Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera).

Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison 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 data set 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 anchored hybrid enrichment 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 data set, 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 the 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. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.].

A molecular phylogeny of the cicadas (Hemiptera: Cicadidae) with a review of tribe and subfamily classification.

A molecular phylogeny and a review of family-group classification are presented for 137 species (ca. 125 genera) of the insect family Cicadidae, the true cicadas, plus two species of hairy cicadas (Tettigarctidae) and two outgroup species from Cercopidae. Five genes, two of them mitochondrial, comprise the 4992 base-pair molecular dataset. Maximum-likelihood and Bayesian phylogenetic results are shown, including analyses to address potential base composition bias. Tettigarcta is confirmed as the sister-clade of the Cicadidae and support is found for three subfamilies identified in an earlier morphological cladistic analysis. A set of paraphyletic deep-level clades formed by African genera are together named as Tettigomyiinae n. stat. Taxonomic reassignments of genera and tribes are made where morphological examination confirms incorrect placements suggested by the molecular tree, and 11 new tribes are defined (Arenopsaltriini n. tribe, Durangonini n. tribe, Katoini n. tribe, Lacetasini n. tribe, Macrotristriini n. tribe, Malagasiini n. tribe, Nelcyndanini n. tribe, Pagiphorini n. tribe, Pictilini n. tribe, Psaltodini n. tribe, and Selymbriini n. tribe). Tribe Tacuini n. syn. is synonymized with Cryptotympanini, and Tryellina n. syn. is synonymized with an expanded Tribe Lamotialnini. Tribe Hyantiini n. syn. is synonymized with Fidicinini. Tribe Sinosenini is transferred to Cicadinae from Cicadettinae, Cicadatrini is moved to Cicadettinae from Cicadinae, and Ydiellini and Tettigomyiini are transferred to Tettigomyiinae n. stat from Cicadettinae. While the subfamily Cicadinae, historically defined by the presence of timbal covers, is weakly supported in the molecular tree, high taxonomic rank is not supported for several earlier clades based on unique morphology associated with sound production.

Cytosolic distribution of Cd, Cu and Zn, and metallothionein levels in relation to physiological changes in gibel carp (Carassius auratus gibelio) from metal-impacted habitats.

In the present study the impact of environmental metal contamination in gibel carp (Carassius auratus gibelio) was investigated coupling disturbances in subcellular metal distribution to effect biomarkers. Gibel carp were caught at six different sampling sites in Flanders (Belgium), characterized by different degrees in environmental metal contamination. Tissue Cd, Cu and Zn concentrations and total metallothioneon (MT) levels were determined in gills, liver and kidney. Cytosolic metal distribution was measured in the main accumulating organs, liver and kidney, revealing tissue- and metal-dependent profiles. The MT pool dominated the cytosolic distribution profile. Although the importance of the MT pool increased with increasing environmental and cytosolic metal concentrations, also an undefined fraction of Cu and Cd fractions (probably free metal ions or metals bound to small organic complexes) increased at the most contaminated sampling sites. Disturbances in serum ion concentrations, serum alanine aminotransferase activity (ALT), hematocrite and condition factor were measured, as indicators of toxic effects. At the sampling site with the highest environmental Cd pollution a significant decrease in serum Ca(2+) concentrations and a significantly increased serum ALT activity were measured suggesting incomplete detoxification of Cd. Increased serum ALT concentrations suggested structural liver damage. The fact that the liver tissue, and probably also the kidney, could not cope with this high Cd burden in combination with the increased uptake of dissolved Cd through the gills most probably contributed to the perturbed serum Ca(2+) homeostasis.

Brominated flame retardants and polychlorinated biphenyls in fish from the river Scheldt, Belgium.

Levels of polybrominated diphenyl ethers (PBDEs), hexabromocyclododecanes (HBCDs), and polychlorinated biphenyls (PCBs) were measured in several fish species originating from the river Scheldt (Belgium). Five sampling locations were chosen in a highly industrialized area along the river, while two ponds in the vicinity of the river served as reference sites. The present study is a follow-up of a survey performed in 2000 which reported extremely high levels of PBDEs and HBCDs in eel (Anguilla anguilla) collected from the same region (Oudenaarde, Flanders). The sum of tri- to hepta-BDE congeners (2270+/-2260 ng/g lipid weight (lw), range 660-11500 ng/g lw) and total HBCDs (4500+/-3000 ng/g lw, range 390-12100 ng/g lw) were one order of magnitude higher than levels usually reported from freshwater systems, indicating the presence of point sources. In most samples, levels of total HBCDs were higher than those of PBDEs, probably due to the high density of factories using HBCD as an additive brominated flame retardant (BFR). The high values of HBCDs were confirmed by both gas- and liquid-chromatography-mass spectrometry. Although BFR levels were between the highest ever reported in freshwater ecosystems, PCBs could be detected at even higher concentrations (16000+/-14300 ng/g lw, range 3900-66600 ng/g lw), being among the highest levels recorded in Belgium. The inter-sampling site variation of PBDEs, HBCDs and PCBs was comparable. All locations presented similar PBDE congener profiles, with BDE 47 being the dominant congener, followed by BDE 100, BDE 99 and BDE 49, probably originating from the former use of the penta-BDE technical mixture. In order to estimate the impact of these point sources on human exposure, we further focussed on eels which showed a considerable decrease in the PBDE and HBCD levels between 2000 and 2006. Due to the wide span in concentrations between the different sampling locations, a variable contribution to the total human exposure through local eel consumption was estimated. The calculated daily intake ranged from 3 ng to 330 ng PBDEs/day for normal eel consumers, but was as high as 9800 ng PBDEs/day for anglers, which may be considered at risk.

