Frédéric Legendre

Evolution on a shaky piece of Gondwana: is local endemism recent in New Caledonia?

New Caledonia is well known as a hot spot of biodiversity whose origin as a land mass can be traced back to the Gondwanan supercontinent. The local flora and fauna, in addition to being remarkably rich and endemic, comprise many supposedly relictual groups. Does the New Caledonian biota date back to Gondwanan times, building up its richness and endemism over 100 Myr or does it result from recent diversifications after Tertiary geological catastrophic events? Here we use a molecular phylogenetic approach to answer this question with the study of the Neocaledonian cockroach genus Angustonicus belonging to the subfamily Tryonicinae from Australia and New Caledonia. Both geological and molecular dating show that the diversification of this group is less than two million years old, whatever the date of its origin itself. This dating is not consistent with hypotheses of Gondwanan richness and endemism in New Caledonian biota. In other terms, local richness and endemism at the specific level are not necessarily related to an old Gondwanan origin of the Neocaledonian groups.

Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence

Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera—and stem-mantises—would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies.

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.

One hundred years of instability in ensiferan relationships

Although Ensifera is a major insect model group, its phylogenetic relationships have been understudied so far. Few phylogenetic hypotheses have been proposed, either with morphological or molecular data. The largest dataset ever used for phylogeny reconstruction on this group is molecular (16S rRNA, 18S rRNA and 28S rRNA sequences for 51 ensiferan species), which has been used twice with different resultant topologies. However, only one of these hypotheses has been adopted commonly as a reference classification. Here we re‐analyse this molecular dataset with different methods and parameters to test the robustness and the stability of the adopted phylogeny. Our study reveals the instability of phylogenetic relationships derived from this dataset, especially for the deepest nodes of the group, and suggests some guidelines for future studies. The comparison between the different classifications proposed in the past 70 years for Ensifera and our results allows the identification of potential monophyletic clades (katydids, mole crickets, scaly crickets + Malgasia, true crickets, leaf roller crickets, cave crickets) and the remaining unresolved clades (wetas, Jerusalem crickets and most of the highest rank clades) in Ensifera phylogeny.

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.

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.

Convergence and parallelism: is a new life ahead of old concepts?

In comparative biology, character observations initially separate similar and dissimilar characters. Only similar characters are considered for phylogeny reconstruction; their homology is attested in a two‐step process, firstly a priori of phylogeny reconstruction by accurate similarity statements, and secondly a posteriori of phylogeny analysis by congruence with other characters. Any pattern of non‐homology is then a homoplasy, commonly, but vaguely, associated with “convergence”. In this logical scheme, there is no way to analyze characters which look similar, but cannot meet usual criteria for homology statements, i.e., false similarity detected a priori of phylogenetic analysis, even though such characters may represent evolutionarily significant patterns of character transformations. Because phylogenies are not only patterns of taxa relationships but also references for evolutionary studies, we propose to redefine the traditional concepts of parallelism and convergence to associate patterns of non‐homology with explicit theoretical contexts: homoplasy is restricted to non‐similarity detected a posteriori of phylogeny analysis and related to parallelism; non‐similarity detected a priori of phylogenetic analysis and necessarily described by different characters would then correspond to a convergence event s. str. We propose to characterize these characters as heterologous (heterology). Heterology and homoplasy correspond to different non‐similarity patterns and processes; they are also associated with different patterns of taxa relationships: homoplasy can occur only in non‐sister group taxa; no such limit exists for heterology. The usefulness of these terms and concepts is illustrated with patterns of acoustic evolution in ensiferan insects.

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.

The Importance of Ambient Sound Level to Characterise Anuran Habitat

Habitat characterisation is a pivotal step of any animal ecology study. The choice of variables used to describe habitats is crucial and need to be relevant to the ecology and behaviour of the species, in order to reflect biologically meaningful distribution patterns. In many species, acoustic communication is critical to individuals’ interactions, and it is expected that ambient acoustic conditions impact their local distribution. Yet, classic animal ecology rarely integrates an acoustic dimension in habitat descriptions. Here we show that ambient sound pressure level (SPL) is a strong predictor of calling site selection in acoustically active frog species. In comparison to six other habitat-related variables (i.e. air and water temperature, depth, width and slope of the stream, substrate), SPL had the most important explanatory power in microhabitat selection for the 34 sampled species. Ambient noise was particularly useful in differentiating two stream-associated guilds: torrents and calmer streams dwelling species. Guild definitions were strongly supported by SPL, whereas slope, which is commonly used in stream-associated habitat, had a weak explanatory power. Moreover, slope measures are non-standardized across studies and are difficult to assess at small scale. We argue that including an acoustic descriptor will improve habitat-species analyses for many acoustically active taxa. SPL integrates habitat topology and temporal information (such as weather and hour of the day, for example) and is a simple and precise measure. We suggest that habitat description in animal ecology should include an acoustic measure such as noise level because it may explain previously misunderstood distribution patterns.

Mapping characters on a tree with or without the outgroups

A character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non‐exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest.