A new procedure to optimize the selection of groups in a classification tree

Agglomerative cluster analyses encompass many techniques, which have been widely used in various fields of science. In biology, and specifically ecology, datasets are generally highly variable and may contain outliers, which increase the difficulty to identify the number of clusters. Here we present a new criterion to determine statistically the optimal level of partition in a classification tree. The criterion robustness is tested against perturbated data (outliers) using an observation or variable with values randomly generated. The technique, called Random Simulation Test (RST), is tested on (1) the well-known Iris dataset [Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Ann. Eugenic. 7, 179–188], (2) simulated data with predetermined numbers of clusters following Milligan and Cooper [Milligan, G.W., Cooper, M.C., 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159–179] and finally (3) is applied on real copepod communities data previously analyzed in Beaugrand et al. [Beaugrand, G., Ibanez, F., Lindley, J.A., Reid, P.C., 2002. Diversity of calanoid copepods in the North Atlantic and adjacent seas: species associations and biogeography. Mar. Ecol. Prog. Ser. 232, 179–195]. The technique is compared to several standard techniques. RST performed generally better than existing algorithms on simulated data and proved to be especially efficient with highly variable datasets.

The Importance of Regional, System-Wide and Local Spatial Scales in Structuring Temperate Estuarine Fish Communities

An extensive literature base worldwide demonstrates how spatial differences in estuarine fish assemblages are related to those in the environment at (bio)regional, estuary-wide or local (within-estuary) scales. Few studies, however, have examined all three scales, and those including more than one have often focused at the level of individual environmental variables rather than scales as a whole. This study has identified those spatial scales of environmental differences, across regional, estuary-wide and local levels, that are most important in structuring ichthyofaunal composition throughout south-western Australian estuaries. It is the first to adopt this approach for temperate microtidal waters. To achieve this, we have employed a novel approach to the BIOENV routine in PRIMER v6 and a modified global BEST test in an alpha version of PRIMER v7. A combination of all three scales best matched the pattern of ichthyofaunal differences across the study area (rho = 0.59; P = 0.001), with estuary-wide and regional scales accounting for about twice the variability of local scales. A shade plot analysis showed these broader-scale ichthyofaunal differences were driven by a greater diversity of marine and estuarine species in the permanently-open west coast estuaries and higher numbers of several small estuarine species in the periodically-open south coast estuaries. When interaction effects were explored, strong but contrasting influences of local environmental scales were revealed within each region and estuary type. A quantitative decision tree for predicting the fish fauna at any nearshore estuarine site in south-western Australia has also been produced. The estuarine management implications of the above findings are highlighted.

Microfaunal communities associated with epiphytic lichens in Belfast

The composition and richness of the microfauna on lime trees was surveyed in relation to the distribution and cover of lichens in Belfast. Parameters used to help interpret the results included distance from the city centre and available data on air quality. The percentage epiphyte cover on the trunks of lime trees was significantly correlated with distance from the city centre whereas that on tree bases as not. In contrast, the number of microfaunal species revealed strong positive correlations with distance for both the bases and the trunks of trees. Most of this increase in microfaunal species richness towards rural areas was due to protistans which are thus proposed as useful bioindicators of air pollution. The total species richness of fauna showed slight negative correlation with smoke but not SO2 levels.

Interchange of entire communities: microbial community coalescence

Microbial communities are enigmatically diverse. We propose a novel view of processes likely affecting microbial assemblages, which could be viewed as the Great American Interchange en miniature: the wholesale exchange among microbial communities resulting from moving pieces of the environment containing entire assemblages. Incidental evidence for such ‘community coalescence’ is accumulating, but such processes are rarely studied, likely because of the absence of suitable terminology or a conceptual framework. We provide the nucleus for such a conceptual foundation for the study of community coalescence, examining factors shaping these events, links to bodies of ecological theory, and we suggest modeling approaches for understanding coalescent communities. We argue for the systematic study of community coalescence because of important functional and applied consequences.

Effects of climate and land management changes on conservation : of mediterranean cork oak woodlands and their bird communities

Tese de doutoramento (co-tutela), Biologia (Biologia da Conservação), Faculdade de Ciências da Universidade de Lisboa, University of East Anglia, School of Environmental Sciences, 2014

Impact of a drier Early-Mid-Holocene climate upon Amazonian forests

This paper uses a palaeoecological approach to examine the impact of drier climatic conditions of the Early-Mid-Holocene (ca 8000-4000 years ago) upon Amazonia's forests and their fire regimes. Palaeovegetation (pollen data) and palaeofire (charcoal) records are synthesized from 20 sites within the present tropical forest biome, and the underlying causes of any emergent patterns or changes are explored by reference to independent palaeoclimate data and present-day patterns of precipitation, forest cover and fire activity across Amazonia. During the Early-Mid-Holocene, Andean cloud forest taxa were replaced by lowland tree taxa as the cloud base rose while lowland ecotonal areas, which are presently covered by evergreen rainforest, were instead dominated by savannahs and/or semi-deciduous dry forests. Elsewhere in the Amazon Basin there is considerable spatial and temporal variation in patterns of vegetation disturbance and fire, which probably reflects the complex heterogeneous patterns in precipitation and seasonality across the basin, and the interactions between climate change, drought- and fire susceptibility of the forests, and Palaeo-Indian land use. Our analysis shows that the forest biome in most parts of Amazonia appears to have been remarkably resilient to climatic conditions significantly drier than those of today, despite widespread evidence of forest burning. Only in ecotonal areas is there evidence of biome replacement in the Holocene. From this palaeoecological perspective, we argue against the Amazon forest 'dieback' scenario simulated for the future.

Quantitative estimates of glacial and Holocene temperature and precipitation change in lowland Amazonian Bolivia

Quantitative estimates of temperature and precipitation change during the late Pleistocene and Holocene have been difficult to obtain for much of the lowland Neotropics. Using two published lacustrine pollen records and a climate-vegetation model based on the modern abundance distributions of 154 Neotropical plant families, we demonstrate how family-level counts of fossil pollen can be used to quantitatively reconstruct tropical paleoclimate and provide needed information on historic patterns of climatic change. With this family-level analysis, we show that one area of the lowland tropics, northeastern Bolivia, experienced cooling (1–3 °C) and drying (400 mm/yr), relative to present, during the late Pleistocene (50,000–12,000 calendar years before present [cal. yr B.P.]). Immediately prior to the Last Glacial Maximum (LGM, ca. 21,000 cal. yr B.P.), we observe a distinct transition from cooler temperatures and variable precipitation to a period of warmer temperatures and relative dryness that extends to the middle Holocene (5000–3000 cal. yr B.P.). This prolonged reduction in precipitation occurs against the backdrop of increasing atmospheric CO2 concentrations, indicating that the presence of mixed savanna and dry-forest communities in northeastern Bolivia durng the LGM was not solely the result of low CO2 levels, as suggested previously, but also lower precipitation. The results of our analysis demonstrate the potential for using the distribution and abundance structure of modern Neotropical plant families to infer paleoclimate from the fossil pollen record.

Struggles over family land? Tree crops, land and labour in Ghana's Brong-Ahafo region

Agricultural land use in much of Brong-Ahafo region, Ghana has been shifting from the production of food crops towards increased cashew nut cultivation in recent years. This article explores everyday, less visible, gendered and generational struggles over family farms in West Africa, based on qualitative, participatory research in a rural community that is becoming increasingly integrated into the global capitalist system. As a tree crop, cashew was regarded as an individual man's property to be passed on to his wife and children rather than to extended family members, which differed from the communal land tenure arrangements governing food crop cultivation. The tendency for land, cash crops and income to be controlled by men, despite women's and young people's significant labour contributions to family farms, and for women to rely on food crop production for their main source of income and for household food security, means that women and girls are more likely to lose out when cashew plantations are expanded to the detriment of land for food crops. Intergenerational tensions emerged when young people felt that their parents and elders were neglecting their views and concerns. The research provides important insights into gendered and generational power relations regarding land access, property rights and intra-household decision-making processes. Greater dialogue between genders and generations may help to tackle unequal power relations and lead to shared decision-making processes that build the resilience of rural communities.

Inter-plant communication through mycorrhizal networks mediates complex adaptive behaviour in plant communities

Adaptive behaviour of plants, including rapid changes in physiology, gene regulation and defence response, can be altered when linked to neighbouring plants by a mycorrhizal network (MN). Mechanisms underlying the behavioural changes include mycorrhizal fungal colonization by the MN or interplant communication via transfer of nutrients, defence signals or allelochemicals. We focus this review on our new findings in ectomycorrhizal ecosystems, and also review recent advances in arbuscular mycorrhizal systems. We have found that the behavioural changes in ectomycorrhizal plants depend on environmental cues, the identity of the plant neighbour and the characteristics of the MN. The hierarchical integration of this phenomenon with other biological networks at broader scales in forest ecosystems, and the consequences we have observed when it is interrupted, indicate that underground ‘tree talk’ is a foundational process in the complex adaptive nature of forest ecosystems.

