Laure Benoit

Identifying phylogeographic breaks and deciphering the relative contributions of environmental extrinsic (e.g., geological barriers, ecological gradients) and organismal intrinsic (e.g., limited dispersal, reproductive incompatibilities) factors to their persistence remain challenging, especially in the absence of genomic data. Here, we address this issue using parapatric lineages of the lizard Acanthodactylus erythrurus in south‐western Morocco. A previous study based on nine nuclear loci identified two phylogeographic units (coastal vs. inland) whose separation did not align with landscape features preventing migration. The coastal lineage was inferred to evolve under isolation by distance (IBD, the regular increase of genetic differentiation with geographic distance), despite the presence of large rivers across its range. This suggests either that phylogeographic breaks do not align with landscape features, or that the restricted marker set prevented an accurate inference of phylogeographic breaks. We tested these hypotheses using RADseq data and recovered three lineages, each separated by phylogeographic breaks and narrow contact zones with restricted admixture. Coastal populations that had been previously identified to evolve under IBD actually included two lineages separated by a major, permanent river, reducing migration. The inland phylogeographic break, correctly identified by the previous study, is located in a continuously distributed habitat. Neither of the breaks aligned with steep changes in bioclimatic variables, suggesting a negligible contribution of local adaptation. We conclude that intrinsic reproductive barriers, as evidenced by narrow clines in allele frequencies at multiple loci spread over the genome, play a major role in maintaining these phylogeographic breaks. Our results also highlight the difficulty of identifying phylogeographic breaks from pre‐genomic molecular data.

Target enrichment methods have provided unprecedented advances in phylogenomics. Targeting hundreds of conserved regions has proven to be a good tradeoff between cost and efficiency, while being useful for museomics and diversified non-model clades. Unfortunately, current methods used for identifying such regions involve high degrees of conservation within targeted elements, usually pushing researchers to rely on flanking data with little guarantee for homology. With a growing number of high quality genomes available throughout the Tree of Life emerges new opportunities to improve marker selection. In this study, we introduce GABBI, a new method for designing target capture probes by taking advantage of genome alignments, avoiding the selection of a single reference genome that can cause notable biases. We compare GABBI-derived markers to the most commonly used probe design method, PHYLUCE, at two taxonomic scales, the weevil superfamily Curculionoidea and the tribe Pachyrhynchini. At both taxonomic scales, results show that our new method allows identifying more variable loci that prove to be more phylogenetically resolutive than the PHYLUCE-derived ones. Doing so, we provide the first probe set specifically designed for weevils, targeting a wide set of 4,255 shared homologous regions, encouraging future research on systematics and macroevolution of one of the most diverse and economically important groups of insects. By providing GABBI as an automated and open-access pipeline, we hope to open new probe design opportunities to other taxonomic groups that face similar phylogenetic obstacles.

Representatives of the weevil tribe Ochyromerini (Coleoptera: Curculionidae: Curculioninae) have been increasingly reported as specialized pollinators of Annonaceae Juss., with some species in the genus Endaeus Schoenherr, 1826 engaging in brood-site pollination with their host. Recent investigations into the poorly documented life history of these pollinators have led to the discovery of new species in the genus Endaeus and provided details of their life histories. The following species are herein described: E. canangae Haran sp. nov. from Southeast Asia, associated with Cananga odorata (Lam.) Hook.f. & Thomson (Annonaceae); E. lenticulatus Haran sp. nov. from Central Africa, associated with Uvariodendron molundense (Diels) R.E.Fr. (Annonaceae); E. xylopiae Haran & Zelvelder sp. nov., E. jaculifer Haran & Zelvelder sp. nov. and E. convexiculus Haran & Zelvelder sp. nov. from Central Africa, associated with Xylopia aethiopica (Dunal) A.Rich. (Annonaceae) and E. staminicola Haran sp. nov. also from Central Africa, associated with Allanblackia floribunda Oliv. (Clusiaceae Lindl.). Pictures of habitus and terminalia of adults, molecular and morphological diagnostic tools along with life history data are provided for each species. These new associations are discussed in light of the general patterns of specialized brood-site pollination mutualism between plants and weevils.

