National Museum

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

Parents affect offspring fitness by propagule size and quality, selection of oviposition site, quality of incubation, feeding of dependent young, and their defence against predators and parasites. Despite many case studies on each of these topics, this knowledge has not been rigorously integrated into individual parental care traits for any taxon. Consequently, we lack a comprehensive, quantitative assessment of how parental care modifies offspring phenotypes. This meta-analysis of 283 studies with 1805 correlations between egg size and offspring quality in birds is intended to fill this gap. The large sample size enabled testing of how the magnitude of the relationship between egg size and offspring quality depends on a number of variables. Egg size was positively related to nearly all studied offspring traits across all stages of the offspring life cycle. Not surprisingly, the relationship was strongest at hatching but persisted until the post-fledging stage. Morphological traits were the most closely related to egg size but significant relationships were also found with hatching success, chick survival, and growth rate. Non-significant effect sizes were found for egg fertility, chick immunity, behaviour, and life-history or sexual traits. Effect size did not depend on whether chicks were raised by their natural parents or were cross-fostered to other territories. Effect size did not depend on species-specific traits such as developmental mode, clutch size, and relative size of the egg, but was larger if tested in captive compared to wild populations and between rather than within broods. In sum, published studies support the view that egg size affects juvenile survival. There are very few studies that tested the relationship between egg size and the fecundity component of offspring fitness, and no studies on offspring survival as adults or on global fitness. More data are also needed for the relationships between egg size and offspring behavioural and physiological traits. It remains to be established whether the relationship between egg size and offspring performance depends on the quality of the offspring environment. Positive effect sizes found in this study are likely to be driven by a causal effect of egg size on offspring quality. However, more studies that control for potential confounding effects of parental post-hatching care, genes, and egg composition are needed to establish firmly this causal link.

Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power of molecular biodiversity assessments, the link between DNA sequences and species and the analytics to discriminate entities remain crucial. Here, we present an analysis of the first DNA barcode library for the freshwater fish fauna of the Mediterranean BH (526 spp.), with virtually complete species coverage (498 spp., 98% extant species). In order to build an identification system supporting conservation, we compared species determination by taxonomists to multiple clustering analyses of DNA barcodes for 3165 specimens. The congruence of barcode clusters with morphological determination was strongly dependent on the method of cluster delineation, but was highest with the general mixed Yule-coalescent (GMYC) model-based approach (83% of all species recovered as GMYC entity). Overall, genetic morphological discontinuities suggest the existence of up to 64 previously unrecognized candidate species. We found reduced identification accuracy when using the entire DNA-barcode database, compared with analyses on databases for individual river catchments. This scale effect has important implications for barcoding assessments and suggests that fairly simple identification pipelines provide sufficient resolution in local applications. We calculated Evolutionarily Distinct and Globally Endangered scores in order to identify candidate species for conservation priority and argue that the evolutionary content of barcode data can be used to detect priority species for future IUCN assessments. We show that large-scale barcoding inventories of complex biotas are feasible and contribute directly to the evaluation of conservation priorities.

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and closely related species distributed across eleven countries, effectively comprising the entire range of the group. We performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of eight mtDNA lineages have ranges >100,000 km2. One of them occupies an area of almost one million km2 encompassing multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.

Abstract With rapid development and the spread of urbanized land, there is an increasing need to understand species' responses to urban conditions. Carnivores are considered to be sensitive to urbanization; however, there is ample evidence that some carnivore species successfully inhabit urban areas, and human‐modified habitats have recently been recognized as an important refuge for several species. Despite the increasing number of studies on urban carnivore ecology, no comprehensive cross‐species comparisons have been made in order to assess the effects of urbanization on the spatial ecology of carnivores and their population densities. Such a review could provide interesting insight into how some carnivore species respond to increasing urbanization. Specifically, we examine changes in population density and home range size of eight carnivore species that occur along the natural–urban environmental gradient. Using data from 411 articles, we provide evidence that the home range size of carnivores decreases in six out of eight species, and population density increases in three out of six species along the natural–urban habitat gradient. The density‐dependent pattern of variation in home range size is consistent in all species studied. Our results emphasize the remarkable ability of some carnivore species to adapt to novel environments through their behavioural flexibility and life history adaptations. We outline ideas for future research that could be adopted in addressing this phenomenon, namely comparative approaches and detailed studies of biotic and abiotic conditions along natural–urban gradients.

