Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans

Description

Methods for delimiting species based on multi-gene nucleotide information are well established and provide the means to complement the classical COI barcoding approach, whose limitations are well known. Our research project aims at establishing a standardized set of single-copy nuclear-encoded markers for genome-wide multi-locus species delimitation by exploiting comparative genomic data and applying target DNA enrichment. Candidate markers are so-called Universal Single-Copy Orthologs (USCOs). The targeted set of gene markers shares a subset among all metazoans and thus sequence data will be comparable across Metazoa. We will assess USCOs exhibiting a conserved gene structure across invertebrates for their discriminative power and universal applicability in selected case studies with either optimal DNA quality or highly degraded DNA from museum samples. Seven planned case studies include cellar spiders, centipedes, parasitoid wasps, scarab beetles, hoverflies, butterflies, nematodes and will use sequence data of hundreds of genes in multispecies-coalescent species delimitation and integrative taxonomy approaches. The analysis pipeline will comprise (1) the design of probes for targeting and enriching invertebrate USCOs, (2) tools for DNA sequence quality filtering, assembly, alignment, and annotation; (3) coalescent-based species delimitation. We will employ a series of alternative protocols to verify the robustness of the total evidence species delimitation with the multi-species coalescent. We will examine congruence with morphology-based a priori species identifications and alternative species delimitation methods. These include character- and tree-based species delimitation based on separate genes (COI barcodes) or concatenated USCOs.

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