The species of the genus Derelomus Schoenherr, 1825 (Curculionidae: Curculioninae: Derelomini) from the Afrotropical (excluding Madagascar) and Mediterranean regions are here revised. In total, 32 valid species are recognized, including 14 described as new: D. acuminatus Haran sp. nov.; D. baka Haran sp. nov.; D. brevis Haran sp. nov.; D. brunneus Haran sp. nov.; D. caldarai Haran sp. nov.; D. crypticus Haran sp. nov.; D. discus Haran sp. nov.; D. karooensis Haran sp. nov.; D. peglerae Haran sp. nov.; D. prochesi Haran sp. nov.; D. setifer Haran sp. nov.; D. strangulatus Haran sp. nov.; D. strelitziae Haran sp. nov. and D. trinotatus Haran sp. nov. The following new synonymies are proposed: D. pallidus Hartmann, 1904 and D. hartmanni Klima, 1934 = D. pallidus Fåhraeus, 1844 syn. nov.; D. rectirostris Hustache, 1937 = D. languidus Fåhraeus, 1844 syn. nov.; D. subcostatus Boheman, 1844 = D. chamaeropis (Fabricius, 1798) syn. nov.; D. kocheri Hoffmann, 1957 = D. piriformis (Hoffamnn, 1938) syn. nov.; D. auberti Hustache, 1932 = D. ephippiger Gyllenhal, 1836 syn. nov and Psilocaulus elatus Richard, 1958 = Derelomus costiger Marshall, 1958 syn. nov. Morphological examination of specimens and molecular analyses enabled recognising four main species groups: the D. signatus Gyllenhal, 1836 group (eight species) associated with the inflorescences of species of Vachellia Wight & Arn. (Fabaceae), the D. pallidus Fåhraeus, 1844 group (three species) associated with Achariaceae and Ebenaceae, the D. nigrovariegatus Hustache, 1936 group (six species) associated with Strelitzia (Strelitziaceae) and Phoenix reclinata Jacq. (Arecaceae) and the D. ephippiger Gyllenhal, 1836 group (12 species) associated with male inflorescences of various palms (Chamaerops L., Cocos L., Phoenix L.; Arecaceae). A key and a description or redescription are provided for each species, with illustrations of habitus of adults and male terminalia.

Aim: Biological invasions result from the combination of (i) population dispersal opportunities and (ii) adaptations to the recipient environment. Identifying complex migration histories, made of long‐distance dispersal from the native range and secondary introductions, or genetic patterns indicative of adaptation is crucial to build coherent management efforts of problematic invasive species. We here aimed at determining the routes of introduction and describing the genetic peculiarities of recent introductions of Wasmannia auropunctata , a destructive invasive ant species with a polymorphic clonal/sexual reproduction system. Location: We focused on three recently established European populations (Cyprus, France and Spain) and their relationship with earlier worldwide introductions and the native South American range of W. auropunctata . Methods: We used a combination of cytochrome c oxidase subunit I (COI) sequencing and genotyping of a total of 686 European individuals at 12 microsatellite loci (from 76 nests and seven localities), together with previous worldwide datasets totalling 503 COI sequences and 6963 genotyped individuals. Phylogenetic reconstruction and genetic differentiation analyses were used to infer the origin, reproduction systems and genetic diversity of the three European populations. Results: We show that the history of the invasion of Europe is a mix of secondary introductions from a Mediterranean bridgehead population (Israel), and a novel long‐distance introduction from a climatically similar area of northeastern Argentina. All newly introduced populations reproduce clonally and display an outbred genotypic pattern, consistent with all prior introductions and with anthropised areas of the native range. Main Conclusions: This study confirms that preventing novel introductions is complex and requires adequate surveillance tools to simultaneously monitor areas of the native range with potential prior adaptation and previous introductions that could act as bridgeheads. Because of their ecological and genetic similarities, the fate of more ancient introductions could help us foresee what the future holds for European introductions.

The bestRAD technique is a reduced genome representation approach with high‐capacity sample multiplexing and physical isolation of biotin‐labelled target DNA fragments using streptavidin beads, which should reduce total cost and genotyping errors. While we here formalise the relevance of this approach within the HTS landscape, our foremost aim was to improve its replicability, validity, and transparency. We first optimised the molecular laboratory protocol and shared the associated protocols (e.g., final detailed methodologies, quality control, best practices) under the FAIR principles. Using 84 worldwide individual samples of the Oriental fruit fly, Bactrocera dorsalis , a major invasive pest, we revealed a low rate of PCR duplicates, robustness to DNA quality and quantity, high genotype call rate, insignificant genotyping error rate, high nuclear and mitochondrial genome representativeness, and a high level of genetic information. This in‐depth data quality assessment, along with total cost and handling time reduced by an estimated one‐third relative to the parent RAD‐Seq version, demonstrates that bestRAD is an excellent compromise between cost and quality. While we generated high‐quality genomic resources for B. dorsalis , we also share details and recommendations for the bestRAD technique that can be readily used in any laboratory and applied to all organisms, even without published genome sequence.

In a context of unprecedented insect decline, it is critical to have reliable monitoring tools to measure species diversity and their dynamic at large‐scales. High‐throughput DNA‐based identification methods, and particularly metabarcoding, were proposed as an effective way to reach this aim. However, these identification methods are subject to multiple technical limitations, resulting in unavoidable false‐positive and false‐negative species detection. Moreover, metabarcoding does not allow a reliable estimation of species abundance in a given sample, which is key to document and detect population declines or range shifts at large scales. To overcome these obstacles, we propose here a human‐assisted molecular identification (HAMI) approach, a framework based on a combination of metabarcoding and image‐based parataxonomic validation of outputs and recording of abundance. We assessed the advantages of using HAMI over the exclusive use of a metabarcoding approach by examining 492 mixed beetle samples from a biodiversity monitoring initiative conducted throughout France. On average, 23% of the species are missed when relying exclusively on metabarcoding, this percent being consistently higher in species‐rich samples. Importantly, on average, 20% of the species identified by molecular‐only approaches correspond to false positives linked to cross‐sample contaminations or mis‐identified barcode sequences in databases. The combination of molecular methodologies and parataxonomic validation in HAMI significantly reduces the intrinsic biases of metabarcoding and recovers reliable abundance data. This approach also enables users to engage in a virtuous circle of database improvement through the identification of specimens associated with missing or incorrectly assigned barcodes. As such, HAMI fills an important gap in the toolbox available for fast and reliable biodiversity monitoring at large scales.