BACKGROUND: Leuciscinae is a subfamily belonging to the Cyprinidae fish family that is widely distributed in Circum-Mediterranean region. Many efforts have been carried out to deciphering the evolutionary history of this group. Thus, different biogeographical scenarios have tried to explain the colonization of Europe and Mediterranean area by cyprinids, such as the "north dispersal" or the "Lago Mare dispersal" models. Most recently, Pleistocene glaciations influenced the distribution of leuciscins, especially in North and Central Europe. Weighing up these biogeographical scenarios, this paper constitutes not only the first attempt at deciphering the mitochondrial and nuclear relationships of Mediterranean leuciscins but also a test of biogeographical hypotheses that could have determined the current distribution of Circum-Mediterranean leuciscins. RESULTS: A total of 4439 characters (mitochondrial + nuclear) from 321 individuals of 176 leuciscine species rendered a well-supported phylogeny, showing fourteen main lineages. Analyses of independent mitochondrial and nuclear markers supported the same main lineages, but basal relationships were not concordant. Moreover, some incongruence was found among independent mitochondrial and nuclear phylogenies. The monophyly of some poorly known genera such as Pseudophoxinus and Petroleuciscus was rejected. Representatives of both genera belong to different evolutionary lineages. Timing of cladogenetic events among the main leuciscine lineages was gained using mitochondrial and all genes data set. CONCLUSIONS: Adaptations to a predatory lifestyle or miniaturization have superimposed the morphology of some species. These species have been separated into different genera, which are not supported by a phylogenetic framework. Such is the case of the genera Pseudophoxinus and Petroleuciscus, which real taxonomy is not well known. The diversification of leuciscine lineages has been determined by intense vicariant events following the paleoclimatological and hydrogeological history of Mediterranean region. We propose different colonization models of Mediterranean region during the early Oligocene. Later vicariance events promoted Leuciscinae diversification during Oligocene and Miocene periods. Our data corroborate the presence of leuciscins in North Africa before the Messinian salinity crisis. Indeed, Messinian period appears as a stage of gradually Leuciscinae diversification. The rise of humidity at the beginning of the Pliocene promoted the colonization and posterior isolation of newly established freshwater populations. Finally, Pleistocene glaciations determined the current European distribution of some leuciscine species.

Reptiles use pterin and carotenoid pigments to produce yellow, orange, and red colors. These conspicuous colors serve a diversity of signaling functions, but their molecular basis remains unresolved. Here, we show that the genomes of sympatric color morphs of the European common wall lizard ( Podarcis muralis ), which differ in orange and yellow pigmentation and in their ecology and behavior, are virtually undifferentiated. Genetic differences are restricted to two small regulatory regions near genes associated with pterin [ sepiapterin reductase ( SPR )] and carotenoid [ beta-carotene oxygenase 2 ( BCO2 )] metabolism, demonstrating that a core gene in the housekeeping pathway of pterin biosynthesis has been coopted for bright coloration in reptiles and indicating that these loci exert pleiotropic effects on other aspects of physiology. Pigmentation differences are explained by extremely divergent alleles, and haplotype analysis revealed abundant transspecific allele sharing with other lacertids exhibiting color polymorphisms. The evolution of these conspicuous color ornaments is the result of ancient genetic variation and cross-species hybridization.

The flowering plants that dominate modern vegetation possess leaf gas exchange potentials that far exceed those of all other living or extinct plants. The great divide in maximal ability to exchange CO(2) for water between leaves of nonangiosperms and angiosperms forms the mechanistic foundation for speculation about how angiosperms drove sweeping ecological and biogeochemical change during the Cretaceous. However, there is no empirical evidence that angiosperms evolved highly photosynthetically active leaves during the Cretaceous. Using vein density (D(V)) measurements of fossil angiosperm leaves, we show that the leaf hydraulic capacities of angiosperms escalated several-fold during the Cretaceous. During the first 30 million years of angiosperm leaf evolution, angiosperm leaves exhibited uniformly low vein D(V) that overlapped the D(V) range of dominant Early Cretaceous ferns and gymnosperms. Fossil angiosperm vein densities reveal a subsequent biphasic increase in D(V). During the first mid-Cretaceous surge, angiosperm D(V) first surpassed the upper bound of D(V) limits for nonangiosperms. However, the upper limits of D(V) typical of modern megathermal rainforest trees first appear during a second wave of increased D(V) during the Cretaceous-Tertiary transition. Thus, our findings provide fossil evidence for the hypothesis that significant ecosystem change brought about by angiosperms lagged behind the Early Cretaceous taxonomic diversification of angiosperms.

. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

Rapid and reliable identification of insects is important in many contexts, from the detection of disease vectors and invasive species to the sorting of material from biodiversity inventories. Because of the shortage of adequate expertise, there has long been an interest in developing automated systems for this task. Previous attempts have been based on laborious and complex handcrafted extraction of image features, but in recent years it has been shown that sophisticated convolutional neural networks (CNNs) can learn to extract relevant features automatically, without human intervention. Unfortunately, reaching expert-level accuracy in CNN identifications requires substantial computational power and huge training data sets, which are often not available for taxonomic tasks. This can be addressed using feature transfer: a CNN that has been pretrained on a generic image classification task is exposed to the taxonomic images of interest, and information about its perception of those images is used in training a simpler, dedicated identification system. Here, we develop an effective method of CNN feature transfer, which achieves expert-level accuracy in taxonomic identification of insects with training sets of 100 images or less per category, depending on the nature of data set. Specifically, we extract rich representations of intermediate to high-level image features from the CNN architecture VGG16 pretrained on the ImageNet data set. This information is submitted to a linear support vector machine classifier, which is trained on the target problem. We tested the performance of our approach on two types of challenging taxonomic tasks: 1) identifying insects to higher groups when they are likely to belong to subgroups that have not been seen previously and 2) identifying visually similar species that are difficult to separate even for experts. For the first task, our approach reached $CDATA[$CDATA[$>$$92% accuracy on one data set (884 face images of 11 families of Diptera, all specimens representing unique species), and $CDATA[$CDATA[$>$$96% accuracy on another (2936 dorsal habitus images of 14 families of Coleoptera, over 90% of specimens belonging to unique species). For the second task, our approach outperformed a leading taxonomic expert on one data set (339 images of three species of the Coleoptera genus Oxythyrea; 97% accuracy), and both humans and traditional automated identification systems on another data set (3845 images of nine species of Plecoptera larvae; 98.6 % accuracy). Reanalyzing several biological image identification tasks studied in the recent literature, we show that our approach is broadly applicable and provides significant improvements over previous methods, whether based on dedicated CNNs, CNN feature transfer, or more traditional techniques. Thus, our method, which is easy to apply, can be highly successful in developing automated taxonomic identification systems even when training data sets are small and computational budgets limited. We conclude by briefly discussing some promising CNN-based research directions in morphological systematics opened up by the success of these techniques in providing accurate diagnostic tools.

Protected Areas (PAs) are the cornerstone of biodiversity conservation. Here, we collated distributional data for >14,000 (~70% of) species of amphibians and reptiles (herpetofauna) to perform a global assessment of the conservation effectiveness of PAs using species distribution models. Our analyses reveal that >91% of herpetofauna species are currently distributed in PAs, and that this proportion will remain unaltered under future climate change. Indeed, loss of species' distributional ranges will be lower inside PAs than outside them. Therefore, the proportion of effectively protected species is predicted to increase. However, over 7.8% of species currently occur outside PAs, and large spatial conservation gaps remain, mainly across tropical and subtropical moist broadleaf forests, and across non-high-income countries. We also predict that more than 300 amphibian and 500 reptile species may go extinct under climate change over the course of the ongoing century. Our study highlights the importance of PAs in providing herpetofauna with refuge from climate change, and suggests ways to optimize PAs to better conserve biodiversity worldwide.

BACKGROUND AND AIMS: Genome size and chromosome numbers are important cytological characters that significantly influence various organismal traits. However, geographical representation of these data is seriously unbalanced, with tropical and subtropical regions being largely neglected. In the present study, an investigation was made of chromosomal and genome size variation in the majority of Curcuma species from the Indian subcontinent, and an assessment was made of the value of these data for taxonomic purposes. METHODS: Genome size of 161 homogeneously cultivated plant samples classified into 51 taxonomic entities was determined by propidium iodide flow cytometry. Chromosome numbers were counted in actively growing root tips using conventional rapid squash techniques. KEY RESULTS: Six different chromosome counts (2n = 22, 42, 63, >70, 77 and 105) were found, the last two representing new generic records. The 2C-values varied from 1.66 pg in C. vamana to 4.76 pg in C. oligantha, representing a 2.87-fold range. Three groups of taxa with significantly different homoploid genome sizes (Cx-values) and distinct geographical distribution were identified. Five species exhibited intraspecific variation in nuclear DNA content, reaching up to 15.1 % in cultivated C. longa. Chromosome counts and genome sizes of three Curcuma-like species (Hitchenia caulina, Kaempferia scaposa and Paracautleya bhatii) corresponded well with typical hexaploid (2n = 6x = 42) Curcuma spp. CONCLUSIONS: The basic chromosome number in the majority of Indian taxa (belonging to subgenus Curcuma) is x = 7; published counts correspond to 6x, 9x, 11x, 12x and 15x ploidy levels. Only a few species-specific C-values were found, but karyological and/or flow cytometric data may support taxonomic decisions in some species alliances with morphological similarities. Close evolutionary relationships among some cytotypes are suggested based on the similarity in homoploid genome sizes and geographical grouping. A new species combination, Curcuma scaposa (Nimmo) Skornick. & M. Sabu, comb. nov., is proposed.

