Thomas Bourguignon

Okinawa Institute of Science and Technology Graduate University | OIST · Evolutionary Genomics Unit

The Neotropics harbor a diverse array of flora and fauna shaped by a complex geological and climatic history. It includes marine invasions, pulses of Andean uplift, glaciations, and the uplift of the Panama Isthmus. These events have shaped organism distribution, which can be described by methods of historical phylogeography. However, the evolution...

Termites digest wood using Carbohydrate-Active Enzymes (CAZymes) produced by gut bacteria with whom they have cospeciated at geological timescales. Whether CAZymes were encoded in the genomes of their ancestor’s gut bacteria and transmitted to modern termites or acquired more recently from bacteria not associated with termites is unclear. We used g...

Social insects have developed a broad diversity of nesting and foraging strategies. One of these, inquilinism, occurs when one species (the inquiline) inhabits the nest built and occupied by another species (the host). Obligatory inquilines must overcome strong constraints upon colony foundation and development, due to limited availability of host...

The higher classification of termites requires substantial revision as the Neoisoptera, the most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa. Here, we produce an updated termite classification using genomic-scale analyses. We reconstruct phylogenies under diverse substitution models with ultraconserved elements...

Genetic changes that enabled the evolution of eusociality have long captivated biologists. More recently, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequ...

Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient‐poor diet. To investigate if host biology has impacted Blattabact...

Fossils encompassing multiple individuals provide rare direct evidence of behavioral interactions among extinct organisms. However, the fossilization process can alter the spatial relationship between individuals and hinder behavioral reconstruction. Here, we report a Baltic amber inclusion preserving a female–male pair of the extinct termite speci...

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among...

The genetic changes that enabled the evolution of eusociality have long captivated biologists. In recent years, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic c...

Microbial symbioses have had profound impacts on the evolution of animals. Conversely, changes in host biology may impact the evolutionary trajectory of symbionts themselves. Blattabacterium cuenoti is present in almost all cockroach species and enables hosts to subsist on a nutrient-poor diet. To investigate if host biology has impacted Blattabact...

While new species of termites are described every year, the description of species distant from every known termite species is rare. In this paper, we describe one such species, Engelitermes zambo sp.n. , an African Termitidae belonging to an entirely new lineage of termites for which we create a new subfamily, Engelitermitinae subfam.n. The subfam...

The neotropical Apicotermitinae is a common and widespread clade of mostly soil-feeding soldierless termites. With few exceptions, species of this group were originally assigned to the genus Anoplotermes Müller, 1873. The application of internal worker morphology coupled with genetic sequencing has recently shed light on the true diversity of this...

Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative import...

Fossils encompassing multiple individuals provide rare direct evidence of behavioral interactions among extinct organisms. However, the fossilization process can alter the spatial relationship between individuals and hinder behavioral reconstruction. Here, we report a Baltic amber inclusion preserving a female-male pair of the extinct termite speci...

Madagascar is home to many endemic plant and animal species owing to its ancient isolation from other landmasses. This unique fauna includes several lineages of termites, a group of insects known for their key role in organic matter decomposition in many terrestrial ecosystems. How and when termites colonised Madagascar remains unknown. In this stu...

The superfamily Blaberoidea is a highly species-rich group of cockroaches. High-level blaberoidean phylogenetics are still under debate owing to variable taxon sampling and incongruence between mitochondrial and nuclear evolution, as well as different methods used in various phylogenetic studies. We here present a phylogenetic analysis of Blaberoid...

The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have t...

Termites (Blattodea: Isoptera) have evolved specialized defensive strategies for colony protection. Alarm communication enables workers to escape threats while soldiers are recruited to the source of disturbance. Here, we study the vibroacoustic and chemical alarm communication in the wood roach Cryptocercus and in 20 termite species including seve...

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among...

Recent attempts to explain the evolutionary prevalence of same-sex sexual behavior (SSB) have focused on the role of indiscriminate mating. However, in many cases, SSB may be more complex than simple mistaken identity, instead involving mutual interactions and successful pairing between partners who can detect each other's sex. Behavioral plasticit...

Group‐living animals coordinate their movements via local interactions, which can be mediated by visual, tactile, and chemical communication channels. Termite mating pairs form tandems with one male imago following one female imago in a synchronised way to explore the environment and search for a nesting site. Imagoes are the only developmental sta...

