Jade Savage

DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits

BackgroundVarious methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate “species” diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues.ResultsOur data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected.ConclusionsOur findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.

Phylogenetic analysis of the genus Thricops Rondani (Diptera: Muscidae) based on molecular and morphological characters

Abstract.  The muscid genus Thricops Rondani comprises forty‐four species and two subspecies restricted to the northern hemisphere. A species‐level phylogenetic analysis of Thricops was conducted using forty‐four morphological characters, 426 bp of the nuclear gene white and 523 bp spanning the 5′ end of the cytochrome c oxidase subunit I (COI), the tRNA leucine gene (L2 region) and the 3′ end of the cytochrome c oxidase subunit II (COII). Thirty‐nine species and two subspecies of Thricops were included in the analysis. Two species of Azelia Robineau‐Desvoidy and one species of Hydrotaea Robineau‐Desvoidy were used as outgroups. Morphological characters were coded for all included species, the mitochondrial gene fragment (COI + II) was sequenced for a subset of seventeen species of Thricops and three outgroup species, and white for twelve of those seventeen Thricops species and two outgroup species. Six separate maximum parsimony analyses were performed on three taxon sets of different sizes (n = 14, n = 20, n = 44). Results from the partition homogeneity test indicated no significant incongruence between data partitions, and four combined maximum parsimony analyses were conducted (DNA + morphology for n = 14; COI + II + morphology for n = 20; DNA + morphology for n = 20; DNA + morphology for n = 44). The relative contribution of each data partition to individual nodes was assessed using partitioned Bremer support. Strict consensus trees resulting from the unweighted analyses of each dataset are presented. Combination of datasets increased resolution for the small taxon set (n = 14), but not for the larger ones (n = 20, n = 44), most probably due to increasing amounts of missing data in the larger taxon sets. Results from both individual and combined analyses of the smaller taxon sets (n = 14, n = 20) provided support for the monophyly of Thricops and a complete division of the genus into two monophyletic subgroups. The strict consensus cladograms resulting from the analysis of the morphological data alone and the combined data for the large taxa set (n = 44) both supported the monophyly of the genus, but placed the species Thricops foveolatus (Zetterstedt) and Thricops bukowskii (Ringdahl) at the base of the ingroup, in a polytomy with a relatively well‐resolved branch comprising all remaining species of the genus. The basal position of these two species, included in the morphological taxon set but absent in the others, illustrates the potential pitfalls of taxon sampling and missing data in phylogenetic analyses. The synonymy of Alloeostylus with Thricops as proposed by previous authors was supported by our results. Relative contributions of different data partitions is discussed, with the mitochondrial sequence generally providing finer resolution and better branch support than white.

Declining diversity and abundance of High Arctic fly assemblages over two decades of rapid climate warming

Insects are particularly vulnerable to rapid environmental changes, which are disproportionally affecting high latitudes. Increased temperature could influence insect species differentially and reshape assemblages over time. We quantified temporal assemblage turnover of Arctic Diptera (flies) in the Muscidae, one of the most diverse and abundant families of Arctic insects, using time series data from Zackenberg, North-East Greenland. We measured temporal patterns of abundance, diversity, and composition of muscid assemblages in wet fen, mesic and arid heath habitats from yearly collections spanning 1996–2014 and tested their relationship to climate. A total of 18,385 individuals representing 16 species of muscid flies were identified. A significant decrease of 80% of total muscid abundance was observed during the study period. Species richness declined in each habitat type but this trend was not significant across habitats. The number of common and abundant species also decreased significantly over time across habitats revealing a temporal modification of species evenness. Significant temporal changes in composition observed in the wet fen and across habitats were mainly driven by a change in relative abundance of certain species rather than by species replacement. Shift in composition in each habitat and decline in muscid abundance across habitats were associated with summer temperature, which has significantly increased over the study period. However, relationships between temperature and muscid abundance at the species level were noticeable for a few species only. Significant directional change in composition was documented in the wet fen but no biotic homogenization across habitats was observed. As one of the few studies of species-level changes in abundance, diversity and composition of an insect taxon in the Arctic over the past two decades, our study shows that habitat types may modulate insect species responses to recent climate change and that contrasting species responses can alter species assemblages within a few decades. This article is protected by copyright. All rights reserved.

