Automatic barcode gap discovery reveals diverse clades of Rhipicephalus spp. and Haemaphysalis spp. ticks from small mammals in 'Asir, Saudi Arabia

Samia Q Alghamdi,John W Mcgarry,Abdulaziz N Alagaili,Van Lun Low,Hadil A Alkathiry,Benjamin L Makepeace

doi:10.1186/s13071-021-05049-x

Abstract

BackgroundThe ixodid tick genera Rhipicephalus and Haemaphysalis contain several species of medical and/or veterinary importance, but their diversity in some regions of the world remains under-explored. For instance, very few modern studies have been performed on the taxonomy of these genera on the Arabian Peninsula.MethodsIn this study, we trapped small mammals in the 'Asir Mountains of south-western Saudi Arabia and collected tick specimens for morphological examination and molecular barcoding, targeting three mitochondrial loci: cox1, 16S rRNA and 12S rRNA.ResultsWe obtained a total of 733 ticks (608 Haemaphysalis spp. and 125 Rhipicephalus spp.) from 75 small mammal hosts belonging to six species. All tick specimens were immature except for nine adults recovered from a hedgehog (Paraechinus aethiopicus). Morphologically, the Rhipicephalus ticks resembled R. camicasi, but the Haemaphysalis ticks showed differences in palp morphology compared with species previously described from Saudi Arabia. Phylogenetic analysis and automatic barcode gap discovery identified a novel clade of Rhipicephalus sp. representing most of the nymphs. This was most closely related to R. leporis, R. guilhoni and R. linnaei. The adult ticks and a small proportion of nymphs clustered with R. camicasi sequences from a previous study. Finally, the Haemaphysalis nymphs formed two distinct clades that were clearly separated from all reference sequences but closest to some African species.ConclusionsThis apparent high level of tick diversity observed in a single study site of only ~ 170 km2, on a relatively small number of hosts, highlights the potential for the discovery of new tick species on the Arabian Peninsula.Graphical

Highlights

The ixodid tick genera Rhipicephalus and Haemaphysalis contain several species of medical and/or veterinary importance, but their diversity in some regions of the world remains under-explored
Material obtained and examined We obtained 75 small mammal hosts across the three sites, which belonged to six species (Table 2): the eastern spiny mouse (Acomys dimidiatus), king jird (Meriones rex), Yemeni mouse (Myomyscus yemeni), black rat (Rattus rattus), house mouse (Mus musculus) and desert hedgehog (Paraechinus aethiopicus)
All specimens subjected to polymerase chain reaction (PCR) [Rhipicephalus spp. nymphs (n = 33), one pool of Rhipicephalus spp. larvae, and eight Haemaphysalis spp. nymphs] generated at least one mitochondrial gene sequence (Table 1)

Summary

Introduction

The ixodid tick genera Rhipicephalus and Haemaphysalis contain several species of medical and/or veterinary importance, but their diversity in some regions of the world remains under-explored. One generic approach to resolving species diversity using objective molecular criteria is automatic barcode gap discovery (ABGD), which is founded on the principle that the genetic divergence should be smaller within species than between species [17]. This allows a confidence limit to be assigned to intraspecific divergence, partitioning gene sequences into bins or operational taxonomic units (OTUs). The ABGD approach and related methods are gaining in popularity in molecular studies of ticks worldwide [18,19,20]

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