A DNA barcode survey of insect biodiversity in Pakistan

Introduction

With an area of 882,000 km², Pakistan includes seven biomes (Deserts & Xeric Shrublands, Flooded Grasslands & Savannas, Mangroves, Montane Grasslands & Shrublands, Temperate Broadleaf & Mixed Forests, Temperate Conifer Forests, Tropical & Subtropical Coniferous Forests) and portions of the Indo-Malayan and Palearctic biogeographic realms (Dinerstein et al., 2017). Because of this physiographic and climatic variation, its faunal diversity is quite high (Anwar, Jasra & Ahmad, 2008). While its vertebrate fauna is well known (Khan, 1976; Roberts, 1997; Grimmett, Roberts & Inskipp, 2008), prior studies on other animal lineages have been restricted to specific taxa or regions (Inayat et al., 2010; Iftikhar et al., 2016a; Manzoor, Khan & Shah, 2020). Although over 5,000 insect species have been reported (Government of Pakistan, 2000), no taxonomically comprehensive or wide-ranging assessments have been undertaken due to the scarcity of taxonomists, and the fact that many insect species remain undescribed (Ward & Lariviere, 2004). Because conventional morphological approaches (Pompeo et al., 2017) are difficult to implement at scale (Fattorini, 2013), the species count for Pakistan remains uncertain as it does globally (Scheffers et al., 2012).

The effectiveness of DNA barcoding (Hebert et al., 2003) in both specimen identification and species discovery (Hebert et al., 2004; Huemer et al., 2014; Kress et al., 2015) has stimulated its rapid adaptation in modern biodiversity studies (Ashfaq & Hebert, 2016; DeSalle & Goldstein, 2019). This work has generated DNA barcode coverage for more than 760,000 animal species on the Barcode of Life Data System (BOLD) (www.boldsystems.org) (Ratnasingham & Hebert, 2007). The effectiveness of the Barcode Index Number (BIN) system (Ratnasingham & Hebert, 2013) as a species proxy (Hausmann et al., 2013) has made it possible to rapidly evaluate species diversity, enabling large-scale biotic inventories (Hebert et al., 2016; Wirta et al., 2016). Because BINs show close congruence with species boundaries established through morphological study (Ortiz et al., 2017; Huemer et al., 2019) they can be used to delineate newly encountered species (Mitchell, Moeseneder & Hutchinson, 2020), to discern cryptic species (Zahiri et al., 2017; Zhou et al., 2019), to plot species distributions (Ren et al., 2018), to estimate species richness in bulk samples (Andújar et al., 2018; Braukmann et al., 2019), to analyze museum collections (Pentinsaari et al., 2020), and to assess faunal similarity at regional and global scales (Ashfaq et al., 2017).

The effectiveness of DNA barcoding coupled with advances in sequencing technology allow it to support large-scale biodiversity analysis (Wilson et al., 2017). However, the intensity of study has varied among regions (Weigand et al., 2019). For example, the BIN count (84,000) for Canada is 8× that for Russia (11,000), although the latter nation is 1.7× larger (www.boldsystems.org, accessed 7 September 2021). In a similar fashion, the BIN count for Germany (23,000) is 4× that for India (5,800), although the latter nation is 9× larger. The current study extends DNA barcode coverage for Pakistan to both advance knowledge of the taxonomic composition of its insect fauna and to develop a barcode reference library that supports routine eDNA and metabarcoding studies in the future.

Materials and Methods

Sample collection and preparation

Insects were sampled at 1,858 sites across Pakistan (Fig. 1) from 2010–2019 using both active and passive collecting methods including sweep nets, hand collections, hostplant beating, light traps, Malaise traps, pitfall traps, and UV illuminated sheets. Plans for the specimen collections/sites were approved by the Director, National Institute for Biotechnology and Genetic Engineering, Faisalabad under the project HEC No. 20-1403/R& D/09. The specimens were identified to an order and, where possible, to lower taxonomic ranks. Large specimens were either pinned and preserved dry or placed in Matrix tubes with 95% ethanol. Small specimens were individually placed in a well containing 30 μl of 95% ethanol in 96-well microplates. Specimen metadata and an image (except for Malaise samples where only representative specimens of each BIN were imaged) were submitted to BOLD where the information can be accessed on both the specimen page and corresponding BIN page. Voucher specimens are archived at the National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan (with sample ID prefix NIBGE) or at the Centre for Biodiversity Genomics (CBG), Guelph, Canada (with ID prefix BIOUG).

