Intraspecific diversity of Meriones persicus (Rodentia; Gerbillinae), the main plague reservoir in Iran, and its connection to enzootic plague in Iran.

Plague, a lethal zoonotic disease, primarily circulates within rodent populations and their fleas. In Iran, the widely distributed jird, Meriones persicus, serves as the principal reservoir for plague, with a belief in the existence of five out of its six recognized subspecies within the country. However, these subspecies are classified into four mitochondrial cytochrome b sub-lineages (IA, IB, IIA, IIB). This discrepancy, combined with the presence of an unnamed sub-lineage in central Iran awaiting taxonomic clarification, has left intraspecific taxonomy unsettled and obscured the true alignment between mtDNA sub-lineages and nominal subspecies. In this study, we investigated the intraspecific variation in the cytb gene across populations sampled throughout Iran, focusing on underexplored regions between the Zagros and Alborz Mountains and central Iran. While our genetic data generally support reported subspecies validity in Iran, we raise questions about M. p. baptistae, emphasizing the need for further data from its type territory in Pakistan. Two main lineages of M. persicus (I and II) exhibit geographical isolation, with limited overlap in the central Zagros Mts., where three subspecies (M. p. ambrosius, M. p. rossicus, and M. p. persicus) coexist. Superimposing infected rodents' geographic coordinates onto updated sub-lineages' distribution revealed a potential association between sub-lineage IA (M. p. rossicus) and all enzootic plague cases from 1946 to 2023. M. persicus rossicus extends into the Caucasus (where plague infections are common), Eastern Turkey, and Iraq. Consequently, interpreting this finding in the context of plague surveillance in Iran and neighboring areas requires caution.

Cryptic diversity of Crocidura shrews in the savannahs of Eastern and Southern Africa.

Crocidura (Eulipotyphla, Soricidae) is the most species-rich genus among mammals, with high cryptic diversity and complicated taxonomy. The hirta-flavescens group of Crocidura represents the most abundant and widespread shrews in savannahs of eastern and southern Africa, making them a suitable phylogeographical model for assessing the role of paleoclimatic changes on current biodiversity in open African habitats. We present the first comprehensive study on the phylogeography, evolutionary history, geographical distribution, systematics, and taxonomy of the group, using the integration of mitochondrial, genome-wide (ddRAD sequencing), morphological and morphometrical data collected from specimens over most of the known geographic distribution. Our genomic data confirmed the monophyly of this group and its sister relationship with the olivieri group of Crocidura. There is a substantial genetic variation within the hirta-flavescens group, with three highly supported clades showing parapatric distribution and which can be distinguished morphologically: C. hirta, distributed in both the Zambezian and Somali-Masai bioregions, C. flavescens, known from South Africa and south-western Zambia, and C. cf. flavescens, which is known to occur only in central and western Tanzania. Morphometric data revealed relatively minor differences between C. hirta and C. cf. flavescens, but they differ in the colouration of the pelage. Diversification of the hirta-flavescens group has most likely happened during phases of grassland expansion and contraction during Plio-Pleistocene climatic cycles. Eastern African Rift system, rivers, and the distinctiveness of Zambezian and Somali-Masai bioregions seem to have also shaped the pattern of their diversity, which is very similar to sympatric rodent species living in open habitats. Finally, we review the group's taxonomy and propose to revalidate C. bloyeti, currently a synonym of C. hirta, including the specimens treated as C. cf. flavescens.

Phylogenetic relations and range history of jerboas of the Allactaginae subfamily (Dipodidae, Rodentia).

Five-toed jerboas of the subfamily Allactaginae comprise several complex taxa occurring over a wide distribution range covering a large part of the Eurasian arid belt. In this study, we employed current methods of molecular phylogenetics based on 15 nuclear genes and the mitochondrial gene cytb to revise relations and systematics within Allactaginae. We also applied species distribution modelling projected on paleo-environmental data to reconstruct the geographic patterns of speciation in Allactaginae. We elucidated the intergeneric relationships within this subfamily and clarified interspecies relations within the genus Scarturus. Moreover, our results demonstrate the species status of S. caprimulga; outline the currently understudied diversity within Orientallactaga, Allactaga, and Pygeretmus; and improve the divergence estimates of these taxa. Based on our results from modelling of geographic range fragmentation in allactagines, we suggest the dating and location of speciation events and present hypotheses regarding general habitat niche conservatism in small mammals.

Plague reservoir species throughout the world.

Plague has been known since ancient times as a re-emerging infectious disease, causing considerable socioeconomic burden in regional hotspots. To better understand the epidemiological cycle of the causative agent of the plague, its potential occurrence, and possible future dispersion, one must carefully consider the taxonomy, distribution, and ecological requirements of reservoir-species in relation either to natural or human-driven changes (e.g. climate change or urbanization). In recent years, the depth of knowledge on species taxonomy and species composition in different landscapes has undergone a dramatic expansion, driven by modern taxonomic methods such as synthetic surveys that take into consideration morphology, genetics, and the ecological setting of captured animals to establish their species identities. Here, we consider the recent taxonomic changes of the rodent species in known plague reservoirs and detail their distribution across the world, with a particular focus on those rodents considered to be keystone host species. A complete checklist of all known plague-infectable vertebrates living in plague foci is provided as a Supporting Information table.

