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Direct Sanger sequencing of a diploid template containing a heterozygous insertion or deletion results in a difficult-to-interpret mixed trace formed by two allelic traces superimposed onto each other. Existing computational methods for deconvolution of such traces require knowledge of a reference sequence or the availability of both direct and reverse mixed sequences of the same template. We describe a simple yet accurate method, which uses dynamic programming optimization to predict superimposed allelic sequences solely from a string of letters representing peaks within an individual mixed trace. We used the method to decode 104 human traces (mean length 294 bp) containing heterozygous indels 5 to 30 bp with a mean of 99.1% bases per allelic sequence reconstructed correctly and unambiguously. Simulations with artificial sequences have demonstrated that the method yields accurate reconstructions when (1) the allelic sequences forming the mixed trace are sufficiently similar, (2) the analyzed fragment is significantly longer than the indel, and (3) multiple indels, if present, are well-spaced. Because these conditions occur in most encountered DNA sequences, the method is widely applicable. It is available as a free Web application Indelligent at http://ctap.inhs.uiuc.edu/dmitriev/indel.asp.

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The genus-level classification of New World Erythroneurini is revised based on results of a phylogenetic analysis of 100 morphological characters. The 704 known species are placed into 18 genera. Erasmoneura Young and Eratoneura Young, previously treated as subgenera of Erythroneura Fitch, and Erythridula Young, most recently treated as a subgenus of Arboridia Zachvatkin, are elevated to generic status. Three species previously included in Erasmoneura are placed in a new genus, Rossmoneura (type species, Erythroneura tecta McAtee). The concept of Erythroneura is thereby narrowed to include only those species previously included in the nominotypical subgenus. New World species previously included in Zygina Fieber are not closely related to the European type species of that genus and are therefore placed in new genera. Neozygina, n. gen., based on type species Erythroneura ceonothana Beamer, includes all species previously included in the “ceonothana group”, and Zyginama, n. gen., based on type species Erythroneura ritana Beamer, includes most species previously included in the “ritana group” of New World Zygina. Five additional new genera are described to include other previously described North American Erythroneurini: Hepzygina, n. gen., based on type species Erythroneura milleri Beamer and also including E. aprica McAtee; Mexigina, n. gen., based on type species Erythroneura oculata McAtee; Nelionidia, n. gen., based on type species N. pueblensis, n. sp., three additional new species, and Erythroneura amicis Ross; Neoimbecilla, n. gen., based on type species Erythroneura kiperi Beamer and one new species; and Illinigina, n. gen., based on type species Erythroneura illinoiensis Gillette. Five new genera, based on previously undescribed species, are also recognized: Aztegina, n. gen, based on A. punctinota, n. sp., from Mexico; Amazygina, n. gen., based on type species A. decaspina, n. sp., and three additional new species from Ecuador; Hamagina, n. gen., based on type species H. spinigera, n. sp., and two additional new species from Peru and Ecuador; Napogina, n. gen., based on type species N. recta, n. sp., and one additional new species from Ecuador; Perugina, n. gen., based on type species P. denticula, n. sp., from Peru; and Spinigina, n. gen., based on type species S. hirsuta, n. sp., and an additional new species from Peru. Phylogenetic analysis suggests that the New World Erythroneurini consist of three lineages resulting from separate invasions from the Old World.

We analysed a phylogenomic dataset comprising 730 terminal taxa and >160,000 nucleotide positions obtained using anchored hybrid enrichment of genomic DNA for a sample of deltocephaline leafhoppers and outgroups. Maximum likelihood analyses of concatenated nucleotide and amino acid sequences as well as coalescent gene tree analysis, yielded well-resolved phylogenetic estimates that were highly congruent with most branches receiving maximum support. Some topological incongruence occurs among the trees resulting from different analyses, mainly distributed among very short branches at intermediate levels in the phylogeny, pertaining to relationships among some tribes and multi-tribe lineages restricted to particular continents. Coalescent gene tree analysis revealed extensive gene tree conflict at these nodes, suggesting that certain relationships may remain difficult to resolve consistently even with genome-scale datasets and dense taxon sampling. Ancestral character state reconstruction of feeding preference indicates that grass specialization has been acquired three or fewer times in some highly diverse but relatively derived lineages. Molecular divergence time estimation suggests that the earliest divergences in the subfamily occurred during the Cretaceous but that most modern tribes did not appear until after the Cretaceous-Palaeogene boundary and that grass specialist lineages generally diversified and spread at the same time as grasslands were becoming widespread globally. These analyses also show a high level of global biogeographic structure, with several large lineages of primarily arboreal deltocephalines restricted to particular regions or continents and long-distance dispersal among continents occurring primarily among grass-specialist lineages. The results represent a major improvement over previous analyses of this diverse subfamily, which were based on 152 or fewer taxa and data from morphology and partial sequences of two genes.