Results

DNA barcodes were recovered from 50,094 (83%) of the 60,273 specimens analyzed. The other 17% either failed to amplify or generated problematic sequences (e.g., contamination, NUMTs, stop codons, endosymbionts) that were excluded from subsequent analysis. Considering orders with 100 or more specimens, sequence recovery ranged from a low of 63% for Blattodea to 95% for Lepidoptera. Sequence recovery for the other four major orders of insects showed considerable variation (Diptera: 91%, Coleoptera: 80%, Hymenoptera: 78%, Hemiptera: 69%).

All 50,592 insects with a barcode were assigned to one of 19 orders while 99.8% received an assignment to one of 362 families (Table 1, Table S1). Five orders represented 92% of the specimens: Diptera (40%), Hymenoptera (21%), Lepidoptera (12%), Hemiptera (11%), and Coleoptera (8%) (Fig. 2). Six orders (Mantodea, Neuroptera, Odonata, Orthoptera, Psocodea, Thysanoptera) were each represented by >100 specimens while the remaining eight possessed fewer representatives (Fig. 2, Table S1). Most of these sequences (98%) received a BIN assignment, leading to a total of 6,590 BINs. The other 1,230 barcode sequences did not meet the criteria for BIN assignment but included 629 OTUs when analyzed using “Cluster Sequences” function on BOLD. The BOLD ID Engine assigned 82 of these OTUs to known BINs, but the other 547 OTUs likely represent taxa new to BOLD. Many (57%) of the 6,590 BINs were represented by two or more sequences, but 43% were represented by just a single specimen. The ratio of these singletons was above 40% in all five major orders but was highest in Hymenoptera (48%). Most BINs (88%; N = 5,754) possessed an image of at least one voucher.

The percentage of records in each of the five major orders with a BIN assignment ranged from 93% (Coleoptera) to 99% (Diptera, Lepidoptera) with Hemiptera and Hymenoptera intermediate (96%) (Table 1). These five orders also contributed most of the BINs (92%) and families (81%) (Table 1, Figs. 3A, 3B). Only 40% of BINs were placed to a genus and 21% to a species, but this still led to records for 1,375 genera and 1,364 species (Table 1, Table S1). Among the five major orders, more BINs were identified to a genus (72%) and species (41%) in Lepidoptera than in the other four orders (Table 1). For example, just 13.8% of Diptera BINs and 10.2% of Hymenoptera BINs were assigned to a species (Table 1).

Specimen counts for the 362 families were highly variable as 15 families were each represented by >1,000 specimens while 38 had just one (Table S1). This pattern was also reflected in the number of BINs as 15 families had >100 BINs while 86 had just one. The Chironomidae (N = 3,258) and Braconidae (N = 2,174) were represented by the most specimens while Cecidomyiidae (238 BINs) and Platygastridae (230 BINs) were most diverse. Figure 4 shows the BIN diversity and BIN:specimen ratio for the 15 families with >100 BINs. The ratio was highest (0.33) for Geometridae (Lepidoptera) and lowest (0.05) for Chironomidae. The species accumulation curve did not reach an asymptote indicating more species await detection (Fig. 5). Species estimates for the country ranged from 9,253 to 12,246 species suggesting that, on average, 40% of species remain to be sampled (Table 2).

BOLD was searched to ascertain if the 6,590 insect BINs from Pakistan were known from other countries. This analysis showed that 2,684 BINs (41%) were shared with at least one of 199 other countries while the others (3,906) are so far only known from Pakistan. The percentage of shared species ranged from 0.02% to 13%. Figure 6 shows the overlap values between Pakistan and countries with >1,000 BINs. BIN overlap was higher with nearby countries (Bangladesh: 13%, India: 12%, China: 8%) than for other regions. For example, Pakistan shared just 5% of its BINs with Australia, South Africa, and Germany (Fig. 6). The overlap between Canada and Costa Rica, both countries with >50,000 insect BINs, was only 4% and 1% respectively (Fig. 6).

