217 results found
Breeschoten T, Doorenweerd C, Tarasov S, et al., 2019, Incorporating older literature into genomic studies: A response to Zunino & Halffter, MOLECULAR PHYLOGENETICS AND EVOLUTION, Vol: 133, Pages: 164-165, ISSN: 1055-7903
Creedy TJ, Ng WS, Vogler A, 2019, Towards accurate species-level metabarcoding of arthropod communities from the tropical forest canopy, Ecology and Evolution, Vol: 6, Pages: 3105-3116, ISSN: 2045-7758
Metabarcoding of arthropod communities can be used for assessing species diversity in tropical forests but the methodology requires validation for accurate and repeatable species occurrences in complex mixtures. This study investigates how the composition of ecological samples affects the accuracy of species recovery. Starting with field-collected bulk samples from the tropical canopy, the recovery of specimens was tested for subsets of different body sizes and major taxa, by assembling these subsets into increasingly complex composite pools. After metabarcoding, we track whether richness, diversity and most importantly composition of any size class or taxonomic subset is affected by the presence of other subsets in the mixture.Operational Taxonomic Units (OTUs) greatly exceeded the number of morphospecies in most taxa, even under very stringent sequencing read filtering. There was no significant effect on the recovered OTU richness of small and medium-sized arthropods when metabarcoded alongside larger arthropods, despite substantial biomass differences in the mixture. The recovery of taxonomic subsets was not generally influenced by the presence of other taxa, although with some exceptions likely due to primer mismatches. Considerable compositional variation within size and taxon-based subcommunities were evident resulting in high beta diversity among samples from within a single tree canopy, but this beta diversity was not affected by experimental manipulation.We conclude that OTU recovery in complex arthropod communities, with sufficient sequencing depth and within reasonable size ranges, is not skewed by variable biomass of the constituent species. This could remove the need for time-intensive manual sorting prior to metabarcoding. However, there remains a chance of taxonomic bias, which may be primer-dependent. There will never be a panacea primer; instead, metabarcoding studies should carefully consider whether the aim is broad-scale turnover, in which case t
Kusy D, Motyka M, Bocek M, et al., 2018, Genome sequences identify three families of Coleoptera as morphologically derived click beetles (Elateridae), Scientific Reports, Vol: 8, ISSN: 2045-2322
Plastoceridae Crowson, 1972, Drilidae Blanchard, 1845 and Omalisidae Lacordaire, 1857 (Elateroidea) are families of the Coleoptera with obscure phylogenetic relationships and modified morphology showing neotenic traits such as soft bodies, reduced wing cases and larviform females. We shotgun sequenced genomes of Plastocerus, Drilus and Omalisus and incorporated them into data matrices of 66 and 4202 single-copy nuclear genes representing Elateroidea. Phylogenetic analyses indicate their terminal positions within the broadly defined well-sclerotized and fully metamorphosed Elateridae and thus Omalisidae should now be considered as Omalisinae stat. nov. in Elateridae Leach, 1815. The results support multiple independent origins of incomplete metamorphosis in Elateridae and indicate the parallel evolution of morphological and ecological traits. Unlike other neotenic elateroids derived from the supposedly pre-adapted aposematically coloured and unpalatable soft-bodied elateroids, such as fireflies (Lampyridae) and net-winged beetles (Lycidae), omalisids and drilids evolved from well-sclerotized click beetles. These findings suggest sudden morphological shifts through incomplete metamorphosis, with important implications for macroevolution, including reduced speciation rate and high extinction risk in unstable habitats. Precise phylogenetic placement is necessary for studies of the molecular mechanisms of ontogenetic shifts leading to profoundly changed morphology.
Linard B, Crampton-Platt A, Moriniere J, et al., 2018, The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera, MOLECULAR PHYLOGENETICS AND EVOLUTION, Vol: 128, Pages: 1-11, ISSN: 1055-7903
Andújar C, Arribas P, Yu DW, et al., 2018, Why the COI barcode should be the community DNA metabarcode for the Metazoa, Molecular Ecology, ISSN: 0962-1083
Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater, and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (i) the extensive coverage of reference-sequence databases for COI, (ii) the variation it presents, (iii) the comparative advantages for denoising protein coding genes, and (iv) recent advances in DNA sequencing protocols argue in favour of standardising for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximise the utility of metabarcoding. This article is protected by copyright. All rights reserved.
Arias MB, Elfekih S, Vogler AP, 2018, Population genetics and migration pathways of the Mediterranean fruit fly Ceratitis capitata inferred with coalescent methods, PeerJ, Vol: 6, ISSN: 2167-8359
BackgroundInvasive species are a growing threat to food biosecurity and cause significant economic losses in agricultural systems. Despite their damaging effect, they are attractive models for the study of evolution and adaptation in newly colonised environments. The Mediterranean fruit fly, Ceratitis capitata, as a member of the family Tephritidae, is one of the most studied invasive species feeding on many fruit crops in the tropics and subtropics worldwide. This study aims to determine the global macrogeographic population structure of Ceratitis capitata and reconstruct its potential migration routes.MethodA partial mitochondrial cytochrome oxidase I gene from >400 individual medflies and 14 populations from four continents was sequenced and subjected to Bayesian demographic modelling.ResultsThe Afrotropical populations (Kenya, South Africa and Ghana) harbour the majority of haplotypes detected, which also are highly divergent, in accordance with the presumed ancestral range of medflies in Sub-Saharan Africa. All other populations in the presumed non-native areas were dominated by a single haplotype also present in South Africa, in addition to a few, closely related haplotypes unique to a single local population or regional set, but missing from Africa. Bayesian coalescence methods revealed recent migration pathways from Africa to all continents, in addition to limited bidirectional migration among many local and intercontinental routes.ConclusionThe detailed investigation of the recent migration history highlights the interconnectedness of affected crop production regions worldwide and pinpoints the routes and potential source areas requiring more specific quarantine measures.
Qin Y-G, Zhou Q-S, Yu F, et al., 2018, Host specificity of parasitoids (Encyrtidae) toward armored scale insects (Diaspididae): Untangling the effect of cryptic species on quantitative food webs, ECOLOGY AND EVOLUTION, Vol: 8, Pages: 7879-7893, ISSN: 2045-7758
Murria C, Doledec S, Papadopoulou A, et al., 2018, Ecological constraints from incumbent clades drive trait evolution across the tree-of-life of freshwater macroinvertebrates, Ecography, Vol: 41, Pages: 1049-1063, ISSN: 0906-7590
The rates of species and trait diversification vary across the Tree‐of‐Life and over time. Whereas species richness and clade age generally are decoupled, the correlation of accumulated trait diversity of clades (trait disparity) with clade age remains poorly explored. Total trait disparity may be coupled with clade age if the growth of disparity (disparification) within and across clades is continuous with time in an additive niche expansion process (linear‐cumulative model), or alternatively if the rate of trait disparification varies over time and decreases as ecological space becomes gradually saturated (disparity‐dependent model). Using a clock‐calibrated phylogenetic tree for 143 freshwater macroinvertebrate families and richness and trait databases covering > 6400 species, we measured trait disparity in 18 independent clades that successively transitioned to freshwater ecosystems and analyzed its relation with clade age. We found a positive correlation between clade age and total disparity within clades, but no relationship for most individual traits. Traits unique to freshwater lifestyle were highly variable within older clades, while disparity in younger clades shifted towards partially terrestrial lifestyles and saline tolerance to occupy habitats previously inaccessible or underutilized. These results argue that constraints from incumbent lineages limit trait disparity in younger clades that evolved for filling unoccupied regions of the trait space, which suggests that trait disparification may follow a disparity‐dependent model. Overall, we provide an empirical pattern that reveals the potential of the disparity‐dependent model for understanding fundamental processes shaping trait dynamics across the Tree‐of‐Life.
Kusy D, Motyka M, Andujar C, et al., 2018, Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera, Frontiers in Zoology, Vol: 15, ISSN: 1742-9994
Background: Rhinorhipidae Lawrence, 1988 is an enigmatic beetle family represented by a single species, Rhinorhipus tamborinensis Lawrence, 1988, from Australia, with poorly established affinities near the superfamily Elateroidea (click beetles, soldier beetles and fireflies) or the more inclusive series (infraorder) Elateriformia. Its evolutionary position may inform the basal relationships of the suborder Polyphaga, the largest clade of Coleoptera.Results: We analyzed four densely sampled DNA datasets of major coleopteran lineages for mitogenomes, rRNA genes and single copy nuclear genes. Additionally, genome sequencing was used for incorporation of R. tamborinensis into a set of 4220 orthologs for 24 terminals representing 12 polyphagan superfamilies. Topologies differed to various degrees, but all consistently refute the proposed placement of Rhinorhipidae in Elateroidea and instead indicate either sister relationships with other Elateriformia, frequently together with Nosodendridae, another divergent small family hitherto placed in Derodontoidea, or in an isolated position among the deepest lineages of Polyphaga. The phylogenomic analyses recovered Rhinorhipus in a sister position to all other Elateriformia composed of five superfamilies. Therefore, we erect the new superfamily Rhinorhipoidea Lawrence, 1988, stat. Nov., with the type-family Rhinorhipidae. The origins of the Rhinorhipidae were dated to the Upper Triassic/Lower Jurassic at the very early phase of polyphagan diversification.Conclusions: Thus, Rhinorhipidae adds another example to several recently recognized ancient relict lineages which are interspersed within contemporaneous hugely species-rich lineages of Coleoptera.
Gillett CPDT, Lyal CH, Vogler AP, et al., 2018, Statistical evaluation of monophyly in the "Broad-Nosed Weevils' through molecular phylogenetic analysis combining mitochondrial genome and single-locus sequences (Curculionidae: Entiminae, Cyclominae, and Hyperinae), Diversity, Vol: 10, ISSN: 1424-2818
Establishing well-supported monophyletic groups is a key requirement for producing a natural classification that reflects evolutionary descent. In a phylogenetic framework this is best achieved through dense taxon sampling and the analysis of a robust character dataset, combined with statistical testing of topological hypotheses. This study assesses the monophyly of tribes and subfamilies within the diverse ‘broad-nosed weevils’ (Curculionidae: Entiminae, Cyclominae and Hyperinae) through analysis of single-locus sequence data for mitochondrial cox1 and rrnL genes, in combination with a ‘backbone’ of complete and near-complete mitochondrial genome sequences. Maximum likelihood phylogenetic analyses incorporating topological constraints for various higher-taxa were statistically tested using the AU, SH, and KH tests, which indicated that three tribes within Entiminae, as presently classified, are not monophyletic. Moderate and high bootstrap support was also consistent with two entimine tribes (Peritelini and Cylydrorhinini) being each recovered as monophyletic in an unconstrained analysis. Furthermore, one genus of cyclomine weevils (Aphela) is recovered outside the clade of ‘broad-nosed weevils’, although its taxonomic placement remains uncertain. It is apparent that the present approach may be hampered by limited taxon sampling in the ‘backbone’ dataset, rendering it difficult for divergent taxa to robustly match to their closest lineages. However, with improved taxon sampling of the mitogenome tree, the general approach can be a useful taxonomic tool for weevils.
Turner SP, Longhorn SJ, Hamilton CA, et al., 2018, Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera, Aphonopelma and Brachypelma, SYSTEMATICS AND BIODIVERSITY, Vol: 16, Pages: 89-107, ISSN: 1477-2000
Andujar C, Arribas P, Gray C, et al., 2017, Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill, Molecular Ecology, Vol: 27, Pages: 146-166, ISSN: 0962-1083
Biomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species‐level resolution is difficult to obtain. Next‐generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 “barcode” and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon “Chironomidae” into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration‐flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between “impacted” vs. “control” samples, detectable with each gene marker, for each major taxonomic group, and for meio‐ and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecolo
Andujar C, Perez-Gonzalez S, Arribas P, et al., 2017, Speciation below ground: Tempo and mode of diversification in a radiation of endogean ground beetles, MOLECULAR ECOLOGY, Vol: 26, Pages: 6053-6070, ISSN: 0962-1083
Murria C, Bonada N, Vellend M, et al., 2017, Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe, Molecular Ecology, Vol: 26, Pages: 6085-6099, ISSN: 0962-1083
Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco‐evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole‐community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage‐ or species‐specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species‐specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels.