Recent focus on plant‐insect associations during the angiosperm radiation from the last 30 million years of the Early Cretaceous has inadvertently de‐emphasized a similar but earlier diversification that occurred among gymnosperms. The existence of gymnosperm‐insect associations during the preangiospermous Mesozoic is evidenced by mouthparts capable of reaching and imbibing pollination drops or similar fluids, availability of pollen types consistent with entomophily, and opportunities for related consumption of pollen, seeds, and reproductively associated tissues in major seed‐plant groups, namely seed ferns, conifers, cycads, bennettitaleans, and gnetaleans. Based on stereotypical plant damage, head‐adherent pollen, gut contents, wing structure, mouthpart morphology and insect damage to plant reproductive organs, the likely nectarivores, pollinivores and pollinators were orthopterans, phasmatodeans, webspinners, sawflies and wasps, moths, beetles, mecopteroids, and true flies. These associations are ranked from possible to probable although the last three insect clades provide the strongest evidence for pollinator activity. We document two mid Cretaceous examples of these associations—cycadeoideaceous bennettitaleans and beetles and a cheirolepidiaceous conifer and flies—for which there are multiple lines of evidence for insect consumption of plant reproductive tissues but also pollination mutualisms. These data highlight the independent origin of a major phase of plant‐insect pollinator‐related associations during the mid Mesozoic that served as a prelude for the separate, iterative and later colonization of angiosperms.

Europe's prehistory oversaw dynamic and complex interactions of diverse societies, hitherto unexplored at detailed regional scales. Studying 271 human genomes dated ~4900 to 1600 BCE from the European heartland, Bohemia, we reveal unprecedented genetic changes and social processes. Major migrations preceded the arrival of "steppe" ancestry, and at ~2800 BCE, three genetically and culturally differentiated groups coexisted. Corded Ware appeared by 2900 BCE, were initially genetically diverse, did not derive all steppe ancestry from known Yamnaya, and assimilated females of diverse backgrounds. Both Corded Ware and Bell Beaker groups underwent dynamic changes, involving sharp reductions and complete replacements of Y-chromosomal diversity at ~2600 and ~2400 BCE, respectively, the latter accompanied by increased Neolithic-like ancestry. The Bronze Age saw new social organization emerge amid a ≥40% population turnover.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

Abstract The phylogeny and evolutionary history of the water scavenger beetles ( C oleoptera: H ydrophilidae) are inferred from comprehensive analyses of DNA sequence data from the mitochondrial genes COI , COII and 16S and the nuclear genes 18S , 28S and arginine kinase . Bayesian and maximum parsimony analyses included 151 taxa, representing all subfamilies, tribes and subtribes that have ever been proposed in the family, as well as representatives of the hydrophiloid families H elophoridae, H ydrochidae, S percheidae, E pimetopidae and G eorissidae. The resulting well‐supported trees strongly disagree with prior classifications of the H ydrophilidae, suggesting that the smaller subfamilies ( H orelophinae, H orelophopsinae and S phaeridiinae) are derived from within the larger H ydrophilinae. The existing tribal classification is more compatible with our results, but many significant differences are evident. Here, we present a new classification of the H ydrophilidae comprising 6 subfamilies and 12 tribes. Each subfamily and tribe is reviewed in detail with (i) a morphological diagnosis, including known or putative morphological synapomorphies, (ii) its taxonomic circumscription, including genera not included in our analyses, and (iii) a review of its general biology and geographic distribution. A new identification key to subfamily and tribe based on adult morphology is also provided. The newly adopted classification requires the following taxonomic changes: the subfamily H ydrophilinae sensu n. is redefined to include only the tribes A mphiopini stat.n. (removed from the synonymy with the C haetarthriini), B erosini, L accobiini, H ydrophilini and H ydrobiusini (= S perchopsini syn.n. ); the subfamily C haetarthriinae stat.n. is removed from synonymy with the H ydrophilinae and includes the tribes C haetarthriini and A nacaenini (= H orelophinae syn.n. ); the A cidocerinae stat.n. (= H orelophopsinae syn.n. ) and R ygmodinae stat.n. (= Andotypini syn.n. , B orborophorini syn.n. and T ormissini syn.n.) are elevated to subfamily rank; and the subfamily E nochrinae subfam.n. is established for the genus Enochrus and its relatives. The implications for the morphological evolution, ecological transitions and biogeography of the family are discussed.

