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The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics., Trends in Genetics, 39 (7), ISSN:0168-9525

Recent developments in museomics enable genetic information to be recovered from previously unusable collection specimens and thus to answer complex taxonomic questions. Here we apply museomics to a taxonomic problem involving several species ofArgyriaHübner (Pyraloidea, Crambinae), with previously unrecognized morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, we aimed to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridization capture protocol, we partially recovered the DNA barcode of the lectotype ofArgyria lacteella(Fabricius, 1794) for comparison with the 229 DNA barcode sequences ofArgyriaspecimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: theArgyria abronalis(Walker, 1859) holotype, thus confirming the synonymy of this name withA. lacteella, the holotype ofA. lusella(Zeller, 1863),rev. syn., the holotype ofA. multifactaDyar, 1914,syn. n., newly synonymized withA. lacteella, and a specimen ofArgyria diplomochalisDyar, 1913, collected in 1992. A complementary sampling composed of nine specimens ofA. lacteella, A. diplomochalis, A. centrifugensDyar, 1914 andA. gonogrammaDyar, 1915, from North to South America, were integrated using classical COI amplification and Sanger sequencing.Argyria gonogrammaDyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified asA. lacteella. Following morphological study of its holotype,Argyria vestalisButler, 1878,syn. n. is also synonymized withA. lacteella. The nameA. pusillalisHübner, 1818, is considered anomen dubiumassociated withA. gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted forA. lacteella, A. diplomochalis, A. centrifugens, andA. gonogrammabased on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the AntilleanA. diplomochalis. Our work highlights the efficiency of the DNA hybrid capture enrichment method to retrieve DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera.

Deceptive pollination often involves volatile organic compound emissions that mislead insects into performing nonrewarding pollination. Among deceptively pollinated plants, Arum maculatum is particularly well-known for its potent dung-like volatile organic compound emissions and specialized floral chamber, which traps pollinators-mainly Psychoda phalaenoides and Psychoda grisescens-overnight. However, little is known about the genes underlying the production of many Arum maculatum volatile organic compounds, and their influence on variation in pollinator attraction rates. Therefore, we performed de novo transcriptome sequencing of Arum maculatum appendix and male floret tissue collected during anthesis and postanthesis, from 10 natural populations across Europe. These RNA-seq data were paired with gas chromatography-mass spectrometry analyses of floral scent composition and pollinator data collected from the same inflorescences. Differential expression analyses revealed candidate transcripts in appendix tissue linked to malodourous volatile organic compounds including indole, p-cresol, and 2-heptanone. In addition, we found that terpene synthase expression in male floret tissue during anthesis significantly covaried with sex- and species-specific attraction of Psychoda phalaenoides and Psychoda grisescens. Taken together, our results provide the first insights into molecular mechanisms underlying pollinator attraction patterns in Arum maculatum and highlight floral chamber sesquiterpene (e.g. bicyclogermacrene) synthases as interesting candidate genes for further study.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Reproductive character displacement occurs when competition for successful breeding imposes a divergent selection on the interacting species, causing a divergence of reproductive traits. Here, we show that a disputed butterfly taxon is actually a case of male wing colour shift, apparently produced by reproductive character displacement. Using double digest restriction-site associated DNA sequencing and mitochondrial DNA sequencing we studied four butterfly taxa of the subgenus Cupido (Lepidoptera: Lycaenidae): Cupido minimus and the taxon carswelli, both characterized by brown males and females, plus C. lorquinii and C. osiris, both with blue males and brown females. Unexpectedly, taxa carswelli and C. lorquinii were close to indistinguishable based on our genomic and mitochondrial data, despite displaying strikingly different male coloration. In addition, we report and analysed a brown male within the C. lorquinii range, which demonstrates that the brown morph occurs at very low frequency in C. lorquinii. Such evidence strongly suggests that carswelli is conspecific with C. lorquinii and represents populations with a fixed male brown colour morph. Considering that these brown populations occur in sympatry with or very close to the blue C. osiris, and that the blue C. lorquinii populations never do, we propose that the taxon carswelli could have lost the blue colour due to reproductive character displacement with C. osiris. Since male colour is important for conspecific recognition during courtship, we hypothesize that the observed colour shift may eventually trigger incipient speciation between blue and brown populations. Male colour seems to be an evolutionarily labile character in the Polyommatinae, and the mechanism described here might be at work in the wide diversification of this subfamily of butterflies., European Regional Development Fund. Grant Numbers: CGL2016‐76322‐P, PID2019‐107078GB‐I00 Ministerio de Economía, Industria y Competitividad, Gobierno de España. Grant Number: BES‐2017‐080641 Ministerio de Ciencia, Innovación y Universidades Generalitat de Catalunya. Grant Number: 2017‐SGR‐991 Academy of Finland. Grant Number: 328895

