MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species

Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils

Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.

Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest

Soils harbour a rich arthropod fauna, but many species are still not formally described (Linnaean shortfall) and the distribution of those already described is poorly understood (Wallacean shortfall). Metabarcoding holds much promise to fill this gap, however, nuclear copies of mitochondrial genes, and other artefacts lead to taxonomic inflation, which compromise the reliability of biodiversity inventories. Here, we explore the potential of a bioinformatic approach to jointly "denoise" and filter nonauthentic mitochondrial sequences from metabarcode reads to obtain reliable soil beetle inventories and address open questions in soil biodiversity research, such as the scale of dispersal constraints in different soil layers. We sampled cloud forest arthropod communities from 49 sites in the Anaga peninsula of Tenerife (Canary Islands). We performed whole organism community DNA (wocDNA) metabarcoding, and built a local reference database with COI barcode sequences of 310 species of Coleoptera for filtering reads and the identification of metabarcoded species. This resulted in reliable haplotype data after considerably reducing nuclear mitochondrial copies and other artefacts. Comparing our results with previous beetle inventories, we found: (i) new species records, potentially representing undescribed species; (ii) new distribution records, and (iii) validated phylogeographic structure when compared with traditional sequencing approaches. Analyses also revealed evidence for higher dispersal constraint within deeper soil beetle communities, compared to those closer to the surface. The combined power of barcoding and metabarcoding contribute to mitigate the important shortfalls associated with soil arthropod diversity data, and thus address unresolved questions for this vast biodiversity fraction.

Richness and resilience in the Pacific: DNA metabarcoding enables parallelized evaluation of biogeographic patterns

Islands make up a large proportion of Earth's biodiversity, yet are also some of the most sensitive systems to environmental perturbation. Biogeographic theory predicts that geologic age, area, and isolation typically drive islands' diversity patterns, and thus potentially impact non-native spread and community homogenization across island systems. One limitation in testing such predictions has been the difficulty of performing comprehensive inventories of island biotas and distinguishing native from introduced taxa. Here, we use DNA metabarcoding and statistical modelling as a high throughput method to survey community-wide arthropod richness, the proportion of native and non-native species, and the incursion of non-natives into primary habitats on three archipelagos in the Pacific - the Ryukyus, the Marianas and Hawaii - which vary in age, isolation and area. Diversity patterns largely match expectations based on island biogeography theory, with the oldest and most geographically connected archipelago, the Ryukyus, showing the highest taxonomic richness and lowest proportion of introduced species. Moreover, we find evidence that forest habitats are more resilient to incursions of non-natives in the Ryukyus than in the less taxonomically rich archipelagos. Surprisingly, we do not find evidence for biotic homogenization across these three archipelagos: the assemblage of non-native species on each island is highly distinct. Our study demonstrates the potential of DNA metabarcoding to facilitate rapid estimation of biogeographic patterns, the spread of non-native species, and the resilience of ecosystems.

Indigenous and introduced Collembola differ in desiccation resistance but not its plasticity in response to temperature

Biological invasions have significant ecological and economic impacts. Much attention is therefore focussed on predicting establishment and invasion success. Trait-based approaches are showing much promise, but are mostly restricted to investigations of plants. Although the application of these approaches to animals is growing rapidly, it is rare for arthropods and restricted mostly to investigations of thermal tolerance. Here we study the extent to which desiccation tolerance and its phenotypic plasticity differ between introduced (nine species) and indigenous (seven species) Collembola, specifically testing predictions of the 'ideal weed' and 'phenotypic plasticity' hypotheses of invasion biology. We do so on the F2 generation of adults in a full factorial design across two temperatures, to elicit desiccation responses, for the phenotypic plasticity trials. We also determine whether basal desiccation resistance responds to thermal laboratory natural selection. We first show experimentally that acclimation to different temperatures elicits changes to cuticular structure and function that are typically associated with water balance, justifying our experimental approach. Our main findings reveal that basal desiccation resistance differs, on average, between the indigenous and introduced species, but that this difference is weaker at higher temperatures, and is driven by particular taxa, as revealed by phylogenetic generalised least squares approaches. By contrast, the extent or form of phenotypic plasticity does not differ between the two groups, with a 'hotter is better' response being most common. Beneficial acclimation is characteristic of only a single species. Laboratory natural selection had little influence on desiccation resistance over 8-12 generations, suggesting that environmental filtering rather than adaptation to new environments may be an important factor influencing Collembola invasions.

