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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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Species' traits and taxonomic distance can predict the hatching phenology of ostracod (Crustacea) resting eggs from tropical floodplain lakes
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Freshwater ostracods are commonly found in temporary ponds and lakes, surviving drought periods by producing resting eggs. We investigated the hatching phenology of ostracod resting eggs from the sediments of temporary floodplain lakes, considering both the taxonomic distance between species and their functional traits, such as carapace size (length and height) and shape, valve ornamentation, and reproductive mode. In addition, we tested the hypotheses: (1) that the hatching time is more similar between congeneric ostracod species than between noncongeneric species; (2) that differences in hatching time between congeneric species are often related to differences in functional traits; (3) that both species composition and functional traits composition of hatchlings change over the incubation time, but with a reduction in the variability over time. The experiment was conducted for 98 days in the laboratory, and the microcosms were monitored weekly. The first hatching of an ostracod was recorded during the second week of incubation after hydration of the sediments. A total of 12 ostracod species hatched, belonging to the families Cyprididae and Candonidae. The above three hypotheses were corroborated. The time between inundation and first hatching was mostly similar for congeneric species in the genus Chlamydotheca, but was different between some species of Strandesia, which might be owing to differences in functional traits. The species composition and functional trait composition of the hatched ostracods were significantly different over the 14 weeks of incubation due to the different hatching phenology of different species. Furthermore, our results show that both taxonomic distance and functional traits can influence the hatching time of ostracod resting eggs from temporary floodplain lakes. Thus, future studies addressing the hatching phenology of ostracod resting eggs (and resting stages from other invertebrates) should also emphasize the use of functional traits.
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RBINS Staff Publications 2021
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A new tribe, two new genera and three new species of Cypridopsinae (Crustacea, Ostracoda, Cyprididae) from Brazil.
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We describe one new tribe, two new genera and three new species of the subfamily Cypridopsinae Kaufmann, 1900 from Brazilian floodplains. Brasilodopsis gen. nov. belongs in the nominal tribe Cypridopsini, and both new species in this new genus were found in both sexual and asexual populations. Brasilodopsis baiabonita gen. et sp. nov. has a wide distribution and was found in three of the four major Brazilian floodplains. Brasilodopsis amazonica gen. et sp. nov. was recorded only from the Amazon floodplain. Brasilodopsis baiabonita gen. et sp. nov. has a subtriangular shape in lateral view, whereas Brasilodopsis amazonica gen. et sp. nov. is more elongated and has more rounded dorsal margins in both valves, as well as more pronounced external valve ornamentation, consisting of rimmed pores in shallow pits. Paranadopsis reducta gen. et sp. nov. was found in asexual populations in the Upper Paraná River floodplain only and differs from other Cypridopsinae in the more elongated carapace, an A1 with strongly reduced chaetotaxy (hence the specific name) and the total absence of caudal rami in females. Because of these strong reductions in valve and limb morphology, Paranadopsini trib. nov. is created within the Cypridopsinae for this intriguing new genus and species.
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RBINS Staff Publications 2021
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The representativeness of protected areas for Amazonian fish diversity under climate change.
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RBINS Staff Publications 2021
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Weird Fish: Defining a role for fish paleopathology
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RBINS Staff Publications 2018
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The new polillensis group in the lanternfly genus Pyrops: Taxonomy, distrubtion and host plant (Hemiptera: Fulgoridae)
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RBINS Staff Publications 2017
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Morphological variability study and review of the distribution area of Metaegosoma annamensis (Pic, 1930) (Coleoptera, Cerambycidae, Prioninae)
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RBINS Staff Publications 2021
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A propos de quelques Raphitomidae (Neogastropoda: Conoidea) de Bretagne, en Mer d’Iroise et en Manche (France)
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RBINS Staff Publications 2020
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A secondary mandibular condylar articulation and collateral effects on a Late Neolithic mandible from Bois Madame rockshelter in Arbre, Belgium
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A Neolithic Belgian mandible from Bois Madame rockshelter in Arbre presents an asymmetrical morphology resulting from a secondary, or false, articulation of the right mandibular condyle. The pathological articulation produced enlarged masseter, medial pterygoid and mylohyoid musculature on the right side as well as a flattening of the right incisal alveolus curvature. The secondary condylar articulation did not lead to pronounced asymmetry of attrition on the antimeres of the dental arcade. This is the most complete mandible from this Late Neolithic collective burial dating to the beginning of the Bronze Age circa 4000 years BP. It is possible that a fall or blow to the mental symphysis during early adolescence could have resulted in the partial intrusion of the mandibular condyle into the articulation disc of the temporomandibular joint capsule. When the affected condyle healed, a secondary, but serviceable articulation developed, producing unique stresses on the involved muscular tissue and ultimately resulted in an asymmetry of mandibular form.
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RBINS Staff Publications 2017
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Pisachini planthoppers of Vietnam: new records of Pisacha and a new Goniopsarites species from Central Vietnam (Hemiptera, Fulgoromorpha, Nogodinidae)
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RBINS Staff Publications 2024
