The first complete mitochondrial genome data of the Afghan pika Ochotona rufescens (Lagomorpha, Ochotonidae), near the type locality.

The Afghan pika Ochotona rufescens (Gray, 1842) is widely distributed across the mountains of Afghanistan, Iran, Pakistan, and southwestern Turkmenistan, most often at elevations between 2,000 and 3,000 m. Here we present, for the first time, the complete mitochondrial genomes of two specimens of the nominotypical subspecies Ochotona rufescens rufescens, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The lengths of the circular mitogenomes are 16,408 bp and 16,407 bp, respectively. Both mitogenomes contain 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA (Gln), tRNA (Ala), tRNA (Asn), tRNA (Cys), tRNA (Tyr), tRNA (Ser), tRNA (Glu), and tRNA (Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was ∼30% for A, 25% for T, 15% for G, and 29% for C. The mitogenome data are available in the GenBank under the accession numbers ON859136 and ON859137.

The first complete mitochondrial genome data of the pygmy rabbit Brachylagus idahoensis, the world's smallest leporid.

The pygmy rabbit Brachylagus idahoensis (Merriam, 1891) is the smallest extant leporid, which naturally occurs in the Great Basin and adjacent areas in western parts of the United States of America. Its distribution is strongly associated with the sagebrush (Artemisia ssp.) vegetation. Here we present, for the first time, the complete mitochondrial genome of Brachylagus idahoensis, de novo assembled from Illumina short reads of fragmented probe-enriched DNA. The circular mitogenome is 17,021 bp in length and contains 13 protein-coding genes (PCGs), two ribosomal RNAs (16S rRNA and 12S rRNA), 22 transfer RNA genes, and a control region. The gene NAD6 and the tRNA(Gln), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), tRNA(Ser), tRNA(Glu) and tRNA(Pro) are encoded on the light strand while the rest are encoded on the heavy strand. The overall nucleotide composition was 30.78% for A, 28.5% for T, 13.62% for G and 27.08% for C. The mitogenome data are available in the GenBank under the accession number OL436257.

Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia.

Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.

Multiple species delimitation approaches applied to the avian lark genus Alaudala.

Species delimitation has advanced from a purely phenotypic exercise to a branch of science that integrates multiple sources of data to identify independently evolving lineages that can be treated as species. We here test species limits in the avian Lesser Short-toed Lark Alaudala rufesens-Sand Lark A. raytal complex, which has an intricate taxonomic history, ranging from a single to three recognised species, with different inclusiveness in different treatments. Our integrative taxonomic approach is based on a combination of DNA sequences, plumage, biometrics, songs, song-flights, geographical distributions, habitat, and bioclimatic data, and using various methods including a species delimitation program (STACEY) based on the multispecies coalescent model. We propose that four species should be recognised: Lesser Short-toed Lark A. rufescens (sensu stricto), Heine's Short-toed Lark A. heinei, Asian Short-toed Lark A. cheleensis and Sand Lark A. raytal. There is also some evidence suggesting lineage separation within A. cheleensis and A. raytal, but additional data are required to evaluate this. The species delimitation based on STACEY agrees well with the non-genetic data. Although computer-based species delimitation programs can be useful in identifying independently evolving lineages, we stress that whenever possible, species hypotheses proposed by these programs should be tested by independent, non-genetic data. Our results highlight the difficulty and subjectivity of delimiting lineages and species, especially at early stages in the speciation process.

A survey on endoparasites in wild rodents of the Jaz Murian depression and adjacent areas, southeast of Iran.

In this survey, rodents and their endoparasites were investigated in the Jaz Murian depression and adjacent areas, southeast Iran. In total, 146 specimens of rodents belong to 13 species were trapped. In general, 10 different genera of endoparasites including 11 species were collected. The endoparasites were identified as follows: (1) Nematodes: Trichuris muris, Syphacia obvelata, Labiostomum sp., Labiostomum naimi, Mastrophorus muris, Aspicularis tetraptera and Heligmosomoides skrjabini, Physaloptera sp. (2) Cestodes: Choanotaenia sp., Raillietina sp., and Hymenolepis diminuta. Of 146 captured rodents, Tatera indica was found with high parasitic infestation (with 93% infested) comparing to Acomys dimidiatus (66%), Rattus rattus (50%), Meriones libycus (15%), Jaculus blanfordi (14%) and Mus musculus (8%) whereas, seven rodent species, Nesokia indica, Gerbillus nanus, Golunda ellioti, Calomyscus hotsoni, Apodemus witherbyi, Cricetulus migratorius and Microtus mystacinus were free from any parasitic infestation. Those six infested rodent species were collected from the center of the Jaz Murian depression, whereas seven non-infested rodents' species except N. indica and G. nanus live in the marginal ranges of the Jaz Murian depression, therefore, these species inhabiting the central parts were supposed to be more important from the health aspect. The species, Labiostomum naimi collected from A. dimidiatus is the first report of this species in rodents from Iran.

Faunistic Study of the Rodents of North Khorasan Province, North East of Iran, 2011-2013.