Choo LQ, Crampton-Platt A, Vogler AP, 2017, Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: phylogeny, species diversity and mitochondrial abundance spectrum, Molecular Ecology, Vol: 26, Pages: 5086-5098, ISSN: 0962-1083
Mitochondrial genomes can be assembled readily from shotgun-sequenced DNAmixtures of mass-trapped arthropods (“mitochondrial metagenomics”), speeding upthe taxonomic characterization. Bulk sequencing was conducted on some 800 indi-viduals of Diptera obtained by canopy fogging of a single tree in Borneo dominatedby small (<1.5 mm) individuals. Specimens were split into five body size classes forDNA extraction, to equalize read numbers across specimens and to study how bodysize, a key ecological trait, interacts with species and phylogenetic diversity. Gen-ome assembly produced 304 orthologous mitochondrial contigs presumed to eachrepresent a different species. The small-bodied fraction was the by far most spe-cies-rich (187 contigs). Identification of contigs was through phylogenetic analysistogether with 56 reference mitogenomes, which placed most of the Bornean com-munity into seven clades of small-bodied species, indicating phylogenetic conserva-tion of body size. Mapping of shotgun reads against the mitogenomes showed wideranges of read abundances within each size class. Ranked read abundance plotswere largely log-linear, indicating a uniformly filled abundance spectrum, especiallyfor small-bodied species. Small-bodied species differed greatly from other sizeclasses in neutral metacommunity parameters, exhibiting greater levels of immigra-tion, besides greater total community size. We suggest that the established uses ofmitochondrial metagenomics for analysis of species and phylogenetic diversity canbe extended to parameterize recent theories of community ecology and biodiversity,and by focusing on the number mitochondria, rather than individuals, a new theo-retical framework for analysis of mitochondrial abundance spectra can be developedthat incorporates metabolic activity approximated by the count of mitochondria.
Bush A, Sollmann R, Wilting A, et al., 2017, Connecting Earth observation to high-throughput biodiversity data, Nature Ecology and Evolution, Vol: 1, ISSN: 2397-334X
Understandably, given the fast pace of biodiversity loss, there is much interest in using Earth observation technology to track biodiversity, ecosystem functions and ecosystem services. However, because most biodiversity is invisible to Earth observation, indicators based on Earth observation could be misleading and reduce the effectiveness of nature conservation and even unintentionally decrease conservation effort. We describe an approach that combines automated recording devices, high-throughput DNA sequencing and modern ecological modelling to extract much more of the information available in Earth observation data. This approach is achievable now, offering efficient and near-real-time monitoring of management impacts on biodiversity and its functions and services.
Lopez-Lopez A, Vogler AP, 2017, The mitogenome phylogeny of Adephaga (Coleoptera), MOLECULAR PHYLOGENETICS AND EVOLUTION, Vol: 114, Pages: 166-174, ISSN: 1055-7903
The beetle suborder Adephaga consists of several aquatic (‘Hydradephaga’) and terrestrial (‘Geadephaga’) families whose relationships remain poorly known. In particular, the position of Cicindelidae (tiger beetles) appears problematic, as recent studies have found them either within the Hydradephaga based on mitogenomes, or together with several unlikely relatives in Geadephaga based on 18S rRNA genes. We newly sequenced nine mitogenomes of representatives of Cicindelidae and three ground beetles (Carabidae), and conducted phylogenetic analyses together with 29 existing mitogenomes of Adephaga. Our results support a basal split of Geadephaga and Hydradephaga, and reveal Cicindelidae, together with Trachypachidae, as sister to all other Geadephaga, supporting their status as Family. We show that alternative arrangements of basal adephagan relationships coincide with increased rates of evolutionary change and with nucleotide compositional bias, but these confounding factors were overcome by the CAT-Poisson model of PhyloBayes. The mitogenome + 18S rRNA combined matrix supports the same topology only after removal of the hypervariable expansion segments. Densely sampled mitogenomes, analyzed with site heterogeneous mixture models, support a plausible hypothesis of basal relationships in the Adephaga.
Andujar C, Arribas P, Vogler AP, 2017, Terra incognita of soil biodiversity: unseen invasions under our feet, MOLECULAR ECOLOGY, Vol: 26, Pages: 3087-3089, ISSN: 0962-1083
Pu T, Vogler AP, 2017, Evolution: Taking the Sting out of Wasp Phylogenetics, CURRENT BIOLOGY, Vol: 27, Pages: R358-R360, ISSN: 0960-9822
Nie R-E, Breeschoten T, Timmermans MJTN, et al., 2017, The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclear rRNA genes, CLADISTICS, Vol: 34, Pages: 113-130, ISSN: 0748-3007
With efficient sequencing techniques, full mitochondrial genomes are rapidly replacing other widely used markers, such as the nuclear rRNA genes, for phylogenetic analysis but their power to resolve deep levels of the tree remains controversial. We studied phylogenetic relationships of leaf beetles (Chrysomelidae) in the tribes Galerucini and Alticini (root worms and flea beetles) based on full mitochondrial genomes (103 newly sequenced), and compared their performance to the widely sequenced nuclear rRNA genes (full 18S, partial 28S). Our results show that: (i) the mitogenome is phylogenetically informative from subtribe to family level, and the per‐nucleotide contribution to nodal support is higher than that of rRNA genes, (ii) the Galerucini and Alticini are reciprocally monophyletic sister groups, if the classification is adjusted to accommodate several ‘problematic genera’ that do not fit the dichotomy of lineages based on the presence (Alticini) or absence (Galerucini) of the jumping apparatus, and (iii) the phylogenetic results suggest a new classification system of Galerucini with eight subtribes: Oidina, Galerucina, Hylaspina, Metacyclina, Luperina, Aulacophorina, Diabroticina and Monoleptina.
Timmermans MJTN, Thompson MJ, Collins S, et al., 2017, Independent evolution of sexual dimorphism and female-limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas), MOLECULAR ECOLOGY, Vol: 26, Pages: 1273-1284, ISSN: 0962-1083
Gomez-Rodriguez C, Timmermans MJTN, Crampton-Platt A, et al., 2016, Intraspecific genetic variation in complex assemblages from mitochondrial metagenomics: comparison with DNA barcodes, Methods in Ecology and Evolution, Vol: 8, Pages: 248-256, ISSN: 2041-210X
Paula DP, Linard B, Crampton-Platt A, et al., 2016, Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents., PLOS One, Vol: 11, ISSN: 1932-6203
Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks.
Breeschoten T, Doorenweerd C, Tarasov S, et al., 2016, Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes, Molecular Phylogenetics and Evolution, Vol: 105, Pages: 86-95, ISSN: 1095-9513
Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini. The analysis defined four major clades of Onthophagini, which was paraphyletic for Oniticellini, with Onitini as sister group to all others. Several (sub)genera considered as members of Onthophagus in the older literature formed separate deep lineages. All New World species of Onthophagus formed a monophyletic group, and the Australian taxa are confined to a single or two closely related clades, one of which forms the sister group of the New World species. Dating the tree by constraining the basal splits with existing calibrations of Scarabaeoidea suggests an origin of Onthophagini sensu lato in the Eocene and a rapid spread from an African ancestral stock into the Oriental region, and secondarily to Australia and the Americas at about 20-24 Mya. The successful assembly of mitogenomes and the well-supported tree obtained from these sequences demonstrates the power of shotgun sequencing from total genomic DNA of species pools as an efficient tool in genus-level phylogenetics.
