Publications

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.

Species of large, testate, rhizarian protists in the genus Gromia are often common in high-latitude coastal environments, including fjords, but are frequently overlooked and almost all are undescribed. Here, we describe three new gromiid species from the Nuuk fjord system on the west coast of southern Greenland. Morphologically, the new species differ in the size and shape of the test. Gromia cucumiformis sp. nov. is elongate, up to 5.5 mm long, with a length:width (L/W) ratio of 4.3–5.5; Gromia botelliformis sp. nov. is up to 2.1 mm long, with a L/W ratio of 3.0–4.8; Gromia brevis is typically less than 1.0 mm long, with a L/W ratio around 2.0. Genetically, they are well-characterised and split between two clades. Gromia cucumiformis and G. brevis branch with several species of deep-water gromiids from the Arabian Sea and the Weddell Sea, while G. botelliformis branches with deep Weddell Sea species and several unnamed and morphologically uncharacterised gromiids from different parts of the world. Gromia botelliformis and G. brevis are currently known only from the Nuuk fjords, but sequences of G. cucumiformis from Greenland group together with sequences from Svalbard and the White Sea. Our genetic data reveal four additional clades of undescribed Gromia species. One contains sequences from Greenland, Svalbard and the White Sea, two comprises sequence from Greenland and the White Sea and one is limited to sequences from Greenland. These results demonstrate the high genetic diversity of gromiids and their widespread distribution in Arctic as well as in deep-sea environments.

We read with great interest the perspective by Bumpus (1), who describes the issue of overrepresenting individuals of European ancestry in pharmacological trials. The author highlights the inequities this can translate into and the efforts needed in reporting ethnicity in trials, in line with the STROPS guideline (2). However, this raises several concerns.

Human leukocyte antigen (HLA) genes are among the most polymorphic of our genome, as a likely consequence of balancing selection related to their central role in adaptive immunity. HLA-A and HLA-B genes were recently suggested to evolve through a model of joint divergent asymmetric selection conferring all populations, including those with severe loss of diversity, an equivalent immune potential. However, the mechanisms by which these two genes might undergo joint evolution while displaying very distinct allelic profiles in populations worldwide are still unknown. To address this issue, we carried out extensive data analyses (among which factorial correspondence and linear modelling) on 2,909 common and rare HLA-A, HLA-B and HLA-C alleles and 200,000 simulated pathogenic peptides by taking into account sequence variation, predicted peptide-binding affinity and HLA allele frequencies in 123 populations worldwide. Our results show that HLA-A and HLA-B (but not HLA-C) molecules maintain considerable functional divergence in almost all populations, which likely plays an instrumental role in their immune defence. We also provide robust evidence of functional complementarity between HLA-A and HLA-B molecules, which display asymmetric relationships in terms of amino acid diversity at both inter- and intra-protein levels and in terms of promiscuous or fastidious peptide-binding specificities. Like two wings of a flying bird, the functional complementarity of HLA-A and HLA-B is a perfect example, in our genome, of duplicated genes sharing their capacity of assuming common vital functions while being submitted to complex and sometimes distinct environmental pressures.

The Late Jurassic Allosaurus is one of the better-studied dinosaurs. A histological and geochemical study of a tibia and a femur of A. fragilis recovered in the Upper Jurassic Cleveland-Lloyd Dinosaur Quarry, Utah, United States has been done in order to address growth characteristics of this species. The two bones, probably belonging to separate individuals, are among the largest known for this species, which make them suitable to address such issues. The inclusion of our data on femur growth markings in the previously published data reflects a range of growth variability rather than two distinct growth strategies. The tibia has a well-developed external fundamental system indicating somatic maturity achievement. Using a quantitative method of superimposition to retrocalculate missing lines of arrested growth, the tibia appears to correspond to an individual that reached its skeletal maturity at 22 years and died at approximately 26 years. In the tibia, the concentration of zinc, a potential biomarker associated with bone formation, displays a higher concentration in zones of rapid growth compared to annuli. There is no direct relationship between the values of δ18Op and the lines of arrested growth distribution. The absence of relations between the histological organization and an enrichment in REE of the bone, indicates that the variations of δ18Op likely represent a diagenetic process rather than a primordial, biologic composition. However, the geochemical composition of the bones is not homogeneous along the sections, indicating that the signal variations have not been completely erased by diagenesis.

The Recent re-/discovery of unusual Lower Cretaceous continental deposits (dysodiles) brings important and exceptional paleontological assets. Dysodile beds are found in many localities across Lebanon and are characterized by their high organic matter content and their richness in exceptionally well-preserved fossils. We focus our study on five sampling localities in the lower Barremian sandstone beds, deposited when Lebanon was located in the north-eastern part of the Gondwana supercontinent. The localities are found associated with volcanic deposits suggesting a close relation between volcanism and their deposition and/or preservation. The present study provides, for the first time, insights on the fossil assemblages found in the dysodiles, including fishes, turtles, gastropods, insects, plant debris (macroflora and palynomorphs), ostracods and coprolites. We provide a preliminary reconstruction of the depositional environment that is common to the five sampling localities. It was a freshwater lake or possibly a series of interconnected lakes, in the vicinity of volcanic edifices, surrounded by a typical Lower Cretaceous flora (open forest environment), and inhabited by basal actinopterygian fishes and teleosts that will constitute the core of subsequent freshwater assemblages. The Lebanon localities have important implications for local palaeoenvironments as well as worldwide biogeography. In addition, the fossil assemblages show some taxonomic and taphonomic differences between the sampling sites, suggesting local differences in environmental conditions during deposition.