Recently, McKenna et al., 2015 (MCK15 hereafter) investigated the higher level phylogenetic relationships of beetles (Insecta, Coleoptera) using the most comprehensive molecular dataset to date, and inferred the absolute ages of major groups using multiple fossil calibrations across the beetle tree of life. Based on the result of their dating analysis, beetles diverged from Strepsiptera in the Early Permian c. 278.33 Ma with a 95% credibility interval (95% CI) of 288.28 to 271.89 Ma, and the crown age of Coleoptera was estimated for the Late Permian c. 252.89 Ma (95% CI: 267.68 to 238.78 Ma), supporting the view that beetles originated before and survived through the End-Permian Mass Extinction that occurred c. 252 Ma (Shen et al., 2011). However, some of the age estimates found in MCK15 are in conflict with current knowledge of the beetle fossil record (e.g. Nikolajev & Ren, 2010; Pan et al., 2011, Prokin & Ren, 2011; Fikáček et al., 2012a; Wang et al., 2013, 2014; Cai et al., 2014b, 2015a; Kirejtshuk et al., 2014; Boucher et al., 2016) and with other recently published molecular age estimates for some major beetle clades (e.g. Zhang & Zhou, 2013; Ahrens et al., 2014; Bloom et al., 2014; Kergoat et al., 2014; Kim & Farrell, 2015; Bocák et al., 2016; Gunter et al., 2016). In some cases, the difference in age estimates is significant and might change our understanding of the mode and tempo of diversification dynamics of these groups. Based on a careful examination of the data and analyses performed in MCK15, we propose that the divergence time estimates which they found are likely to underestimate clade ages. We believe this is due to the subset of fossil Coleoptera that MCK15 selected as calibration points, as well as the methodological approach used in their analyses. To explore the impact of fossil selection on the age of Coleoptera, we derived an alternative set of fossil calibration points based on best-practice recommendations (e.g. Parham et al., 2012), and performed new molecular dating analyses to investigate the effect of fossil selection and maximum ages, on posterior estimates of divergence times. We first replicated the results of MCK15 using the same dataset (File S2 in MCK15) and settings. To do so, we recovered the molecular matrix from MCK15 comprising eight gene fragments for a total of ∼9000 bp (see MCK15 for more details). We then specified the same fossil constraints as in MCK15 following the procedure described in the original paper. Calibrated nodes as well as some suprafamilial nodes were constrained to be monophyletic. The Tree Model was set to a Yule: speciation prior in beauti 1.8.2 (Drummond et al., 2012). All fossil calibrations were specified using a lognormal prior (mean = 30, log-SD = 0.75) on the stem of the targeted clades except for the root that received a normal prior density (mean = 302, SD = 30). The prior distribution of the root was then truncated to the interval 270–396 Ma as in MCK15. The partitions (one partition for the ribosomal gene fragments, one partition for first and second positions of protein-coding gene fragment codons, and one partition for third positions of protein-coding gene fragment codons) and substitution models (GTR + Γ + I for all partitions) were the same as in MCK15. Preliminary analyses revealed that most parameters were critically undersampled and their associated ESS values <100 when using only a 100 million generations sampled every 1000 generations, as described in MCK15. Therefore, we ran two independent analyses with a Markov chain Monte Carlo (MCMC) running for 300 million generations and a parameter sampling every 3000 generations. The posterior trees and log files were resampled at a frequency of 30 000 then combined in LogCombiner 1.8.2 (Drummond et al., 2012) before applying a conservative burn-in of 50%. Second, we replicated these analyses but instead of using monophyletic constraints, we used a fixed topology the same as the time tree of MCK15 (provided by Duane McKenna) as a starting tree, and unchecked the parameters allowing topology changes in beauti 1.8.2. The objective of this analysis was to show that by enforcing a fixed topology we would recover similar ages as in the analysis using monophyletic constraints. We found very similar ages between the original chronogram from MCK15 and our analyses with or without fixing the tree topology (see Files S1 and S2). Therefore, we conducted the rest of the analyses with a fixed topology. In order to calibrate the tree from MCK15, we carefully checked the fossil record of Coleoptera. We selected beetle fossils known as the most ancient representatives of clades recovered in MCK15. We checked fossils for the presence of synapomorphies or relevant diagnostic characters, based partly on consultations with specialists on particular groups (see File S3 and Acknowledgements). The selection was not solely based on published data because in some instances, original descriptions had incomplete or even lacked reliable justification for the systematic placement of the fossils. Fossils were selected on the basis of shared apomorphies with a specific clade of the tree to allow their confident placement on the stem of each focal clade. Our search targeted all beetle clades and selected all available oldest representatives that we could possibly fit in the tree using the same stringent criteria. Our final fossil set consisted of 34 fossils listed in detail in Table 1. Justification for their placement in the tree is provided following the recommendation of Parham et al. (2012) when possible. It is noteworthy that Table 1 lists only the specimens that were ultimately retained to provide a minimum age; however, in many cases additional fossils of nearly the same age were available and