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Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
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Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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RBINS Staff Publications 2021
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Familie-indeling en diversiteit van wespen (Hymenoptera) in de Lage Landen
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De classificatie van de families van de orde Hymenoptera is de afgelopen vijf jaar aanzienlijk veranderd, onder meer door meer moleculair onderzoek. De evolutionaire geschiedenis van de orde wordt ook steeds duidelijker. Op basis van onderzoek uit recente literatuur en in lijn met nieuwe inzichten presenteren wij een nieuw familieoverzicht voor Nederland en België. In Nederland en België zijn vertegenwoordigers gevonden van 88 families. Om een idee te krijgen van de diversiteit van de verschillende families wordt een overzicht gegeven van het aantal genera en het (geschatte) aantal soorten voor elke familie. Deze cijfers zijn gebaseerd op literatuuronderzoek, websites of deskundig oordeel van specialisten. Een groot aantal foto’s toont de enorme soortendiversiteit van de wespen. Er valt echter ook in beide landen nog veel te ontdekken, vooral in de Parasitica-groep.
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RBINS Staff Publications 2024
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Faunal Remains from Archaeological Sites Document Human Impact on the Terrestrial and Aquatic Environment: examples from the last thousand years in Belgium
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The aim of this article is to demonstrate how animal remains from archaeological sites can contribute to a better understanding of human impact on the terrestrial and aquatic environment over time. A number of case studies, mainly from Belgium, illustrate the possible effects of deforestation, overhunting, overfishing and water pollution on wildlife. Species extinctions and introductions from the last millennium are also discussed. It is shown how relevant these results are and how they can be communicated to the general public, the wider scientific community and stakeholders.
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RBINS Staff Publications 2023
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Faunal remains from Early Bronze Age al-Lāhūn (Jordan) and a comparison to contemporaneous assemblages in the southern Levant
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RBINS Staff Publications 2022
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Faunistic survey of myrmecophilous and other ant-associated beetles and spiders in the Belgian province of Limburg (Araneae, Coleoptera, Hymenoptera: Formicidae)
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Many researchers have been fascinated by the social organisation within an ant colony. They have noticed that several other invertebrates are found in or near the ants’ nests, notably a variety of Coleoptera and to a lesser extent, some spiders. Many of these observations have been written down, some just as a brief statement but sometimes a detailed report of these interactions as a result of accurate and prolonged monitoring was published. All this information allowed us to make a comparison with the ant species associated with beetles and spiders in the Belgian province of Limburg. We will discuss a large number of species within their respective families and mention in particular a certain connection between the guest and its host, a relationship which cannot necessarily be called myrmecophilous
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RBINS Staff Publications 2023
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Faunistics, shell morphology, and reproductive anatomy of the genus Bensonies Baker, 1938 In Nepal (Gastropoda: Pulmonata: Ariophantidae)
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RBINS Staff Publications 2023 OA
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Suction feeding preceded filtering in baleen whale evolution
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RBINS Staff Publications 2016
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Field Data on the Little Known and, Endangered Lepilemur Mittermeieri
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RBINS Staff Publications
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Field guide to the brittle and basket stars (Echinodermata: Ophiuroidea) of South Africa
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Brittle and basket stars (ophiuroids) are one of five extant classes of the phylum Echinodermata and have a fossil record dating back almost 500 million years to the Early Ordovician. Today, they remain diverse and widespread, with over 260 described genera and 2,077 extant species globally (Stöhr et al. 2018), more than any other class of echinoderm. Ophiuroid species are found across all marine habitats from the intertidal shore to the abyss. In southern Africa, the ophiuroid fauna has been studied extensively by a number of authors and is relatively wellknown. The last published review of the southern African Ophiuroidea however was by Clark & Courtman-Stock in 1976. It included 101 species reported from within the boundaries of South Africa. In the 40 years since that publication the number of species has risen to 136. This identification guide includes a taxonomic key to all 136 species, and gives key references, istribution maps, diagnoses, scaled photographs (where possible), and a synthesis of known ecological and depth information for each. The guide is designed to be comprehensive, well illustrated and easy to use for both naturalists and professional biologists. Taxonomic terms, morphological characteristics and technical expressions are defined and described in detail, with illustrations to clarify some aspects of the terminology. A checklist of all species in the region is also included, and indicates which species are endemic (33), for which we report significant range extensions (23), which have been recorded as new to the South African fauna (28) since the previous monograph of Clark & Courtman-Stock (1976) and which have undergone taxonomic revisions since that time (28).
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RBINS Staff Publications 2019
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Field Intercomparison of Radiometer Measurements for Ocean Colour Validation
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A field intercomparison was conducted at the Acqua Alta Oceanographic Tower (AAOT) in the northern Adriatic Sea, from 9 to 19 July 2018 to assess differences in the accuracy of in- and above-water radiometer measurements used for the validation of ocean colour products. Ten measurement systems were compared. Prior to the intercomparison, the absolute radiometric calibration of all sensors was carried out using the same standards and methods at the same reference laboratory. Measurements were performed under clear sky conditions, relatively low sun zenith angles, moderately low sea state and on the same deployment platform and frame (except in-water systems). The weighted average of five above-water measurements was used as baseline reference for comparisons. For downwelling irradiance ( E d ), there was generally good agreement between sensors with differences of <6\% for most of the sensors over the spectral range 400 nm–665 nm. One sensor exhibited a systematic bias, of up to 11\%, due to poor cosine response. For sky radiance ( L s k y ) the spectrally averaged difference between optical systems was <2.5\% with a root mean square error (RMS) <0.01 mWm−2 nm−1 sr−1. For total above-water upwelling radiance ( L t ), the difference was <3.5\% with an RMS <0.009 mWm−2 nm−1 sr−1. For remote-sensing reflectance ( R r s ), the differences between above-water TriOS RAMSES were <3.5\% and <2.5\% at 443 and 560 nm, respectively, and were <7.5\% for some systems at 665 nm. Seabird-Hyperspectral Surface Acquisition System (HyperSAS) sensors were on average within 3.5\% at 443 nm, 1\% at 560 nm, and 3\% at 665 nm. The differences between the weighted mean of the above-water and in-water systems was <15.8\% across visible bands. A sensitivity analysis showed that E d accounted for the largest fraction of the variance in R r s , which suggests that minimizing the errors arising from this measurement is the most important variable in reducing the inter-group differences in R r s . The differences may also be due, in part, to using five of the above-water systems as a reference. To avoid this, in situ normalized water-leaving radiance ( L w n ) was therefore compared to AERONET-OC SeaPRiSM L w n as an alternative reference measurement. For the TriOS-RAMSES and Seabird-HyperSAS sensors the differences were similar across the visible spectra with 4.7\% and 4.9\%, respectively. The difference between SeaPRiSM L w n and two in-water systems at blue, green and red bands was 11.8\%. This was partly due to temporal and spatial differences in sampling between the in-water and above-water systems and possibly due to uncertainties in instrument self-shading for one of the in-water measurements.
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RBINS Staff Publications 2020