Direct and indirect effects of landscape structure on a tri-trophic system within agricultural lands

Although several studies have examined the influence of landscape structure and agricultural intensification on species abundance and diversity, few have addressed how these impact populations across multiple trophic levels. We investigated the effects of landscape structure on the tri-trophic interactions between a bird host (the Tree Swallow Tachycineta bicolor (Vieillot)), its blowfly ectoparasites (Protocalliphora Hough), and their parasitoid wasps (Nasonia Ashmead) across 13 spatial scales, along a gradient of agricultural intensification covering 10,200 km 2 in southern Quebec, Canada. We showed that the three taxa responded to landscape structure at distinctive spatial scales that are relative to their size rather than their trophic rank. This response, however, differed according to habitat type. The three organisms responded to the amount of intensive cultures (maize, soybean and other cereals) at smaller spatial scales than to the amount of extensive cultures (hayfields and pastures). Although the number of Tree Swallow fledglings, the number of Protocalliphora sialia Shannon & Dobroscky pupae and the number of P. sialia pupae parasitized by Nasonia sp. per nest were negatively affected by agricultural intensification, our data do not support the prediction that organisms at the higher trophic levels are more susceptible to habitat degradation. Here, ectoparasites at the second trophic level were disproportionally affected by agricultural intensification; the abundance of P. sialia decreased by 80% along the gradient of agricultural intensification compared to a 20% and 35% reduction in the number of Tree Swallow fledglings and in the level of parasitism by Nasonia sp., respectively. Our work highlights the importance of designing protocols that take spatial aspects of trophic interactions into account when studying the impact of habitat loss and fragmentation on populations and communities, as these interactions dictate local biodiversity and community function. Furthermore, our results highlight the importance of considering multiple landscape parameters when identifying the functional spatial scales of an organism, as a failure to do so could lead to an underestimation of the area it uses.

Diversity and Abundance of Ectoparasitic Blow Flies Protocalliphora (Diptera: Calliphoridae) and their Nasonia (Hymenoptera: Pteromalidae) Parasitoids in Tree Swallow Nests within Agricultural Lands of Southern Québec, Canada

ABSTRACT We described the community composition of the ectoparasitic flies Protocalliphora Hough (Diptera: Calliphoridae) and their Nasonia (Ashmead) (Hymenoptera: Pteromalidae) parasitoids collected from tree swallow, Tachycineta bicolor (Vieillot), nests in southern Québec, Canada, in 2008 and 2009. The prevalence of nest infestation by Protocalliphora was 70.8% in 2008 and 34.6% in 2009. The average parasitic burden of Protocalliphora spp. was estimated at 5.53 (±5.61 SD) pupae per nestling for 2008 and 4.66 (±9.31 SD) pupae per nestling for 2009. The percentage of nests containing Protocalliphora pupae parasitized by Nasonia spp. was of 85.3% in 2008 and 67.2% in 2009. Three species of Protocalliphora were collected—Protocalliphora sialia Shannon & Dobroscky, Protocalliphora bennetti Whitworth, and Protocalliphora metallica (Townsend)—and two species of Nasonia, Nasonia vitripennis (Walker) and Nasonia giraulti Darling. This is the first record of P. bennetti and N. giraulti in the province of Québec. Our findings provide further evidence for observation made previously that altricial bird nests are more frequently and more heavily infested by blow flies in western than in eastern North America. Our data also suggest that more than a quarter of the tree swallow within the study area are exposed to high levels of ectoparasitism that could negatively affect their health.

Systematics of Cetema Hendel (Diptera: Chloropidae): revision of the Nearctic species and phylogeny and zoogeography of the Holarctic fauna

The Holarctic genus Cetema Hendel is revised, with special reference to the Nearctic fauna. There are four Nearctic species: C. elongata Meigen; C. nigripalpis sp. n., C. procera Loew, and C. subvittata Loew. This is the first record of the Palaearctic species C. elongata in the Nearctic region. All Nearctic species are described and illustrated. The Palaearctic species C. paramyopina Collin is synonymized with C. neglecta Tonnoir and a key to all described species of Cetema is provided. A phylogenetic analysis supports the monophyly of the genus, as well as the monophyly of the subgenera Archecetema Nartshuk and Cetema. The Nearctic species do not form a monophyletic group. Zoogeographic analysis suggests that the genus originated in the eastern Palaearctic and subsequently colonized North America via a Beringian connection, probably in the early to mid-Tertiary. Following speciation in the eastern Nearctic, the more derived lineages of Cetema recolonized the western Palaearctic, probably via a North Atlantic land connection prior to the late Miocene.

Comprehensive inventory of true flies (Diptera) at a tropical site

Estimations of tropical insect diversity generally suffer from lack of known groups or faunas against which extrapolations can be made, and have seriously underestimated the diversity of some taxa. Here we report the intensive inventory of a four-hectare tropical cloud forest in Costa Rica for one year, which yielded 4332 species of Diptera, providing the first verifiable basis for diversity of a major group of insects at a single site in the tropics. In total 73 families were present, all of which were studied to the species level, providing potentially complete coverage of all families of the order likely to be present at the site. Even so, extrapolations based on our data indicate that with further sampling, the actual total for the site could be closer to 8000 species. Efforts to completely sample a site, although resource-intensive and time-consuming, are needed to better ground estimations of world biodiversity based on limited sampling.Brian Brown et al. report the results of the Zurquí All Diptera Biodiversity Inventory project, one of the largest efforts to date to directly assess species richness of a megadiverse order of insects. The authors identified 41,001 flies to 4332 species, including 73 of the worlds 160 Diptera families.