Publications

The positive correlation between speciation rates and morphological evolution expressed by body size is a macroevolutionary trait of vertebrates. Although taxic diversification and morphological evolution are slow in coelacanths, their fossil record indicates that large and small species coexisted, which calls into question the link between morphological and body size disparities. Here, we describe and reassess fossils of giant coelacanths. Two genera reached up to 5 m long, placing them among the ten largest bony fish that ever lived. The disparity in body size adjusted to taxic diversity is much greater in coelacanths than in ray-finned fishes. Previous studies have shown that rates of speciation and rates of morphological evolution are overall low in this group, and our results indicate that these parameters are decoupled from the disparity in body size in coelacanths. Genomic and physiological characteristics of the extant Latimeria may reflect how the extinct relatives grew to such a large size. These characteristics highlight new evolutionary traits specific to these "living fossils"

Humans are a highly mobile species that has colonized the entire globe in a few tens of thousands of years after it went out of Africa. There are still many unknowns about the routes followed by our ancestors during this expansion process, which has been influenced by various environmental, biological, and cultural factors, but these migrations have contributed to shape the genetic diversity of our species. A powerful approach to study the consequences of human dispersal on our genome is the modelling of complex evolutionary scenarios via computer simulation. In this chapter, we present three types of approaches used to simulate human dispersal in a geographic landscape. We focus on a spatially explicit method, simulating the demographic and migratory dynamic of populations forward in time and their resulting genetic diversity backward in time using the coalescent. We describe this approach and illustrate its interest with two important results: the process of gene surfing during population expansion and the genetic consequences of hybridization during species expansions. We show that a relatively simple scenario of global expansion of Homo sapiens from Africa, with rare hybridization events with archaic humans, such as Neanderthals or Denisovans, over a large geographic area reasonably explains the introgression pattern of archaic DNA in the genome of our species.

Deep-sea biodiversity, a source of critical ecological functions and ecosystem services, is increasingly subject to the threat of disturbance from existing practices (e.g., fishing, waste disposal, oil and gas extraction) as well as emerging industries such as deep-seabed mining. Current scientific tools may not be adequate for monitoring and assessing subsequent changes to biodiversity. In this paper, we evaluate the scientific and budgetary trade-offs associated with morphology-based taxonomy and metabarcoding approaches to biodiversity surveys in the context of nascent deep-seabed mining for polymetallic nodules in the Clarion-Clipperton Zone, the area of most intense interest. For the dominant taxa of benthic meiofauna, we discuss the types of information produced by these methods, and use cost-effectiveness analysis to compare their abilities to yield biological and ecological data for use in environmental assessment and management. Based on our evaluation, morphology-based taxonomy is less cost-effective than metabarcoding but offers scientific advantages, such as the generation of density, biomass, and size structure data. Approaches that combine the two methods during the environmental assessment phase of commercial activities may facilitate future biodiversity monitoring and assessment for deep-seabed mining and for other activities in remote deep-sea habitats, for which taxonomic data and expertise are limited. This article is protected by copyright. All rights reserved.

Advances in phylogenomics contribute towards resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and UCE reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2945 loci with a mean of 1788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax nested within the genus Calosoma demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma (Ctenosta) burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level datasets informative at deep evolutionary scales.

Glyphosate is the most used pesticide around the world. Although different studies have evidenced its negative effect on honey bees, including detrimental impacts on behavior, cognitive, sensory and developmental abilities, its use continues to grow. Recent studies have shown that it also alters the composition of the honey bee gut microbiota. In this study we explored the impact of chronic exposure to sublethal doses of glyphosate on the honey bee gut microbiota and its effects on the immune response, infection by and Deformed wing virus (DWV) and honey bee survival. Glyphosate combined with infection altered the structure and composition of the honey bee gut microbiota, for example by decreasing the relative abundance of the core members and . Glyphosate increased the expression of some immune genes, possibly representing a physiological response to mitigate its negative effects. However, this response was not sufficient to maintain honey bee health, as glyphosate promoted the replication of DWV and decreased the expression of , which were accompanied by a reduced life span. Infection by also alters honey bee immunity although no synergistic effect with glyphosate was observed. These results corroborate previous findings suggesting deleterious effects of widespread use of glyphosate on honey bee health, and they contribute to elucidate the physiological mechanisms underlying a global decline of pollination services.