reliably assigned to the same or sister clades, thereby providing even more evidence for the calibration of particular stems (see File S3 for more details). We chose not to use the fossil calibrations used to enforce minimum ages for Hymenoptera and Neuroptera in MCK15 for several reasons. First, the taxon sampling in these two clades is extremely reduced and most major branching events are missing. Second, multiple orders of insects closely related to Coleoptera were not included in the dataset. In order to use such fossil calibrations, it would have been advisable to sample representatives of the other megadiverse orders Diptera and Lepidoptera that are representatives of the sister group of beetles and their closest relatives (e.g. Misof et al., 2014). Third, the fact that all fossil calibrations from MCK15 were originally enforced at the stem of focal clades means that the fossil calibration used to constrain Hymenoptera actually enforced a minimum age on the root of the tree. This is problematic because it means that the root has in fact two different constraints that are not enforcing the same age prior. If the root was constrained with the Hymenoptera fossil calibration, then 95% of the age distribution would be found between 240 and 330 Ma. These ages are far younger than the original root calibration in MCK15 where the truncated normal distribution encompassed an older interval (270–396 Ma). A similar issue was found for the Chrysomeloidea and Curculionoidea calibrations where the stems of both clades were constrained with different fossil taxa. However, because both calibrations were on the stem of sister lineages, the only node being constrained was the crown of Chrysomeloidea + Curculionoidea (=Phytophaga). Fortunately, in that case, both calibrations encapsulate the same information because the chrysomeloid and curculionoid fossils are from the same geological stratum in Kazakhstan. Nonetheless, these imprecisions lowered the number of informative fossil calibrations from 15 to 13 in MCK15. Although MCK15 would not have been able to know at the time of their analyses, the root calibration they used (270–396 Ma) has proven to be problematic in light of contemporary studies. The minimum bound of the root prior in MCK15 conflicts with the most recent reviews of the beetle fossil record (e.g. Kirejtshuk et al., 2014) and also with the most recent phylogenomic studies of insect evolution. In Misof et al. (2014) and Tong et al. (2015), the lower bound of the age credibility interval for the Holometabola node was estimated at 320 and 350 Ma, respectively. For future studies, a more justifiable way to place an interval on the age of the root is to use the age estimates of the recent dating studies of Misof et al. (2014) and Tong et al. (2015) in which the age of the crown Holometabola was found to be ∼345 Ma (CI: ∼320–370 Ma) and ∼370 Ma (CI: ∼350–400 Ma), respectively. These studies are based on the same phylogenomic dataset. Tong et al. (2015) only revisited the ages of Misof et al. (2014) using additional fossil evidence and different parametrisation of the Bayesian molecular dating analyses. We therefore chose to use an interval encompassing both estimates (320–400 Ma). The new fossil calibrations were enforced in beauti 1.8.2 (Drummond et al., 2012) using the same priors used in MCK15, a lognormal density with mean = 30 and log (SD) = 0.75 was assigned to every fossil calibration. All other settings were left identical as in MCK15. As for the previous runs, we conducted two independent analyses of 300 million generations with a sampling every 3000 cycles. The .xml file generated in beauti to perform this analysis is provided in File S4. The resulting log and tree files were then resampled at a lower frequency (30 000) and combined in LogCombiner 1.8.2 with a conservative burn-in of 50% (Drummond et al., 2012). All beast analyses performed with 300 million generations converged, with all parameters properly sampled as indicated by ESS values >200. The chronograms recovered in the preliminary tests (monophyletic constraints vs fixed topology) are presented in Files S1 and S2. Using the same settings as specified in MCK15, we recovered very similar age estimates, as indicated in File S1. Likewise, when constraining the topology to the time tree of MCK15 as presented in File S4 of the original paper, we did not recover major differences in divergence time estimates in comparison to the unconstrained analysis (File S2). The median age estimates from these two analyses are very similar to the ones of MCK15 presented in Table 2. The chronogram derived from the new fossil calibration set is available with full annotations in File S5 and summarised in Fig. 1. We recovered large differences between our estimates and the estimates of MCK15 (Figs 1, 2 and Table 2). The root of the tree (crown Holometabola) was found at 385.27 Ma with a 95% credibility interval (CI) of 365.49–400.00 Ma. We recovered the split between Strepsiptera and Coleoptera at 356 Ma (95% CI: 336–375 Ma) in the Early Carboniferous. The estimated origin of extant beetle clades was found to be as old as 332 Ma (95% CI: 317–349 Ma) in the Mid Carboniferous. Most superfamilies were found to have originated in the Permian or Triassic (Fig. 2). In a substantial number of clades, the credibility intervals we recovered do not overlap with the ones estimates in MCK15, as highlighted in Fig. 2. Our recalibrated time tree of Coleoptera based on MCK15 sequence data and topology, and a revised set of fossil calibrations resulted in node ages significantly older than in MCK15 and in other dated phylogenies focusing on the whole beetle tree of life (e.g. Hunt et al., 2007; McKenna & Farrell, 2009; Misof et al., 2014). However, our estimates