Community assembly and metaphylogeography of soil biodiversity: insights from haplotype-level community DNA metabarcoding within an oceanic island

Most of our understanding of island diversity comes from the study of aboveground systems, while the patterns and processes of diversification and community assembly for belowground biotas remain poorly understood. Here, we take advantage of a relatively young and dynamic oceanic island to advance our understanding of ecoevolutionary processes driving community assembly within soil mesofauna. Using whole organism community DNA (wocDNA) metabarcoding and the recently developed metaMATE pipeline, we have generated spatially explicit and reliable haplotype‐level DNA sequence data for soil mesofaunal assemblages sampled across the four main habitats within the island of Tenerife. Community ecological and metaphylogeographic analyses have been performed at multiple levels of genetic similarity, from haplotypes to species and supraspecific groupings. Broadly consistent patterns of local‐scale species richness across different insular habitats have been found, whereas local insular richness is lower than in continental settings. Our results reveal an important role for niche conservatism as a driver of insular community assembly of soil mesofauna, with only limited evidence for habitat shifts promoting diversification. Furthermore, support is found for a fundamental role of habitat in the assembly of soil mesofauna, where habitat specialism is mainly due to colonization and the establishment of preadapted species. Hierarchical patterns of distance decay at the community level and metaphylogeographical analyses support a pattern of geographic structuring over limited spatial scales, from the level of haplotypes through to species and lineages, as expected for taxa with strong dispersal limitations. Our results demonstrate the potential for wocDNA metabarcoding to advance our understanding of biodiversity.

SLAM Project - Long Term Ecological Study of the Impacts of Climate Change in the natural forest of Azores: I - the spiders from native forests of Terceira and Pico Islands (2012-2019)

Background

Long-term monitoring of invertebrate communities is needed to understand the impact of key biodiversity erosion drivers (e.g. habitat fragmentation and degradation, invasive species, pollution, climatic changes) on the biodiversity of these high diverse organisms.

The data we present are part of the long-term project SLAM (Long Term Ecological Study of the Impacts of Climate Change in the natural forest of Azores) that started in 2012, aiming to understand the impact of biodiversity erosion drivers on Azorean native forests (Azores, Macaronesia, Portugal). In this contribution, the design of the project, its objectives and the first available data for the spider fauna of two Islands (Pico and Terceira) are described.

Passive flight interception SLAM traps (Sea, Land and Air Malaise traps) were used to sample native forest plots in several Azorean islands, with one trap being set up at each plot and samples taken every three months following the seasons.

The key objectives of the SLAM project are: 1) collect long-term ecological data to evaluate species distributions and abundance at multiple spatial and temporal scales, responding to the Wallacean and Prestonian shortfalls, 2) identify biodiversity erosion drivers impacting oceanic indigenous assemblages under global change for conservation management purpose, 3) use species distribution and abundance data in model-based studies of environmental change in different islands, 4) contribute to clarifying the potential occurrence of an "insect decline" in Azores and identifying the spatial and temporal invasion patterns of exotic arthropod species, 5) contribute with temporal data to re-assess the Red-list status of Azorean endemic arthropods and 6) perform studies about the relationship between diversity (taxonomic, functional and phylogenetic) and ecosystem function.

New information

The project SLAM (Long Term Ecological Study of the Impacts of Climate Change in the natural forest of Azores) is described in detail.

Seasonal distribution and abundance data of Azorean spiders, based on a long-term study undertaken between 2012 and 2019 in two Azorean Islands (Terceira and Pico), is presented. A total of 14979 specimens were collected, of which 6430 (43%) were adults. Despite the uncertainty of juvenile identification, juveniles are also included in the data presented in this paper, since the low diversity allows a relatively precise identification of this life-stage in Azores.

A total of 57 species, belonging to 50 genera and 17 families, were recorded from the area, which constitutes baseline information of spiders from the studied sites for future long-term comparisons. Linyphiidae were the richest and most abundant family, with 19 (33%) species and 5973 (40%) specimens. The ten most abundant species are composed mostly of endemic or native non-endemic species and only one exotic species (Tenuiphantestenuis (Blackwall, 1852)). Those ten most abundant species include 84% of all sampled specimens and are clearly the dominant species in the Azorean native forests. Textrixcaudata L. Koch, 1872 was firstly reported from Terceira and Pico Islands, Araneusangulatus Clerck, 1757 was firstly reported from Terceira Island, Nerieneclathrata (Sundevall, 1830) and Macaroerisdiligens (Blackwall, 1867) were firstly reported from Pico Island.

This publication contributes not only to a better knowledge of the arachnofauna present in native forests of Terceira and Pico, but also to understand the patterns of abundance and diversity of spider species, both seasonally and between years.

Standardised arthropod (Arthropoda) inventory across natural and anthropogenic impacted habitats in the Azores archipelago

Background

In this paper, we present an extensive checklist of selected arthropods and their distribution in five Islands of the Azores (Santa Maria. São Miguel, Terceira, Flores and Pico). Habitat surveys included five herbaceous and four arboreal habitat types, scaling up from native to anthropogenic managed habitats. We aimed to contribute to the ongoing effort to document the terrestrial biodiversity of the world, in particular the Portuguese archipelago of the Azores, as islands harbour a significant portion of unique terrestrial biodiversity. Selection of Arthropoda groups for the current checklist was based on their known richness and abundance (Arachnida, Collembola, Hemiptera, Neuroptera, Coleoptera, Hymenoptera), in almost all terrestrial ecosystems, as well as their importance in current Integrated Pest Management and alternative Biocontrol protocols at large (i.e. hymenopteran parasitoids and beneficial Coleoptera). In addition, we include the list of Dermaptera, Orthoptera, Psocoptera and Thysanoptera species. These assembled groups represent part of the monitoring programme EDEN Azores (2008-2014), where all Arthropod fauna, at all strata, within nine representative habitats of the abovementioned five Islands of the Azores was recorded.

New information

In this study, a total of 116,523 specimens, belonging to 483 species and subspecies of selected groups of arthropods, are reported by order, family and, when possible, genus and species. Hymenopteran, mostly parasitoids, accounted for the most represented taxa across all the monitoring and sampling phase of EDEN Azores (193 species and mophospecies), followed by Coleoptera (95 species); Collembola (89 species); and Araneae (72 species).

A total of 37 non-native species are reported for the first time in the Azores. Coleoptera: Asaphidionflavipes (Linnaeus, 1761) (Carabidae); Tachyporusdispar (Paykull, 1789) (Staphylinidae). Hemiptera: Acrosternumheegeri Fieber, 1861 (Pentatomidae). Collembola: Entomobryaregularis Stach, 1963 (Entomobryidae); Lepidocyrtuslusitanicuspiezoensis (Simón-Benito, 2007) (Entomobryidae); Jordanathrixarticulata (Ellis, 1974) (Sminthuridae); Sminthurinusquadrimaculatus (Ryder, 1879) (Katiannidae); Himalanura sp. (Entomobryidae); Protophorura sp. (Onychiuridae). Hymenoptera, parasitoids: Aphidiuscolemani Viereck, 1912 (Braconidae); Aphidiuservi Haliday, 1834 (Braconidae); Aphidiusmatricariae Viereck, 1912 (Braconidae); Aphidiusrhopalosiphi Stefani-Perez, 1902 (Braconidae); Aphidiusrosae (Haliday, 1834) (Braconidae); Aphidiusurticae Haliday, 1834 (Braconidae); Centistideaectoedemiae Rohwer, 1914 (Braconidae); Meteorusunicolor (Wesmael, 1835) (Braconidae); Meteoruscollaris (Spin.) Hal. – Ruschka, Fulmek, 1915 (Braconidae); Orthostigmacratospilum (Thomson, 1895) (Braconidae); Orthostigmalatriventris Ratzeburg, 1844 (Braconidae); two other species of Orthostigma sp.; Pseudopezomachusbituberculatus (Marshall, 1905) (Braconidae); Tanycarpapunctata (van Achterberg, 1976) (Braconidae); Gonatopusclavipes (Thunberg, 1827) (Dryinidae). New genera not previously recorded for the Azores include: Pycnetron sp. (Chalcidoidea: Pteromalidae); four species of Aspilota sp. (Braconidae: Alysiinae); four species of Chorebus sp. (Braconidae: Aphidiinae: Alysiinae); Microgaster sp. (Braconidae: Microgastrinae); Homolobus sp. (Braconidae: Homolobinae); Lodbrokia sp. (Braconidae: Alysiinae).

These 37 taxa were found in several Islands and five are new species for Flores Island, 10 species are new for Pico Island, 12 species are new for Terceira Island, 19 species are new for S. Miguel Island and five species are new for S. Maria Island.

Additional species records for the Islands included: Flores (5 Collembola, 9 Araneae; 2 Hemiptera; 8 Coleoptera, 8 Hymenoptera), Pico (4 Collembola; 7 Araneae; 4 Hemiptera; 11 Coleoptera; 9 Hymenoptera), Terceira (4 Collembola; 1 Araneae; 3 Hymenoptera), S. Miguel (1 Araneae; 2 Coleoptera; 3 Hymenoptera), S. Maria (5 Collembola; 3 Araneae; 2 Hemiptera; 2 Hymenoptera).

Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis

High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.

Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data

Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.

Eradicating the large white butterfly from New Zealand eliminates a threat to endemic Brassicaceae

In May 2010 the large white butterfly, Pieris brassicae L. (Lepidoptera: Pieridae), was discovered to have established in New Zealand. It is a Palearctic species that-due to its wide host plant range within the Brassicaceae-was regarded as a risk to New Zealand's native brassicas. New Zealand has 83 native species of Brassicaceae including 81 that are endemic, and many are threatened by both habitat loss and herbivory by other organisms. Initially a program was implemented to slow its spread, then an eradication attempt commenced in November 2012. The P. brassicae population was distributed over an area of approximately 100 km2 primarily in urban residential gardens. The eradication attempt involved promoting public engagement and reports of sightings, including offering a bounty for a two week period, systematically searching gardens for P. brassicae and its host plants, removing host plants, ground-based spraying of insecticide to kill eggs and larvae, searching for pupae, capturing adults with nets, and augmenting natural enemy populations. The attempt was supported by research that helped to progressively refine the eradication strategy and evaluate its performance. The last New Zealand detection of P. brassicae occurred on 16 December 2014, the eradication program ceased on 4 June 2016 and P. brassicae was officially declared eradicated from New Zealand on 22 November 2016, 6.5 years after it was first detected and 4 years after the eradication attempt commenced. This is the first species of butterfly ever to have been eradicated worldwide.

Population genetics and diversity structure of an invasive earthworm in tropical and temperate pastures from Veracruz, Mexico

Pontoscolexcorethrurus (Müller, 1857) is an invasive tropical earthworm, globally distributed. It reproduces through parthenogenesis, which theoretically results in low genetic diversity. The analysis of the population structure of P.corethrurus using molecular markers may significantly contribute to understanding the ecology and reproductive system of this earthworm species. This work assessed the genetic diversity and population structure of P.corethrurus with 34 polymorphic inter simple sequence repeat markers, covering four populations in tropical and temperate pastures from Veracruz State. Nuclear markers distinguished two genetic clusters, probably corresponding to two distinct genetic lineages. The number of clones detected in the AC population was lower than expected for a parthenogenetic species. Also, the apparent lack of differences in population structures related to the geographic region among the populations studied may indicate that human-mediated transference is prevalent in these areas. Still, most individuals apparently belong to lineage A, and only a few individuals seem to belong to the lineage B. Thus, the admixture signatures found among the four populations of P.corethrurus may have facilitated a successful invasion by directly increasing fitness. In summary, addressing the genetic variation of P.corethrurus with ISSR markers was a suitable approach, as it evidenced the genetic diversity and relationships in the populations evaluated.

Basal tolerance but not plasticity gives invasive springtails the advantage in an assemblage setting

As global climates change, alien species are anticipated to have a growing advantage relative to their indigenous counterparts, mediated through consistent trait differences between the groups. These insights have largely been developed based on interspecific comparisons using multiple species examined from different locations. Whether such consistent physiological trait differences are present within assemblages is not well understood, especially for animals. Yet, it is at the assemblage level that interactions play out. Here, we examine whether physiological trait differences observed at the interspecific level are also applicable to assemblages. We focus on the Collembola, an important component of the soil fauna characterized by invasions globally, and five traits related to fitness: critical thermal maximum, minimum and range, desiccation resistance and egg development rate. We test the predictions that the alien component of a local assemblage has greater basal physiological tolerances or higher rates, and more pronounced phenotypic plasticity than the indigenous component. Basal critical thermal maximum, thermal tolerance range, desiccation resistance, optimum temperature for egg development, the rate of development at that optimum and the upper temperature limiting egg hatching success are all significantly higher, on average, for the alien than the indigenous components of the assemblage. Outcomes for critical thermal minimum are variable. No significant differences in phenotypic plasticity exist between the alien and indigenous components of the assemblage. These results are consistent with previous interspecific studies investigating basal thermal tolerance limits and development rates and their phenotypic plasticity, in arthropods, but are inconsistent with results from previous work on desiccation resistance. Thus, for the Collembola, the anticipated advantage of alien over indigenous species under warming and drying is likely to be manifest in local assemblages, globally.

From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe

Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.

Springtail phylogeography highlights biosecurity risks of repeated invasions and intraregional transfers among remote islands

Human-mediated transport of species outside their natural range is a rapidly growing threat to biodiversity, particularly for island ecosystems that have evolved in isolation. The genetic structure underpinning island populations will largely determine their response to increased transport and thus help to inform biosecurity management. However, this information is severely lacking for some groups, such as the soil fauna. We therefore analysed the phylogeographic structure of an indigenous and an invasive springtail species (Collembola: Poduromorpha), each distributed across multiple remote sub-Antarctic islands, where human activity is currently intensifying. For both species, we generated a genome-wide SNP data set and additionally analysed all available COI barcodes. Genetic differentiation in the indigenous springtail Tullbergia bisetosa is substantial among (and, to a lesser degree, within) islands, reflecting low dispersal and historic population fragmentation, while COI patterns reveal ancestral signatures of postglacial recolonization. This pronounced geographic structure demonstrates the key role of allopatric divergence in shaping the region's diversity and highlights the vulnerability of indigenous populations to genetic homogenization via human transport. For the invasive species Hypogastrura viatica, nuclear genetic structure is much less apparent, particularly for islands linked by regular shipping, while diverged COI haplotypes indicate multiple independent introductions to each island. Thus, human transport has likely facilitated this species' persistence since its initial colonization, through the ongoing introduction and inter-island spread of genetic variation. These findings highlight the different evolutionary consequences of human transport for indigenous and invasive soil species. Crucially, both outcomes demonstrate the need for improved intraregional biosecurity among remote island systems, where the policy focus to date has been on external introductions.

Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing

In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems.

Mitochondrial Genome Diversity in Collembola: Phylogeny, Dating and Gene Order

Collembola (springtails) are an early diverging class of apterygotes, and mark the first substantial radiation of hexapods on land. Despite extensive work, the relationships between major collembolan lineages are still debated and, apart from the Early Devonian fossil Rhyniella praecursor, which demonstrates their antiquity, the time frame of springtail evolution is unknown. In this study, we sequence two new mitochondrial genomes and reanalyze all known Collembola mt-genomes, including selected metagenomic data, to produce an improved phylogenetic hypothesis for the group, develop a tentative time frame for their differentiation, and provide a comprehensive overview of gene order diversity. Our analyses support most taxonomically recognized entities. We find support for an Entomobryomorpha + Symphypleona clade, while the position of Neelipleona could not be assessed with confidence. A Silurian time frame for their basal diversification is recovered, with an indication that divergence times may be fairly old overall. The distribution of mitochondrial gene order indicates the pancrustacean arrangement as plesiomorphic and dominant in the group, with the exception of the family Onychiuridae. We distinguished multiple instances of different arrangements in individual genomes or small clusters. We further discuss the opportunities and drawbacks associated with the inclusion of metagenomic data in a classic study on mitochondrial genome diversity.

Terra incognita of soil biodiversity: unseen invasions under our feet

Whilst cartographers of the 19th century endeavoured to chart the last unknown lands, the great challenge for biologists in the 21st century is to fill the gaps on the biodiversity map of the Earth. And one of the largest gaps concerns the biodiversity of soils, a terra incognita right under our feet. The study of soil biodiversity, and particularly the complex communities of small invertebrates, has suffered from a severe 'taxonomic impediment' (Decaëns ) leading to great uncertainties about total species richness, phylogenetic diversity, geographical structure, temporal dynamics of soil organisms, and consequently about their role on ecosystem function (Bardgett & van der Putten ). However, the revolution in high-throughput sequencing is now revealing the hidden biodiversity of the soil with unprecedented detail (e.g. Arribas et al. ). In a noteworthy from the Cover article in this issue of Molecular Ecology, Cicconardi et al. () apply these new tools to study soil communities of Collembola in three distant oceanic islands of volcanic origin, obtaining a striking result: only 38 of 70 species (54%) are exclusively found in a single island, with the remaining shared among islands or with other distant regions, suggesting a massive recent introduction of soil species, whose impact is entirely unknown.

