Genetic basis and expression of ventral colour in polymorphic common lizards.

Colour is an important visual cue that can correlate with sex, behaviour, life history or ecological strategies, and has evolved divergently and convergently across animal lineages. Its genetic basis in non-model organisms is rarely known, but such information is vital for determining the drivers and mechanisms of colour evolution. Leveraging genetic admixture in a rare contact zone between oviparous and viviparous common lizards (Zootoca vivipara), we show that females (N = 558) of the two otherwise morphologically indistinguishable reproductive modes differ in their ventral colouration (from pale to vibrant yellow) and intensity of melanic patterning. We find no association between female colouration and reproductive investment, and no evidence for selection on colour. Using a combination of genetic mapping and transcriptomic evidence, we identified two candidate genes associated with ventral colour differentiation, DGAT2 and PMEL. These are genes known to be involved in carotenoid metabolism and melanin synthesis respectively. Ventral melanic spots were associated with two genomic regions, including a SNP close to protein tyrosine phosphatase (PTP) genes. Using genome re-sequencing data, our results show that fixed coding mutations in the candidate genes cannot account for differences in colouration. Taken together, our findings show that the evolution of ventral colouration and its associations across common lizard lineages is variable. A potential genetic mechanism explaining the flexibility of ventral colouration may be that colouration in common lizards, but also across squamates, is predominantly driven by regulatory genetic variation.

Chromosome-Level Genome Assembly of the Cape Cliff Lizard (Hemicordylus capensis).

Squamates represent a highly diverse and species-rich vertebrate group that is remarkably understudied from a genomic perspective. A scarcity of genomic data is particularly evident for scincomorph lizards, which encompass over 10% of all living squamates, and for which high-quality genomic resources are currently lacking. To address this knowledge gap, we present the first chromosome-level reference genome for this group, generated from a male Cape cliff lizard (Hemicordylus capensis), using highly accurate PacBio HiFi long-read sequencing data, long-range Omni-C chromosomal conformation capture data and transcriptomic data for annotation. The rHemCap1.1 genome assembly spans 2.29 Gb, with a scaffold N50 of 359.65 Mb, and includes 25,300 protein-coding genes, with a BUSCO completeness score of 95.5% (sauropsida_odb10). We have generated the most contiguous and complete chromosome-level squamate reference genome assembly publicly available to date. Furthermore, we used short-read resequencing of 35 males and females and applied a differential coverage approach to infer the sex-determination system of the species, which was previously unknown. Our results suggest this species has XX/XY sex chromosomes, representing the first evidence of sex determination in the family Cordylidae. This reference genome will help to establish this species as an evolutionary model for studying variation in body armor, a key trait in cordylids and other squamate groups. Lastly, this is the first squamate reference genome from a continental African species and, as such, represents a valuable resource not only for further evolutionary research in cordylids but also in closely related groups.

The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.

Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat in terms of mortality, morbidity, and economic burden.2,3 Because AMR can be exchanged between humans, livestock, and wildlife, wild animals can be used as indicators of human-associated AMR contamination of the environment.4 However, AMR is a normal function of natural environments and is present in host-associated microbiomes, which makes it challenging to distinguish between anthropogenic and natural sources.4,5 One way to overcome this difficulty is to use historical samples that span the period from before the mass production of antibiotics to today. We used shotgun metagenomic sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears collected over the last 180 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is consistent with patterns of national human antibiotic use. We also demonstrated a significant decrease in total AMR load in bears in the last two decades, which coincides with Swedish strategies to mitigate AMR. Our study suggests that public health policies can be effective in limiting human-associated AMR contamination of the environment and wildlife.

Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.

Too much to tell: Narrative styles of the first descriptions of the natural world of the Indies.

Describing a Mundus Novus was a very singular task in the sixteenth century. It was an effort shaped by a permanent inherent tension between novelty and normality, between the immense variety of new facts (some extraordinary) and the demand of credibility. How did these inner strains affect the narrative style of the first descriptions of the natural world of 'the Indies'? How were the first European observers of the nature of America able to simultaneously transmit the idea of immensity and regularity ( mundus), and that of novelty ( novus)? How did they attempt to describe new worlds knowing that there was a lot - perhaps too much - to tell? This paper focuses not on the much-discussed epistemological issues related to those questions, but on their narrative and stylistic consequences. We argue that the first Europeans meeting the new realities of the Americas or India had to meet new challenges, and these translated into texts with specific characteristics. Thus, their first descriptions are essentially different from the texts about the natural world that were written before or after the 'discovery'. We show that they adopted very specific discursive approaches, and were deeply influenced by the credibility strategies of the medical profession in which they had been trained.

Zilsel's Thesis, Maritime Culture, and Iberian Science in Early Modern Europe.

Zilsel's thesis on the artisanal origins of modern science remains one of the most original proposals about the emergence of scientific modernity. We propose to inspect the scientific developments in Iberia in the early modern period using Zilsel's ideas as a guideline. Our purpose is to show that his ideas illuminate the situation in Iberia but also that the Iberian case is a remarkable illustration of Zilsel's thesis. Furthermore, we argue that Zilsel's thesis is essentially a sociological explanation that cannot be applied to isolated cases; its use implies global events that involve extended societies over large periods of time.

Giant placental chorioangioma: a rare cause of fetal hydrops.

Giant choriangiomas are rare placental tumours, associated with a high prevalence of pregnancy complications and a poor perinatal outcome. Neonatal consequences include severe microangiopathic haemolytic anaemia, thrombocytopaenia and hydrops. The associated high perinatal death rate (30-40%) has led to a number of prenatal therapeutic interventions with limited success in most cases. The authors present a case of non-immune fetal hydrops caused by a giant chorioangioma, diagnosed at 27 weeks of gestational age. Despite tocolytic therapy, the baby was born prematurely (28 weeks of gestational age) and required transfusion of blood derivatives, intensive phototherapy and exchange transfusion. She had an uncomplicated recovery and was discharged home in the second month of life. The authors emphasise the need to consider chorioangioma as a cause of non-immune fetal hydrops and microangiopathic haemolytic anaemia.

Idiopathic congenital chylothorax treated with octreotide.

Idiopathic congenital chylothorax is defined as an abnormal accumulation of lymphatic fluid within the pleural space and is a relatively rare condition. It is a cause of progressive respiratory distress with nutritional and immunological consequences. Treatment of congenital chylothorax has been conservative management and cases unresponsive usually require surgery. We report a case of idiopathic congenital chylothorax treated with octreotide (a somatostatin analogue), avoiding surgery after failed conservative medical treatment. The patient promptly improved after initiation of endovenous octreotide treatment (10 µg/kg/h) with no observed side effects.