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ABSTRACT The Importance of the Regional Species PoolThe regional species pool—the set of species capable of entering a local community—is a foundational concept for understanding ecological processes that occur between local and extensive (biogeographic) spatial scales. However, the lack of precise definitions for the regional species pool, coupled with limited research into the dynamics of regional biodiversity, has impeded the development of a comprehensive framework to explain the mechanisms shaping these pools. Processes Governing Regional Species PoolsAlthough ecological processes at local and extensive scales are relatively well understood, the mechanisms shaping regional biota remain less clear. Regional species pools are likely shaped by a unique set of processes that often overlap minimally with those operating at local or extensive scales. Despite their significance, our understanding of the specific mechanisms driving the dynamics of regional species pools remains incomplete. The Need for a Theory of Regional Species PoolsWe argue that it is essential to prioritise the study of the regional species pool for two reasons. First, the regional species pool bridges spatial and temporal scales from ecological dynamics in landscapes to the long‐term processes shaping the biotas of entire biogeographic provinces. As such, understanding the dynamics of species pools addresses fundamental questions about the origin, maintenance, and dynamics of biodiversity. Second, effective biodiversity conservation in the Anthropocene hinges on understanding the processes that operate at regional scales. 

Abstract BackgroundIn light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). FindingsUsing a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. ConclusionsSequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities. 

Abstract The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the presence of these evolutionary processes in the Hawaiian spiny‐legTetragnathaadaptive radiation, which includes four microhabitat‐specialists or ecomorphs, with different body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). We investigated the evolutionary history of this radiation using 76 newly generated low‐coverage, whole‐genome resequenced samples, along with phylogenetic and population genomic tools. Considering the Green ecomorph as the ancestral state, our results suggest that the Green ecomorph likely re‐evolved once, the Large Brown and Maroon ecomorphs evolved twice and the Small Brown evolved three times. We found that the evolution of the Maroon and Small Brown ecomorphs likely involved ancestral hybridization events, while the Green and Large Brown ecomorphs likely evolved through novel mutations, despite a high rate of incomplete lineage sorting in the dataset. Our findings demonstrate that the repeated evolution of ecomorphs in the Hawaiian spiny‐legTetragnathais influenced by multiple evolutionary processes.