The Angiosperm Terrestrial Revolution buffered ants against extinction.

With ~14,000 extant species, ants are ubiquitous and of tremendous ecological importance. They have undergone remarkable diversification throughout their evolutionary history. However, the drivers of their diversity dynamics are not well quantified or understood. Previous phylogenetic analyses have suggested patterns of diversity dynamics associated with the Angiosperm Terrestrial Revolution (ATR), but these studies have overlooked valuable information from the fossil record. To address this gap, we conducted a comprehensive analysis using a large dataset that includes both the ant fossil record (~24,000 individual occurrences) and neontological data (~14,000 occurrences), and tested four hypotheses proposed for ant diversification: co-diversification, competitive extinction, hyper-specialization, and buffered extinction. Taking into account biases in the fossil record, we found three distinct diversification periods (the latest Cretaceous, Eocene, and Oligo-Miocene) and one extinction period (Late Cretaceous). The competitive extinction hypothesis between stem and crown ants is not supported. Instead, we found support for the co-diversification, buffered extinction, and hyper-specialization hypotheses. The environmental changes of the ATR, mediated by the angiosperm radiation, likely played a critical role in buffering ants against extinction and favoring their diversification by providing new ecological niches, such as forest litter and arboreal nesting sites, and additional resources. We also hypothesize that the decline and extinction of stem ants during the Late Cretaceous was due to their hyper-specialized morphology, which limited their ability to expand their dietary niche in changing environments. This study highlights the importance of a holistic approach when studying the interplay between past environments and the evolutionary trajectories of organisms.

Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects.

Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass-extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites (altogether included in Dictyoptera) have experienced episodic pulses of speciation or extinction and how these pulses may be associated with environmental fluctuations or mass extinctions. We relied on molecular phylogeny and fossil data to shed light on the times and rates at which dictyopterans diversified. The diversification of Dictyoptera has alternated between (i) periods of high diversification in the late Carboniferous, Early-Middle Triassic, Early Cretaceous and middle Palaeogene, and (ii) periods of high extinction rates particularly at the Permian-Triassic boundary, but not necessarily correlated with the major global biodiversity crises as in the mid-Cretaceous. This study advocates the importance of analyzing, when possible, both molecular phylogeny and fossil data to unveil diversification and extinction periods for a given group. The causes and consequences of extinction must be studied beyond mass-extinction events alone to gain a broader understanding of how clades wax and wane.

An integrative phylogenomic approach illuminates the evolutionary history of cockroaches and termites (Blattodea).

Phylogenetic relationships among subgroups of cockroaches and termites are still matters of debate. Their divergence times and major phenotypic transitions during evolution are also not yet settled. We addressed these points by combining the first nuclear phylogenomic study of termites and cockroaches with a thorough approach to divergence time analysis, identification of endosymbionts, and reconstruction of ancestral morphological traits and behaviour. Analyses of the phylogenetic relationships within Blattodea robustly confirm previously uncertain hypotheses such as the sister-group relationship between Blaberoidea and remaining Blattodea, and Lamproblatta being the closest relative to the social and wood-feeding Cryptocercus and termites. Consequently, we propose new names for various clades in Blattodea: Cryptocercus + termites = Tutricablattae; Lamproblattidae + Tutricablattae = Kittrickea; and Blattoidea + Corydioidea = Solumblattodea. Our inferred divergence times contradict previous studies by showing that most subgroups of Blattodea evolved in the Cretaceous, reducing the gap between molecular estimates of divergence times and the fossil record. On a phenotypic level, the blattodean ground-plan is for egg packages to be laid directly in a hole while other forms of oviposition, including ovovivipary and vivipary, arose later. Finally, other changes in egg care strategy may have allowed for the adaptation of nest building and other novelties.

When Darwin's Special Difficulty Promotes Diversification in Insects.

