Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae)

Winkler, Isaac S.; Blaschke, Jeremy D.; Davis, Daniel R.; Stireman, John O.; O’Hara, James E.; Cerretti, Pierfilippo; Moulton, John K.

doi:10.1016/j.ympev.2015.03.021

Cited by 57 publications

(93 citation statements)

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“…The amplification of the various fragments of this gene proved to be much more difficult than in traditional markers, so the inclusion of more protein-coding nuclear genes has not been possible with current material, which includes many rare species, available as only one or two specimens, usually collected several years ago. As soon as more fresh material (especially of Sciaroidea incertae sedis ) is available for next-gen sequencing, which may take several years or more, it should be possible to design specific primers for Sciaroidea and amplify the supposedly more informative protein-coding nuclear genes, such as MCS and MAC (see Winkler et al, 2015). Our attempts to amplify MCS and MAC markers from most of the specimens of Bibionomorpha using the primers designed for other groups of Diptera failed.…”

Section: Resultsmentioning

confidence: 99%

Molecular phylogeny of the megadiverse insect infraorder Bibionomorphasensu lato(Diptera)

Ševčı́k

Kaspřák

Mantič

et al. 2016

PeerJ

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The phylogeny of the insect infraorder Bibionomorpha (Diptera) is reconstructed based on the combined analysis of three nuclear (18S, 28S, CAD) and three mitochondrial (12S, 16S, COI) gene markers. All the analyses strongly support the monophyly of Bibionomorpha in both the narrow (sensu stricto) and the broader (sensu lato) concepts. The major lineages of Bibionomorpha sensu lato (Sciaroidea, Bibionoidea, Anisopodoidea, and Scatopsoidea) and most of the included families are supported as monophyletic groups. Axymyiidae was not found to be part of Bibionomorpha nor was it found to be its sister group. Bibionidae was paraphyletic with respect to Hesperinidae and Keroplatidae was paraphyletic with respect to Lygistorrhinidae. The included Sciaroidea incertae sedis (except Ohakunea Edwards) were found to belong to one clade, but the relationships within this group and its position within Sciaroidea require further study.

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Section: Resultsmentioning

confidence: 99%

Molecular phylogeny of the megadiverse insect infraorder Bibionomorphasensu lato(Diptera)

Ševčı́k

Kaspřák

Mantič

et al. 2016

PeerJ

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“…Certainly, a large amount of works on mitochondrial genes (Weirauch and Munro, 2009, Maekawa et al, 2001, Liu and Beckenbach, 1992, Howland and Hewitt, 1995, Scheffer and Wiegmann, 2000 and ribosomal structural RNAs (Weller et al, 1992, Shull et al, 2001, Whiting et al, 1997, Carmean et al, 1992 paved the way of insect phylogenetics, but more recent studies which included nuclear protein coding genes provided further advancements in the field (Gibson et al, 2011, Winkler et al, 2015, Sahoo et al, 2016, Wahlberg and Wheat, 2008, Regier et al, 2013, Wahlberg et al, 2016.…”

Section: The Changing Landscape Of Insect Molecular Systematicsmentioning

confidence: 99%

“…However, phylogenetic studies which combine information from five or more protein coding genes (excluding Next Generation Sequencing based study) are not common in insects , Winkler et al, 2015. Sanger sequencing applied to phylogenetic studies started more than two decades ago, and since the early application of this technology in phylogenetics, increasing the amount of data has always been one of the major concerns.…”

Section: The Changing Landscape Of Insect Molecular Systematicsmentioning

confidence: 99%

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Molecular phylogeny of bark and ambrosia beetles (Curculionidae: Scolytinae) based on 18 molecular markers

Pistone

Gohli

Jordal

2017

Systematic Entomology

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“…Group after group is being sequenced and the resultant phylogenies abound (e.g., Buenaventura et al, 2016;Caravas & Friedrich, 2013;Chapman et al, 2012;Ding et al, 2015;Haseyama et al, 2015;Semelbauer, 2016;Ševčík, 2016;Wang et al, 2016;Winkler et al, 2015;Winterton et al, 2016;Young et al, 2016a;. Molecular analyses are promising to give final answers (Trautwein et al, 2017;Yeates et al, 2016) and morphological analyses are often as straightforward as scoring variable character states in a matrix, choosing a few taxa as outgroups and determining the most parsimonious tree with a program (and options) of choice (usually PAUP or Mesquite + TNT).…”

Section: Introductionmentioning

confidence: 99%

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

Borkent

2018

Zootaxa

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The order Diptera is remarkably diverse, not only in species but in morphological variation in every life stage, making them excellent candidates for phylogenetic analysis. Such analysis has been hampered by methods that have severely restricted character state interpretation. Morphological-based phylogenies should be based on a deep understanding of the morphology, development and function of character states, and have extensive outgroup comparisons made to determine their polarity. Character states clearly vary in their value for determining phylogenetic relationships and this needs to be studied and utilized. Characters themselves need more explicit discussion, including how some may be developmentally or functionally related to other characters (and potentially not independent indicators of genealogical relationship). The current practice by many, of filling a matrix with poorly understood character states and highly limited outgroup comparisons, is unacceptable if the results are to be a valid reflection of the actual history of the group.Parsimony analysis is not an objective interpretation of phylogenetic relationships when all characters are treated as equal in value. Exact mathematical values applied to characters are entirely arbitrary and are generally used to produce a phylogeny that the author considers as reasonable. Mathematical appraisal of a given node is similarly inconsequential because characters do not have an intrinsic mathematical value. Bremer support, for example, provides values that have no biological reality but provide the pretence of objectivity. Cladists need to focus their attention on testing the validity of each synapomorphy proposed, as the basis for all further phylogenetic interpretation, rather than the testing of differing phylogenies through various comparative programs.Current phylogenetic analyses have come to increasingly depend on DNA sequence-based characters, in spite of their tumultuous history of inconsistent results. Until such time as sequences can be shown to produce predictive phylogenies (i.e., using Hennigian logic), independent of morphological analysis, they should be viewed with caution and certainly not as a panacea as they are commonly portrayed.The purported comprehensive analyses of phylogenetic relationships between families of Diptera by Wiegmann et al. (2011) andLambkin et al. (2013) have serious flaws and cannot be considered as the "Periodic Table" of such relationships as originally heralded.Systematists working on Diptera have a plethora of complex and informative morphological synapomorphies in every life stage, either described or awaiting study. Many lineages have the potential of providing a wealth of evolutionary stories to share with other biologists if we produce stable phylogenies based on weighted synapomorphies and interpreted to elucidate the zoogeographic and bionomic divergence of the group. Some lineages are devoid of convincing synapomorphies and, in spite of our desires, should be recognized as being largely uninterpretab...

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Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae)

Cited by 57 publications

References 100 publications

Molecular phylogeny of the megadiverse insect infraorder Bibionomorphasensu lato(Diptera)

Molecular phylogeny of the megadiverse insect infraorder Bibionomorphasensu lato(Diptera)

Molecular phylogeny of bark and ambrosia beetles (Curculionidae: Scolytinae) based on 18 molecular markers

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

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