Progress, pitfalls and parallel universes: a history of insect phylogenetics

Abstract

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies , dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

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

“…This suggests to me a strong uncertainty regarding molecular analysis in such groups in which there are a significant number of high-weight synapomorphies and a solid morphologicallybased phylogeny (at least known to the systematist, even if not published). It is similarly striking that the nodes in insect phylogeny that are morphologically well supported are also those well supported by published molecular results, while those that are difficult to interpret morphologically (e.g., Ephemeroptera, hemimetabolous insects) have also produced contentious molecular results (Kjer et al, 2016;Yeates et al, 2016). In my opinion, it would be valuable and interesting to test molecular and morphological approaches with a number of double-blind studies to test their level of congruence.…”

“…Beginning with sequences of a single gene for a taxonomic group, which "proved" various relationships that were often vehemently denied by morphologists (e.g., bats evolving at least twice, gorillas being the sister species of humans, etc.) to the debates among geneticists when second genes provided conflicting patterns, to an increase in the number of genes utilized, always indicating accurate results and always providing new and fresh phylogenies (Kjer et al, 2016). Today we are still on the border of the Promised Land with the assurance that transcriptomes, representing complete sequences of a group of mRNA molecules, will provide access to the final answers (Jiménez-Guri et al, 2013).…”

“…Many of these programs are quickly outdated, making repetition of older analyses difficult. least some groups are providing some irregularities (e.g., Fernández et al, 2016), there is the ever-present caveat that this will all soon be sorted out (although Kjer et al, 2016 invoke a fundamental scientific premise and warn that merely more data may not provide better answers). Yeates et al (2016) for example, state "We predict that insect phylogenomic analyses will become much more sophisticated, and produce more reliable results, in the near future".…”

Computational biomechanics changes our view on insect head evolution

“…The so-called 'Palaeoptera problem'-the unclear relationships of dragonflies (Odonata), mayflies (Ephemeroptera) and all other winged insects (Neoptera)-was identified as one of the few remaining challenges in deep-level insect systematics [1]. The Palaeoptera problem is of special interest, because it also relates to the evolution of insect flight which evolved approximately 400 Ma [2,3].…”

Editorial overview: Insect phylogenetics: an expanding toolbox to resolve evolutionary questions

“…The past decade has seen major breakthroughs in our understanding of the evolutionary relationships of insects, due largely to novel tools for the discovery and analysis of phylogenetically informative characters. Many insights, especially on ancient nodes of the insect evolutionary tree, are a direct result of recent phylogenomic studies [1,2]. New technologies for the discovery of morphological characters provide another valuable source of phylogenetic information, help cross-validate phylogenetic hypotheses based on genomic data, and enhance our understanding of character transformation and adaptation.…”