are more in agreement with the few recent studies that looked at divergence times of major beetle clades (e.g. Zhang & Zhou, 2013; Ahrens et al., 2014; Bloom et al., 2014; Kergoat et al., 2014; Kim & Farrell, 2015; Bocák et al., 2016; Gunter et al., 2016). Our estimates place the origin of Coleoptera during the Mid Carboniferous. We also infer an origin of the four extant beetle suborders in the Late Carboniferous to Early Permian, and an origin of many principal clades (series and superfamilies) predating the End-Permian Mass Extinction. Finally, our results support an origin of the large phytophagan families Curculionidae, Cerambycidae and Chrysomelidae during the Late Triassic to Mid Jurassic. These new age estimates and derived credibility intervals are consistent with the latest dating for the crown of flowering plants in the Jurassic (e.g. Bell et al., 2010; Clarke et al., 2011; but see Beaulieu et al., 2015). These estimates push back in time the old hypothesis of coevolution between phytophagan beetles and angiosperms (e.g. McKenna et al., 2009). The ancestral plant association of phytophagan beetles therefore remains somewhat enigmatic as their origin largely pre-dates the diversification and dominance of angiosperms in the Cretaceous (Friis et al., 2011). The Mid Carboniferous origin of Coleoptera is older than all previous estimates that dated it back to the Late Carboniferous/Early Permian (Hunt et al., 2007; McKenna & Farrell, 2009; Misof et al., 2014, MCK15). On one hand, a Mid–Late Carboniferous origin was suggested in recent studies for major holometabolan lineages including Hymenoptera – the clade strongly supported as sister to other Holometabola (Ronquist et al., 2012; Misof et al., 2014). On the other hand, the oldest definite beetle fossils with clearly developed elytra (i.e. bearing the principal apomorphy of the order) are known from the Early Permian deposits of Germany, Russia, Czech Republic and USA dated as 295 to 260 Ma (Kukalová, 1969; Ponomarenko, 1969; Lubkin & Engel, 2005; Beckemeyer & Engel, 2008; Kirejtshuk et al., 2014). This indicates a c. 35–40 Ma-long gap between the supposed origin of Coleoptera and the oldest confirmed fossil of the clade (Coleopsis archaica, ∼295 Ma; see Table 1 and File S3), which is comparable to the gaps between the estimated origin and oldest fossil of other holometabolan orders (e.g. Hymenoptera, see Ronquist et al., 2012). The Late Carboniferous to Early Permian origin of all four beetle suborders (Adephaga, Archostemata, Myxophaga and Polyphaga) and the Late Permian origin of several major clades (superfamilies) are the most surprising result of our analysis. If accurate, this suggests that the basic diversity of Coleoptera evolved during the Late Paleozoic, with 8–11 modern lineages surviving the End-Permian Mass Extinction (Fig. 1). Our analysis dates the divergences of most principal polyphagan clades in a rather narrow window in the Late Permian and Early Triassic, around the Palaeozoic–Mesozoic boundary. These results stand in contrast to the current understanding of the Permian–Triassic fossil record of Coleoptera, in which the oldest definite representatives of all four modern suborders date to Early Triassic or earliest Middle Triassic (Ponomarenko, 1969, 1977, 1992; Lawrence, 1999; Chatzimanolis et al., 2012; Grebennikov & Newton, 2012; Tan et al., 2012; Lawrence & Ślipiński, 2013; Prokin et al., 2013a, 2013b). The crown ages of the superfamilies as well as origins of families pre-date the first fossils known for these groups, and our estimates at this level differ from those of MCK15, in which origins of many clades were younger than known fossils of the respective clade. For example, the crown age of Hydrophiloidea s.s. in MCK15 was estimated as 124 Ma (CI: 88–155 Ma) and the divergence of modern hydrophiloid families was dated to c. 100 Ma (CI not provided). However, the oldest fossils of the modern hydrophiloid families Helophoridae, Spercheidae and Hydrophilidae are already known from the Late Jurassic (c. 145–155 Ma; Prokin, 2009; Fikáček et al., 2012a, 2012b, 2014). Increased congruence between estimates of family-level divergence times in our analysis and the fossil record were expected, as we mainly used fossils reliably assigned to the deeper nodes of modern clades (subfamilies, tribes, genera) to calibrate the divergence dates at family/subfamily levels. Consequently, we also estimate a much older origin for the largest beetle families (e.g. Staphylinidae: Late Triassic; Tenebrionidae: Early Jurassic) including the phytophagous groups (Middle Triassic origin of stem chrysomeloids and curculionoids, and Late Triassic origin of Chrysomelidae and Mid–Late Jurassic origins of Curculionidae and Cerambycidae). These results are largely congruent with the time tree analyses of phytophagous clades by Wang et al. (2014) based on a recently discovered fossil prionine beetle, and of Tenebrionidae by Kergoat et al. (2014) based on combination of fossil and geological calibrations. The exercise of this paper was to provide an alternative temporal framework of beetle evolution given the MCK15 topology by comparing the fossil set of MCK15 with a new and more comprehensive one. To do so, we replicated the analyses of MCK15 using two sets of fossils. However, we want to emphasise that we do not believe some of the parameter settings used in MCK15 (and therefore in this study) are the most appropriate considering the latest developments in molecular dating (some of which were not available at the time of MCK15). For instance, recent studies have shown that the effect of clock partitioning on estimates of evolutionary rates and timescales can be important in empirical datasets (e.g. Duchêne & Ho, 2014). Some methods have been