Eusociality, Darwin's special difficulty, has been widely investigated but remains a topic of great debate in organismal biology. Eusocial species challenge existing theories, and the impact of highly integrated societies on diversification dynamics is controversial with opposing assertions and hypotheses in the literature. Here, using phylogenetic approaches in termites-the first group that has evolved eusociality-we assessed the fundamental prediction that eusocial lineages have higher diversification rates than non-eusocial clades. We found multiple lines of evidence that eusociality provided higher diversification as compared to non-eusociality. This is particularly exacerbated for eusocial species with "true" workers as compared to species with "false" workers. Because most species with "true" workers have an entirely prokaryotic microbiota, the latter feature is also related to higher diversification rates, but it should be investigated further, notably in relation to angiosperm diversification. Overall, this study suggests that societies with "true" workers are not only more successful at ecological timescales but also over millions of years, which further implies that both organism- and species-level traits act on species selection.

The Increasing Disconnection of Primary Biodiversity Data from Specimens: How Does It Happen and How to Handle It?

Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based (OB) occurrences is overthrowing the collection of specimen-based (SB) occurrences. Although this change in practice is a major upheaval with significant consequences in the study of biodiversity, it remains understudied and has not attracted yet the attention it deserves. Analyzing 536 million occurrences from the Global Biodiversity Information Facility (GBIF) mediated data, we show that this spectacular change affects the 24 eukaryote taxonomic classes we targeted: from 1970 to 2016 the proportion of occurrences marked as traceable to tangible material (i.e., SB occurrences) fell from 68% to 18%; moreover, most of those specimen based-occurrences cannot be readily traced back to a specimen because the necessary information is missing. Ethical, practical or legal reasons responsible for this shift are known, and this situation appears unlikely to be reversed. Still, we urge scholars to acknowledge this dramatic change, embrace it and actively deal with it. Specifically, we emphasize why SB occurrences must be gathered, as a warrant to allow both repeating evolutionary studies and conducting rich and diverse investigations. When impossible to secure, voucher specimens must be replaced with OB occurrences combined with ancillary data (e.g., pictures, recordings, samples, DNA sequences). Ancillary data are instrumental for the usefulness of biodiversity occurrences and we show that, despite improving technologies to collate them, they remain rarely shared. The consequences of such a change are not yet clear but we advocate collecting material evidence or ancillary data to ensure that primary biodiversity data collected lately do not partly become obsolete when doubtful.

The evolution of sociality in termites from cockroaches: A taxonomic and phylogenetic perspective.

Despite multiple studies and advances, sociality still puzzles evolutionary biologists in numerous ways, which might be partly addressed with the advent of sociogenomics. In insects, the majority of sociogenomic studies deal with Hymenoptera, one of the two groups that evolved eusociality with termites. But, to fully grasp the evolution of sociality, studies must obviously not restrict to eusocial lineages. Multiple kinds of social system transitions have been recorded and they all bring complementary insights. For instance, cockroaches, the closest relatives to termites, display a wide range of social interactions and evolved convergently subsocial behaviors (i.e., brood care). In this context, we emphasize the need for natural history, taxonomic, and phylogenetic studies. Natural history studies provide the foundations on which building hypotheses, whereas taxonomy provides the taxa to sample to test these hypotheses, and phylogenetics brings the historical framework necessary to test evolutionary scenarios of sociality evolution.

Topological support and data quality can only be assessed through multiple tests in reviewing Blattodea phylogeny.

Assessing support for molecular phylogenies is difficult because the data is heterogeneous in quality and overwhelming in quantity. Traditionally, node support values (bootstrap frequency, Bayesian posterior probability) are used to assess confidence in tree topologies. Other analyses to assess the quality of phylogenetic data (e.g. Lento plots, saturation plots, trait consistency) and the resulting phylogenetic trees (e.g. internode certainty, parameter permutation tests, topological tests) exist but are rarely applied. Here we argue that a single qualitative analysis is insufficient to assess support of a phylogenetic hypothesis and relate data quality to tree quality. We use six molecular markers to infer the phylogeny of Blattodea and apply various tests to assess relationship support, locus quality, and the relationship between the two. We use internode-certainty calculations in conjunction with bootstrap scores, alignment permutations, and an approximately unbiased (AU) test to assess if the molecular data unambiguously support the phylogenetic relationships found. Our results show higher support for the position of Lamproblattidae, high support for the termite phylogeny, and low support for the position of Anaplectidae, Corydioidea and phylogeny of Blaberoidea. We use Lento plots in conjunction with mutation-saturation plots, calculations of locus homoplasy to assess locus quality, identify long branch attraction, and decide if the tree's relationships are the result of data biases. We conclude that multiple tests and metrics need to be taken into account to assess tree support and data robustness.

