Towards conserving natural diversity: A biotic inventory by observations, specimens, DNA barcoding and high-throughput sequencing methods

Abstract

The Kenai National Wildlife Refuge has been given a broad conservation mandate to conserve natural diversity. A prerequisite for fulfilling this purpose is to be able to identify the species and communities that make up that biodiversity. We tested a set of varied methods for inventory and monitoring of plants, birds and terrestrial invertebrates on a grid of 40 sites in a 938 ha study area in the Slikok Creek watershed, Kenai Peninsula, Alaska. We sampled plants and lichens through observation and specimen-based methods. We surveyed birds using bird call surveys on variable circular plots. We sampled terrestrial arthropods by sweep net sampling, processing samples with High Throughput Sequencing methods. We surveyed for earthworms, using the hot mustard extraction method and identified worm specimens by morphology and DNA barcoding. We examined community membership using clustering methods and Nonmetric Multidimensional Scaling. We documented a total of 4,764 occurrences of 984 species and molecular operational taxonomic units: 87 vascular plants, 51 mosses, 12 liverworts, 111 lichens, 43 vertebrates, 663 arthropods, 9 molluscs and 8 annelid worms. Amongst these records, 102 of the arthropod species appeared to be new records for Alaska. We found three non-native species: Deroceras agreste (Linnaeus, 1758) (Stylommatophora: Agriolimacidae), Dendrobaena octaedra (Savigny, 1826) (Crassiclitellata: Lumbricidae) and Heterarthrus nemoratus (Fallén, 1808) (Hymenoptera: Tenthredinidae). Both D. octaedra and H. nemoratus were found at sites distant from obvious human disturbance. The 40 sites were grouped into five community groups: upland mixed forest, black spruce forest, open deciduous forest, shrub-sedge bog and willow. We demonstrated that, at least for a subset of species that could be detected using these methods, we were able to document current species distributions and assemblages in a way that could be efficiently repeated for the purposes of biomonitoring. While our methods could be improved and additional methods and groups could be added, our combination of techniques yielded a substantial portion of the data necessary for fulfilling Kenai National Wildlife Refuge's broad conservation purposes.

European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation

“…This information can be subsequently translated to the function and role of taxa in the environment and used to other applied research fields. Omics data can support the conservation of ecosystems and the sustainable use of marine resources (for example Bowser et al, 2020;Turunen et al, 2021), as well as the monitoring of wild animal populations such as fish (Andruszkiewicz et al, 2017) or mammals (Suarez-Bregua et al, 2022). In addition, omics data can be integrated into ecosystem models to develop innovative investigations in food security (for example Grützke et al, 2019;Sequino et al, 2022), biodiscovery (for example Mahapatra et al, 2020;Shaaban et al, 2022), novel treatments in biofuels (Sartaj et al, 2022) and bioremediation (Rodrıǵuez et al, 2022), and other services such as disease detection in the environment (Wurtzer et al, 2022) or clinical diagnostics (Forbes et al, 2017).…”

The gender-specific impact of starvation on mitotypes diversity in adults of Drosophila melanogaster

“…With the accumulation of barcode sequences, some databases such as NCBI and BOLD system [36] have recorded a large number of species barcodes, among which the commonly used DNA barcode in animals is the 5 0 end region of the mitochondrial cox1 gene [37][38][39], particularly in insects [40]. Currently, the high-throughput cox1 amplicon sequencing can be used for rapid identification of members in ecological communities [41], determination of animal diets [42,43], biodiversity surveys [40,44], discovery of cryptic species [45] and conservation biology [46], along with the estimation of intraspecific genetic diversity [47]. According to the sequencing principle, cox1 amplicon sequencing can also be used to study intra-individual genetic diversity, enabling the identification of cox1 haplotypes within individuals, with the advantage of a well-stocked cox1 reference database that can eliminate contamination introduced during the experimental processes.…”