The long-term coevolution between insects and their obligate endosymbionts is accompanied by increasing levels of genome integration, sometimes to the point that metabolic pathways require enzymes encoded in two genomes, which we refer to as “collaborative pathways”. To date, collaborative pathways have only been reported from sap-feeding insects.

Termites (Blattodea: Isoptera) have evolved specialized defensive strategies for colony protection. Alarm communication enables workers to escape threats while soldiers are recruited to the source of disturbance. Here, we studied the vibroacoustic and chemical alarm communication in the wood roach Cryptocercus and in 20 termite species including se...

Recent attempts to explain the evolutionary prevalence of same-sex sexual behaviour (SSB) have focused on the role of indiscriminate mating. However, in many cases, SSB involves plastically adjusting sex roles to achieve successful courtship or pairing. To evaluate this overlooked factor, we tested whether ancestral sex-role plasticity facilitated...

Background Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of t...

The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-...

Termites feed on vegetal matter at various stages of decomposition. Lineages of wood- and soil-feeding termites are distributed across terrestrial ecosystems located between 45°N and 45°S of latitude, a distribution they acquired through many transoceanic dispersal events. While wood-feeding termites often live in the wood on which they feed and ar...

Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging...

Termites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites roamed the earth during the early Cretaceous, suggesting that both vicariance and overseas dispersal may have shaped the distribution of early diverging termites. We investigate the historical biogeography of three early di...

Machadotermes is one of the basal Apicotermitinae genera, living in tropical West Africa. Old observations suggested the presence of a new gland, the intramandibular gland, in Machadotermes soldiers. Here, by combining micro-computed tomography, optical and electron microscopy, we showed that the gland exists in Machadotermes soldiers only as an ac...

Colonies of social insects contain large amounts of resources often exploited by specialized social parasites. While some termite species host numerous parasitic arthropod species, called termitophiles, others host none. The reason for this large variability remains unknown. Here we report that the evolution of termitophily in rove beetles is linke...

The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved...

Madagascar is home to many endemic plant and animal species owing to its ancient isolation from other landmasses. This unique fauna includes several lineages of termites, a group of insects known for their key role in organic matter decomposition in many terrestrial ecosystems. How and when termites colonised Madagascar remains unknown. In this stu...

Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species, but remains largely unknown in other taxa. We intend to feel this gap and provide a global understanding of the functional evolution of termite gut...

Termites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites (crown-Isoptera) occurred during the earliest Cretaceous, approximately 140 million years ago, suggesting that both vicariance through continental drift and overseas dispersal may have shaped the distribution of early diver...

Termites are social cockroaches. Because non-termite cockroaches are larger than basal termite lineages, which themselves include large termite species, it has been proposed that termites experienced a unidirectional body size reduction since they evolved eusociality. However, the validity of this hypothesis remains untested in a phylogenetic frame...

Termites are social cockroaches. Because non-termite cockroaches are larger than basal termite lineages, which themselves include large termite species, it has been proposed that termites experienced a unidirectional body size reduction since they evolved eusociality. However, the validity of this hypothesis remains untested in a phylogenetic frame...

Termites are major decomposers of organic matter in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae, the second-largest termite family, are widely distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals...

Cryptocercus Scudder, a genus of wingless, subsocial cockroaches, has low vagility but exhibits a disjunct distribution in eastern and western North America, and in China, South Korea and the Russian Far East. This distribution provides an ideal model for testing hypotheses of vicariance through plate tectonics or other natural barriers versus tran...

Soil-feeding termites are abundant in tropical regions and play an important role in soil bioturbation and in the organic matter cycle. The Apicotermitinae are arguably the most diverse lineage of soil-feeding termites, but they are also the most understudied, probably because many species are soldierless, which makes identification difficult. Alth...

Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete ge...

Soil‐burrowing cockroaches (Blaberidae: Geoscapheinae) are large insects endemic to Australia. Originally thought to represent a monophyletic group, these enigmatic species have in fact evolved burrowing behaviour, associated fossorial morphological modifications, and dietary transitions to dry leaf litter feeding multiple times from the wood‐feedi...

Termites are a clade of eusocial wood-feeding roaches with > 3000 described species. Eusociality emerged ~ 150 million years ago in the ancestor of modern termites, which, since then, have acquired and sometimes lost a series of adaptive traits defining of their evolution. Termites primarily feed on wood, and digest cellulose in association with th...