Laying the foundations of evolutionary and systematic studies in crickets (Insecta, Orthoptera): a multilocus phylogenetic analysis.

Orthoptera have been used for decades for numerous evolutionary questions but several of its constituent groups, notably crickets, still suffer from a lack of a robust phylogenetic hypothesis. We propose the first phylogenetic hypothesis for the evolution of crickets sensu lato, based on analysis of 205 species, representing 88% of the subfamilies and 71% tribes currently listed in the database Orthoptera Species File (OSF). We reconstructed parsimony, maximum likelihood and Bayesian phylogenies using fragments of 18S, 28SA, 28SD, H3, 12S, 16S, and cytb (~3600 bp). Our results support the monophyly of the cricket clade, and its subdivision into two clades: mole crickets and ant-loving crickets on the one hand, and all the other crickets on the other (i.e. crickets sensu stricto). Crickets sensu stricto form seven monophyletic clades, which support part of the OSF families, "subfamily groups", or subfamilies: the mole crickets (OSF Gryllotalpidae), the scaly crickets (OSF Mogoplistidae), and the true crickets (OSF Gryllidae) are recovered as monophyletic. Among the 22 sampled subfamilies, only six are monophyletic: Gryllotalpinae, Trigonidiinae, Pteroplistinae, Euscyrtinae, Oecanthinae, and Phaloriinae. Most of the 37 tribes sampled are para- or polyphyletic. We propose the best-supported clades as backbones for future definitions of familial groups, validating some taxonomic hypotheses proposed in the past. These clades fit variously with the morphological characters used today to identify crickets. Our study emphasizes the utility of a classificatory system that accommodates diagnostic characters and monophyletic units of evolution. Moreover, the phylogenetic hypotheses proposed by the present study open new perspectives for further evolutionary research, especially on acoustic communication and biogeography.

Phylogenetic analyses of termite post-embryonic sequences illuminate caste and developmental pathway evolution.

Termites are highly eusocial insects with a caste polyphenism (i.e., discontinuous morphological differences between castes) and elaborated behaviors. While the developmental pathways leading to caste occurrence are well-known in many species, the evolutionary origin of these pathways is still obscure. Recent molecular phylogenetic studies suggest multiple independent origins of sterile castes in termites, reviving a 30 years old debate. We demonstrate here that diploid sterile castes ("true" workers) evolved several times independently in this group and that this caste was lost at least once in a lineage with developmentally more flexible workers called pseudergates or "false" workers. We also infer that flexibility in post-embryonic development was acquired multiple times independently during termite evolution. We suggest that focusing on detailed developmental pathways in phylogenetic analyses is essential for elucidating the origin of caste polyphenism in termites.

Multiple drivers and lineage-specific insect extinctions during the Permo-Triassic.

The Permo-Triassic interval encompasses three extinction events including the most dramatic biological crisis of the Phanerozoic, the latest Permian mass extinction. However, their drivers and outcomes are poorly quantified and understood for terrestrial invertebrates, which we assess here for insects. We find a pattern with three extinctions: the Roadian/Wordian (≈266.9 Ma; extinction of 64.5% insect genera), the Permian/Triassic (≈252 Ma; extinction of 82.6% insect genera), and the Ladinian/Carnian boundaries (≈237 Ma; extinction of 74.8% insect genera). We also unveil a heterogeneous effect of these extinction events across the major insect clades. Because extinction events have impacted Permo-Triassic ecosystems, we investigate the influence of abiotic and biotic factors on insect diversification dynamics and find that changes in floral assemblages are likely the strongest drivers of insects' responses throughout the Permo-Triassic. We also assess the effect of diversity dependence between three insect guilds; an effect ubiquitously found in current ecosystems. We find that herbivores held a central position in the Permo-Triassic interaction network. Our study reveals high levels of insect extinction that profoundly shaped the evolutionary history of the most diverse non-microbial lineage.