Linard B, Arribas P, Andujar C, et al., 2016, Lessons from genome skimming of arthropod-preserving ethanol, Molecular Ecology Resources, Vol: 16, Pages: 1365-1377, ISSN: 1755-098X
Field-collected specimens of invertebrates are regularly killed and preserved in ethanol, prior to DNA extraction from the specimens, while the ethanol fraction is usually discarded. However, DNA may be released from the specimens into the ethanol, which can potentially be exploited to study species diversity in the sample without the need for DNA extraction from tissue. We used shallow shotgun sequencing of the total DNA to characterize the preservative ethanol from two pools of insects (from a freshwater habitat and terrestrial habitat) to evaluate the efficiency of DNA transfer from the specimens to the ethanol. In parallel, the specimens themselves were subjected to bulk DNA extraction and shotgun sequencing, followed by assembly of mitochondrial genomes for 39 of 40 species in the two pools. Shotgun sequencing from the ethanol fraction and read-matching to the mitogenomes detected ~40% of the arthropod species in the ethanol, confirming the transfer of DNA whose quantity was correlated to the biomass of specimens. The comparison of diversity profiles of microbiota in specimen and ethanol samples showed that ‘closed association’ (internal tissue) bacterial species tend to be more abundant in DNA extracted from the specimens, while ‘open association’ symbionts were enriched in the preservative fluid. The vomiting reflex of many insects also ensures that gut content is released into the ethanol, which provides easy access to DNA from prey items. Shotgun sequencing of DNA from preservative ethanol provides novel opportunities for characterizing the functional or ecological components of an ecosystem and their trophic interactions.
Andujar C, Arribas P, Linard B, et al., 2016, The mitochondrial genome of Iberobaenia (Coleoptera: Iberobaeniidae): first rearrangement of protein-coding genes in the beetles., Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, ISSN: 2470-1394
The complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochondrial genome of Iberobaeniidae includes 13 protein-coding genes, 2 rRNAs, 22 tRNAs genes, and 1 putative control region, and showed a unique rearrangement of protein-coding genes. This is the first rearrangement affecting the relative position of protein-coding and ribosomal genes reported for the order Coleoptera.
Bocak L, Kundrata R, Fernandez CA, et al., 2016, The discovery of Iberobaeniidae (Coleoptera: Elateroidea): a new family of beetles from Spain, with immatures detected by environmental DNA sequencing, Proceedings of the Royal Society B: Biological Sciences, Vol: 283, ISSN: 0962-8452
The ongoing exploration of biodiversity and the implementation of new molecular tools continue to unveil hitherto unknown lineages. Here, we report the discovery of three species of neotenic beetles for which we propose the new family Iberobaeniidae. Complete mitochondrial genomes and rRNA genes recovered Iberobaeniidae as a deep branch in Elateroidea, as sister to Lycidae (net-winged beetles). Two species of the new genus Iberobaenia, Iberobaenia minuta sp. nov. and Iberobaenia lencinai sp. nov. were found in the adult stage. In a separate incidence, a related sequence was identified in bulk samples of soil invertebrates subjected to shotgun sequencing and mitogenome assembly, which was traced to a larval voucher specimen of a third species of Iberobaenia. Iberobaenia shows characters shared with other elateroid neotenic lineages, including soft-bodiedness, the hypognathous head, reduced mouthparts with reduced labial palpomeres, and extremely small-bodied males without strengthening structures due to miniaturization. Molecular dating shows that Iberobaeniidae represents an ancient relict lineage originating in the Lower Jurassic, which possibly indicates a long history of neoteny, usually considered to be evolutionarily short-lived. The apparent endemism of Iberobaeniidae in the Mediterranean region highlights the importance of this biodiversity hotspot and the need for further species exploration even in the well-studied European continent.
Ahrens D, Fujisawa T, Krammer H-J, et al., 2016, Rarity and Incomplete Sampling in DNA-Based Species Delimitation, Systematic Biology, Vol: 65, Pages: 478-494, ISSN: 1076-836X
DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including “singleton” representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by “clade addition” of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size (NeNe), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in NeNe among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in NeNe and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable NeNe. This effect was less pronounced for methods of species d
Song F, Li H, Jiang P, et al., 2016, Capturing the phylogeny of holometabola with mitochondrial genome data and bayesian site-heterogeneous mixture models, Genome Biology and Evolution, Vol: 8, Pages: 1411-1426, ISSN: 1759-6653
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
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