The Neotropical family Serritermitidae is a monophyletic group of termites including two genera, Serritermes and Glossotermes, with different way-of-life, the former being the sole obligatory inquiline among “lower” termites, while the latter is a single-site nester feeding on dry rotten red wood. Like the most advanced termite’s family, the Termit...

An iconic group of arid‐adapted insects is the Australian soil‐burrowing cockroaches (Blaberidae: Geoscapheinae), large, wingless insects that evolved burrowing behaviour and associated forms in parallel from wood feeding ancestors in the subfamily Panesthiinae. A particularly problematic taxon within the Geoscapheinae is Geoscapheus dilatatus (Sau...

All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feedi...

Despite their ecological importance, nothing is known about the diversity and abundance of RNA viruses in termites (Termitoidae). We used a metatranscriptomics approach to determine the RNA virome structure of 50 diverse species of termite that differ in both phylogenetic position and colony composition. From these samples, we identified 67 novel R...

Termites are important plant biomass decomposers. Their digestive activity typically relies on pro-karyotes and protozoa present in their guts. In some cases, such as in fungus-growing termites, digestion also relies on ectosymbiosis with specific fungal taxa. To date, the mycobiome of termites has yet to be investigated in detail. We evaluated the...

The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (Ne) is thought to play an important role in shaping genome size [1, 2, 3]—a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the exi...

Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protist species in these communities, as estimated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that chaotic advection by...

Animal collective behaviors give rise to various spatial patterns, such as the nests of social insects. These structures are built by individuals following a simple set of rules, slightly varying within and among species, to produce a large diversity of shapes. However, little is known about the origin and evolution of the behavioral mechanisms reg...

Trail-following behavior is a key to ecological success of termites, allowing them to orient themselves between the nesting and foraging sites. This behavior is controlled by specific trail-following pheromones produced by the abdominal sternal gland occurring in all termite species and developmental stages. Trail-following communication has been s...

Oceans host communities of plankton composed of relatively few abundant species and many rare species. The number of rare protists species in these communities, as esti- mated in metagenomic studies, decays as a steep power law of their abundance. The ecological factors at the origin of this pattern remain elusive. We propose that oceanic currents...

Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigat...

Thousands of eukaryotes transcriptomes have been generated, mainly to investigate nuclear genes expression, and the amount of available data is constantly increasing. A neglected but promising use of this large amount of data is to assemble organelle genomes. To assess the reliability of this approach, we attempted to reconstruct complete mitochond...

Termitidae comprises ∼80% of all termite species [1] that play dominant decomposer roles in tropical ecosystems [2, 3]. Two major events during termite evolution were the loss of cellulolytic gut protozoans in the ancestor of Termitidae and the subsequent gain in the termitid subfamily Macrotermitinae of fungal symbionts cultivated externally in "c...

Most people consider cockroaches to be quintessential urban pests, even though very few of the 5000 cockroach species live in urban areas. The German cockroach is the most widespread and common cockroach in urban areas, however how this invasive species has spread globally is poorly understood. We reviewed the published and grey literatures, and mu...

Bacterial endosymbionts evolve under strong host-driven selection. Factors influencing host evolution might affect symbionts in similar ways, potentially leading to correlations between the molecular evolutionary rates of hosts and symbionts. Although there is evidence of rate correlations between mitochondrial and nuclear genes, similar investigat...

Termites have evolved diverse defence strategies to protect themselves against predators, including a complex alarm communication system based on vibroacoustic and/or chemical signals. In reaction to alarm signals, workers and other vulnerable castes flee away while soldiers, the specialized colony defenders, actively move toward the alarm source....

Termites are the principal decomposers in tropical and subtropical ecosystems around the world. Time-calibrated molecular phylogenies show that some lineages of Neoisoptera diversified during the Oligocene and Miocene, and acquired their pantropical distribution through transoceanic dispersal events, probably by rafting in wood. In this paper, we i...

Termites have developed a wide array of defensive mechanisms. One of them is the mandibulate soldier caste that crushes or pierces their enemies. However, in several lineages of Termitinae, soldiers have long and slender mandibles that cannot bite but, instead, snap and deliver powerful strikes to their opponents. Here, we use morphological and mol...