Systematics and evolution of predatory flower flies (Diptera Syrphidae) based on exon-capture sequencing

Flower flies (Diptera: Syrphidae) are one of the most species-rich dipteran families and provide important ecosystem services such as pollination, biological control of pests, recycling of organic matter and redistributions of essential nutrients. Flower fly adults generally feed on pollen and nectar, but their larval feeding habits are strikingly diverse. In the present study, high-throughput sequencing was used to capture and enrich phylogenetically and evolutionary informative exonic regions. With the help of the baitfisher software, we developed a new bait kit (SYRPHIDAE1.0) to target 1945 CDS regions belonging to 1312 orthologous genes. This new bait kit was successfully used to exon capture the targeted loci in 121 flower fly species across the different subfamilies of Syrphidae. We analysed different amino acid and nucleotide data sets (1302 loci and 154 loci) with maximum likelihood and multispecies coalescent models. Our analyses yielded highly supported similar topologies, although the degree of the SRH (global stationarity, reversibility and homogeneity) conditions varied greatly between amino acid and nucleotide data sets. The sisterhood of subfamilies Pipizinae and Syrphinae is supported in all our analyses, confirming a common origin of taxa feeding on soft-bodied arthropods. Based on our results, we define Syrphini stat.rev. to include the genera Toxomerus and Paragus. Our divergence estimate analyses with beast inferred the origin of the Syrphidae in the Lower Cretaceous (125.5-98.5 Ma) and the diversification of predatory flower flies around the K-Pg boundary (70.61-54.4 Ma), coinciding with the rise and diversification of their prey.Peer reviewe

Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Abstract Species are the fundamental units of life and evolution. Their recognition is essential for science and society. Molecular methods have been increasingly used for the identification of animal species, despite several challenges. Here, we explore with genomic data from nine animal lineages a set of nuclear markers, namely metazoan‐level universal single‐copy orthologs (metazoan USCOs), for their use in species delimitation. Our data sets include arthropods and vertebrates. We use various data assembly strategies and use coalescent‐based species inference as well as population admixture analyses and phenetic methods. We demonstrate that metazoan USCOs distinguish well closely related morphospecies and consistently outperform classical mitochondrial DNA barcoding in discriminating closely related species in different animal taxa, as judged by comparison with morphospecies delimitations. USCOs overcome the general shortcomings of mitochondrial DNA barcodes, and due to standardization across Metazoa, also those of other approaches. They accurately assign samples not only to lower but also to higher taxonomic levels. Metazoan USCOs provide a powerful and unifying framework for DNA‐based species delimitation and taxonomy in animals and their employment could result in a more efficient use of research data and resources