Dataset Information

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.

SUBMITTER: Ashfaq M

PROVIDER: S-EPMC6037371 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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

Ashfaq Muhammad M Sabir Jamal S M JSM El-Ansary Hosam O HO Perez Kate K Levesque-Beaudin Valerie V Khan Arif M AM Rasool Akhtar A Gallant Carlene C Addesi Joseph J Hebert Paul D N PDN

PloS one 20180709 7

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 understand ...[more]

PMID: 29985924

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Project description:AimUnderstanding diversity patterns and identifying the environmental factors that shape these patterns are essential for ecology and conservation. The Afro-Arabian region comprises one of the most important biogeographic areas connecting continents. Yet, little emphasis has been put on understanding its endemic fauna in relation to its biogeographic realms. Our objective is to fill the gaps in knowledge on diversity patterns and biogeography that are essential for prioritizing the overdue conservation efforts.LocationThe study area covers mostly the hot desert climate region in North Africa and Arabia, and includes the Mediterranean, Sahel, and Ethiopian highlands (hereafter "Afro-Arabian region").MethodsWe used distribution maps developed by IUCN and BirdLife for species endemic to the Afro-Arabian region belonging to the four tetrapod classes, amphibians, reptiles, birds, and mammals, to identify the endemic richness hotspots. We then used multivariate analyses to delineate biogeographic regions and evaluate their relationship with the environmental factors.ResultsOur study reveals a complex map of the richness hotspots for the endemic tetrapod classes. The main hotspots of endemism were concentrated at the margins of the study area, along the Mediterranean coast, Ethiopian highlands, and along the Red Sea Mountains. We propose classifying the Afro-Arabian region into three discrete biogeographic realms for endemic amphibians, four for reptiles and birds, and five discrete biogeographic realms for endemic mammals. The identified realms are defined by their environmental conditions and the historical geological processes.Main conclusionsRichness hotspots of endemic tetrapod classes were heterogeneously distributed in the Afro-Arabian region. Our results support the hypothesis that species diversity patterns and endemism have been shaped by the environmental conditions and the paleogeographic processes. Each of the identified bioregions is associated with a characteristic set of tetrapod species. Our results are a benchmark for assessing the effectiveness of the protected areas and for implementing conservation plans for biodiversity.

Project description:BackgroundThe megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region.ResultsOf the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.ConclusionsOur study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.

Project description:BACKGROUND: Previous studies on insect DNA barcoding provide contradictory results and suggest not consistent performances across orders. This work aims at providing a general evaluation of insect DNA barcoding and "mini-barcoding" by performing simulations on a large database of 15,948 DNA barcodes. We compared the proportions of correctly identified queries across a) six insect orders (Coleoptera, Diptera, Hemiptera, Hymenoptera, Lepidoptera and Orthoptera), b) four identification criteria (Best Match: BM; Best Close Match: BCM; All Species Barcodes: ASB; tree-based identification: NJT), and c) reference databases with different taxon coverage (100, 500, 1,000, 1,500 and 1,995 insect species). RESULTS: Analysis of variance revealed highly significant differences among ID criteria and insect orders. A posteriori comparisons of means showed that NJT had always a significantly lower identification success (NJT = 0.656, S.D. = 0.118) compared to both BM and BCM (BM = 0.948, S.D. = 0.026; BCM = 0.946, S.D. = 0.031). NJT showed significant variations among orders, with the highest proportion of correctly identified queries in Hymenoptera and Orthoptera and the lowest in Diptera. Conversely, the proportions of correct matches of BM and BCM were consistent across orders but a progressive increase in false identification was observed when larger reference databases were used. CONCLUSIONS: Regardless the relatively low proportion of Type I errors (misidentification of queries which are represented in the reference database) of BM and BCM, the lack of reference DNA barcodes for 98% of the known insect species implies that insect DNA barcoding is heavily biased by Type II errors (misidentification of queries without conspecifics in the database). The detrimental effects of Type II errors could be circumvented if insect DNA barcoding is used to verify the lack of correspondence between a query and a list of properly referenced target species (e.g. insect pests). This "negative identification" would only be subjected to Type I errors and could be profitably adopted in insect quarantine procedures.

Dataset Information

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

Publications

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

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