BACKGROUND: Rodents are one of the most important hosts for some zoonotic diseases and also act as a reservoir of some ectoparasites and endoparasites. They cause damage to the farms and inflict public health. The aim of this study was to investigate the faunal composition of rodent in North Khorasan Province, Northeast of Iran. METHODS: The sampling was carried out between 2011 to 2013. The specimens were collected using different methods including rodent death and live traps, digging of their burrow, and hand net from 75 different sample sites. RESULTS: The total number of 396 specimens belonging to 22 species and six families were identified. The results illustrated the high numbers and densities of Meriones persicus (17.68%), Meriones libycus (15.15%), Nesokia indica (7.32%) and Rhombomys opimus (6.82%), as the most important reservoirs for different zoonotic diseases. Moreover, significant number of other rodent species including Mus musculus (15.66%), Apodemus witherbyi (13.89%), A. hyrcanicus (0.25%), Rattus norvegicus (1.01%), Meriones crassus (0.25%), Gerbillus nanus (0.51%), Microtus paradoxus (2.27%), M. transcaspicus (0.76%), Ellobius fuscocapillus (0.25%), Cricetulus migratorius (4.29%), Calomyscus elburzensis (4.29%), C. mystax (1.26%), Spermophilus fulvus (0.25%), Dryomys nitedula (3.54%), Allactaga elater (3.54%), Jaculus blanfordi (0.25%), Meriones zarudnyi (0.25%), M. meridianus (0.51%), and Hystrix indica as hosts for parasites and zoonotic diseases were identified. CONCLUSION: The high biodiversity including at least 22 species and six families of rodents were found in North Khorasan Province, some of them were medically important species.

Molecular Survey of Tularemia and Plague in Small Mammals From Iran.

Introduction: Plague and tularemia are zoonoses and their causative bacteria are circulating in certain regions of Iran. This study was conducted to investigate potential disease reservoirs amongst small wildlife species in different regions of Iran. Methods: Rodents, insectivores and hares from 17 different provinces of the country were collected in 2014 and 2015. Samples were taken from the spleens of the animals and Real-time PCR was applied to detect nucleic acid sequences that are specific to Francisella tularensis and Yersinia pestis, respectively. Results: Among 140 collected rodents, 25 distinct species were identified out of which five were the most common: Microtus paradoxus (21% out of 140 rodents), Apodemus witherbyi (12%), Microtus irani (11%), Mus musculus (11%) and Microtus socialis (10%). Seventeen insectivores were collected and identified as Crocidura suaveolens (82%) and C. leucodon (18%). Fifty-one hares were collected and identified as Lepus europaeus (57%), Lepus tolai (14%) and Lepus sp. (29%). Three out of 140 explored rodents (1.91%) were positive for F. tularensis, an A. witherbyi, a Mus musculus domesticus, and a Chionomys nivalis collected from Golestan, Khuzestan and Razavi Khorasan provinces, respectively. Two hares (3.92%) were F. tularensis-positive, a L. europaeus from Khuzestan and a Lepus sp. from the Sistan and Baluchistan province. None of the tested animals were positive for Y. pestis. Conclusion: This is the first report of direct detection of F. tularensis in mammals of Iran and the first-time observation of the agent in a snow vole, C. nivalis worldwide. The results indicate that tularemia is more widespread in Iran than previously reported including the Northeast and Southwestern parts of the country. Future studies should address genetic characterization of F. tularensis positive DNA samples from Iran to achieve molecular subtyping and rule out assay cross-reactivity with near neighbor Francisella species.

Intestinal Helminths in Different Species of Rodents in North Khorasan Province, Northeast of Iran.

BACKGROUND: Rodents are an important source of zoonotic diseases for human. The aim of this study was to determine the infectivity of rodents with intestinal helminths in North Khorasan Province, Iran. METHODS: One hundred and thirteen rodents were collected using different collection methods such as kill and live traps, digging of their burrow, filling of their hiding places with water and hand net during 2011-2013. Their alimentary canals were removed in the laboratory and helminths were determined in the department of parasitology, Tehran University of Medical Sciences. RESULTS: Thirteen species of helminths parasites were found in 13 species of rodents, including Aspiculuris tetraptera, Hymenolepis diminuta, Nippostrongylus brasiliensis, Protospirura Seurat, Rictolaria ratti, Skrjabinitaenia lobata, Streptopharagus kuntzi, Syphacia obvelata, Taenia taeniaeformis, Trichuris muris, Cysticercus fasciolaris, Acanthocephal. spp and Trichuris spp. Some of them were reported for the first time in new host in Iran. S. obvelata and A. tetraptera were the most frequent parasites and P. Seurat, R. ratti and C. fasciolaris were found only in one rodent. CONCLUSION: This is the first study to investigate the intestinal parasites in rodents in this area. Among different species identified, some of helminths were reported in new host.

A Field Study of Plague and Tularemia in Rodents, Western Iran.

INTRODUCTION: Kurdistan Province in Iran is a historical focus for plague and tularemia. This study aimed at assessing the current status of these two foci by studying their rodent reservoirs. MATERIALS AND METHODS: Rodents were trapped and their ectoparasites were collected. The genus and species of both rodents and ectoparasites were determined. Serological analyses of rodent blood samples were done by enzyme-linked immunosorbent assay for plague and by standard tube agglutination assay for tularemia. Rodent spleen samples were subjected to bacterial culture, microscopic examination, and real-time PCR to search for active plague or tularemia infection. RESULTS: During this study, 245 rodents were trapped, of which the most abundant genera were Apodemus (40%), Mus (24.49%), and Meriones (12.65%). One hundred fifty-three fleas, 37 mites, and 54 ticks were collected on these rodents. The results of all direct and indirect tests were negative for plague. Serological tests were positive for tularemia in 4.8% of trapped rodents. DISCUSSION: This study is the first report on the presence of tularemia infection in rodents in Western Iran. Since Meriones persicus is a known reservoir for plague and tularemia, and this rodent carried plague and tularemia vectors in Marivan and Sanandaj districts, there is a real potential for the occurrence of these two diseases in this region.