Eusocial Transition in Blattodea: Transposable Elements and Shifts of Gene Expression.

(1) Unravelling the molecular basis underlying major evolutionary transitions can shed light on how complex phenotypes arise. The evolution of eusociality, a major evolutionary transition, has been demonstrated to be accompanied by enhanced gene regulation. Numerous pieces of evidence suggest the major impact of transposon insertion on gene regulation and its role in adaptive evolution. Transposons have been shown to be play a role in gene duplication involved in the eusocial transition in termites. However, evidence of the molecular basis underlying the eusocial transition in Blattodea remains scarce. Could transposons have facilitated the eusocial transition in termites through shifts of gene expression? (2) Using available cockroach and termite genomes and transcriptomes, we investigated if transposons insert more frequently in genes with differential expression in queens and workers and if those genes could be linked to specific functions essential for eusocial transition. (3) The insertion rate of transposons differs among differentially expressed genes and displays opposite trends between termites and cockroaches. The functions of termite transposon-rich queen- and worker-biased genes are related to reproduction and ageing and behaviour and gene expression, respectively. (4) Our study provides further evidence on the role of transposons in the evolution of eusociality, potentially through shifts in gene expression.

Mapping extrinsic traits such as extinction risks or modelled bioclimatic niches on phylogenies: does it make sense at all?

An increasing variety of extrinsic traits are used in comparative studies aimed at testing evolutionary hypotheses. After briefly reviewing the relevant literature, it appears that three different problems are implied by this trend. Some extrinsic traits are only surrogates for phenotypic traits, and should be redefined to better fit the requisites for phylogenetic analysis, such as selective regimes and extinction risks. Some others are already adequately defined and cannot be made less extrinsic, such as taxon age, geographical distribution, associates (parasites, symbionts, etc.), and bioclimatic modelled niches. Because they are not heritable, they should not be analysed by optimization onto a tree, but are better considered in sister-group comparisons or within a reconciliation procedure, as already done for areas of biogeography. © The Willi Hennig Society 2010.

Sound vs. light: wing-based communication in Carboniferous insects.

Acoustic communication is well-known in insects since the Mesozoic, but earlier evidence of this behavior is rare. Titanoptera, an 'orthopteroid' Permian-Triassic order, is one of the few candidates for Paleozoic intersex calling interactions: some specimens had highly specialized broadened zones on the forewings, which are currently considered-despite inconclusive evidence-as 'resonators' of a stridulatory apparatus. Here we argue that the stridulatory apparatus hypothesis is unlikely because the Titanoptera lack a stridulatory file on their bodies, legs or wings. Instead, comparing these broadened zones with similar structures in extant locusts, flies, and fossil damselflies, we find evidence that the Titanoptera used their wings to produce flashes of light and/or crepitated sounds. Moreover, we describe the first Carboniferous (~310 Mya) Titanoptera, which exhibits such specialized zones, thus corresponding to the oldest record of wing communication in insects. Whether these communication systems were used to attract sexual partners and/or escape predators remain to be demonstrated.

The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: Implications for the evolution of the worker and pseudergate castes, and foraging behaviors.

A phylogenetic hypothesis of termite relationships was inferred from DNA sequence data. Seven gene fragments (12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA, cytochrome oxidase I, cytochrome oxidase II and cytochrome b) were sequenced for 40 termite exemplars, representing all termite families and 14 outgroups. Termites were found to be monophyletic with Mastotermes darwiniensis (Mastotermitidae) as sister group to the remainder of the termites. In this remainder, the family Kalotermitidae was sister group to other families. The families Kalotermitidae, Hodotermitidae and Termitidae were retrieved as monophyletic whereas the Termopsidae and Rhinotermitidae appeared paraphyletic. All of these results were very stable and supported with high bootstrap and Bremer values. The evolution of worker caste and foraging behavior were discussed according to the phylogenetic hypothesis. Our analyses suggested that both true workers and pseudergates ("false workers") were the result of at least two different origins. Our data support a traditional hypothesis of foraging behavior, in which the evolutionary transition from a one-piece type to a separate life type occurred through an intermediate behavioral form.

