Hanna Tuomisto

Dissecting amazonian biodiversity.

Biogeographical and biodiversity studies in Iowland Amazonian rain forests typically refer to observed or postulated distribution barriers such as past unfavorable climates, mountains, rivers, and river floodplains that divide the uniform tierra firme (noninundated) forest. Present-day ecological heterogeneity within tierra firme has hardly been discussed in this context, although edaphic differences are known to affect species distribution patterns in both inundated areas and tierra firme. Quantification of landscape heterogeneity in Peruvian Iowland Amazonia (500,000 kilometers squared), based on field studies and satellite image analysis, shows that Peruvian Amazonia is considerably more heterogeneous than previously reported. These observations have implications for the research, management, and conservation of Amazonian biodiversity.

ANALYZING OR EXPLAINING BETA DIVERSITY? UNDERSTANDING THE TARGETS OF DIFFERENT METHODS OF ANALYSIS

It has been actively discussed recently what statistical methods are appropriate when one is interested in testing hypotheses about the origin of beta diversity, especially whether one should use the raw-data approach (e.g., canonical analysis such as RDA and CCA) or the distance approach (e.g., Mantel test and multiple regression on distance matrices). Most of the confusion seems to stem from uncertainty as to what is the response variable in the different approaches. Here our aim is to clarify this issue. We also show that, although both the raw-data approach and the distance approach can often be used to address the same ecological hypothesis, they target fundamentally different predictions of those hypotheses. As the two approaches shed light on different aspects of the ecological hypotheses, they should be viewed as complementary rather than alternative ways of analyzing data. However, in some cases only one of the approaches may be appropriate. We argue that S. P. Hubbells neutral theory can only be tested using the distance approach, because its testable predictions are stated in terms of distances, not in terms of raw data. In all cases, the decision on which method is chosen must be based on which addresses the question at hand, it cannot be based on which provides the highest proportion of explained variance in simulation studies.

A consistent terminology for quantifying species diversity? Yes, it does exist

The prevailing terminological confusion around the concept ‘diversity’ has hampered accurate communication and caused diversity issues to appear unnecessarily complicated. In fact, a consistent terminology for phenomena related to (species) diversity is already available. When this terminology is adhered to, diversity emerges as an easily understood concept. It is important to differentiate between diversity itself and a diversity index: an index of something is just a surrogate for the thing itself. The conceptual problem of defining diversity also has to be separated from the practical problem of deciding how to adequately quantify diversity for a community of interest. In practice, diversity can be quantified for any dataset where units of observation (such as individuals) have been classified into types (such as species). All that needs to be known is what proportion of the observed units belong to a type of mean abundance. Diversity equals the inverse of this mean, and it quantifies the effective number of the types of interest. In ecology, interest often (but not always) focuses on species diversity. If the dataset consists of (or gets divided into) subunits, then the total effective number of species (gamma diversity) can be partitioned into the effective number of compositionally distinct subunits (beta diversity) and the mean effective number of species per such subunit (alpha diversity). Species richness is related to species diversity, but they are not the same thing; richness does not take the proportional abundances into account and is therefore the actual—rather than the effective—number of types. Most of the phenomena that have been called ‘beta diversity’ in the past do not quantify an effective number of types, so they should be referred to by names other than ‘diversity’ (for example, species turnover or differentiation).

LINKING FLORISTIC PATTERNS WITH SOIL HETEROGENEITY AND SATELLITE IMAGERY IN ECUADORIAN AMAZONIA

Florisitic ground surveys in tropical rain forests are laborious and time consuming, so we tested to what degree reflectance differences visible in Landsat Thematic Mapper (TM) satellite images can be used to predict differences in florisitic composition and species richness among rain forest sites. To gain ecological understanding of the rain forest ecosystem, we also tested to what extent variation in these vegetation characteristics can be explained by edaphic site conditions. The study was conducted in a relatively homogeneous area of Amazonian rain forest in Yasuni National Park, Ecuador. We established 27 transects of 5 m × 500 m within an area of ∼20 km × 25 km to study edaphic and floristic patterns mainly within the tierra firme (non-inundated) forest. In each transect, soil samples were collected for chemical and textural analyses, and the abundance of each species belonging to two understory plant groups, pteridophytes (ferns and fern allies) and the Melastomataceae, was assessed. Floristic similarity between transect pairs varied widely and ranged from almost no overlap in species composition to very high overlap. The among-transect floristic similarity patterns of the two plant groups were strongly correlated with each other no matter whether presence–absence or abundance data were used. The floristic similarity patterns were also strongly correlated with the similarity in pixel values of the infrared bands in the Landsat TM satellite image and with the similarity in most of the measured soil variables. Similarity in species richness, on the contrary, was neither correlated with similarity in pixel values nor with similarity in most of the soil variables. We conclude that reflectance patterns in satellite images can be efficiently used to predict landscape-scale floristic and edaphic patterns in tierra firme rain forest. Predicting patterns in species richness, on the other hand, is not possible in the same straightforward manner. These results have important practical implications for land use and conservation planning as well as for ecological and biodiversity research. Corresponding Editor: C. A. Wessman.

Distribution of Pteridophyta and Melastomataceae along an edaphic gradient in an Amazonian rain forest

Abstract. Pteridophyta and Melastomataceae were studied in an area of non-flooded (tierra firme) rain forest in Peruvian Amazonia, close to the village of Mishana (River Nanay, in the vicinity of Iquitos City). The general objective of the study was to establish a method for rapidly documenting changes in the floristic composition among and within rain forests in geologically different areas. More specifically, the changes in the plant communities were documented along an edaphic and topographic gradient from clay soil on level ground to quartzitic sand on a hill top. Two 5-m-wide, parallel transects were established 50 m apart. A total of 40 species of pteridophytes were found; 18 of these were confined to clayey soil and 11 to sandy soil. The total number of Melastomataceae on the transects was 22, and 14 of these were confined to clayey soil while only two were confined to sandy soil. Further differences in the abundance of many species correlated with drainage conditions and the accumulation of organic matter on the soil surface. Cluster analyses were made using both edaphic and floristic criteria, and in all cases the transects could be divided into distinct sections. Both transects gave rather similar results, and therefore it was concluded that the chosen transect width was sufficient to document the prevalent floristic patterns.

A community-derived classification for extant lycophytes and ferns

Phylogeny has long informed pteridophyte classification. As our ability to infer evolutionary trees has improved, classifications aimed at recognizing natural groups have become increasingly predictive and stable. Here, we provide a modern, comprehensive classification for lycophytes and ferns, down to the genus level, utilizing a community‐based approach. We use monophyly as the primary criterion for the recognition of taxa, but also aim to preserve existing taxa and circumscriptions that are both widely accepted and consistent with our understanding of pteridophyte phylogeny. In total, this classification treats an estimated 11 916 species in 337 genera, 51 families, 14 orders, and two classes. This classification is not intended as the final word on lycophyte and fern taxonomy, but rather a summary statement of current hypotheses, derived from the best available data and shaped by those most familiar with the plants in question. We hope that it will serve as a resource for those wanting references to the recent literature on pteridophyte phylogeny and classification, a framework for guiding future investigations, and a stimulus to further discourse.

USE OF MELASTOMATACEAE AND PTERIDOPHYTES FOR REVEALING PHYTOGEOGRAPHICAL PATTERNS IN AMAZONIAN RAIN FORESTS

Similarities and differences among eight upland rain forest sites in Peruvian Amazonia were measured separately by using Melastomataceae, pteridophyte and tree species compositions and edaphic characteristics of the sites. All three plant groups showed a similar pattern among the sites, and this pattern could be explained by edaphic differences but not by geographical distances among the sites. The explicability of site-specific edaphic characteristics on the basis of geological history is discussed. The results suggest that both pteridophytes and Melastomataceae can be used as indicators of floristically different rain forest types that are edaphically defined. Distribution patterns of these plant groups can be studied much more rapidly than the patterns of trees and therefore both Melastomataceae and pteridophytes may be used in large scale phytogeographical studies that are urgently needed in the face of rapidly advancing deforestation.

Geological control of floristic composition in Amazonian forests

Aim Conservation and land-use planning require accurate maps of patterns in species composition and an understanding of the factors that control them. Substantial doubt exists, however, about the existence and determinants of large-area floristic divisions in Amazonia. Here we ask whether Amazonian forests are partitioned into broad-scale floristic units on the basis of geological formations and their edaphic properties. Location Western and central Amazonia. Methods We used Landsat imagery and Shuttle Radar Topography Mission (SRTM) digital elevation data to identify a possible floristic and geological discontinuity of over 300 km in northern Peru. We then used plant inventories and soil sampling to document changes in species composition and soil properties across this boundary. Data were obtained from 138 sites distributed along more than 450 km of road and river. On the basis of our findings, we used broad-scale Landsat and SRTM mosaics to identify similar patterns across western and central Amazonia. Results The discontinuity identified in Landsat and SRTM data corresponded to a 15-fold change in soil cation concentrations and an almost total change in plant species composition. This discontinuity appears to be caused by the widespread removal of cation-poor surface sediments by river incision to expose cation-rich sediments beneath. Examination of broad-scale Landsat and SRTM mosaics indicated that equivalent processes have generated a north–south discontinuity of over 1500 km in western Brazil. Due to similarities with our study area, we suggest that this discontinuity represents a chemical and ecological limit between western and central Amazonia. Main conclusions Our findings suggest that Amazonian forests are partitioned into large-area units on the basis of geological formations and their edaphic properties. The evolution of these units through geological time may provide a general mechanism for biotic diversification in Amazonia. These compositional units, moreover, may correspond to broad-scale functional units. The existence of large-area compositional and functional units would suggest that protected-area, carbon sequestration, and other land-use strategies in Amazonia be implemented on a region-by-region basis. The methods described here can be used to map these patterns, and thus enable effective conservation and management of Amazonian forests.

The role of ecological knowledge in explaining biogeography and biodiversity in Amazonia

Biogeographical studies in Amazonia have commonly taken a historical, rather than an ecological approach. General patterns have been sought in the distribution maps of different species, and these have been explained in terms of past or present distribution barriers, especially past climates and large rivers. Implicitly, and often also explicitly, it is assumed that Amazonia is ecologically so uniform that present-day ecological conditions are rather insignificant in determining species distribution patterns and speciation. However, this assumption is more based on the lack of relevant data than on actual observations of environmental uniformity or ecological unspecialization of the species. Recent studies have indeed documented ecological heterogeneity and floristic differences among sites that were previously thought similar. In the absence of direct knowledge of the past, more complete ecological and environmental understanding of the present-day Amazonia are needed for evaluating the relative roles of historical and ecological factors in Amazonian biogeography and biodiversity.

Commentary: do we have a consistent terminology for species diversity? Yes, if we choose to use it

Meaningful quantification of species diversity requires that both ‘species’ and ‘diversity’ are unambiguously defined. Rigorous rules of nomenclature exist to ensure that each species has a single unique name, but the naming of concepts is much more variable. As a consequence, ‘diversity’ has been defined in so many different ways that its ability to transfer accurate information has been compromised. This problem can be solved by defining ‘diversity’ as the effective number of species (or other types of interest), and using the term ‘true diversity’ to specify that this narrow concept is being used (analogously to using the term ‘true bugs’ when adhering to a narrow circumscription of ‘bugs’). Other measures related to diversity (such as entropies and probabilities) continue to be useful, but they represent different phenomena and should therefore be referred to by different names. Total species diversity in a dataset can be partitioned into two components in several different ways. The components of a specific multiplicative partitioning can be called true alpha diversity and true beta diversity. When the partitioning is done in some other way, the resulting components are different and should be called by other names. For example, the beta component of additive partitioning does not equal true beta diversity, but can logically be called species turnover. All the phenomena that have been called ‘beta diversity’ in the ecological literature have also been called by alternative unique names. Consequently, a consistent terminology is already available; only a general agreement to use it is lacking.