The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double-digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes., Financial support was provided by projects PID2019-107078GB-I00 funded by MCIN/AEI/10.13039/501100011033 and 2017-SGR-991 funded by Generalitat de Catalunya to R.V., by grant BES-2017-080641, funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future” to J.C.H. and by the project “Ricerca e conservazione sugli Impollinatori dell’Arcipelago Toscano e divulgazione sui Lepidotteri del parco” to L.D. Computational resources used by D.K. were supplied by the project "e-Infrastruktura CZ" (e-INFRA LM2018140) provided within the program Projects of Large Research, Development and Innovations Infrastructures.

Caves put strong constraints on organisms living there, which results in acquisition of variety of troglomorphic traits, most obvious ones being depigmentation and degradation of visual system (Christiansen 2012). Cave habitats are considered fragmented, and the animals living there face limited connectivity between potential habitats (Barr 1967, Bregović and Zagmajster 2016, Trontelj 2018). Additionally, once adapted to underground conditions, cave-dwellers are thought to be unable to use the surface for dispersal, thus demonstrating population dynamics similar to those of the species found in islands (Barr and Holsinger 1985). We compared the population genetic structure of several cave spider species with different biology and ecology from different caves in the Dinarides. Namely, depigmented and anophthalmic Dysderidae species which were never collected outside caves, and several species from the genus Troglohyphantes, which exhibit different levels of troglomorphisms and dependency on cave habitat (some, like T. excavatus and T. kordunlikanus, can be occasionally found in surface habitats). Additionally, Dysderidae are wandering active hunters, while all Troglohyphantes species spin webs. In our study, we applied a hybridization-capture approach, i.e., HyRAD (Suchan et al. 2016) to extract and capture DNA from historical samples. We compared the population genetic structures among the species, and studied isolation by distance, and identified contrasted genetic structures related to the biology and ecology of each species. We identified a deeper population structuring and more pronounced patterns of isolation by distance in the highly troglomorphic species compared to the less troglomorphic ones. Species that can occasionally be found in surface habitats showed less structured populations compatible with higher dispersal ability. Additionally, we detected several common breaks in gene flow for most studied species, some of which can be explained by geographic and geologic features.

The rapid development of ancient DNA (aDNA) analysis in the last decades has induced a paradigm shift in ecology and evolution. Driven by a combination of breakthroughs in DNA isolation techniques, high-throughput sequencing and bioinformatics, ancient genome-scale data for a rapidly growing variety of taxa is now available, allowing researchers to directly observe demographic and evolutionary processes over time. However, the vast majority of palaeogenomic studies still focuses on human or animal remains. In this article, we make the case for a vast untapped resource of ancient plant material that is ideally suited for palaeogenomic analyses: Plant remains such as needles, leaves, wood, seeds or fruits that are deposited in natural archives, such as lake sediments, permafrost or even ice caves. Such plant remains are commonly found in large numbers and in stratigraphic sequence through time and have so far been used primarily to reconstruct past local species presences and abundances. However, they are also unique repositories of genetic information with the potential to revolutionize the fields of ecology and evolution by directly studying microevolutionary processes over time. Here, we give an overview of the current state-of-the-art, address important challenges, and highlight new research avenues to inspire future research.