Rodent-borne diseases and their public health importance in Iran.

BACKGROUND: Rodents are reservoirs and hosts for several zoonotic diseases such as plague, leptospirosis, and leishmaniasis. Rapid development of industry and agriculture, as well as climate change throughout the globe, has led to change or increase in occurrence of rodent-borne diseases. Considering the distribution of rodents throughout Iran, the aim of this review is to assess the risk of rodent-borne diseases in Iran. METHODOLOGY/PRINCIPAL FINDING: We searched Google Scholar, PubMed, Science Direct, Scientific Information Database (SID), and Magiran databases up to September 2016 to obtain articles reporting occurrence of rodent-borne diseases in Iran and extract information from them. Out of 70 known rodent-borne diseases, 34 were reported in Iran: 17 (50%) parasitic diseases, 13 (38%) bacterial diseases, and 4 (12%) viral diseases. Twenty-one out of 34 diseases were reported from both humans and rodents. Among the diseases reported in the rodents of Iran, plague, leishmaniasis, and hymenolepiasis were the most frequent. The most infected rodents were Rattus norvegicus (16 diseases), Mus musculus (14 diseases), Rattus rattus (13 diseases), Meriones persicus (7 diseases), Apodemus spp. (5 diseases), Tatera indica (4 diseases), Meriones libycus (3 diseases), Rhombomys opimus (3 diseases), Cricetulus migratorius (3 diseases), and Nesokia indica (2 diseases). CONCLUSIONS/SIGNIFICANCE: The results of this review indicate the importance of rodent-borne diseases in Iran. Considering notable diversity of rodents and their extensive distribution throughout the country, it is crucial to pay more attention to their role in spreading infectious diseases for better control of the diseases.

Glacial allopatry vs. postglacial parapatry and peripatry: the case of hedgehogs.

Although hedgehogs are well-known examples of postglacial recolonisation, the specific processes that shape their population structures have not been examined by detailed sampling and fast-evolving genetic markers in combination with model based clustering methods. This study aims to analyse the impacts of isolation within glacial refugia and of postglacial expansion on the population structure of the Northern White-breasted hedgehog (Erinaceus roumanicus). It also discusses the role of the processes at edges of species distribution in its evolutionary history. The maternally inherited mitochondrial control region and the bi-parentally inherited nuclear microsatellites were used to examine samples within the Central Europe, Balkan Peninsula and adjacent islands. Bayesian coalescent inference and neutrality tests proposed a recent increase in the population size. The most pronounced pattern of population structure involved differentiation of the insular populations in the Mediterranean Sea and the population within the contact zone with E. europaeus in Central Europe. An interspecies hybrid was detected for the first time in Central Europe. A low genetic diversity was observed in Crete, while the highest genetic distances among individuals were found in Romania. The recent population in the post-refugial area related to the Balkan Peninsula shows a complex pattern with pronounced subpopulations located mainly in the Pannonian Basin and at the Adriatic and Pontic coasts. Detailed analyses indicate that parapatry and peripatry may not be the only factors that limit range expansion, but also strong microevolutionary forces that may change the genetic structure of the species. Here we present evidence showing that population differentiation may occur not only during the glacial restriction of the range into the refugia, but also during the interglacial range expansion. Population differentiation at the Balkan Peninsula and adjacent regions could be ascribed to diversification in steppe/forest biomes and complicated geomorphology, including pronounced geographic barriers as Carpathians.

A redescription of the Long-tailed Nesokia, Nesokia bunnii, and designation of a neotype (Rodentia: Muridae).

Long-tailed Nesokia, Nesokia bunnii, is a large rat restricted to the Mesopotamian marshes in Basra Province in southern Iraq. The species is known from five museum vouchers collected between March 1974 and January 1977. The type and the paratype, deposited in the Natural History Research Centre and Museum, University of Baghdad, Iraq, were destroyed during War on Iraq in 2003. By studying morphological details on three museum specimens in the Senckenberg Institution, Frankfurt a. M., Germany, we show that N. bunnii is unique among the Bandicoot rats (Nesokia and Bandicota) in having (1) rufous dorsal pelage, (2) facial mask of rufous, dark brown, grey and whitish areas, (3) whitish belly which is clearly demarcated along flanks, (4) ventral hairs white to bases, (5) woolly underfur, (6) long front claws, and (7) large tail annulation. Similar to N. indica, but in contrast to Bandicota, N. bunnii displays short incisive foramina, posterior margin of hard palate which terminates at the level of the third molar, and robust, hypsodont and laminate molars which lack posterior cingula. To objectively define the taxon we designate a neotype, which was collected at Saraifa, 30 km north of Qurna, Iraq. Our study highlights the importance of museum collections in documenting biodiversity and the indifference of decision makers and international institutions regarding their safe future.

