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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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The upper Eocene-Oligocene carnivorous mammals from the Quercy Phosphorites (France) housed in Belgian collections
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The Quercy Phosphorites Formation in France is world famous for its Eocene to Miocene faunas, especially those from the upper Eocene to lower Oligocene, the richest of all. The latter particularly helped to understand the ‘Grande Coupure’, a dramatic faunal turnover event that occurred in Europe during the Eocene-Oligocene transition. Fossils from the Quercy Phosphorites were excavated from the middle 19th century until the early 20th century in a series of sites and became subsequently dispersed over several research institutions, while often losing the temporal and geographical information in the process. In this contribution, we provide an overview and reassess the taxonomy of these barely known collections housed in three Belgian institutions: the Université de Liège, KU Leuven, and the Royal Belgian Institute of Natural Sciences. We focus our efforts on the carnivorous mammals (Hyaenodonta and Carnivoramorpha) and assess the stratigraphic intervals covered by each collection. These fossils are derived from upper Eocene (Priabonian), lower Oligocene (Rupelian), and upper Oligocene (Chattian) deposits in the Quercy area. The richness of the three collections (e.g., the presence of numerous postcranial elements in the Liège collection), the presence of types and figured specimens in the Leuven collection, and some identified localities in the RBINS collection make these collections of great interest for further studies on systematics and the evolution of mammals around the ‘Grande Coupure’.
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RBINS Staff Publications 2021
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Ocean acidification modifies behaviour of shelf seabed macrofauna: A laboratory study on two ecosystem engineers, Abra alba and Lanice conchilega
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The feeding activity and burrow ventilation by benthic invertebrates importantly affect the biodiversity and functioning of seafloor sediments. Here we investigated how ocean acidification can modify these behavioural activities in two common and abundant macrofaunal ecosystem engineering species in temperate continental shelf communities: the white furrow shell Abra alba and the sand mason Lanice conchilega. Using time-lapse imagery and sediment porewater hydraulic signatures we show that both species adapt their behaviour in response to predicted future pH conditions (-0.3 units). During a three-week laboratory experiment, A. alba reduced the duration per feeding event when suspension and deposit feeding (by 86 and 53%, respectively), and almost completely ceased suspension feeding under reduced seawater pH in comparison to ambient seawater pH (pH ~ 8.2). This behavioural change reduces the intake of low pH water during feeding and respiration. L. conchilega increased its piston-pumping frequency by 30 and 52%, respectively, after one and two weeks of exposure to future pH conditions (-0.3 units) relative to ambient conditions. This change in irrigation activity suggests higher metabolic demands under low seawater pH, and also extended low water column pH conditions deeper into the seafloor. Because the distribution of other populations depends on the physicochemical setting by our focal species, we argue that the demonstrated behavioural plasticity will likely have cascading effects on seafloor diversity and functioning, highlighting the complexity of how ocean acidification, and climate change in general, will affect seafloor ecology.
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RBINS Staff Publications 2023
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Catypnes marazziorum sp. nov. (Coleoptera: Cerambycidae: Prioninae) from Papua New Guinea
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RBINS Staff Publications 2021
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Polydictya lanternflies of Java: New species, taxonomy and identification key (Hemiptera: Fulgoromorpha: Fulgoridae)
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RBINS Staff Publications 2024
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Case 3826 – Propappus Michaelsen, 1905 and Propappidae Coates, 1986 (Annelida, Clitellata): proposed conservation by suppression of Propappus Seeley, 1888 (Vertebrata, Reptilia)
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RBINS Staff Publications 2021
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Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin
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RBINS Staff Publications 2020
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Mainstreaming biodiversity conservation into development cooperation—highlights from an ALTER-NET-EKLIPSE workshop
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RBINS Staff Publications 2020
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The changing ecosystem of East Africa’s Mare Nostrum: Using ichthyology collections to identify the changes in the Lake Victoria region
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RBINS Staff Publications 2024