International audience; Flowering plants emit complex bouquets of volatile organic compounds (VOCs) to mediate interactions with their pollinators. These bouquets are undoubtedly influenced by pollinatormediated selection, particularly in deceptively-pollinated species that rely on chemical mimicry. However, many uncertainties remain regarding how spatially and temporally heterogeneous pollinators affect the diversity and distribution of floral odour variation. Here, we characterized and compared the floral odours of ten populations of deceptively-pollinated Arum maculatum (Araceae), and inter-annual and decadal variation in pollinator attraction

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of phylogenetically unrelated plant and insect species, typical of the Eurasian steppes. We contrast three explicit demographic hypotheses by applying a novel approach combining Convolutional Neural Networks with Approximate Bayesian Computation. We identified congruent demographic responses of cold stage expansions and warm stage contractions across all species, but also species-specific effects. The demographic history of Eurasian steppe biota reflects major paleoecological turning points of the late Quaternary, and emphasizes the role of the climate as a driving force behind patterns of genetic variance.

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level.

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.

Domestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture., The work by G. Boeskorov is done on state assignment of DPMGI SB RAS. This project was supported by the University Paul Sabatier IDEX Chaire d’Excellence (OURASI); Villum Funden miGENEPI research programme; the CNRS ‘Programme de Recherche Conjoint’ (PRC); the CNRS International Research Project (IRP AMADEUS); the France Génomique Appel à Grand Projet (ANR-10-INBS-09-08, BUCEPHALE project); IB10131 and IB18060, both funded by Junta de Extremadura (Spain) and European Regional Development Fund; Czech Academy of Sciences (RVO:67985912); the Zoological Institute ZIN RAS (АААА-А19-119032590102-7); and King Saud University Researchers Supporting Project (NSRSP–2020/2). The research was carried out with the financial support of the Russian Foundation for Basic Research (19-59-15001 and 20-04-00213), the Russian Science Foundation (16-18-10265, 20-78-10151, and 21-18-00457), the Government of the Russian Federation (FENU-2020-0021), the Estonian Research Council (PRG29), the Estonian Ministry of Education and Research (PRG1209), the Hungarian Scientific Research Fund (Project NF 104792), the Hungarian Academy of Sciences (Momentum Mobility Research Project of the Institute of Archaeology, Research Centre for the Humanities); and the Polish National Science Centre (2013/11/B/HS3/03822). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie (grant agreement 797449). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements 681605, 716732 and 834616).

[Aim]: Coastal plants are terrestrial organisms for which ocean surface currents often act as long‐distance dispersal vectors (thalassochorous species) favouring broad distributions and connecting distant populations. However, few studies have statistically assessed the role of currents in modulating gene flow and species distributions of terrestrial organisms. Here we evaluate the hypothesis that some thalassochorous plants exhibit population connectivity, presumably due to effective seed dispersal driven by sea currents. Location Galápagos Islands (Ecuador). Taxon Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm. Methods Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance. Results Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal., [Location]: Galápagos Islands (Ecuador)., [Taxon]: Salt bush (Cryptocarpus pyriformis Kunth), a Galápagos native and locally widespread coastal angiosperm., [Methods]: Using 1806 SNPs obtained by ddRADseq, we evaluated the genetic structure and differentiation of the Galápagos salt bush. To assess the role of sea currents in modulating inter‐population gene flow, four explicit hypotheses were tested using reciprocal causal modelling and spatial eigenvector analysis: (a) isolation by sea resistance, considering that only sea dispersal is possible; (b) isolation by sea and inland resistance, considering that inland dispersal is also possible; (c) isolation by barrier, considering the sea as an obstacle to seed dispersal; and (d) isolation by geographical distance., [Results]: Low differentiation and little genetic structure were detected among populations of C. pyriformis. Pairwise genetic distances between populations from different islands were significantly correlated with cost distances calculated from sea‐current direction and speed. Nonetheless, inland dispersal also accounted for some gene flow within each island. Main conclusion Extensive and frequent seed dispersal by sea has apparently favoured strong inter‐island genetic connectivity within Galápagos. A combination of methods developed for terrestrial and marine domains (landscape and seascape genetics) aids in understanding how landscape features modulate gene flow of coastal plant species, as these terrestrial organisms are highly dependent on the sea for seed dispersal., This study is framed within a project also financed by the Ministerio de Economía y Competitividad (CGL2012‐C02‐01).

