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.

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.

Summary1. 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.

Aim Large‐scale DNA barcoding allows the simultaneous assessment of variation in community composition at species level and below. We here propose that the patterns emerging across multiple hierarchical levels can be used to discern the effects of neutral and non‐neutral macroecological processes, which otherwise have proven difficult to separate. Location Iberian Peninsula. Methods We performed cox1 barcoding on 20 complete assemblages of leaf beetles for 4533 individuals of 203 species. The neutrality of cox1 sequence evolution was tested using Tajima's test. Haplotypes (n = 2020) were grouped into nested n‐step networks of up to five intraspecific hierarchical levels. We then assessed whether the spatial variation in assemblage composition at all hierarchical levels from haplotype to species was self‐similar (fractal) and predictable from level to level. Results Tajima's test on a subset of widely sampled species (n = 136) was consistent with neutral evolution in 83% of the species, but only 3% of cases exhibited balancing selection. Multiple hierarchical levels representing haplotype genealogies of various ages showed a similar rate of distance decay of assemblage similarity. In addition, we found strong log‐log correlations between hierarchical level (lineage age) and number of lineages, lineage range size and assemblage similarity. Similarity at the species level was strongly correlated to similarity at the haplotype level for the whole assemblage (r2 = 0.75) or for within‐species haplotype similarity (mean r2 = 0.17, SE = 0.03). Main conclusions These findings suggest great regularities in the pattern of assemblage variation at all lineage ages that are best explained by the enduring action of stochastic (neutral) processes of mutation and dispersal. The multi‐hierarchical analysis therefore bridges predictions of the neutral theory of molecular evolution and the neutral theory of biodiversity. Neutral processes thus emerge as a unifying principle of ecology and evolution, which has deep implications in biodiversity assessment and conservation.