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Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family
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The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.
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RBINS Staff Publications 2023
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Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.
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Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4\% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.
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RBINS Staff Publications 2019
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Revision of the genus Baltoplana (Rhabdocoela: Schizorhynchia: Cheliplanidae) with the description of two new species
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RBINS Staff Publications 2024
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Unraveling chromosomal inversions and their evolutionary dance in a wing polymorphic beetle
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RBINS Staff Publications 2024
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Symbiotic interactions challenged by environmental stress in aquatic transitional habitats
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RBINS Staff Publications 2024
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Comparison of the pollinator microbiome: management practices, altitude and sex as drivers for change
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RBINS Staff Publications 2024
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The green heart of Africa, the Lomami Primer
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RBINS Staff Publications 2024
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Evolution in the tides: unravelling adaptive strategies in Pogonus chalceus beetles
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RBINS Staff Publications 2024
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Morphological study of the anterior dentition in Raoellidae (Mammalia, Artiodactyla), new insight on their dietary habits
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Raoellidae are small artiodactyls from the Indian subcontinent closely related to stem cetaceans. They bring crucial information to understand the early phase of the land-to- water transition in Cetacea. If they are considered to be partly aquatic, the question of their dietary habits remains partly understood due to their “transitional” morphology. Raoellidae are largely documented by their cheek teeth and getting a better knowledge of their anterior dentition constitutes an additional proxy to discuss their feeding habits. In this work, we document the anterior dentition of Indohyus indirae from an unprecedented sample of in situ and isolated teeth from the locality of East Aiji-2 in the Kalakot area (Rajouri district, India). We propose identification criteria for upper and lower incisors and canines in raoellids. Based on CT scan data, virtual reconstruction of in situ dentition, and identification of the isolated incisors and canines, we reconstruct a composite anterior dentition of Indohyus supported by the correspondence of wear facets between upper and lower teeth. This constitutes the first attempt at reconstruction of the anterior dentition of a raoellid. We show that the upper incisors are caniniform and very similar morphologically, whereas the lower incisors are pointed but remain incisiform and quite different from one another. We also describe noticeable intraspecific variation, at the level of upper canines, suggesting a potential sexual dimorphism in this species. Upper and lower incisors are recurved, with the upper incisor row arranged on a widely opened arch. Taken altogether the anterior dentition forms a grasping device, allowing the animal to capture and secure food, a characteristic shared with stem cetaceans. This would mark the first step towards the carnivorous diet in these peculiar artiodactyls.
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RBINS Staff Publications 2025 OA
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Bioerosional marks in the shells of two sea turtle taxa from the middle Eocene of Belgium
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This study analyses the diverse types of bioerosion marks on the shells of two sea turtle specimens from the Lutetian (middle Eocene) of Belgium. The objective is to understand the physical stressors affecting these organisms in ancient marine environments and to identify the potential factors responsible for these changes. The first specimen, the holotype of Eochelone brabantica, presents multiple erosive anomalies on its costal plates. The second individual, corresponding to Puppigerus camperi, exhibits different types of shell deviations, also of an erosive character. The combination of macroscopic and imaging techniques (i.e., CT scanning and 3D surface scanning) allow us the precise observation and identification of the different alterations. Comparative analyses suggest several external factors as potential causes of the anomalies of the two specimens (i.e., invertebrate feeding traces and trauma). This detailed examination provides specific insights into the types and causes of shell alterations in these Eocene turtles, offering a clearer understanding of their interactions in the marine ecosystem in which they lived.
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RBINS Staff Publications 2025 OA