Floral odor is a complex trait that mediates many biotic interactions, including pollination. While high intraspecific floral odor variation appears to be common, the ecological and evolutionary drivers of this variation are often unclear. Here, we investigated the influence of spatially and temporally heterogeneous pollinator communities on floral odor variation inArum maculatum(Araceae). Through Europe-wide field surveys, we identified high floral odor diversity and shifts in the dominant pollinator species within severalA. maculatumpopulations compared to pollinator data from the same sites ten years ago. Using common-garden experiments, we further confirmed that inflorescences from native and foreign pollinator backgrounds were equally efficient at attracting local pollinators. The substantial within-population floral odor variation we observed may therefore be advantageous when facing temporally heterogeneous pollinator communities. We propose spatio-temporal heterogeneity in pollinators as one potential mechanism maintaining diverse floral odor bouquets in angiosperms.

Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.

Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the spatial scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation extending back several millions of years. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation., This research was supported by Spanish MINECO grants CGL2013‐42589‐P and CGL2017‐85718‐P, co‐financed by FEDER and awarded to B.C.E, and by the ERA‐Net Net‐Biome research framework, financed through Canary Island Government ACIISI grants SE‐12/04 and SE‐12/02, co‐financed by FEDER and awarded to P.O. and B.C.E respectively. A.S.‐C. was funded by the Ministerio de Educación y Formación Profesional through the FPU PhD fellowship (FPU014/02948). J.P. was funded by the MINECO through the Juan de la Cierva Program ‐ Incorporation (IJCI‐2014‐19691) and Ramón y Cajal Program (RYC‐2016‐20506), and Marie Sklodowska‐Curie COFUND, Researchers' Night and Individual Fellowships Global (MSCA grant agreement No 747238, 'UNISLAND').

International audience; Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analyzing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this manuscript, we apply such a method, i.e., HyRAD, to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. We show in the localities for which the data retrieved has sufficient power to accurately examine genetic dynamics through time, that genetic erosion has increased across the last hundred years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies, i.e., Erebia embla, isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.

The habitat template concept applied to a freshwater system indicates that lotic species, or those which occupy permanent habitats along stream courses, are less dispersive than lentic species, or those that occur in more ephemeral aquatic habitats. Thus, populations of lotic species will be more structured than those of lentic species. Stream courses include both flowing water and small, stagnant microhabitats that can provide refuge when streams are low. Many species occur in these microhabitats but remain poorly studied. Here, we present population genetic data for one such species, the tropical diving beetle Exocelina manokwariensis (Dytiscidae), sampled from six localities along a ~300 km transect across the Birds Head Peninsula of New Guinea. Molecular data from both mitochondrial (CO1 sequences) and nuclear (ddRAD loci) regions document fine-scale population structure across populations that are ~45 km apart. Our results are concordant with previous phylogenetic and macroecological studies that applied the habitat template concept to aquatic systems. This study also illustrates that these diverse but mostly overlooked microhabitats are promising study systems in freshwater ecology and evolutionary biology. With the advent of next-generation sequencing, fine-scale population genomic studies are feasible for small nonmodel organisms to help illuminate the effect of habitat stability on species' natural history, population structure and geographic distribution.

Tropical mountains are areas of high species richness and endemism. Two historical phenomena may have contributed to this: (i) fragmentation and isolation of habitats may have promoted the genetic differentiation of populations and increased the possibility of allopatric divergence and speciation and (ii) the mountain areas may have allowed long-term population persistence during global climate fluctuations. These two phenomena have been studied using either species occurrence data or estimating species divergence times. However, only few studies have used intraspecific genetic data to analyse the mechanisms by which endemism may emerge at the microevolutionary scale. Here, we use landscape analysis of genomic SNP data sampled from two high-elevation plant species from an archipelago of tropical sky islands (the Trans-Mexican Volcanic Belt) to test for population genetic differentiation, synchronous demographic changes and habitat persistence. We show that genetic differentiation can be explained by the degree of glacial habitat connectivity among mountains and that mountains have facilitated the persistence of populations throughout glacial/interglacial cycles. Our results support the ongoing role of tropical mountains as cradles for biodiversity by uncovering cryptic differentiation and limits to gene flow., Part of the analyses were carried out on the High Performance Computing Cluster supported by the Research and Specialist Computing Support service at UEA and at the City University of New York High Performance Computing Center, with support from the National Science Foundation (CNS‐0855217 and CNS‐0958379). This work was supported by Consejo Nacional de Ciencia y Tecnología (grant number CONACYT 213538 to AMY and CONACYT 178245 to DP), by Rosemary Grant Award for Graduate Student Research from the Society for the Study of Evolution granted to AMY, by grants from National Science Foundation (DEB‐1253710 to M.J.H.; DEB‐1343578 to Ana C. Carnaval, M.J.H., and Kyle C. McDonald); FAPESP (BIOTA, 2013/50297‐0 to A.C.C., M.J.H., and K.C.M.); and NASA through the Dimensions of Biodiversity Program.