A field survey of metal binding to metallothionein and other cytosolic ligands in liver of eels using an on-line isotope dilution method in combination with size exclusion (SE) high pressure liquid chromatography (HPLC) coupled to Inductively Coupled Plasma time-of-flight Mass Spectrometry (ICP-TOFMS).

The effect of metal exposure on the accumulation and cytosolic speciation of metals in livers of wild populations of European eel with special emphasis on metallothioneins (MT) was studied. Four sampling sites in Flanders showing different degrees of heavy metal contamination were selected for this purpose. An on-line isotope dilution method in combination with size exclusion (SE) high pressure liquid chromatography (HPLC) coupled to Inductively Coupled Plasma time-of-flight Mass Spectrometry (ICP-TOFMS) was used to study the cytosolic speciation of the metals. The distribution of the metals Cd, Cu, Ni, Pb and Zn among cytosolic fractions displayed strong differences. The cytosolic concentration of Cd, Ni and Pb increased proportionally with the total liver levels. However, the cytosolic concentrations of Cu and Zn only increased above a certain liver tissue threshold level. Cd, Cu and Zn, but not Pb and Ni, were largely associated with the MT pool in correspondence with the environmental exposure and liver tissue concentrations. Most of the Pb and Ni and a considerable fraction of Cu and Zn, but not Cd, were associated to High Molecular Weight (HMW) fractions. The relative importance of the Cu and Zn in the HMW fraction decreased with increasing contamination levels while the MT pool became progressively more important. The close relationship between the cytosolic metal load and the total MT levels or the metals bound on the MT pool indicates that the metals, rather than other stress factors, are the major factor determining MT induction.

Spatial variations and temporal trends between 1994 and 2005 in polychlorinated biphenyls, organochlorine pesticides and heavy metals in European eel (Anguilla anguilla L.) in Flanders, Belgium.

In Flanders, the northern region of Belgium, European yellow eel muscle tissue was used as an indicator of environmental and potential human dietary exposure by hazardous chemicals of surface waters and sediments. Between 1994 and 2005, over 2800 eel captured at 365 stations were analysed for PCBs, pesticides and heavy metals. Contamination of eel in Flanders fell within the range of reported concentrations in other watersheds of Western Europe. A spatial analysis of the data demonstrated that the variation in pollutant concentration tended towards higher values. This was especially evident for PCBs, lindane, endrin, dieldrin and DDE. The concentration of almost all banned substances decreased significantly during the study period.

Perfluorooctane sulfonic acid and organohalogen pollutants in liver of three freshwater fish species in Flanders (Belgium): relationships with biochemical and organismal effects.

A perfluorooctane sulfonic acid (PFOS) assessment was conducted on gibel carp (Carassius auratus gibelio), carp (Cyprinus carpio), and eel (Anguilla anguilla) in Flanders (Belgium). The liver PFOS concentrations in fish from the Ieperlee canal (Boezinge, 250-9031 ng/g wet weight, respectively) and the Blokkersdijk pond (Antwerp, 633-1822 ng/g wet weight) were higher than at the Zuun basin (Sint-Pieters-Leeuw, 11.2-162 ng/g wet weight) and among the highest in feral fish worldwide. Eel from the Oude Maas pond (Dilsen-Stokkem) and Watersportbaan basin (Ghent) had PFOS concentrations ranging between 212 and 857 ng/g wet weight. The hepatic PFOS concentration was significantly and positively related with the serum alanine aminotransferase activity, and negatively with the serum protein content in eel and carp. The hepatic PFOS concentration in carp correlated significantly and negatively with the serum electrolyte concentrations whereas a significant positive relation was found with the hematocrit in eel. Although 13 organochlorine pesticides, 22 polychlorinated biphenyl (PCB) congeners and 7 polybrominated diphenyl ethers (PBDEs) were also measured in the liver tissue, only PCB 28, PCB 74, gamma-hexachlorocyclohexane (gamma-HCH) and hexachlorobenzene (HCB) were suggested to contribute to the observed serological alterations in eel.

Vitellogenin content in European eel (Anguilla anguilla) in Flanders, Belgium.

As part of a large-scale monitoring program of bioaccumulating contaminants in the European eel (Anguilla anguilla) in Flanders (Belgium), we investigated potential effects of xenoestrogens in these fish. The present paper describes the results of the plasma vitellogenin (VTG) content, measured in 142 eels sampled at 20 different locations, in relation to the internal pollution levels. To validate the blood VTG assays, a small number of eels (n=8) was exposed to 10 microg ethinylestradiol/l (EE2) for 9 days. In this experiment, VTG was detected as a protein with a molecular weight of 214 kDa and confirmed by Western blotting. Compared with the solvent controls, significantly higher concentrations of VTG were measured in EE2 exposed eel. However, the VTG content was relatively low compared with other fish species exposed to high concentrations of estrogens. The plasma VTG content of eels from the field study was very low, despite a very high internal load of endocrine disrupters. These results, together with previously published studies, suggest that immature yellow European eel might not be the best sentinel species to study the effects of estrogenic compounds on VTG levels of wild fish populations.