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[Background] In recent years, Next Generation Sequencing (NGS) has accelerated the generation of full mitogenomes, providing abundant material for studying different aspects of molecular evolution. Some mitogenomes have been observed to harbor atypical sequences with bizarre secondary structures, which origins and significance could only be fully understood in an evolutionary framework. ; [Results] Here we report and analyze the mitochondrial sequences and gene arrangements of six closely related spiders in the sister genera Parachtes and Harpactocrates, which belong to the nocturnal, ground dwelling family Dysderidae. Species of both genera have compacted mitogenomes with many overlapping genes and strikingly reduced tRNAs that are among the shortest described within metazoans. Thanks to the conservation of the gene order and the nucleotide identity across close relatives, we were able to predict the secondary structures even on arm-less tRNAs, which would be otherwise unattainable for a single species. They exhibit aberrant secondary structures with the lack of either DHU or TψC arms and many miss-pairings in the acceptor arm but this degeneracy trend goes even further since at least four tRNAs are arm-less in the six spider species studied.[Conclusions] The conservation of at least four arm-less tRNA genes in two sister spider genera for about 30 myr suggest that these genes are still encoding fully functional tRNAs though they may be post-transcriptionally edited to be fully functional as previously described in other species. We suggest that the presence of overlapping and truncated tRNA genes may be related and explains why spider mitogenomes are smaller than those of other invertebrates. ; This work was supported by the Spanish Ministry of Science and Innovation (MICINN) grant CGL2006–08617 (MA) which provided funds to design this study and collection, analysis, and interpretation of data and in writing the manuscript. LBB was also supported by a graduate fellowship (FI-DGR 2009). Further research fellowship support was provided by Sistema Nacional de Investigadores (Agencia Nacional de Investigación e Innovación) and Programa de Desarrollo de las Ciencias Básicas to LBB, and by the Catalan Government through a 2014SGR1604 grant and an ICREA Academia award for excellence in research. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).

There is an increasing demand for databases including species trait information for biodiversity and community ecology studies. The existence of trait databases is useful for comparative studies within taxa or geographical regions, but there is low availability of databases for certain organisms. Here we present an open access functional trait database for spiders from Macaronesia and the Iberian Peninsula, recording several morphological and ecological traits related to the species life histories, microhabitat and trophic preferences. ; Marie Sklodowska-Curie Individual Fellowships (H2020-MSCA-IF-2015706482); ERA-Net Net-Biome research framework (0003/201); Organismo Autonomo de Parques Nacionales Spain (485/2012); Catalan Government (2017SGR83); AZORESBIOPORTAL-PORBIOTA (ACORES-01-0145FEDER-000072); University of Barcelona ; info:eu-repo/semantics/publishedVersion

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies. ; Marie Sklodowska-Curie Individual Fellowships (H2020-MSCA-IF-2015); ERA-Net Net-Biome research framework, financed through Portuguese FCT-NETBIOME grant 0003/2011; ERA-Net Net-Biome financed through Canary Islands Government ACIISI grants SE-12/02, SE-12/03, SE-12/04; FEDER; FCT MACDIV-FCT-PTDC/BIABIC/0054/2014; Organismo Autonomo de Parques Nacionales Spain (OAPN #485/2012); Catalan Government; APIF PhD fellowship from the University of Barcelona; Juan de la Cierva Fellowship (FJCI-2015-23723); FCT-Fundação para a Ciência e a Tecnologia (Norma Transitoria-DL57/2016/CP1375/CT0003); University of Helsinki. ; info:eu-repo/semantics/publishedVersion