Geomorphology has increasingly considered the role of biotic factors as controls upon geomorphic processes across a wide range of spatial and temporal scales. Where timescales are long (centennial and longer), it has been possible to quantify relationships between geomorphic processes and vegetation using, for example, the pollen record. However, where the biotic agents are fauna, longer term reconstruction of the impacts of biological activity upon geomorphic processes is more challenging. Here, we review the prospect of using environmental DNA as a molecular proxy to decipher the presence and nature of faunal influences on geomorphic processes in both present and ancient deposits. When used appropriately, this method has the potential to improve our understanding of biotic drivers of geomorphic processes, notably fauna, over long timescales and so to reconstruct how such drivers might explain the landscape as we see it today.

Aim: The seed beetle Callosobruchus maculatus is an important tropical and subtropical pest of legumes distributed world-wide. Archaeological evidence suggests an African origin with later world-wide invasion facilitated by the last centuries' legume trading and exchange. To date, no studies could identify the routes or timing of dispersal of the species. Here, we investigate the global phylogeography of this pest to shed light on the main inter-continental dispersal routes that led to it becoming a cosmopolitan pest. Location: World-wide. Methods: We sampled seed beetles over a large fraction of the species' range and sequenced one nuclear and three mitochondrial loci. Using this data, we estimated spatio-temporal phylogeographical reconstructions, and the demographic history of the species. We also used our dataset to evaluate the effect of panmixia on Bayesian demographic estimations. Results: Callosobruchus maculatus exhibited regional and continental genetic structure, with the highest genetic diversity found in Africa. Our discrete Bayesian phylogeographical approach indicated that the species first dispersed to Asia and then colonized the pantropical belt. The three methods used for inferring the demographic history of C. maculatus indicated a recent demographic expansion in the world-wide dataset, as well as in the subset restricted to African samples. Such a signal was, however, not observed in the subset composed of Asian specimens. This demographic expansion occurred in the Holocene and is likely explained by the spread of cowpea and other host legumes across and out of Africa. Main conclusions: The inferred dispersal routes support the idea that the evolutionary history of C. maculatus relates to the trade of its main host plant, Vigna unguiculata. Human-mediated processes appear to have shaped the global genetic structure of this pest. As a methodological implication, we demonstrate that coalescent-based demographic reconstructions can be erroneous if the dataset violates the assumption of panmixia.

We examine the genetics, morphology and ecology of the widely distributed Megachile concinna species complex (Hymenoptera: Megachilidae), which is composed of numerous taxa of unclear taxonomic status in Africa and the Palearctic. In the Western Palearctic, three genetically distinct operational taxonomic units (OTUs) are found around the Mediterranean Sea: the western Mediterranean OTU M. pusilla, the eastern Mediterranean OTU M. anatolica and the predominantly Arabian OTU M. leucostoma. A morphological cline is present between anatolica and leucostoma in the Near East, despite a lack of mitochondrial introgression between the two; one nuclear marker suggests some gene flow between these OTUs. The contact zone between pusilla and leucostoma could not be sampled but phenotypic intergradation is also observed between these OTUs in northern Africa. In contrast, study of the contact zone between pusilla and anatolica indicates that both OTUs retain phenotypic and genomic integrity in sympatry over a contact zone spanning 1000 km. The arrangement of these three OTUs suggests a ring of interconnected populations around the Mediterranean Sea and sympatry between pusilla and anatolica at both ends of the ring in southeastern Europe. The latter two OTUs exhibit ecological differences, including phenology and host-plant preferences, which may contribute to their isolation. In addition, our results suggest that two OTUs, M. venusta and M. concinna, maintain genetic and phenotypic integrity in sympatry in parts of Africa; the latter is recognized as a valid species here. Lastly, our results indicate that two OTUs have been introduced independently into the New World, pusilla in North America and Argentina, and concinna in the Antilles.

