Andrés Baselga

A multiple-site similarity measure independent of richness

The Diserud–Ødegaard multiple-site similarity index makes use of data on species shared by two or more sites, but produces equal similarity values in two different circumstances: species loss and true species turnover. We developed a new multiple-site similarity measure, which is independent of richness and performs better than the Diserud–Ødegaard index under conditions of equal richness between sites, because it discriminates between situations in which shared species are distributed evenly among sites or concentrated in few pairs of sites. We conducted several simulations to assess the relative performance of both the indices. The use of the new measure is recommended, enabling the simultaneous analysis of turnover and richness gradients based on two independent measures.

Multiplicative partition of true diversity yields independent alpha and beta components; additive partition does not

The need for a measure of beta diversity independent of alpha diversity was stressed long time ago (Wilson and Shmida 1984), in order to ensure a ‘‘useful application of a measure [of beta diversity] to systems with different alpha diversities.’’ It should be noted that this requirement refers to the independence of beta diversity of mean alpha diversity, and not to the independence of beta diversity with regard to differences in alpha diversity between sites. The latter issue was addressed by several authors (Harrison et al. 1992, Lennon et al. 2001, Koleff et al. 2003, Baselga 2007) because beta diversity measures that are dependent on the variation in alpha diversity consider spatial turnover and nestedness patterns as being equivalent (Baselga et al. 2007). However, the dependence of beta diversity on the mean value of alpha diversity is even more critical because it compromises the comparability of beta diversity Manuscript received 25 February 2009; revised 13 April 2009; accepted 16 April 2009. Corresponding Editor: A. M. Ellison. For reprints of this Forum, see footnote 1, p. 1962. 1 E-mail: andres.baselga@usc.es FORUM 1974 Ecology, Vol. 91, No. 7

Comparing methods to separate components of beta diversity

Summary Two alternative frameworks have been proposed to partition compositional dissimilarity into replacement and nestedness-resultant component or into replacement and richness-difference components. These are, respectively, the BAS (Baselga 2010, Global Ecology and Biogeography, 19, 134–143) and POD (Podani & Schmera 2011. Oikos, 120, 1625–1638) frameworks. We conduct a systematic comparison of parallel components in alternative approaches. We test whether the replacement components derived from the BAS and POD frameworks are independent of richness difference. We also evaluate whether previously reported tests of monotonicity between indices and ecological processes are informative to assess the performance of indices. Finally, we illustrate the consequences of differences between the BAS and POD frameworks using the North American freshwater fish fauna as an empirical example. In the BAS framework, the nestedness-resultant component (βjne or βsne) accounts only for richness differences derived from nested patterns while, in the POD framework, richness-difference dissimilarity (βrich or βrich.s) accounts for all kind of richness differences. Likewise, the replacement components of both alternative methods account for different concepts. Only the replacement component of the BAS framework (βjtu or βsim) is independent of richness difference, while the parallel component in the POD framework (β−3 or β−3.s) is not (i.e. it is mathematically constrained by richness difference). Therefore, only the BAS framework allows separating (i) the variation in species composition derived from species replacement which is independent of richness difference (i.e. not mathematically constrained by it) and (ii) the variation in species composition derived from nested patterns.

Separating the two components of abundance‐based dissimilarity: balanced changes in abundance vs. abundance gradients

Summary Dissimilarity measures can be formulated using matching components that can be defined as the intersection in terms of species composition of both sets (a) and the relative complements of each set (b and c respectively). Previous work has extended these matching components to abundance-based measures of dissimilarity. Using these matching components in terms of species abundances I provide a novel partition separating two components of abundance-based dissimilarity: (i) balanced variation in abundance, whereby the individuals of some species in one site are substituted by the same number of individuals of different species in another site; and (ii) abundance gradients, whereby some individuals are lost from one site to the other. New indices deriving from the additive partition of Bray-Curtis dissimilarity are presented, each one accounting separately for these two antithetic components of assemblage variation. An example comparing the patterns of increase of assemblage dissimilarity with spatial distance in two tropical forests is provided to illustrate the usefulness of the novel partition to discern the different sources of assemblage variation. The widely used Bray-Curtis index of dissimilarity is the result of summing these two sources of dissimilarity, and therefore might consider equivalent patterns that are markedly different. Therefore, the novel partition may be useful to assess biodiversity patterns and to explore their causes, as substitution and loss of individuals are patterns that can derive from completely different processes.

Historical Legacies in World Amphibian Diversity Revealed by the Turnover and Nestedness Components of Beta Diversity

Historic processes are expected to influence present diversity patterns in combination with contemporary environmental factors. We hypothesise that the joint use of beta diversity partitioning methods and a threshold-based approach may help reveal the effect of large-scale historic processes on present biodiversity. We partitioned intra-regional beta diversity into its turnover (differences in composition caused by species replacements) and nestedness-resultant (differences in species composition caused by species losses) components. We used piecewise regressions to show that, for amphibian beta diversity, two different world regions can be distinguished. Below parallel 37, beta diversity is dominated by turnover, while above parallel 37, beta diversity is dominated by nestedness. Notably, these regions are revealed when the piecewise regression method is applied to the relationship between latitude and the difference between the Last Glacial Maximum (LGM) and the present temperature but not when present energy-water factors are analysed. When this threshold effect of historic climatic change is partialled out, current energy-water variables become more relevant to the nestedness-resultant dissimilarity patterns, while mountainous areas are associated with higher spatial turnover. This result suggests that nested patterns are caused by species losses that are determined by physiological constraints, whereas turnover is associated with speciation and/or Pleistocene refugia. Thus, the new threshold-based view may help reveal the role of historic factors in shaping present amphibian beta diversity patterns.

Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels

A correlation of species and genetic diversity has been proposed but not uniformly supported. Large-scale DNA barcoding provides qualitatively novel data to test for correlations across hierarchical levels (genes, genealogies and species), and may help to unveil the underlying processes. Here we analyse sequence variation in communities of aquatic beetles across Europe (>5,000 individuals) to test for self-similarity of beta diversity patterns at multiple hierarchical levels. We show that community similarity at all levels decreases exponentially with geographic distance, and initial similarity is correlated with the lineage age, consistent with a molecular clock. Log-log correlations between lineage age, number of lineages, and range sizes, reveal a fractal geometry in time and space, indicating a spatio-temporal continuum of biodiversity across scales. Simulations show that these findings mirror dispersal-constrained models of haplotype distributions. These novel macroecological patterns may be explained by neutral evolutionary processes, acting continuously over time to produce multi-scale regularities of biodiversity.

Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages

Summary 1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real-world communities; and (iii) a custom set of DNA barcode (cox1-5 0 ) sequences. 3. Species detection against the custom-built reference genomes was very high (>90%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundance 9 body length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance. 4. A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications. 5. The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.

Challenging species distribution models : the case of Maculinea nausithous in the Iberian Peninsula

Maculinea nausithousis the most endangered Iberian butterfly, being included in the Bern and Habitat directives and in the Spanish Red Book for invertebrates. We map its potential distribution in the Iberian Peninsula, identifying potentially suitable areas where to focus future surveys. Using presence/absence data and a set of environmental variables, the distribution of M. nausithous was modelled using Generalized Additive Models. Model results were filtered using land cover data to identify the anthropogenic grasslands inhabited by the species. The model obtained indicates that some Iberian areas that currently do not support M. nausithous populations could be environmentally suitable for the species. The reasons for these absences are discussed. Indeed, field surveys identified possible sources of uncertainty at finer scale, highlighting that deficiencies in land use GIS data might constitute an important source of error, able to explain both commission and omission errors (i.e., over and underpredictions) of the model.

Diversity of Chrysomelidae (Coleoptera) in Galicia, Northwest Spain: estimating the completeness of the regional inventory

The diversity of Chrysomelidae (Coleoptera) in Galicia, Northwest Spain was examined. A long-term sampling was conducted during 1996–2001 and 267 species were collected, but including bibliographic citations a total of 276 species were recorded. As a result of this study the regional inventory has grown from 83 taxa cited before 1998 to the current 276 species. Species accumulation models were used to measure the inventory completeness and estimate the actual species richness of Chrysomelidae occurring in Galicia. Estimates were generated by analyzing both the rarefaction curve from the long-term sampling and the cumulative number of species recorded from Galicia since 1866. Values of total richness predicted by these different methods range between 290 and 323 species. Therefore, it seems that between 85 and 95% of the leaf beetle fauna was recorded and thus the inventory has reached an acceptable level of completeness.

Environmental and geographical determinants of beta diversity of leaf beetles (Coleoptera: Chrysomelidae) in the Iberian Peninsula

Abstract 1. The effect and relative importance of both environmental and geographic factors on species turnover of Chrysomelidae assemblages in the Iberian Peninsula was explored.