
@article {112947,
	title = {Detecting and removing sample contamination in phylogenomic data: an example and its implications for Cicadidae phylogeny (Insecta: Hemiptera).},
	journal = {Syst Biol},
	year = {2022},
	month = {2022 Jun 16},
	abstract = {<p>Contamination of a genetic sample with DNA from one or more non-target species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and Next-Generation Sequencing (NGS) studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on detection of bimodal distributions of patristic distances across gene trees. When the contamination occurs between samples within a dataset, comparisons between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a dataset generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the AHE markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned dataset, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution.</p>
},
	issn = {1076-836X},
	doi = {10.1093/sysbio/syac043},
	author = {Owen, Christopher L and Marshall, David C and Wade, Elizabeth J and Meister, Russ and Goemans, Geert and Kunte, Krushnamegh and Moulds, Max and Hill, Kathy and Villet, M and Pham, Thai-Hong and Kortyna, Michelle and Lemmon, Emily Moriarty and Lemmon, Alan R and Simon, Chris}
}
@article {95776,
	title = {The molecular systematics and diversification of a taxonomically unstable group of Asian cicada tribes related to Cicadini Latreille, 1802 (Hemiptera : Cicadidae)},
	journal = {INVERTEBRATE SYSTEMATICS},
	year = {2021},
	month = {06/2021},
	abstract = {<p>The cicadas (Hemiptera: Cicadidae) related to tribe Cicadini exhibit some of the most remarkable phenotypes in the family, with many genera possessing striking colour patterns and unusual morphological features. This largely Asian group of 13 tribes has proven challenging for cicada taxonomists, in part because of likely convergent evolution or losses of these phenotypes. We present the first focused molecular phylogeny of this clade, including similar to 60 described genera. The genetic dataset contains 839 ingroup-informative sites (out of 2575) from mitochondrial cytochrome c oxidase subunit I, nuclear elongation factor-1 alpha, and nuclear acetyltransferase. We use Bayesian and maximum likelihood trees to test recent changes in tribe- and subtribe- level classification, and we reconstruct ancestral character states for potentially convergent traits influencing tribe descriptions. We use fossil and molecular clock calibrations to estimate the temporal and geographic context of the radiation. The tribes Gaeanini, Leptopsaltriini, Platypleurini, Psithyristriini, and Tosenini appear polyphyletic and in need of revision, in part because of convergent evolution of opaque wings and multiple convergent gains or losses of abdominal tubercles. Kalabita Moulton, 1923 is transferred from Platypleurini to Leptopsaltriini. Vittagaeana gen. nov. is established for Vittagaeana paviei comb. nov. and Vittagaeana dives comb. nov., formerly in Tosena. Sinosenini syn. nov. is synonymised with Dundubiina. Ayuthiini trib. nov. is established with two new subtribes for Ayuthia Distant, 1919 and Distantalna Boulard, 2009, formerly in Tosenini. For the earliest split in the tree, one common ancestor appears to have been Indian + Asian in geographic distribution and the other Asian. We estimate that the radiation began in the middle Cenozoic Era, possibly as recently as the early Miocene. The recent and steady pattern of diversification suggests that refinement of tribe diagnoses will prove challenging.</p>
},
	doi = {10.1071/IS20079},
	author = {Hill, Kathy B. R. and Marshall, David C and Marathe, Kiran and Moulds, Maxwell S. and Lee, Young June and Pham, Thai-Hong and Mohagan, Alma B. and Sarkar, Vivek and Price, Benjamin W. and Duffels, J. P. and Schouten, Marieke A. and de Boer, Arnold J. and Kunte, Krushnamegh and Simon, Chris}
}
