Phylogenetic synthesis of morphological and molecular data reveals new insights into the higher-level classification of Tipuloidea (Diptera)

Abstract

Tipuloidea, the crane flies, are a diverse lineage of true flies (Insecta: Diptera) whose phylogenetic classification and taxonomy remain a challenge. Here we present the results of a quantitative phylogenetic analysis of Tipuloidea based on combined morphological characters (adult, larvae and pupae) and nuclear gene sequence data (28S rDNA and CAD). Forty‐five species, from 44 genera and subgenera, were sampled, representing the four putative families of Tipuloidea (Cylindrotomidae, Limoniidae, Pediciidae and Tipulidae sensu stricto). Analyses of individual datasets, although differing in overall topology, support the monophyly of several major lineages within Tipuloidea. Parsimony and Bayesian analyses using individual morphological and molecular datasets resulted in incongruent topologies. Increased resolution and tree support was obtained when both datasets (morphology and genes) were combined, in both combined evidence parsimony and Bayesian analyses, than when analysed separately. The recovered consensus phylogeny was not consistent with any previously proposed Tipuloidea classification, with previous importance assigned to character states shown here to represent losses and reversals seen as a major factor influencing erroneous classification. The results provided here, together with evidence from previous analyses, were used to append the Tipuloidea classification to supported evolutionary lineages. Tipuloidea is presented as two families: Pediciidae and Tipulidae. Pediciidae is recovered as the sister group to all remaining Tipuloidea. Our current phylogenetic hypothesis is not consistent with the existing subfamilial classification of the ‘Limoniidae’, which is paraphyletic with respect to a well‐supported Tipulinae + Cylindrotominae clade, whereas the three ‘limoniid’ subfamilies are para‐ or polyphyletic. The recognition of ‘Limoniidae’ as a valid monophyletic family is discouraged and the subfamilies of ‘Limoniidae’ are amended and placed within Tipulidae. A revised phylogenetic classification is proposed for the crane flies based on a synthesis of evidence from multiple genes and morphology.

The State of Phylogenetic Analysis: Narrow Visions and Simple Answers—Examples from the Diptera (flies)

“…As such, I am uncertain whether others noticed that the "Periodic Table" of Diptera phylogeny by Wiegmann et al (2011) did not provide the morphological data they claimed to have included, in some manner, in their analysis. Those authors do not stand alone as an example of 'total evidence' papers that are clearly biased toward the molecular portion of the paper (e.g., Petersen et al, 2010;Su et al, 2008;Tóthová et al, 2013;Winterton & Ware, 2015). The second strong trend is the unfortunate belief by many non-systematists that phylogenies are as easy to produce as determining a barcode or another limited set of sequences for each species and popping the results into a program, whether they do it themselves or farm the process out to someone who knows the techniques and is awarded coauthorship.…”

“…On the other hand, there are numbers of publications in which both sequences and morphology (at least partially) are examined. Some are combined studies that partition morphological and molecular characters at least as an initial approach to examine levels of congruence (e.g., Germann et al, 2010;Hash et al, 2017;Petersen et al, 2010;Roháček & Tóthová, 2014;Skevington & Yeates, 2000;Su et al, 2008;Williams et al, 2016). Some others combine the characters, appearing to effectively swamp the morphological characters with the molecular characters (e.g., Fu et Pu et al, 2017;Semelbauer, 2016;Tachi, 2013;Tkoč et al, 2016;Wang et al, 2014;Watts et al, 2016).…”

“…Today the use of limited exemplars has become the modus operandi and is nearly universal in studies using an approach combining and/or comparing molecular and morphological data (e.g., Kitching et al, 2015;Petersen et al, 2010;Tkoč et al, 2016;Winterton & Ware, 2015). Such limited examination is inherent to current methods utilized in sequence analyses but is unacceptably reductionist for studies including morphological features.…”

New records of Limoniidae and Pediciidae (Diptera) from Croatia

“…Pedicia (Amalopis) occulta (Meigen, 1830), Dicranota (Paradicranota) pavida (Haliday, 1833)). Limoniidae or short-palped crane flies are a paraphyletic group (Petersen et al 2010) of various sized tipuloid like flies, which larvae occupy different habitats (Ujvárosi 2005, Ujvárosi and Póti 2006, Kolcsár et al 2013). A large part of genera bind to wet environments and some are truly aquatic (e.g.…”

Checklist of the infraorder Tipulomorpha (Trichoceridae, Tipuloidea) (Diptera) of Finland

“…Alexander, usually prefer a single family, Tipulidae; other families, sensu Starý, are there subfamilies or tribes (Byers 1992, Petersen et al 2010). According to a recent phylogenetic analysis (Petersen et al 2010), two families are recognized, Tipulidae and Pediciidae, but the consensus tree of that analysis had many unresolved polytomies. Crane fly larvae occur usually in moist or (semi)aquatic habitats, but larvae may also be found on mosses, in dry soil, fungal fruiting bodies and dead wood.…”