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies

Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.

Standardised inventories of spiders (Arachnida, Araneae) of Macaronesia I: The native forests of the Azores (Pico and Terceira islands)

Background

The data presented here come from samples collected as part of two recent research projects (NETBIOME - ISLANDBIODIV and FCT - MACDIV) which aimed at understanding the drivers of community assembly in Macaronesian islands. We applied the sampling protocol COBRA (Conservation Oriented Biodiversity Rapid Assessment, Cardoso 2009) in sixteen 50 m x 50 m native forest plots in the Azorean Islands of Pico (6 plots) and Terceira (10 plots) to assess spider diversity. Through this publication, we contribute to the knowledge of the arachnofauna of the Azores and, more specifically, to that of the islands of Pico and Terceira.

New information

The collected samples yielded 8,789 specimens, of which 45% were adults (3,970) belonging to 13 families, 36 species and three morphospecies that have yet to be described. Species of the family Linyphiidae dominated the samples, with 17 species and two morphospecies that have yet to be described (48% of the taxa). Out of the identified (morpho)species, 16 were introduced, 13 Azorean endemic (three of which were undescribed) and seven native (five of them Macaronesian endemics). We report the first record of the introduced species Haplodrassussignifer and Agynetadecora in Pico Island.

New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods

Insect metabarcoding has been mainly based on PCR amplification of short fragments within the “barcoding region” of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein‐coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon‐based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.

Basal resistance enhances warming tolerance of alien over indigenous species across latitude

How climate change and biological invasions interact to affect biodiversity is of major concern to conservation. Quantitative evidence for the nature of climate change–invasion interactions is, however, limited. For the soil ecosystem fauna, such evidence is nonexistent. Yet across the globe, soil-dwelling animals regulate belowground functioning and have pronounced influences on aboveground dynamics. Using springtails as an exemplar taxon, widely known to have species-specific effects on below- and aboveground dynamics, we show that across a wide latitudinal span (16–54°S), alien species have greater ability to tolerate climate change-associated warming than do their indigenous counterparts. The consequences of such consistent differences are profound given globally significant invasions of soil systems by springtails.

Soil systems are being increasingly exposed to the interactive effects of biological invasions and climate change, with rising temperatures expected to benefit alien over indigenous species. We assessed this expectation for an important soil-dwelling group, the springtails, by determining whether alien species show broader thermal tolerance limits and greater tolerance to climate warming than their indigenous counterparts. We found that, from the tropics to the sub-Antarctic, alien species have the broadest thermal tolerances and greatest tolerance to environmental warming. Both groups of species show little phenotypic plasticity or potential for evolutionary change in tolerance to high temperature. These trait differences between alien and indigenous species suggest that biological invasions will exacerbate the impacts of climate change on soil systems, with profound implications for terrestrial ecosystem functioning.

Recommendations for developing and applying genetic tools to assess and manage biological invasions in marine ecosystems

The European Union's Marine Strategy Framework Directive (MSFD) aims to adopt integrated ecosystem management approaches to achieve or maintain "Good Environmental Status" for marine waters, habitats and resources, including mitigation of the negative effects of non-indigenous species (NIS). The Directive further seeks to promote broadly standardized monitoring efforts and assessment of temporal trends in marine ecosystem condition, incorporating metrics describing the distribution and impacts of NIS. Accomplishing these goals will require application of advanced tools for NIS surveillance and risk assessment, particularly given known challenges associated with surveying and monitoring with traditional methods. In the past decade, a host of methods based on nucleic acids (DNA and RNA) analysis have been developed or advanced that promise to dramatically enhance capacity in assessing and managing NIS. However, ensuring that these rapidly evolving approaches remain accessible and responsive to the needs of resource managers remains a challenge. This paper provides recommendations for future development of these genetic tools for assessment and management of NIS in marine systems, within the context of the explicit requirements of the MSFD. Issues considered include technological innovation, methodological standardization, data sharing and collaboration, and the critical importance of shared foundational resources, particularly integrated taxonomic expertise. Though the recommendations offered here are not exhaustive, they provide a basis for future intentional (and international) collaborative development of a genetic toolkit for NIS research, capable of fulfilling the immediate and long term goals of marine ecosystem and resource conservation.