturbed site (LHD), (ii) a heavily human disturbed site (HHD), and (iii) a cattle disturbed site (CD). While all three sites were selectively logged in the 1940s, the main signs of disturbance today are footpaths at the LHD site, tree stumps at the HHD site, and wide cattle paths at the CD site. Not surprisingly, of the disturbed sites, the LHD site was in the best condition. Trees at the HHD site exhibited extremely poor recruitment into the small size classes, a condition that can probably be attributed to human exploitation of small trees for poles. The CD site appeared to be at an earlier successional stage than the other disturbed sites with its low mean DBH, high overall stem density, and high pioneer species stem density. Browsing and trampling of vegetation by cattle may be the source of the light gaps that have led to the abundance of pioneer species at this site. We conclude that conservation measures applied to central Isecheno, including the establishment of a forest station nearby and ranger patrols, appear to have succeeded, but that the prognosis for the Kakamega Forest in general is bleak if protection efforts are not increased in other parts of the forest, where anthropogenic disturbance remains high. We also note the considerable variation in tree population structure and composition that can occur within a small area depending on the local history of disturbance.     

Spatial variation in population dynamics of juvenile Atlantic salmon: implications for conservation and management

Application of habitat models for predicting expected local densities of Atlantic Salmon Salmo salar in healthy populations has been hampered by a lack of generality in their fit to data from different systems. It is believed that this problem results at least in part from difficulties of effectively integrating factors that act across a range of spatial and temporal scales. Here, as an aid to developing more robust modelling and sampling methodologies, a simple process‐based model for local‐scale dynamics of Atlantic salmon juveniles is developed from first principles by integrating contemporary understanding of self‐thinning, density‐dependent growth and dispersal. The aim is to present a readily understood structure to illustrate the links between spawning and stocking strategies, habitat, migration and fish production. Based on this structure, contemporary understanding of the more complex biological processes that affect density, growth and habitat are discussed in relation to some of the key requirements of managers, including stocking for rehabilitation, assessment of predation impact and development of strategies for sampling populations effectively when deriving habitat‐production models. A major conclusion is that more structured, integrated research is required to provide the basic variables needed to model links between local and global scale habitat and fish production effectively. Nevertheless, application of the current understanding of the biology of Atlantic salmon should be of great benefit to managers in extracting key information from field surveys.     

Modelling Chlamydia–koala interactions: coexistence, population dynamics and conservation implications

1. Considerable research has been conducted on koala Phascolarctos cinereus population dynamics and the epidemiology of Chlamydia psittaci infection in koalas, but the impact of Chlamydia on koala populations has been difficult to assess.
2. I developed a model of koala and Chlamydia population dynamics to examine interactions between Chlamydia transmission and pathogenicity, koala mating behaviour and demography, and koala population persistence.
3. Simulations based on sexual and parent–offspring parasite transmission demonstrate that stable Chlamydia–koala coexistence is possible in a small population for a broad range of demographic, behavioural, pathogenicity and transmission parameter estimations. Koala population persistence was most sensitive to reduced annual survivorship of adults (4–10-year-old males and 2–12-year-old females), highlighting the need for accurate field estimates of adult survivorship in order to assess Chlamydia 's impact on specific populations.
4. If koalas become less resistant to disease in fragmented, high-stress habitats (i.e. experience increased Chlamydia -induced mortality and sterility rates), Chlamydia is not predicted to cause koala extinctions under most conditions. Extinctions are only predicted if Chlamydia transmission rates also increase (e.g. due to new transmission pathways or increased mating frequency), or other non-disease factors change birth and mortality rates to reduce the koala population's intrinsic rate of increase below 0·1.
5. The most important predicted effect of habitat fragmentation and other forms of human disturbance on this unique host–parasite relationship is the extinction of Chlamydia in populations where koala resistance to disease decreases.     

Modeling the population dynamics of annual plants with seed bank and density dependent effects

A model is proposed for the population dynamics of an annual plant (Sesbania vesicaria) with a seed bank (i.e. in which a proportion of seeds remain dormant for at least one year). A simple linear matrix model is deduced from the life cycle graph. The dominant eigenvalue of the projection matrix is estimated from demographic parameters derived from field studies. The estimated values for population growth rate () indicates that the study population should be experiencing a rapid exponential increase, but this was not the case in our population.The addition of density dependent effects on seedling survivorship and adult fecundity, effects for which field studies provide evidence, considerably improves our model. Depending on the demographic parameters, the model leads to stable equilibrium, oscillations, or chaos. Study of the behaviour of this model in the parameter space shows that the existence of a seed bank allows higher among-year variation of adult fecundity, without leaving the region of demographic stability. Field data obtained over 3 years confirm this prediction.     

Nitrogen dynamics in seasonally flooded soils in the Amazon floodplain

Large areas of the Amazon are subject to seasonal flooding due to water level changes of the river. This flood pulse causes rapidly changing conditions for microorganisms living in the soils which affects the cycling of nitrogen in the ecosystem. An understanding of the nitrogen dynamics in the seasonally flooded soils is essential for the development of productive and sustainable management concepts. We measured nitrogen concentrations, denitrifier enzyme activity (DEA), cell numbers of nitrifying and denitrifying bacteria, respiration, pH and total carbon in the seasonally flooded soils over one entire annual hydrological cycle. By comparing three sites with different vegetation (forest, aquatic macrophyte stand and bare sediment with annual herbs) we assessed the effect of vegetation on soil nitrogen dynamics. Inorganic nitrogen was always dominated by ammonium indicating reduced conditions in the soil even during the terrestrial phase. Although conditions were generally poor for nitrification we observed high numbers of nitrifying bacteria between 10⁴ and 10⁷cells g^–1. Pulses of ammonium as well as high DEA were observed during the transition periods between aquatic and terrestrial phase. Thus the alternation between aquatic and terrestrial phase promotes nitrogen mineralization and denitrification in the soils. There were no plausible correlations between microbial activities and numbers with soil physical or chemical parameters except a relation between the numbers of nitrate reducing bacteria and soil moisture (R² = 0.81) and ammonium (R² = 0.92) at one site. This shows the complex regulation patterns in this habitat. Different vegetation did not alter the general patterns of nitrogen dynamics but the absolute extend of fluctuations. We conclude that both the soil physical and chemical changes directly caused by the flood pulse and the vegetation have a great impact on microbial nitrogen turnover in the soils. The effects of the flood pulse can be buffered by a fine soil texture or a litter layer which prevents desiccation of the soil during the terrestrial phase.     