Synthesis and evaluation of new phosphonolipid compounds for gene delivery.

The preparation of a series of novel water soluble cationic lipid derivatives possessing phosphonate ester groups linked to the para-position of N-methyl pyridinium moieties and bearing either identical or different alkyl chains is reported. The obtained phospholipids were tested for transfection efficiency into three different mammalian cell lines alone and in conjunction with diphytanoylphosphatidylethanolamine (DiPPE) or dioleylphosphatidylethanolamine (DOPE), using an assay adapted for 96-well microplates based on the detection of a colorimetric change caused by the production of a chromogen induced by expressed secreted human placental alkaline phosphatase. In our conditions, the highest transfection activities of cells HEK293 and hard-to-transfect cell lines B16 and CHO were achieved with a 4-phosphonobutylpyridinium compound used at 1:5, 1:10 or 3:6 DNA/lipid ratio bearing two myristyl chains in the presence of the fusogenic helper lipid DiPPE.

Distinguishing between convergence and parallelism is central to comparative biology: a reply to Williams and Ebach.

The definitions of character similarity, homology, homoplasy, heterology, parallelism and convergence are clarified in the framework of current phylogenetic methodology. They are all associated with definite patterns of character change and can consequently be tested by phylogeny building. Their crucial significance in comparative biology is illustrated using demonstrative examples.

Taxonomic bias in biodiversity data and societal preferences.

Studying and protecting each and every living species on Earth is a major challenge of the 21st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

Updating the Phylogenetic Dating of New Caledonian Biodiversity with a Meta-analysis of the Available Evidence.

For a long time, New Caledonia was considered a continental island, a fragment of Gondwana harbouring old clades that originated by vicariance and so were thought to be locally ancient. Recent molecular phylogenetic studies dating diversification and geological data indicating important events of submergence during the Paleocene and Eocene (until 37 Ma) brought evidence to dismiss this old hypothesis. In spite of this, some authors still insist on the idea of a local permanence of a Gondwanan biota, justifying this assumption through a complex scenario of survival by hopping to and from nearby and now-vanished islands. Based on a comprehensive review of the literature, we found 40 studies dating regional clades of diverse organisms and we used them to test the hypothesis that New Caledonian and inclusive Pacific island clades are older than 37 Ma. The results of this meta-analysis provide strong evidence for refuting the hypothesis of a Gondwanan refuge with a biota that originated by vicariance. Only a few inclusive Pacific clades (6 out of 40) were older than the oldest existing island. We suggest that these clades could have extinct members either on vanished islands or nearby continents, emphasizing the role of dispersal and extinction in shaping the present-day biota.

Phylogenetic analysis and alignment of behavioral sequences by direct optimization.

We propose a new approach to consider behavioral data in phylogenetic analyses. We show that behavior can be described as sequences of repeated units, and that these behavioral sequences can be analyzed under direct optimization in a way similar to molecular data. This approach provides repeatable hypotheses of homology for behavior when traditional criteria result in multiple alternatives or do not allow to propose any. We exemplify this approach by analyzing the calling songs of the North American Gryllus species under direct optimization. We first use two alternative coding schemes to describe the temporal patterns of the songs as sequences of repeated simple behaviors. We submit these behavioral data to phylogenetic analysis under direct optimization, first as separate analyses, and second in combination with molecular data and additional acoustic characters. The results show that the coding option that consists of discretizing the silent parts of the songs: (1) allows description of the songs in a more precise way; (2) discriminates further the songs between species; and (3) enhances the phylogenetic content of the behavioral sequences. Our study demonstrates that behavioral sequences can be transformed so that they can be used in genuine phylogenetic analysis, in isolation or combined with other data sets. We discuss how this approach may provide phylogenetic signal where none or little is usually available, and the applications to the study of the evolution of behavioral evolution.