Sensitivity analysis, molecular systematics and natural history evolution of Scathophagidae (Diptera: Cyclorrhapha: Calyptratae)

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects

The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species-level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species-comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine-readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species-comprehensive phylogenies for biological research.

No evidence for mitochondrial genetic variability in the largest population of critically endangered Tonkin snub-nosed monkeys in Vietnam

The Tonkin snub-nosed monkey (Rhinopithecus avunculus) with a global population of <250 is listed as critically endangered. It is endemic to northeastern Vietnam and was feared extinct until its rediscovery in 1989. The largest single population of R. avunculus consists of 125-130 individuals in an area of forest called Khau Ca in Ha Giang Province. We used non-invasively collected fecal samples to establish the amount of genetic diversity in this population based on mitochondrial information. We amplified and sequenced a 467- to 650-bp section of the hypervariable region I (HVI) of the mitochondrial D-loop for 201 samples and reconstructed the full mitochondrial genomes for five samples based on metagenomic data. All 201 HVI sequences were identical and no variability was found in the five mitochondrial genomes. Our results highlight the immediate need for a comprehensive assessment of the genetic diversity of all populations of R. avunculus based on mitochondrial and nuclear markers. The latter need to be developed for this species.

Is qualitative and quantitative metabarcoding of dung fauna biodiversity feasible?

In biodiversity assessments, especially of small-bodied organisms for which taxonomic expertise is lacking, identification by genetic barcoding may be a cost-effective and efficient alternative to traditional identification of species by morphology, ecology, and behavior. The authors tested the feasibility and accuracy of such an approach using dung insects of practical relevance in ecotoxicological assessments of veterinary pharmaceutical residues in the environment. They produced 8 known mixtures that varied in absolute and relative composition of small-bodied and large-bodied species to see whether mitochondrial cytochrome c oxidase subunit 1 barcoding picks up all species qualitatively and quantitatively. As demonstrated before in other contexts, such metabarcoding of large numbers of dung insect specimens is principally possible using next-generation sequencing. The authors recovered most species in a sample (low type I error), at minimum permitting analysis of species richness. They obtained even quantitative responses reflecting the body size of the species, although the number of specimens was not well detected. The latter is problematic when calculating diversity indices. Nevertheless, the method yielded too many closely related false positives (type II error), thus generally overestimating species diversity and richness. These errors can be reduced by refining methods and data filtering, although this requires bioinformatics expertise often unavailable where such research is carried out. Identification by barcoding foremost hinges on a good reference database, which does not yet exist for dung organisms but would be worth developing for practical applications. Environ Toxicol Chem 2016;35:1970-1977. © 2015 SETAC.

Molecules and morphology unite Sarcophaga (Stackelbergeola) Rohdendorf and S. (Rohdendorfisca) Grunin within megadiverse Sarcophaga Meigen (sensu lato) (Diptera, Sarcophagidae)

The largest genus of the family Sarcophagidae (Insecta, Diptera), Sarcophaga Meigen (sensu lato), has ~160 subgenera; however, the validity and phylogenetic relationships of these are still unclear, impeding progress in evolutionary studies. This study presents a phylogenetic hypothesis for selected subgenera of Sarcophaga s.l. based on COI sequences (685 bp) for 87 species representing 27 valid subgenera. The subgenera Stackelbergeola Rohdendorf and Rohdendorfisca Grunin are reconsidered in the light of new molecular, morphological and biological data. The female is described for the first time for a representative of both subgenera, and Sarcophaga (Rohdendorfisca) flagellifera (Grunin) is shown to be a parasitoid of tettigoniid grasshoppers. As the male of Sarcophaga (Stackelbergeola) sushkini (Rohdendorf) is insufficiently documented in the literature, a redescription is provided based on material from Xinjiang, thereby providing the first record of this subgenus and species from China. Detailed documentation through photographs, scanning electron microscopy and illustrations of the adult morphology is also provided. The subgenera Stackelbergeola and Rohdendorfisca are shown to be monophyletic, together forming a monophylum supported by molecular and morphological data, and they are placed in a wider phylogenetic context of the megadiverse genus Sarcophaga s.l.

DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae)

Phormia regina (the black fly) is a common Holarctic blow fly species which serves as a primary indicator taxon to estimate minimal post mortem intervals. It is also a major research model in physiological and neurological studies on insect feeding. Previous studies have shown a sequence divergence of up to 4.3% in the mitochondrial COI gene between W European and N American P. regina populations. Here, we DNA barcoded P. regina specimens from six N American and 17 W European populations and confirmed a mean sequence divergence of ca. 4% between the populations of the two continents, while sequence divergence within each continent was a ten-fold lower. Comparable mean mtDNA sequence divergences were observed for COII (3.7%) and cyt b (5.3%), but mean divergence was lower for 16S (0.4-0.6%). Intercontinental divergence at nuclear DNA was very low (≤ 0.1% for both 28S and ITS2), and we did not detect any morphological differentiation between N American and W European specimens. Therefore, we consider the strong differentiation at COI, COII and cyt b as intraspecific mtDNA sequence divergence that should be taken into account when using P. regina in forensic casework or experimental research.