Mineral lick distribution modeling and NW Amazon conservation planning alternatives

Mineral licks are faunal attractors, whose distribution determines the structure and composition of Amazonian landscapes and the way they are used by wildlife and traditional communities. Research on the distribution of mineral licks is scarce, limiting the possibility of using them in conservation beyond local scales. Using the species distribution modeling framework, we predicted the distribution of suitable conditions for mineral licks in the Northwest Amazon, compiling localities from academic and traditional sources and using environmental variables associated with geology, geomorphology, edaphology, topography, and hydrology. Best models, selected according to evaluation metrics incorporated in the ENMeval “R” package, showed to be robust and predict sectors with different areas, but similar distributions. Suitable areas covered up to 14.6% of the study area and confirmed the association of mineral licks with the drainage system. The erosive capacities of the rivers and their roles in terms of sediment deposition allowed the generation of ideal conditions for the expression of mineral licks in past and present riparian zones. Closeness to salt deposits and the seacoast was also important, giving information about the underground and aboveground mineral availability, crucial aspects for mineral lick formation. Considering the extension and distribution of our predictions, we proposed its use as input for other spatial modeling exercises, for example, as part of a complex resistance matrix to evaluate ecological connectivity or as criteria to prioritize sectors for restoration in the Colombian Amazon, where it is imperative to consolidate functional networks to prevent isolation between the Amazon and Andes regions.

     

Floodplain lake fish assemblages in the Amazon River: directions in conservation biology

The Neotropical region is renowned for its high biodiversity, and the Amazon River basin contains the highest number of fish species of any river system in the world. In recent years, habitat fragmentation and exploitation of biotic resources have threatened biological integrity and provoked to need for sustainable management and conservation of the Amazon River system. We studied 36 floodplain lakes along 2000 km of the Amazon River. The fish assemblages associated with flood forests are moderately diverse, with low species dominance and reduced populations. To detect nestedness of fish assemblage composition in floodplain lakes, a nested subset analysis was performed on species presence–absence. The incidence matrix (species × lakes) was maximally packed using the Nestedness Temperature Calculator software. The results of ranking lakes and species allow us to establish targets for conservation. Such strategy for sustainable management should be focused on maintaining the Amazonian biodiversity.     

Capillostrongyloides arapaimae sp. n. (Nematoda: Capillariidae), a new intestinal parasite of the arapaima Arapaima gigas from the Brazilian Amazon

A new nematode species, Capillostrongyloides arapaimae sp. n., is described from the intestine and pyloric caeca of the arapaima, Arapaima gigas (Schinz), from the Mexiana Island, Amazon river delta, Brazil. It is characterized mainly by the length of the spicule (779-1,800 microm), the large size of the body (males and gravid females 9.39-21.25 and 13.54-27.70 mm long, respectively) and by the markedly broad caudal lateral lobes in the male. It is the third species of genus Capillostrongyloides reported to parasitize Neotropical freshwater fishes.     

Quaternary population dynamics of an endemic conifer, Picea omorika, and their conservation implications

Serbian spruce, Picea omorika (Pan?.) Purk., is a cold-adapted conifer confined to an area of c. 10,000 km² within the Balkans. This area, which has not been exposed to severe anthropogenic disturbances in the recent past, represents a long-term cryptic refugium of this species. We studied Quaternary dynamics of fragmentary distributed Serbian spruce populations to uncover genetic and demographic processes accounting for high levels of genetic diversities in this endemic species within its long-term cryptic refugium. Based on our data set [499 trees from ten populations, five nuclear microsatellites (EST-SSRs) and a mitochondrial (mtDNA) locus], we found the following: (i) continuous increase of genetic distinctiveness of populations caused by various genetic and/or demographic processes, (ii) decreasing over generations pollen flow, and (iii) almost complete lack of seed flow, are trends applicable not only for post-glacial but also for glacial populations. As a result, populations distant few kilometers or less were poorly connected and highly differentiated (nuclear DNA: average ρ _ST , Hedrick’s G′ _ST and Jost’s D of 0.165, 0.429 and 0.385, respectively; mtDNA: G _ST  = 0.632). They were characterized as independent gene pools at the nuclear DNA level. Nonetheless, levels of genetic diversity were high at both nuclear (average allelic richness = 16.14; average H _E  = 0.776) and mtDNA (H _T  = 0.231) levels. They were maintained not by pronounced gene flow but rather by frequent admixtures of highly differentiated populations, and also by species longevity and overlapping generations in the populations. However, admixtures had been possible only if populations encountered each other over time. Particular genetic and/or demographic changes of populations, such as fragmentations, admixture, size reductions/expansions and extinctions, could not be associated exclusively neither to the post-glacial nor to the last glacial as they were detected during both periods. In accordance with expectations on range alternations in cold-adapted taxa confined to refugia during warm Quaternary periods, our study species was expanding range during the last glacial and contracting range post-glacially. Recommendations for conservation of this IUCN red-listed, endemic and relict species have been provided.