New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae)

Abstract

The Syrphoidea (families Pipunculidae and Syrphidae) has been suggested to be the sister group of the Schizophora, the largest species radiation of true flies. A major challenge in dipterology is inferring the phylogenetic relationship between Syrphoidea and Schizophora in order to understand the evolutionary history of flies. Using newly sequenced transcriptomic data of Syrphidae, Pipunculidae and closely related lineages, we were able to fully resolve phylogenetic relationships of Syrphoidea using a supermatrix approach with more than 1 million amino acid positions derived from 3145 genes, including 19 taxa across nine families. Platypezoidea were inferred as a sister group to Eumuscomorpha, which was recovered monophyletic. While Syrphidae were also found to be monophyletic, the superfamily Syrphoidea was not recovered as a monophyletic group, as Pipunculidae were inferred as sister group to Schizophora. Within Syrphidae, the subfamily Microdontinae was resolved as sister group to the remaining taxa, Syrphinae and Pipizinae were placed as sister groups, and the monophyly of Eristalinae was not recovered. Although our results are consistent with previously established hypotheses on Eumuscomorphan evolution, our approach is new to dipteran phylogeny, using larger‐scale transcriptomic data for the first time for this insect group.

Old World and New World Phasmatodea: Phylogenomics Resolve the Evolutionary History of Stick and Leaf Insects

“…robertlanfear.com/partitionfinder/; Lanfear et al, 2014Lanfear et al, , 2016 in combination with RaxML v.8.2.4 (Stamatakis, 2014) (options -rcluster -rcluster-max 6000 (for AA SOS ) -rcluster-max 2000 (for AA decisive ) -rcluster-percent 100 -q -p 24 -weights 1,1,0,1 -all-states -min-subset-size 100). We further restricted the PartitionFinder search to 11 amino-acid substitution models as these are the most selected models for empirical studies on Hexapoda (Misof et al, 2014;Pauli et al, 2018), namely LG+G, WAG+G, DCMUT+G, JTT+G, BLOSUM62+G, LG+G+F, WAG+G+F, DCMUT+G+F, JTT+G+F, BLOSUM62+G+F, LG4X (Yang, 1994;Gu et al, 1995;Müller and Vingron, 2000;Whelan and Goldman, 2001;Veerassamy et al, 2003;Kosiol and Goldman, 2005;Le and Gascuel, 2008;Soubrier et al, 2012).…”

“…In recent years, numerous large-scale, highly resolved phylogenies for several insect lineages have been published and these have led to workable classifications for nearly all major groups traditionally referred to as insect orders, for instance, major groups of Polyneoptera (Wipfler et al, 2019), Blattodea (Evangelista et al, 2019), true bugs (Heteroptera) and other hemipteroid lineages (Johnson et al, 2018), Hymenoptera , Coleoptera (Zhang et al, 2018), Lepidoptera (Breinholt et al, 2018), and dipteran lineages (Pauli et al, 2018). Stick and leaf insects (Phasmatodea) however, stand out as one of the last remaining insect lineages traditionally referred to as orders for which a robust higher-level phylogenetic hypothesis is still lacking, as highlighted in numerous textbooks (e.g., Grimaldi and Engel, 2005;Tilgner, 2009;Beutel et al, 2014;Gullan and Cranston, 2014).…”

Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error

“…As a result, the authors of many studies have excluded saturated or compositionally heterogeneous sites prior to their phylogenetic analyses (e.g. Breinholt and Kawahara, 2013;Jarvis et al, 2014;Misof et al, 2014;Pauli et al, 2018;. The second codon positions are arguably the most homogeneous sites among the codon triplets of a supermatrix (e.g.…”

Anchored hybrid enrichment challenges the traditional classification of flesh flies (Diptera: Sarcophagidae)

“…To ensure that loci captured with the probe set and used in the phylogenetic analysis are clusters of orthologous sequences of selected reference species [single-copy orthologues, also called orthologue groups (OGs)], an additional orthology assessment was carried out using the program orthograph v.0.5.14 (Petersen et al, 2017) with the orthologue set 'Mecopterida', which includes a set of 3145 single-copy nuclear genes. The 'Mecopterida' orthologue set is available on Mendeley (Pauli et al, 2018) and includes five reference species: Bombyx mori Linnaeus (Lepidoptera: Bombycidae), Danaus plexippus (Linnaeus) (Lepidoptera: Nymphalidae), Aedes aegypti (Linnaeus) (Diptera: Culicidae), Drosophila melanogaster (Diptera: Drosophilidae) and Glossina morsitans Westwood (Diptera: Glossinidae). In our orthograph implementation, we used default settings except that, for 'substitute-u-with X' (activated) and 'extend-orf', we replaced putative internal stop codons and the amino acid Selenocysteine U with 'X' (amino acid level) or 'NNN' (nucleotide level) with a custom Perl script of Misof et al (2014) Alignment and trimming FASTA files of sequences were created for each orthologous gene set and aligned using mafft (v.7.273) with the L-INS-i algorithm (Katoh & Standley, 2013).…”