: Phytophagous insects have specialized on virtually every plant lineage. Parasitic plants, however, are uncommon hosts. Among insects, only a single lineage of weevils, the Smicronychini, has successfully radiated on both parasitic and non-parasitic plants in a large panel of distantly related Asterid families. This unusual pattern suggests that major host plant shifts have occurred over the course of their diversification. Through the analysis of a phylogenomic dataset, we reconstruct for the first time their evolutionary history and ancestral host plant associations. Our results show that independent host plant shifts occurred both from parasitic to non-parasitic hosts and between distinct parasitic lineages. These results suggest that host shift mechanisms can be driven by ecological opportunities provided by plant-plant interactions. This first evidence of extreme insect host plant shifts mediated by parasitic plant-plant interactions emphasizes the core importance of ecological interactions as driving forces behind insect host plant shifts.

The potential for population genomics to elucidate invasion pathways of a species is limited by taxonomic identification issues. The Oriental fruit fly pest, Bactrocera dorsalis (Hendel) belongs to a complex in which several sympatric species are attracted to the same lure used in trapping and are morphologically cryptic and/or reported to hybridize. In this study, we evaluated the taxonomic ambiguity between B. dorsalis and 2 major cryptic species, based on morphological expertise and 289 target specimens sampled across the whole distribution range. Specimens were then subjected to DNA sequence analyses of the COI mitochondrial barcode and the EIF3L nuclear marker to evaluate the potential for molecular identification, in particular for specimens for which morphological identification was inconclusive. To this aim, we produced reference datasets with DNA sequences from target specimens whose morphological identification was unambiguous, which we complemented with 56 new DNA sequences from closest relatives and 76 published and curated DNA sequences of different species in the complex. After the necessary morphological observation, about 3.5% of the target dataset and 47.6% of the specimens from Southeast Asian islands displayed ambiguous character states shared with B. carambolae and/or B. occipitalis. Critical interpretation of DNA sequence data solved morphological ambiguities only when combining both mitochondrial and nuclear markers. COI discriminated B. dorsalis from 5 species; EIF3L and ITS from another species. We recommend this procedure to ensure correct identification of B. dorsalis specimens in population genetics studies and surveillance programs.

The weevil genus Cryptolarynx Van Schalkwyk, 1966 is endemic to the Northern and Western Cape provinces of South Africa. The two previously known species of the genus, C. vitis (Marshall, 1957) and C. estriatus (Marshall, 1957), have an aberrant globular body and head shape, which has made it difficult to place the genus into the classification systems of the Curculionoidea. This paper presents the description of 21 new species of Cryptolarynx from South Africa (C. subglaber Haran sp. nov., C. squamulatus Haran sp. nov., C. muellerae Haran sp. nov., C. hirtulus Haran sp. nov., C. robustus Haran sp. nov., C. namaquanus Haran sp. nov., C. carinatus Haran sp. nov., C. variabilis Haran sp. nov., C. pyrophilus Haran sp. nov., C. pilipes Haran sp. nov., C. armatus Haran sp. nov., C. falciformis Haran sp. nov., C. oberprieleri Haran sp. nov., C. spinicornis Haran sp. nov., C. cederbergensis Haran sp. nov., C. homaroides Haran sp. nov., C. marshalli Haran sp. nov., C. endroedyi Haran sp. nov., C. oberlanderi Haran sp. nov., C. san Haran sp. nov., and C. luteipennis Haran sp. nov.) and of one new genus and species, Hadrocryptolarynx major Haran gen. et sp. nov., also from South Africa. A redescription of the genus Cryptolarynx is provided to incorporate the characters of the new species. The plant genus Oxalis (Oxalidaceae) is recorded as larval host for several species of Cryptolarynx and for Hadrocryptolarynx Haran gen. nov., as their larvae develop in the subterranean bulbs of members of the genus, and the egg, larva and pupa of C. variabilis are described. The characters of the Cryptolarynx larva confirm that Cryptolaryngini are an early-diverging group of Curculionidae, with a placement among taxa currently classified in the subfamily Brachycerinae sensu lato, and although their exact taxonomic position remains unresolved, some larval characters, and also pupal ones, suggest a close relationship between Cryptolaryngini and Stenopelmus Schoenherr. Potential use of species of Cryptolarynx in the biological control of weedy South African species of Oxalis is discussed.