Host and habitat filtering in seedling root-associated fungal communities: taxonomic and functional diversity are altered in ‘novel’ soils

Climatic and land use changes have significant consequences for the distribution of tree species, both through natural dispersal processes and following management prescriptions. Responses to these changes will be expressed most strongly in seedlings near current species range boundaries. In northern temperate forest ecosystems, where changes are already being observed, ectomycorrhizal fungi contribute significantly to successful tree establishment. We hypothesised that communities of fungal symbionts might therefore play a role in facilitating, or limiting, host seedling range expansion. To test this hypothesis, ectomycorrhizal communities of interior Douglas-fir and interior lodgepole pine seedlings were analysed in a common greenhouse environment following growth in five soils collected along an ecosystem gradient. Currently, Douglas-fir’s natural distribution encompasses three of the five soils, whereas lodgepole pine’s extends much further north. Host filtering was evident amongst the 29 fungal species encountered: 7 were shared, 9 exclusive to Douglas-fir and 13 exclusive to lodgepole pine. Seedlings of both host species formed symbioses with each soil fungal community, thus Douglas-fir did so even where those soils came from outside its current distribution. However, these latter communities displayed significant taxonomic and functional differences to those found within the host distribution, indicative of habitat filtering. In contrast, lodgepole pine fungal communities displayed high functional similarity across the soil gradient. Taxonomic and/or functional shifts in Douglas-fir fungal communities may prove ecologically significant during the predicted northward migration of this species; especially in combination with changes in climate and management operations, such as seed transfer across geographical regions for forestry purposes.

Nutrition in Transition: Dietary Patterns of Rural Amazonian Women During a Period of Economic Change

Objectives: The goal of this study was to understand the relationship between economic change (wage labor, retirement, and the Bolsa Familia program) and dietary patterns in the rural Amazon and to determine the extent to which these changes followed the pattern of the nutrition transition. Methods: The study was longitudinal. The weighed-inventory method and economic interviews were used to collect data on dietary intake and household economics in a sample of 30 and 52 women in 2002 and 2009, respectively. Twenty of the women participated in both years and make-up the longitudinal sub-sample. Comparative statistics were used to identify changes in dietary patterns over time and multiple linear regressions were used to explore the relationship between economics, subsistence strategies, and diet. Results: There was a significant decline in kcal (P < 0.01) and carbohydrate (P < 0.01) but no change in protein intake over time in both the larger and smaller, longitudinal subsample. The percent of energy, carbohydrate, protein, and fat purchased increased in the larger and longitudinal samples (P <= 0.02) and there was an increase in refined carbohydrate and processed, fatty-meat consumption over time. The abandonment of manioc gardens was associated with increased dependence on purchased food (P = 0.03) while receipt of the Bolsa Familia was associated with increased protein intake and adequacy (P = 0.02). Conclusions: The dietary changes observed are only in partial agreement with predictions of the nutrition transition literature. The relationship between the economic and diet changes was shaped by the local context which should be considered when implementing CCT programs, like the Bolsa Familia. Am. J. Hum. Biol. 23:458-469, 2011. (C) 2011 Wiley-Liss, Inc.

A Plant Needs Ants like a Dog Needs Fleas: Myrmelachista schumanni Ants Gall Many Tree Species to Create Housing

Hundreds of tropical plant species house ant colonies in specialized chambers called domatia. When, in 1873, Richard Spruce likened plant-ants to fleas and asserted that domatia are ant-created galls, he incited a debate that lasted almost a century. Although we now know that domatia are not galls and that most ant-plant interactions are mutualisms and not parasitisms, we revisit Spruce`s suggestion that ants can gall in light of our observations of the plant-ant Myrmelachista schumanni, which creates clearings in the Amazonian rain forest called ""supay-chakras,"" or ""devil`s gardens."" We observed swollen scars on the trunks of nonmyrmecophytic canopy trees surrounding supay-chakras, and within these swellings, we found networks of cavities inhabited by M. schumanni. Here, we summarize the evidence supporting the hypothesis that M. schumanni ants make these galls, and we hypothesize that the adaptive benefit of galling is to increase the amount of nesting space available to M. schumanni colonies.

Malaria on the Amazonian frontier: Transmission dynamics, risk factors, spatial distribution, and prospects for control

Little follow-up data on malaria transmission in communities originating from frontier settlements in Amazonia are available. Here we describe a cohort study in a frontier settlement in Acre, Brazil, where 509 subjects contributed 489.7 person-years of follow-up. The association between malaria morbidity during the follow-up and individual, household, and spatial covariates was explored with mixed-effects logistic regression models and spatial analysis. Incidence rates for Plasmodium vivax and Plasmodium falciparum malaria were 30.0/100 and 16.3/100 person-years at risk, respectively. Malaria morbidity was strongly associated with land clearing and farming, and decreased after five years of residence in the area, suggesting that clinical immunity develops among subjects exposed to low malaria endemicity. Significant spatial clustering of malaria was observed in the areas of most recent occupation, indicating that the continuous influx of nonimmune settlers to forest-fringe areas perpetuates the cycle of environmental change and colonization that favors malaria transmission in rural Amazonia.