Discussion

Current estimates of the number of insect species which occur in Pakistan range from 5,000 (Ministry of Climate Change, Pakistan, 2019) to 20,000 species (Hasnain, 1998), but they are certainly too low (Baig & Al-Subaiee, 2009). The current study aimed to refine estimates of species richness by coupling DNA barcoding with the BIN system. With over 50,000 specimens sequenced, this study represents, by far, the largest effort to assemble a DNA barcode registry for the insect fauna of any South Asian country. While success (83%) in DNA barcode recovery was good, it varied considerably among orders from 63% for Blattodea to 95% for Lepidoptera. Similar variation in barcode recovery among different insect taxa has been reported in other studies (Geiger et al., 2016; Pentinsaari et al., 2020). For example, a study on the insect fauna of French Polynesia reported 91% recovery for Diptera vs 63% for Coleoptera (Ramage et al., 2017). Similarly, a large-scale Canadian study revealed 95% recovery for Diptera vs 77% for Hemiptera and 74% for Hymenoptera (deWaard et al., 2019a). Although DNA quantity and quality play an important role (Ballare et al., 2019; Velasco-Cuervo et al., 2019), failures in primer binding often underlie low sequence recovery (Hajibabaei et al., 2005, Hebert et al., 2016). Such failures can lead to the underestimation of species richness in insect groups where recovery is low (Hebert et al., 2016). Other factors, such as co-amplification of pseudogenes (Song et al., 2008), Wolbachia (Smith et al., 2012), recent speciation (van Velzen et al., 2012), or incomplete lineage sorting (Mallo & Posada, 2016) may also limit the efficacy of barcodes to delimitate species, consequently affecting the diversity estimates. Moreover, there are instances where the BIN system overestimated species diversity in certain insect groups, such as Chironomidae (Lin, Stur & Ekrem, 2015; Ekrem et al., 2018).

The coupling of morphological inspection with barcode matches on BOLD (deWaard et al., 2019a, 2019b) was very effective at placing BINs to an order (100%) and family (>99%). However, just 40% of the BINs could be assigned to a genus and 21% to a species indicating the need for better parameterization of the barcode reference library. This was particularly true for the three most diverse orders where species assignments were less than 15% (Diptera: 13.8%, Coleoptera: 13.3%, Hymenoptera: 10.2%). Considerably higher assignment success has been reported for Malaise samples from Germany (34%) and Canada (38%) (Geiger et al., 2016; deWaard et al., 2019a) reflecting the more comprehensive DNA barcode reference libraries available for these nations. Despite the limited reference database (Virgilio et al., 2010), the present analysis identified representatives from 1,375 genera and 1,364 species showing the value of the global reference library (BOLD) which far exceeds the results obtained by morphology alone (Marshall, Paiero & Buck, 2009). The present analysis revealed 6,590 BINs with species richness estimates indicating that the fauna of Pakistan certainly includes more than 10,000 species. As these estimates are based on specimens collected with uneven sampling and limited geographic coverage, they are likely to increase with more comprehensive efforts.

Although 19 insect orders were detected, five (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera) were dominant (92%), reinforcing prior results from morphological (Stork, 2018) and barcoding studies (Ritter et al., 2019; Pentinsaari et al., 2020). Malaise traps preferentially capture low-flying insects such as Diptera and Hymenoptera (Cooksey & Barton, 1981; deWaard et al., 2019b), the two orders that made 61% of the collections. Other studies have reported a similar pattern (Brown, 2005; Karlsson et al., 2020). For example, a Canadian study found that Diptera comprised 57% of the collections (deWaard et al., 2019b).

Fifteen of the 362 families dominated with 1,000 or more specimens and this pattern was also reflected in the BIN diversity. The uneven detection of families in the survey is supported by the fact that 38 families were represented by just one specimen and 88 by one BIN. Interestingly, nine of the 15 families with the most BINs were dipterans and hymenopterans with Cecidomyiidae and Ichneumonidae comprising the highest BIN:specimen ratio.

Because BOLD now hosts around nine million DNA barcode records for more than 760,000 animal species, it provides a good basis for assessing faunal overlap using BINs. Only 41% of the 6,590 insect BINs from Pakistan are currently known from other countries. As expected, BIN overlap was highest with neighboring countries. This result reflects the endemism of biodiversity (Werneck et al., 2012) and underscores the need to develop local biodiversity inventories. The current survey represents a first step towards building an inventory for the insect fauna of Pakistan.

Supplemental Information