introduced to take into account this issue, by identifying the best clock partitioning strategy in a Bayesian framework (Duchêne et al., 2014). Likewise, the choice of fossil calibration prior densities should be examined in a comparative framework (Ho & Phillips, 2009). At a minimum, it is recommended to conduct comparative approaches using different prior densities to understand their impact on posterior age estimates, in particular when maximum ages are not easy to justify (Toussaint & Condamine, 2016). The fit of different parameter settings to empirical datasets can be tested by comparing the marginal likelihoods of different analyses using statistical tests (e.g. Bayes Factors; Kass & Raftery, 1995). The latest developments of dating programs such as beast (Drummond et al., 2012) incorporate means to estimate these marginal likelihoods in a more sensitive and sound way than before (Baele et al., 2012), thereby improving the robustness of the statistical framework in which comparative dating analyses are conducted. We want to thank Shaun Winterton as well as three anonymous reviewers for helpful comments on an earlier version of this paper. We thank Duane McKenna for sending us the original dataset and chronogram published in Systematic Entomology (MCK15). We also want to thank Petr Švácha and Steve Davis for discussions on chrysomeloid and curculionoid fossils and latest opinions about the phylogenies of these clades, Rafał Ruta for discussions concerning the fossil record of the Scirtoidea, Alexey Solodovnikov for advice concerning the current views of the phylogeny of the Staphylinoidea, Zbyněk Kejval for comments on fossil Anthicidae, and Alexander Prokin for providing many relevant literature and discussions on fossils from the Russian deposits. This work was supported in part by NSF-DEB grant #1453452 to AEZS, the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 542241 to MS and EAV, the Ministry of Culture of the Czech Republic (DKRVO 2016/14, National Museum, 00023272) to MF, JH and LS, and the institutional support from resources of the Ministry of Education, Youth and Sports of the Czech Republic to DK. The work of MS and EAV at the Department of Zoology, Charles University in Prague was partly supported by grant SVV 260 313/2016. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Abstract The classification of the tetrahedrite group minerals in keeping with the current IMA-accepted nomenclature rules is discussed. Tetrahedrite isotypes are cubic, with space group symmetry I43m. The general structural formula of minerals belonging to this group can be written as M(2)A6M(1)(B4C2)X(3) D4S(1)Y12S(2)Z, where A = Cu+, Ag+, ☐ (vacancy), and (Ag6)4+ clusters; B = Cu+, and Ag+; C = Zn2+, Fe2+, Hg2+, Cd2+, Mn2+, Cu2+, Cu+, and Fe3+; D = Sb3+, As3+, Bi3+, and Te4+; Y = S2– and Se2–; and Z = S 2–, Se2–, and ☐. The occurrence of both Me+ and Me2+ cations at the M(1) site, in a 4:2 atomic ratio, is a case of valency-imposed double site-occupancy. Consequently, different combinations of B and C constituents should be regarded as separate mineral species. The tetrahedrite group is divided into five different series on the basis of the A, B, D, and Y constituents, i.e., the tetrahedrite, tennantite, freibergite, hakite, and giraudite series. The nature of the dominant C constituent (the so-called “charge-compensating constituent”) is made explicit using a hyphenated suffix between parentheses. Rozhdestvenskayaite, arsenofreibergite, and goldfieldite could be the names of three other series. Eleven minerals belonging to the tetrahedrite group are considered as valid species: argentotennantite-(Zn), argentotetrahedrite-(Fe), kenoargentotetrahedrite-(Fe), giraudite-(Zn), goldfieldite, hakite-(Hg), rozhdestvenskayaite-(Zn), tennantite-(Fe), tennantite-(Zn), tetrahedrite-(Fe), and tetrahedrite-(Zn). Furthermore, annivite is formally discredited. Minerals corresponding to different end-member compositions should be approved as new mineral species by the IMA-CNMNC following the submission of regular proposals. The nomenclature and classification system of the tetrahedrite group, approved by the IMA-CNMNC, allows the full description of the chemical variability of the tetrahedrite minerals and it is able to convey important chemical information not only to mineralogists but also to ore geologists and industry professionals.

Over decades it has been unclear how individual migratory songbirds cross large ecological barriers such as seas or deserts. By deploying light-level geolocators on four songbird species weighing only about 12 g, we found that these otherwise mainly nocturnal migrants seem to regularly extend their nocturnal flights into the day when crossing the Sahara Desert and the Mediterranean Sea. The proportion of the proposed diurnally flying birds gradually declined over the day with similar landing patterns in autumn and spring. The prolonged flights were slightly more frequent in spring than in autumn, suggesting tighter migratory schedules when returning to breeding sites. Often we found several patterns for barrier crossing for the same individual in autumn compared to the spring journey. As only a small proportion of the birds flew strictly during the night and even some individuals might have flown non-stop, we suggest that prolonged endurance flights are not an exception even in small migratory species. We emphasise an individual's ability to perform both diurnal and nocturnal migration when facing the challenge of crossing a large ecological barrier to successfully complete a migratory journey.

Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re-analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species' history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM.