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

Abstract

Background 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. For instance, very few modern studies have been performed on the taxonomy of these genera on the Arabian Peninsula. Methods In 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. Results We 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. Conclusions This 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 Abstract

One Health in practice: Multi-season survey of ixodid tick species collected from domestic dogs in Chad

“…by molecular characterization. The 16S rRNA gene sequence (400 bp) was most similar to several Haemaphysalis species from rodents in Saudi Arabia [e.g., MW763058, (Alghamdi et al, 2021)] followed by H. hispanica (355/380bp, 93.4%) from rabbits in Portugal (OL656102) and Spain (MZ420715) (Figure 6). The partial cytochrome oxidase I gene sequence (709 bp) for this Haemaphysalis sp.…”

Multi-Locus Sequence Analysis Indicates Potential Cryptic Speciation in the Chigger Mite Neoschoengastia gallinarum (Hatori, 1920) Parasitising Birds in Asia

“…Multi-locus sequence analysis studies have increased in popularity over the years due to the reduced impact of evolutionary rates for individual genes [ 76 , 77 ]; for instance, several such studies have been performed in ticks, usually using concatenated mitochondrial markers [ 78 , 79 , 80 , 81 ]. While mitochondrial DNA undergoes a more rapid rate of mutation compared to nuclear DNA [ 82 ] and recombination in animal mitogenomes is considered rare [ 83 ], its utility in identifying distinct maternal lineages is counterbalanced by caveats when applied to the detection of reproductive isolation [ 84 ].…”

Exploration of Multi-Gene DNA Barcode Markers to Reveal the Broad Genetic Diversity of Field Ticks (Acari: Ixodidae) in a Tropical Environment of Hainan Island, China

“…Intraspecific and interspecific genetic distances were calculated using the K2P model. Gaps in the DNA barcodes between intra-and interspecific genetic distances were identified using Automatic Barcode Gap Discovery (ABGD) software with the default options, i.e., P min = 0.001, P max = 0.1, steps = 10, X (relative gap width) = 1.5, and the K2P model [Puillandre et al, 2012;Alghamdi et al, 2021]. DNA barcode markers with significant intra-and interspecific divergence and obvious gaps were applied to effectively distinguish species.…”