Why is the molecular identification of the forensically important blowfly species Lucilia caesar and L. illustris (family Calliphoridae) so problematic?

Species of the fly genus Lucilia are commonly used in forensic investigations to estimate the postmortem interval (PMI). Two close-related species Lucilia caesar and L. illustris are difficult to identify. Previous studies showed that the mitochondrial cytochrome c oxidase subunit I (COI) marker could be used to identify many Lucilia species. However, mixed results were obtained for L. caesar and L. illustris due to some European specimens showing identical haplotypes. Here, we investigated 58 new European male specimens of L. illustris and L. caesar whose morphological identifications were checked and for which COI fragments were sequenced. In addition, two other mitochondrial (cytochrome c oxidase subunit II and 16S) and two nuclear (internal transcribed spacer 2 and 28S ribosomal RNA) markers were obtained for a subset of these samples. For each marker, genetic divergence within each species was in the same range as between species, confirming the close relationship between both species. Moreover, for each of the gene fragments, both species shared at least one haplotype/genotype. Hence, none of the molecular markers tested could be used, alone or in combination, to discriminate between L. illustris and L. caesar.

Infections with Wolbachia and Spiroplasma in the Scathophagidae and other Muscoidea

The microbes Wolbachia and Spiroplasma are common reproductive parasites of arthropods and may strongly influence reproduction of infected hosts and also impact on reproductive isolation. Such infections could hence influence results of many studies assessing reproductive behaviour and fitness of possible hosts, as well as reproductive isolation. Previous work indicates that infections with the microbes Wolbachia and Spiroplasma are common in the Drosophilidae. However, extensive and targeted surveys of other Dipteran families are lacking. Here we survey the yellow dung fly Scathophaga stercoraria and a range of other species from the Muscoidea (families Scathophagidae, Anthomyiidae, Fanniidae and Muscidae) collected in the field or obtained from museum collections for infection with the widespread reproductive parasites Wolbachia and Spiroplasma. Both have been shown to be heritable symbionts and affect reproduction in other Diptera. S. stercoraria is a very important model for the study of sexual selection, and in particular of postcopulatory processes, as it has played a major role in the history of research on sperm competition and cryptic female choice. Infections with Wolbachia were found to be widespread across the Muscoidea, whereas infections with Spiroplasma were rarer. We discuss the consequences of these findings and directions for future research on the impact of reproductive parasites on host reproduction in the Scathophagidae.

Molecular data sheds light on the classification of long-legged flies (Diptera:Dolichopodidae)

Dolichopodidae (long-legged flies) is the world’s fourth largest dipteran family, but a phylogeny based on a broad global taxon sample is still lacking. We present here a first molecular phylogenetic hypothesis for Dolichopodidae, based on 157 dolichopodid species in 68 genera and 15 subfamilies from the Old and New World, and seven empidoid species (Empididae, Hybotidae) as outgroups. Both relatively fast-evolving mitochondrial markers (COI, 12S, 16S) and a more conserved nuclear marker (18S) were used, the latter being widely employed to study the phylogeny at higher taxonomic levels. We present strong evidence for Microphorinae as sister group to Dolichopodidae sensu stricto, and for the monophyletic Parathalassiinae as part of Dolichopodidae sensu stricto. Monophyly of Achalcinae, Dolichopodinae, and Sciapodinae is supported and Stolidosomatinae are placed within Sympycninae. Diaphorinae, Medeterinae, Neurigoninae, Rhaphiinae, and Sympycninae are paraphyletic, and Hydrophorinae and Peloropeodinae polyphyletic. Our broad taxon sample allows us to gain new insights into the complex systematics of Dolichopodidae. Our results highlight several problems with the traditional classification, which have considerable consequences for the systematic status of some taxa. The poor resolution observed in deep divergences supports previous hypotheses suggesting a rapid early radiation of Dolichopodidae.

Conflict, convergent evolution, and the relative importance of immature and adult characters in endopterygote phylogenetics

We use two episodes from systematic history to illustrate how conflict between immature and adult data was important for the development of phylogenetic systematics. A reference search in Zoological Record reveals that most phylogenetic analyses of endopterygote insects continue to utilize morphological rather than DNA sequence data. However, the use of immature and adult data is established for only a few taxa. An assessment of the phylogenetic utility of 73 matrices with immature and adult data reveals that the immature partitions have fewer characters and that immature characters provide lower node support through homoplasy levels in immatures, and adult partitions are comparable. Despite much conflict, analyses based on all available evidence yield better tree resolution and higher support. We argue that DNA sequence-based matching of immature and adult stages will greatly help with the study of endopterygote immatures and facilitate the assembly of combined character matrices with data from all life-history stages.