DNA metabarcoding allows non-invasive identification of arthropod prey provisioned to nestling Rufous hummingbirds (Selasphorus rufus)

Abstract

Hummingbirds consume sugars from nectar, sap and honeydew, and obtain protein, fat and minerals from arthropods. To date, the identity of arthropod taxa in hummingbird diets has been investigated by observation of foraging or examination of alimentary tract contents. Direct examination of nestling provisioning adds the extra complication of disturbance to the young and mother. Here, we show that arthropod food items provisioned to Rufous hummingbird (Selasphorus rufus) nestlings can be identified by a safe and non-invasive protocol using next-generation sequencing (NGS) of DNA from nestling fecal pellets collected post-fledging. We found that females on southern Vancouver Island (British Columbia, Canada) provisioned nestlings with a wide range of arthropod taxa. The samples examined contained three Classes, eight Orders, 48 Families, and 87 Genera, with from one to 15 Families being identified in a single pellet. Soft-bodied Dipterans were found most frequently and had the highest relative abundance; hard-bodied prey items were absent from almost all samples. Substantial differences in taxa were found within season and between years, indicating the importance of multi-year sampling when defining a prey spectrum.

Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists

“…This is because markers considered universal for a given taxonomic clade may still have considerable variations in affinity across taxa within that clade, and thus may not amplify some important items in the diet (Aizpurua et al, 2018;Alberdi et al, 2019Alberdi et al, , 2017Bowser et al, 2013;Clarke et al, 2014;Kaunisto et al, 2017;Piñol et al, 2015). The problem was clearly illustrated by the high level of bias detected for ZBJ, which is sometimes regarded as universal for arthropods and is still the only marker used in many studies (Gordon et al, 2019;McClenaghan et al, 2019;Moran et al, 2019). In our study ZBJ completely missed Formicidae and other Hymenoptera, which was a key component of the diet identified through other methods, and probably overestimated the dietary importance of Lepidoptera and Diptera.…”

“…Likewise, many studies on insectivore diets often used the ZBJ primer amplifying a fragment of the COI mitochondrial gene (Razgour et al, ; Zeale, Butlin, Barker, Lees, & Jones, ). This single marker approach has been widely used in many studies (Gordon et al, ; McClenaghan, Nol, & Kerr, ; Moran, Prosser, & Moran, ), but it may produce significant biases due to differential primer affinity for different taxa. For instance, although ZBJ is often used as a ‘universal’ marker for arthropods (Crisol‐Martínez, Moreno‐Moyano, Wormington, Brown, & Stanley, ; Jedlicka, Vo, & Almeida, ; Trevelline, Latta, Marshall, Nuttle, & Porter, ; Trevelline et al, ), it may have strong positive or negative bias depending on the taxa (Clarke, Soubrier, Weyrich, & Cooper, ; Piñol, Mir, Gomez‐Polo, & Agustí, ).…”

Vertebrate-Aedes aegypti and Culex quinquefasciatus (Diptera)-arbovirus transmission networks: Non-human feeding revealed by meta-barcoding and next-generation sequencing

“…Host DNA was prepared for deep sequencing using a two-stage fusion primer approach [13] with vertebrate-specific primers. Two microliters of DNA extract was added to a PCR reaction consisting of 6.25 μL of 10% D-(+)-trehalose dihydrate (Fluka Analytical), 2.0 μL of Hyclone ultra-pure water (Thermo Scientific), 1.25 μL of 10X Platinum Taq buffer (Invitrogen), 0.625 μL of 50 mM MgCl2 (Invitrogen), 0.125 μL of each 10 μM primer, 0.0625 μL of 10 mM dNTP (KAPA Biosystems), and 0.060 μL of 5U/lL Platinum Taq DNA Polymerase (Invitrogen) for a total reaction volume of 12.5 μL.…”

“…DNA metabarcoding is a rapidly evolving method for biodiversity assessment of bulk samples using the COI gene and next-generation sequencing. It has been used in diverse applications including biodiversity monitoring, reconstruction of paleo-communities, and animal gut contents [13]. Given the importance of correctly identifying the preferred vector when examining host-vector contact [a concept expressed by the Human Blood Index (HBI)], which is defined as the proportion of insects in a vector population with human blood [14], we investigated the host feeding pattern of Ae.…”

Strengthening marine amphipod DNA barcode libraries for environmental monitoring

“…eDNA technology has been shown to be useful in spatial and temporal monitoring in a wide variety of settings, as the methods are relatively inexpensive, reliable and quicker than conventional monitoring (Lecaudey et al 2019;Preissler et al 2019;Reinhardt et al 2019;Sutter and Kinziger 2019;Sales et al 2020). The breakthrough in eDNA barcoding technology is in its ability to monitor the ecosystem without causing unnecessary harm to ecosystem or their organisms by non-invasive sampling strategy (Antognazza et al 2019;Mora et al 2019;Leempoel et al 2020) and to detect elusive, rare, and cryptic species effectively even in low density occurrences (Franklin et al 2019;Shelton et al 2019;Takahara et al 2020). Single eDNA sampling could simultaneously monitor biodiversity in the given environment over a broad taxonomic spectrum (Sawaya et al 2019;Thomsen and Sigsgaard 2019;Zhang et al 2020).…”