Insect diversity in the Saharo-Arabian region: Revealing a little-studied fauna by DNA barcoding

Abstract

Although insects dominate the terrestrial fauna, sampling constraints and the poor taxonomic knowledge of many groups have limited assessments of their diversity. Passive sampling techniques and DNA-based species assignments now make it possible to overcome these barriers. For example, Malaise traps collect specimens with minimal intervention while the Barcode Index Number (BIN) system automates taxonomic assignments. The present study employs Malaise traps and DNA barcoding to extend understanding of insect diversity in one of the least known zoogeographic regions, the Saharo-Arabian. Insects were collected at four sites in three countries (Egypt, Pakistan, Saudi Arabia) by deploying Malaise traps. The collected specimens were analyzed by sequencing 658 bp of cytochrome oxidase I (DNA barcode) and assigning BINs on the Barcode of Life Data Systems. The year-long deployment of a Malaise trap in Pakistan and briefer placements at two Egyptian sites and at one in Saudi Arabia collected 53,092 specimens. They belonged to 17 insect orders with Diptera and Hymenoptera dominating the catch. Barcode sequences were recovered from 44,432 (84%) of the specimens, revealing the occurrence of 3,682 BINs belonging to 254 families. Many of these taxa were uncommon as 25% of the families and 50% of the BINs from Pakistan were only present in one sample. Family and BIN counts varied significantly through the year, but diversity indices did not. Although more than 10,000 specimens were analyzed from each nation, just 2% of BINs were shared by Pakistan and Saudi Arabia, 4% by Egypt and Pakistan, and 7% by Egypt and Saudi Arabia. The present study demonstrates how the BIN system can circumvent the barriers imposed by limited access to taxonomic specialists and by the fact that many insect species in the Saharo-Arabian region are undescribed.

Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests

“…Taxonomic identification of vertebrate species is generally not challenging, but low abundances and shy behavior of the often-crepuscular animals can make direct surveys time-and labor intense, especially in remote areas and in areas with dense vegetation. Given the difficulty of their identification, molecular analyses are increasingly applied to identify the taxonomic contents of bulk arthropod samples (Ashfaq et al, 2018;Elbrecht et al, 2017;Gibson et al, 2014;Kocher, Gantler et al, 2017;Liu et al, 2018;Morinière et al, 2016;Oliverio, Gan, Wickings, & Fierer, 2018;Shokralla et al, 2015;Yu et al, 2012). In contrast, while arthropods occur in high abundance and are easily sampled (Rosenberg et al, 1986), morphology-based taxonomic identification of arthropod community samples requires not only taxonomic expertise for multiple taxonomic groups but also a significant time investment to identify all the taxonomic constituents (Basset et al, 2012).…”

“…For this, DNA metabarcoding approaches are the most frequently applied. Metabarcoding of bulk insect samples has, for example, been used to characterize the diversity of insects in montane landscapes in tropical southern China (Zhang et al, 2016), explore the insect diversity in a Saharo-Arabian region with otherwise sparse fauna information (Ashfaq et al, 2018), and monitor temporal changes in arthropod communities in different forest types (Brandon-Mong et al, 2018). Unique identifiers are added to sample amplicons before they are sequenced in parallel on a high-throughput sequencing platform.…”

“…In contrast, while arthropods occur in high abundance and are easily sampled (Rosenberg et al, 1986), morphology-based taxonomic identification of arthropod community samples requires not only taxonomic expertise for multiple taxonomic groups but also a significant time investment to identify all the taxonomic constituents (Basset et al, 2012). Given the difficulty of their identification, molecular analyses are increasingly applied to identify the taxonomic contents of bulk arthropod samples (Ashfaq et al, 2018;Elbrecht et al, 2017;Gibson et al, 2014;Kocher, Gantler et al, 2017;Liu et al, 2018;Morinière et al, 2016;Oliverio, Gan, Wickings, & Fierer, 2018;Shokralla et al, 2015;Yu et al, 2012). For this, DNA metabarcoding approaches are the most frequently applied.…”

“…The targeted nature of metabarcoding means that it is a cost-effective and efficient method for identifying the taxonomic contents of hundreds to thousands of samples in parallel (Galan et al, 2018;Taberlet et al, 2012). Metabarcoding of bulk insect samples has, for example, been used to characterize the diversity of insects in montane landscapes in tropical southern China (Zhang et al, 2016), explore the insect diversity in a Saharo-Arabian region with otherwise sparse fauna information (Ashfaq et al, 2018), and monitor temporal changes in arthropod communities in different forest types (Brandon-Mong et al, 2018).…”

BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

“…BINs are an effective species proxy because they correspond closely with species designated through morphological study [36,37]. As a result, BINs are now routinely employed for biodiversity assessments, counting species, analyzing cryptic species complexes, and assessing species ranges [38–40]. These developments have generated a high level of interest in DNA barcoding, leading to reference barcode libraries for certain groups at continental and global scales [32,41–45].…”