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
Metacommunity studies using the deconstruction approach based on biological traits have received a great deal of attention in recent years as they often better describe characteristics of the species that reflect adaptations to a specific environment. This approach has not yet been used for ostracods, which are nevertheless highly diverse crustaceans and abundant in continental aquatic environments. Here, we investigate the influence of environmental and spatial factors on the metacommunity structure of periphytic ostracods in 27 tropical floodplain lakes in the Upper Paraná River floodplain (Brazil). An analysis of variance partitioning was used to estimate the relative importance of these factors (environmental and spatial) on both the entire community as well as after its deconstruction according to the biological traits (size and locomotion mode). Ostracods, regardless of body size, are good dispersers at regional scales. In addition, as expected, swimming ostracods were better dispersers at local scales than non-swimmers, which were influenced mainly by the diversity of aquatic macrophytes. Environmental factors (species sorting mechanism) seem important in structuring the entire ostracods metacommunity, as well as for most categories of biological traits. The unexplained variability remained high showing that other variables, not measured here, must be important. The analysis based on deconstruction, when compared to the analysis based on the metacommunity as a whole, contributed to a better assessment of ostracod metacommunity structuring.
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RBINS Staff Publications 2018