[Aim] How non-dispersive taxa colonize islands is generalized as being by wind, or rafting, with the implicit assumption that such events involve one (wind) or a few (rafting) individuals. However, because of the evolutionary time-scale for colonization events, the fit of individual species to a conceptual model of wind or rafting is difficult to assess. Here, we describe an alternative testable geological model for inter-island colonization that can result in larger effective founding population sizes than traditionally accepted colonization mechanisms. We then test for the fit of genetic data to this model using weevils from the Laparocerus tessellatus species complex. [Location] Canary Islands. Methods: Using a combination of geological data for the Canary Islands, and mtDNA data from a weevil radiation within the Canary Islands, we test three species-level predictions for mega-landslides as drivers of oceanic rafting between islands and subsequent speciation: (1) colonization should involve multiple female lineages, (2) founding lineages should have a common geographical origin, consistent with a mega-landslide event, and (3) colonization direction should be consistent with ocean currents. [Results] Both individual-level and population-level analyses support a mega-landslide event as the driver of colonization from the island of Tenerife to La Palma. At least four female lineages colonized La Palma from Tenerife, with the geographical range of ancestral sequences to these four lineages describing the limits of the La Orotava mega-landslide in Tenerife. [Main conclusions] In the context of island biogeographical theory, mega-landslides may be an important driver of colonization, and subsequent lineage diversification. They provide a framework for hypothesis testing using genetic data from species, or closely related species, with ranges that encompass landslides and potential areas of colonization., Fieldwork was supported by permits granted by the Cabildo of La Palma (No. ref. A/EST‐020/2014), the Cabildo of Gran Canaria (No. exp.: 167/15), and the Cabildo of Tenerife (No. sigma: 2015‐00218). We are also grateful to the Cabildo of La Palma for providing accommodation. This work was supported by Spanish MINECO grant CGL2013‐42589‐P, co‐financed by FEDER. VGO is funded by a Spanish MINECO FPI contract and JP is funded by a Spanish MINECO Fellowship (Juan de la Cierva Program – Incorporation); IJCI‐2014‐19691.

Background and aims – Despite their vicariant distribution and slightly distinct morphologies, the Dotted Loosestrife ( L. punctata L.) and the Whorled Loosestrife ( L. verticillata (Green) Hand.-Mazz.) have sometimes been treated as synonyms, or even confounded by several authors. Here we examine the genetic divergence of these two taxa in order to clarify their species status.Methods – We apply AFLP genome fingerprinting to samples from eleven wild and two naturalized populations, and compile occurrence data from herbaria and public data depositories.Key results – The distribution of genotypes in a multivariate space confirms the distinct species status of the two species, and highlights the absence of natural hybrids between the two in their native area. This result contrasts with the hybrid nature of naturalized populations from northern Europe, likely produced through horticultural practices.

We present an original method to de novo call variants for Restriction site associated DNA Sequencing (RAD-Seq). RAD-Seq is a technique characterized by the sequencing of specific loci along the genome, that is widely employed in the field of evolutionary biology since it allows to exploit variants (mainly SNPs) information from entire populations at a reduced cost. Common RAD dedicated tools, as STACKS or IPyRAD, are based on all-versus-all read comparisons, which require consequent time and computing resources. Based on the variant caller DiscoSnp, initially designed for shotgun sequencing, DiscoSnp-RAD avoids this pitfall as variants are detected by exploring the De Bruijn Graph built from all the read datasets. We tested the implementation on RAD data from 259 specimens of Chiastocheta flies, morphologically assigned to 7 species. All individuals were successfully assigned to their species using both STRUCTURE and Maximum Likelihood phylogenetic reconstruction. Moreover, identified variants succeeded to reveal a within species structuration and the existence of two populations linked to their geographic distributions. Furthermore, our results show that DiscoSnp-RAD is at least one order of magnitude faster than state-of-the-art tools. The overall results show that DiscoSnp-RAD is suitable to identify variants from RAD data, and stands out from other tools due to his completely different principle, making it significantly faster, in particular on large datasets.LicenseGNU Affero general public licenseAvailabilityhttps://github.com/GATB/DiscoSnpContactjeremy.gauthier@inria.fr

