Assessing the equilibrium between assemblage composition and climate: A directional distance-decay approach.

The variation of assemblage composition in space is characterised by the decrease in assemblage similarity with spatial distance. Climatic constraint and dispersal limitation are major drivers of distance-decay of similarity. Distance-decay of similarity is usually conceptualised and modelled as an isotropic pattern, that is, assuming that similarity decays with the same rate in all directions. Because climatic gradients are markedly anisotropic, that is, they have different strength in different directions, if species distributions were in equilibrium with climate, the decay of assemblage similarity should be anisotropic in the same direction as the climatic gradient, that is, faster turnover in the direction that maximises the climatic gradient. Thus, deviations from equilibrium between assemblage composition and climatic conditions would result in differences in anisotropy between distance-decay of similarity and climatic gradients. We assessed anisotropy in distance-decay patterns in marine plankton assemblages, terrestrial vertebrates and European beetles, using two procedures: (a) measuring the correlation between the residuals of a distance-decay model and the angle in which pairs of sites are separated and (b) computing two separate distance-decay models for each dataset, one using only pairwise cases that are separated on North-South direction and another one using pairwise cases separated on East-West direction. We also analysed whether the degree of anisotropy in distance-decay is related to dispersal ability (proportion of wingless species and body size) and ecological niche characteristics (main habitat and trophic position) by assessing these relationships among beetle taxonomic groups (n = 21). Anisotropy varied markedly across realms and biological groups. Despite climatic gradients being steeper in North-South direction than in East-West direction in all datasets, North-South distance-decays tended to be steeper than East-West distance-decays in plankton and most vertebrate assemblages, but flatter in European amphibians and most beetle groups. Anisotropy also markedly varied across beetle groups depending on their dispersal ability, as the proportion of wingless species explained 60% of the variance in the difference between North-South and East-West distance-decay slopes. Our results suggest that the degree of equilibrium decreases from marine to terrestrial realms, and is markedly different between vertebrates and beetles. This has profound implications on the expected ability of different groups to track their suitable climates, and thus on the impact of climate change on biodiversity.

The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.

A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.

Climatic niche divergence drives patterns of diversification and richness among mammal families.

A major goal of evolutionary biology is to understand why clades differ dramatically in species richness. A key to this challenge is to uncover the correlates of variation in diversification rate (speciation - extinction) among clades. Here, we explore the relationship between diversification rates and the climatic niches of species and clades among 92 families of terrestrial mammals. We use a time-calibrated molecular phylogeny of mammals and climatic data from 3335 species. We show that considerable variation in net diversification rates among mammal families is explained by niche divergence (59%) and rates of niche change (51%). Diversification rates in turn explain most variation in species richness among families (79%). Contrary to expectations, patterns of diversification are not explained by differences in geographic range areas of clades, nor by their climatic niche position (i.e. whether they are primarily tropical or temperate). Overall, these results suggest that speciation through climatic niche divergence may help drive large-scale patterns of diversification and richness. Our results help explain diversification patterns in a major clade of vertebrates, and suggest that similar underlying principles may explain the diversification of many terrestrial clades.

Rare failures of DNA barcodes [corrected] to separate morphologically distinct species in a biodiversity survey of Iberian leaf beetles.

During a survey of genetic and species diversity patterns of leaf beetle (Coleoptera: Chrysomelidae) assemblages across the Iberian Peninsula we found a broad congruence between morphologically delimited species and variation in the cytochrome oxidase (cox1) gene. However, one species pair each in the genera Longitarsus Berthold and Pachybrachis Chevrolat was inseparable using molecular methods, whereas diagnostic morphological characters (including male or female genitalia) unequivocally separated the named species. Parsimony haplotype networks and maximum likelihood trees built from cox1 showed high genetic structure within each species pair, but no correlation with the morphological types and neither with geographic distributions. This contrasted with all analysed congeneric species, which were recovered as monophyletic. A limited number of specimens were sequenced for the nuclear 18S rRNA gene, which showed no or very limited variation within the species pair and no separation of morphological types. These results suggest that processes of lineage sorting for either group are lagging behind the clear morphological and presumably reproductive separation. In the Iberian chrysomelids, incongruence between DNA-based and morphological delimitations is a rare exception, but the discovery of these species pairs may be useful as an evolutionary model for studying the process of speciation in this ecological and geographical setting. In addition, the study of biodiversity patterns based on DNA requires an evolutionary understanding of these incongruences and their potential causes.

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.

The European reference condition concept: A scientific and technical approach to identify minimally-impacted river ecosystems.

One objective of the European Union (EU)'s Water Framework Directive (WFD: Directive 2000/60/EC) is for all European surface waters to achieve 'good status' by 2015. In support of this objective, the EU has facilitated an intercalibration exercise to ensure harmonized definitions of the status of water bodies, reflecting the deviation of their properties (mainly biotic assemblages) from a minimally disturbed state, termed the "reference condition". One of the major challenges of the WFD has been to find common approaches for defining reference conditions and to define the level of anthropogenic intervention allowed in reference sites. In this paper we describe how river reference sites were selected in the Central-Baltic region of Europe. A list of pressure criteria was provided and 14 Member States (MSs) categorized each criterion according to the method (i.e. measured, field inspection, etc.) used for reference site screening. Additionally, reference land-use and water-chemistry thresholds were agreed among countries in order to base reference site selection on objective criteria. For land-use criteria, a reference threshold and a rejection threshold were established. Sites with all criteria below the reference threshold were considered to be reference sites; sites having most criteria below the reference threshold and only some parameters between the reference and rejection threshold were "possible reference sites". These sites were retained only after carefully checking the cumulative effects of the pressures using local expertise, and a posteriori water-chemistry evaluation was necessary. In general, the most widespread method for defining a reference site was the measurement of pressures, followed by field inspections and expert judgment. However, some major pressures (e.g. hydromorphological alteration) were evaluated in a number of different ways (e.g. measured, field inspection, expert judgment). Our meta-analyses reveal a need to reinforce standardization in the application of pressure criteria by Member States. The pressure criteria identified in this exercise should be refined and tested with biological data to help in the further validation of minimally disturbed sites (i.e. the WFD "reference condition") and to provide a firm foundation for ecological status assessment. This in turn would ensure that there is pan-European comparability when evaluating the achievement of environmental objectives.

Spatial network structure and amphibian persistence in stochastic environments.

In the past few years, the framework of complex networks has provided new insight into the organization and function of biological systems. However, in spite of its potential, spatial ecology has not yet fully incorporated tools and concepts from network theory. In the present study, we identify a large spatial network of temporary ponds, which are used as breeding sites by several amphibian species. We investigate how the structural properties of the spatial network change as a function of the amphibian dispersal distance and the hydric conditions. Our measures of network topology suggest that the observed spatial structure of ponds is robust to drought (compared with similar random structures), allowing the movement of amphibians to and between flooded ponds, and hence, increasing the probability of reproduction even in dry seasons.