Between the Balkans and the Baltic: Phylogeography of a Common Vole Mitochondrial DNA Lineage Limited to Central Europe.

The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern Europe, analyzing contemporary genetic structure to identify the role of a potential 'northern glacial refugium', i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe.

Risk assessment of metals and PAHs for receptor organisms in differently polluted areas in Slovenia.

Samples from receptor organisms (small mammals, passerine birds) and their food sources (herbaceous plants, leaves and fruits of wood plants, earthworms) were collected during 2011-2014 from the vicinity of a former lead smelter, from the vicinity of the largest Slovenian thermal power plant, from along a state road and also from a reference area. The samples were then analysed to determine the degree of contamination with the metals (Pb, Cd, Zn, Hg, Cu, Mo) and with polycyclic aromatic hydrocarbons (PAHs). This study provides the first data on metal and PAH exposure to small mammals and passerine birds in southeast Europe, focussing on the transfer of metals and PAHs through the food chain and on risk assessment for differently polluted areas in Slovenia. The results indicate that: (i) earthworms and herbaceous plants (especially roots) can be a source of metal exposure for organisms higher in the food chain; (ii) a risk from Pb and Cd (HQ > 1) in the vicinity of the former lead smelter exists for Myodes glareolus feeding in part on roots and for Apodemus flavicollis and Parus major feeding in part on earthworms; and (iii) mean Pb and Cd concentrations in the liver of small mammal species inhabiting the vicinity of the lead smelter reach effect concentrations in a significant proportion of the specimens (Pb: 40%, Cd: 67%); (iv) the results for P. major confirm that the study area is exposed to Pb, Cd, Hg; (v) metals contribute the major part of the total risk for receptor organisms from vicinity of lead smelter. On the contrary, the risk of PAHs for small mammals trapped close to the state road is insignificant. We can summarize, that the hazards experienced by the local ecosystem due to metal exposure may persist for decades in the vicinity of large emission sources (especially smelters).

Small mammals as biomonitors of metal pollution: a case study in Slovenia.

The transfer of lead, cadmium, zinc, mercury, copper and molybdenum from soil to the tissues of small mammals inhabiting differently polluted areas in Slovenia was investigated. Metals were determined in soil samples and in the livers of 139 individuals of five small mammal species, collected in 2012 in the vicinity of a former lead smelter, the largest Slovenian thermal power plant, along a main road and in a control area. The area in the vicinity of former lead smelter differs considerably from other study areas. The soil from that area is heavily polluted with Pb and Cd. The mean metal concentrations in the liver, irrespective of species, varied in the following ranges-Pb: 0.40-7.40 mg/kg fw and Cd: 0.27-135 mg/kg fw and reached effect concentrations at which toxic effects can be expected in a significant proportion of the livers of the small mammal specimens (Pb 40 %, Cd 67 %). These findings indicate that the majority of small mammals trapped in the area of the former lead smelter are at risk of toxic effects due to the very high bioaccumulation of Pb and Cd in the organism. On the contrary, Pd and Cd concentrations in the livers of small mammals sampled in the vicinity of the thermal power plant and along the main road were comparable with reference values and considerably lower than effect concentrations. Additionally, the study suggests that Apodemus flavicollis and Myodes glareolus are very suitable biomonitors of metal pollution.

Phylogeography of the rare Balkan endemic Martino's vole, Dinaromys bogdanovi, reveals strong differentiation within the western Balkan Peninsula.

The spatial genetic structure of Martino's vole, a rare palaeoendemic species of the western Balkans, was investigated using DNA isolated from archived museum samples. The study was based on partial sequencing (555 bp) of the mitochondrial cytochrome b gene for 63 specimens from 20 different localities throughout the species' range. Three highly divergent allopatric phylogenetic lineages (Northwestern, Central and Southeastern) were recognized among 47 haplotypes, suggesting three independent glacial differentiation centres within the western Balkans. The Northwestern lineage, which showed the highest divergence from all other samples (mean sequence divergence of 6.64% +/- 1.10), comprised samples collected from northwest of the Neretva River in Croatia, western Bosnia and Herzegovina. The Central and Southeastern lineages were separated by an average sequence divergence of 2.95% +/- 0.66 and were geographically divided by the Drim River (the Kosovo Basin in Serbia). Overall, haplotype diversity decreased from the Northwestern lineage to the Central and subsequently the Southeastern lineage, in a geographical pattern consistent with a stepping stone colonization. The observed distribution indicates a gradual southerly expansion with subsequent allopatry across the Neretva River and Drim River approximately 1 and 0.3 million years ago, respectively. Such a scenario is concordant with palaeontological evidence. Several highly divergent sublineages within the Northwestern and Central lineages showed no significant geographical structuring, suggesting secondary contact of allopatrically evolved lineages. We hypothesize that the topographical complexity of the Balkans promoted allopatry and isolation on a small geographical scale during interglacial periods, with secondary contact during glacial maxima. Furthermore, the three main lineages should be regarded as evolutionary significant units with important implications for conservation. Ecological data show that the Northwestern lineage in particular fulfils all criteria for a highly endangered, evolutionarily significant unit.