© The Author(s). 2019, [Background] The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant eaters among its approximately 315,000 species. In particular, plants defend themselves with a diversity of specialized toxic chemicals. These may impose selective pressures that drive genomic diversification and speciation in phytophagous beetles. However, evidence of changes in beetle gene repertoires driven by such interactions remains largely anecdotal and without explicit hypothesis testing., [Results] We explore the genomic consequences of beetle-plant trophic interactions by performing comparative gene family analyses across 18 species representative of the two most species-rich beetle suborders. We contrast the gene contents of species from the mostly plant-eating suborder Polyphaga with those of the mainly predatory Adephaga. We find gene repertoire evolution to be more dynamic, with significantly more adaptive lineage-specific expansions, in the more speciose Polyphaga. Testing the specific hypothesis of adaptation to plant feeding, we identify families of enzymes putatively involved in beetle-plant interactions that underwent adaptive expansions in Polyphaga. There is notable support for the selection hypothesis on large gene families for glutathione S-transferase and carboxylesterase detoxification enzymes., [Conclusions] Our explicit modeling of the evolution of gene repertoires across 18 species identifies putative adaptive lineage-specific gene family expansions that accompany the dietary shift towards plants in beetles. These genomic signatures support the popular hypothesis of a key role for interactions with plant chemical defenses, and for plant feeding in general, in driving beetle diversification., This work was supported by the United States National Science Foundation (DEB 1355169) and the United States Department of Agriculture (cooperative agreement 8130-0547-CA) to DDM, the Spanish grant CGL2013-42589-P awarded by the MINECO and co-financed by FEDER to BCE, the Science Foundation DFG grant BA2152/11-1, 2, the BGI-Shenzhen, the China National Genebank, and the following Swiss National Science Foundation grants: 31003A_143936 (PI), 31003A_173048 (MRR), PP00P3_170664 (RMW), and PP00P3_172899 (NA). Funding for open access charge: Geneva Natural History Museum.

The life-history traits of the most important storage pest of cowpea seeds Callosobruchus maculatus (Fabricius) were examined on the basis of oviposition preference and adult emergence on three cowpea varieties Baye Ngagne, Mame Fama and Ndiaga Aw. Fecundity and emergence rate were assessed by using both free choice and no-choice scenarios. Our results showed that, when females were in no-choice scenarios, they did not demonstrate any preferences for oviposition. In contrast, in choice scenarios, there was significant difference for oviposition between the three varieties: Mame Fama was the most preferred (fecundity rate = 30.50), while Ndiaga Aw was the least preferred (fecundity rate = 19.85). Further, in both no-choice and choice scenarios, adult emergences were significantly different between the three varieties, the emergence rates were higher on Baye Ngagne and Mame Fama varieties, than on Ndiaga Aw variety. Even though in an indirect way, our results provide a chemical and biological explanation to the observed farmer preference for the Ndiaga Aw variety. This study is also an important contribution to the construction of knowledge necessary to better understand the life-history traits of this pest and hopefully help its control.

International audience; The size-advantage model (SAM) explains the temporal variation of energetic investment on reproductive structures (i.e. male and female gametes and reproductive organs) in long-lived hermaphroditic plants and animals. It proposes that an increase in the resources available to an organism induces a higher relative investment on the most energetically costly sexual structures. In plants, pollination interactions are known to play an important role in the evolution of floral features. Because the SAM directly concerns flower characters, pollinators are expected to have a strong influence on the application of the model. This hypothesis, however, has never been tested. Here, we investigate whether the identity and diversity of pollinators can be used as a proxy to predict the application of the SAM in exclusive zoophilous plants. We present a new approach to unravel the dynamics of the model and test it on several widespread Arum (Araceae) species. By identifying the species composition, abundance and spatial variation of arthropods trapped in inflorescences, we show that some species (i.e. A. cylindraceum and A. italicum) display a generalist reproductive strategy, relying on the exploitation of a low number of dipterans, in contrast to the pattern seen in the specialist A. maculatum (pollinated specifically by two fly species only). Based on the model presented here, the application of the SAM is predicted for the first two and not expected in the latter species, those predictions being further confirmed by allometric measures. We here demonstrate that while an increase in the female zone occurs in larger inflorescences of generalist species, this does not happen in species demonstrating specific pollinators. This is the first time that this theory is both proposed and empirically tested in zoophilous plants. Its overall biological importance is discussed through its application in other non-Arum systems.