Globally, one of the two most common shallow-marine and estuarine foraminiferal genera is Ammonia. Over the past 50 years, the majority of workers have identified specimens in this genus as belonging to just 1-3 cosmopolitan species - A. beccarii, A. tepida and A. parkinsoniana. This has been partly because of the problems of discriminating the Ammonia species based entirely on shell morphology and partly because of a 1974 laboratory study that claimed to have shown that all morphologies were merely ecophenotypic variants of one species - a conclusion that molecular studies have proven to be unequivocally wrong. In this study we recognize, describe and figure sixty-seven living species and infraspecies of Recent Ammonia and two closely-related genera (Acarotrochus, Pseudoeponides) from around the world and summarize their ecological and biogeographic distribution. Twenty-six species and two subspecies are recognized by DNA sequencing and shown to be morphologically distinguishable. A further 39 morphospecies and one subspecies, that have not yet been sequenced, have sufficiently distinct morphology to be recognized. Canonical variates analysis using 42 measured or assessed morphological characters shows that the majority of these species can be readily discriminated by their test morphologies, although a few of the less-ornamented molecular species are verging on being pseudocryptic. Molecular sequencing of the type species of Challengerella (C. bradyi) and Helenina (H. anderseni) places them within our Ammonia clade. Here we continue to recognize the morphologically highly distinct genera Pseudoeponides (subjective senior synonym of Helenina) and allied Acarotrochus. Twenty new species or subspecies are described (molecular T types in brackets): Ammonia abramovichae (T8), A. akitaae, A. aoteana australiensis (T5A), A. arabica (T26), A. ariakensis quiltyi, A. buzasi (T11), A. fajemilai, A. goldsteinae, A. goodayi, A. haigi (T25), A. hattai, A. jorisseni (T23), A. justinparkeri, A. kitazatoi (T10), A. morleyae (T12), A. shchedrinae, A. turgida almogilabinae (T22M), Acarotrochus lippsi, Pseudoeponides hottingeri and P. dubuissoni. Aneotype is designated for A. veneta (Schultze 1854) (T1). We recognize 67 Ammonia and related taxa in this study but speculate that there may be 30 or more additional living species that we are not yet confident to discriminate without molecular sequencing. Ammonia species live in most parts of the world between 62 degrees N (Faeroe Islands) and 55 degrees S (Strait of Magellan), where seasonal sea-surface temperatures are 4-10 degrees C and above. One estuarine species (A. veneta, T1) is cosmopolitan, euryhaline and eurythermic. Several species are widespread in one or two ocean regions (e.g., Atlantic and Mediterranean; South Pacific), whereas the majority are endemic to smaller areas (e.g., eastern Mediterranean; Caribbean-Gulf of Mexico). Eleven biogeographic "provinces" are recognized by cluster analysis of presence/absence records with the highest diversities in the Australian and northwest Pacific provinces with 18 and 19 species each). Levels of endemism in our "provinces" range between 0 (temperate Atlantic) and 44% (Australian).

Vision is usually assumed to be sensitive to the light intensity and spectrum but not to its spectral phase. However, experiments performed on retinal proteins in solution showed that the first step of vision consists in an ultrafast photoisomerization that can be coherently controlled by shaping the phase of femtosecond laser pulses, especially in the multiphoton interaction regime. The link between these experiments in solution and the biological process allowing vision was not demonstrated. Here, we measure the electric signals fired from the retina of living mice upon femtosecond multipulse and single-pulse light stimulation. Our results show that the electrophysiological signaling is sensitive to the manipulation of the light excitation on a femtosecond time scale. The mechanism relies on multiple interactions with the light pulses close to the conical intersection, like pump-dump (photoisomerization interruption) and pump-repump (reverse isomerization) processes. This interpretation is supported both experimentally and by dynamics simulations.

We previously showed that the adult ocellated lizard skin colour pattern is effectively generated by a stochastic cellular automaton (CA) of skin scales. We additionally suggested that the canonical continuous 2D reaction-diffusion (RD) process of colour pattern development is transformed into this discrete CA by reduced diffusion coefficients at the borders of scales (justified by the corresponding thinning of the skin). Here, we use RD numerical simulations in 3D on realistic lizard skin geometries and demonstrate that skin thickness variation on its own is sufficient to cause scale-by-scale coloration and CA dynamics during RD patterning. In addition, we show that this phenomenon is robust to RD model variation. Finally, using dimensionality-reduction approaches on large networks of skin scales, we show that animal growth affects the scale-colour flipping dynamics by causing a substantial decrease of the relative length scale of the labyrinthine colour pattern of the lizard skin.

Predators must frequently balance competing approach and defensive behaviors elicited by a moving and potentially dangerous prey. Several brain circuits supporting predation have recently been localized. However, the mechanisms by which these circuits balance the conflict between approach and defense responses remain unknown. Laboratory mice initially show alternating approach and defense responses toward cockroaches, a natural prey, but with repeated exposure become avid hunters. Here, we used in vivo neural activity recording and cell-type specific manipulations in hunting male mice to identify neurons in the lateral hypothalamus and periaqueductal gray that encode and control predatory approach and defense behaviors. We found a subset of GABAergic neurons in lateral hypothalamus that specifically encoded hunting behaviors and whose stimulation triggered predation but not feeding. This population projects to the periaqueductal gray, and stimulation of these projections promoted predation. Neurons in periaqueductal gray encoded both approach and defensive behaviors but only initially when the mouse showed high levels of fear of the prey. Our findings allow us to propose that GABAergic neurons in lateral hypothalamus facilitate predation in part by suppressing defensive responses to prey encoded in the periaqueductal gray. Our results reveal a neural circuit mechanism for controlling the balance between conflicting approach and defensive behaviors elicited by the same stimulus.

Even in well-characterized genomes, many transcripts are considered noncoding RNAs (ncRNAs) simply due to the absence of large open reading frames (ORFs). However, it is now becoming clear that many small ORFs (smORFs) produce peptides with important biological functions. In the process of characterizing the ribosome-bound transcriptome of an important cell type of the seminal fluid-producing accessory gland of , we detected an RNA, previously thought to be noncoding, called (). Notably, is nested in the HOX gene cluster of the Bithorax complex and is known to contain a micro-RNA within one of its introns. We find that this RNA encodes a "micropeptide" (9 or 20 amino acids, MSAmiP) that is expressed exclusively in the secondary cells of the male accessory gland, where it seems to accumulate in nuclei. Importantly, loss of function of this micropeptide causes defects in sperm competition. In addition to bringing insights into the biology of a rare cell type, this work underlines the importance of small peptides, a class of molecules that is now emerging as important actors in complex biological processes.