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A recent molecular phylogeny of the genus Crematogaster reclassified some members of the former subgenera Paracrema and Physocrema into the C. inflata -group, now comprised of five species: C. ampullaris , C. inflata , C. modiglianii , C. onusta and C. subcircularis. Here, a molecular analysis of the Crematogaster inflata -group and eight other species of the former subgenus Physocrema (C. aurita , C. difformis , C. mucronata , C. physothorax , C. sewardi , C. tanakai , C. vacca and C. yamanei) is conducted using a total of c. 4 kb of sequence data from six nuclear protein-coding genes and two mitochondrial genes. Monophyly of the C. inflata -group is strongly supported. A revised morphological delineation of the subgroups is proposed, supported by the molecular phylogeny: three morphologically distinct subgroups, the C. difformis -subgroup, the C. vacca -subgroup and the C. inflata -subgroup. Molecular dating and biogeographical analyses indicate that the C. inflata -group originated in the Sundaic region around the Middle Miocene 12 Mya and diversified from the Late Miocene to Pliocene. Ancestral state reconstructions indicate that the C. inflata -group diversified from an ancestor with a swollen propodeum and circular-shaped metapleural gland opening. Biogeographical reconstruction indicates that dispersal to peripheral areas and allopatry due to sea-level changes shaped the evolutionary history of the C. inflata -group. [ABSTRACT FROM AUTHOR]

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.] [ABSTRACT FROM AUTHOR]

The redbay ambrosia beetle, Xyleborus glabratus Eichhoff, is native to Southeast Asia, where it specializes on Lauraceae trees. It forms a symbiosis with the ambrosia fungus Raffaelea lauricola T.C. Harr. Fraedrich & Aghayeva, which can act as a pathogen in living host trees. The beetle and fungus were recently introduced into the United States, where they have killed millions of native Lauraceae trees and threaten the avocado industry. These introduced populations have limited genetic variation. In the native range, the fungi are genetically variable, but the native genetic variability of the beetles is unknown. It is important to assess the beetle's native genetic variation because different lineages may vary in the capacity to vector this fungus, which may affect disease etiology. Here, we analyzed genetic variation in several Chinese, Taiwanese, and Vietnamese populations of X. glabratus using mitochondrial (COI) and nuclear DNA (CAD) markers. Phylogenetic analysis revealed nine COI haplotypes and four CAD genotypes. Uncorrected 'p' distance for intrapopulation comparisons ranged from 0 to 0.1 and 0 to 0.013 and interpopulation comparisons ranged from 0.137 to 0.168 and 0.015 to 0.032 for COI and CAD, respectively. Two populations exceeded the range of intraspecific nucleotide differences for both genes. Given that individuals from these populations also exhibited consistent morphological differences, they are described as two new species: Xyleborus insidiosus Cognato & Smith, n. sp. and Xyleborus mysticulus Cognato & Smith, n. sp. Xyleborus glabratus was redescribed and a lectotype was designated to facilitate its recognition in light of these new species. These results indicate that X. glabratus is genetically variable and is related to two morphologically similar species. Whether these new species and X. glabratus lineages associate with different fungal strains is unknown. Given that the biology and host colonization of these new species are unknown, preventing their introduction to other regions is prudent. [ABSTRACT FROM AUTHOR]