Due to their static nature, protected areas (PAs) are vulnerable to global change, and resident species will likely need to colonize new sites and exchange migrants to sustain viable local populations. Alpine habitats often have a high level of protection, yet extensive environmental heterogeneity and the limited dispersal ability of many endemic species makes it unclear whether PA networks provide sufficient connectivity to protect vulnerable species. We assess landscape connectivity in the European alpine PA network by combining measures of habitat and genetic connectivity using community landscape genetics approaches. Examining 27 plant species, we compare levels of genetic diversity in PA and non-PA sites, and rank non-PA sites for their potential value in facilitating genetic and habitat connectivity, as well as preserving species richness in 893 alpine plants. Non-PA sites do not significantly enhance overall levels of genetic variability across species. However, spatial genetic turnover (allele frequency variation across space) is influenced by geographical and environmental distance, suggesting that genetic connectivity, and by extension landscape connectivity, is impacted by gaps in the PA network. A subset of non-PA sites, when measured for habitat connectivity, genetic connectivity and species richness using spatial graphs, substantially increase landscape connectivity for alpine plants, although there are discrepancies among metrics in ranking sites. We provide the first example of the evaluation and prediction of new PAs including levels of intraspecific genetic diversity for a whole community. This has significance for the management and extension of the European alpine network, especially in identifying valuable unprotected sites.

Background and Aims Various studies and conservationist reports have warned about the contraction of the last subtropical Afro-Macaronesian forests. These relict vegetation zones have been restricted to a few oceanic and continental islands around the edges of Africa, due to aridification. Previous studies on relict species have generally focused on glacial effects on narrow endemics; however, little is known about the effects of aridification on the fates of previously widespread subtropical lineages. Methods Nuclear microsatellites and ecological niche modelling were used to understand observed patterns of genetic diversity in two emblematic species, widely distributed in these ecosystems: Canarina eminii (a palaeoendemic of the eastern Afromontane forests) and Canarina canariensis (a palaeoendemic of the Canarian laurel forests). The software DIYABC was used to test alternative demographic scenarios and an ensemble method was employed to model potential distributions of the selected plants from the end of the deglaciation to the present. Key Results All the populations assessed experienced a strong and recent population decline, revealing that locally widespread endemisms may also be alarmingly threatened. Conclusions The detected extinction debt, as well as the extinction spiral to which these populations are subjected, demands urgent conservation measures for the unique, biodiversity-rich ecosystems that they inhabit., This work was supported by a PhD research grant (BES-2010–037261) to M.M., including short research stays at JBCVC-CSIC (J.C.C.), University of Lausanne (N.A.) and University of Fribourg (L.P. and M.H.) funded by MINECO (grants CGL2009-1332-C03-01 (MICINN), CGL2012- 40129-C02-01 and CGL2015-67849-P) (MINECO/FEDER) to I.S.; grant CGL2012-40129-C02-02 (MINECO) and a Marie Curie Intra-European Fellowship (PIEF-GA-2012-329088) to M.H. and project grant DEMIURGO MAC/1/C20) to J.C.C.

Since Ehrlich & Raven's seminal paper 50 years ago, coevolution has been seen as a major driver of species diversification. Here, we review classical and more recent case studies on the coevolution of plants and associated insects, to examine whether the coevolutionary component holds as an explanation of their current diversity. We discuss the main dogmas in coevolution and argue that coevolutionary processes should not be considered as major drivers of diversification in plants and insects. Instead, we suggest that coevolution essentially occurs through relatively short ‘interludes’, making the pattern difficult to detect. We also criticize the use of comparative phylogenetics to investigate coevolutionary processes, as coevolution may not necessarily produce congruent phylogenies among interacting lineages and, in turn, other processes may produce patterns of codivergence. Finally, we propose new lines of investigation for future research.