Cytonuclear discordance among Southeast Asian black rats ( Rattus rattus complex)

Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events

Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages.

Serological detection of Rickettsia spp. and evaluation of blood parameters in pet dogs and cats from Bangkok and neighboring provinces

Rickettsiosis is caused by Orientia spp. and Rickettsia spp., arthropod-borne zoonotic intracellular bacteria. The close relationships between pet dogs, cats and owners increase the risk of rickettsial transmission, with limited studies on the seroprevalence in pets. This study investigated the prevalence of rickettsia exposure among dogs and cats in Bangkok and neighboring provinces. The samples from 367 dogs and 187 cats used in this study were leftover serum samples from routine laboratory testing stored at the Veterinary Teaching Hospital. In-house Enzyme-linked immunosorbent assay (ELISA) tests included IgG against the scrub typhus group (STG), typhus group (TG), and spotted fever group (SFG). The seroprevalence in pet dogs was 30.25% (111/367), including 21.53% for STG, 4.36% for TG, and 1.09% for SFG. Co-seroprevalence consisted of 2.72% for STG and TG, 0.27% for STG and SFG, and 0.27% for pangroup infection. The prevalence in cats was 62.56% (117/187), including 28.34% for STG, 4.28% for TG, and 6.42% for STG. Co-seroprevalence in cats consisted of STG and TG (4.28%), STG and SFG (5.35%), TG and SFG (3.21%), and three-group infection (10.69%). No significant difference in seroprevalence for the three serogroups was observed in any of the 64 districts sampled. The mean hematocrit level significantly decreased in seropositive dogs (P<0.05). Seropositive dogs and cats were detected in significantly greater numbers of anemia cases than nonanemia cases (P<0.05) (odds ratio: 7.93, 0.44, p = 0.00, p = 0.01). A significantly higher number of seropositive cats had decreased hemoglobin levels (P<0.05) (odds ratio: 3.63, p = 0.00). The seropositive samples significantly differed among older cats (P<0.05). These high exposures in pet dogs and cats could constitute important relationship dynamics between companion animals and rickettsial vectors. Significantly decreased hematocrit and hemoglobin levels indicated anemia in the exposed dogs and cats. The study findings will raise awareness of this neglected disease among pet owners and veterinary hospital personnel and aid in future public health preventative planning.

Phylogeny of Rhynchium and Its Related Genera (Hymenoptera: Eumeninae) Based on Universal Single-Copy Orthologs and Ultraconserved Elements

The subfamily Eumeninae is a large group of fierce predatory insects that prey mainly on the larvae of Lepidoptera pests. Because of the highly similar morphologies of the genus Rhynchium and its related genera in the subfamily, including Rhynchium Spinola, Allorhynchium van der Vecht, Anterhynchium de Saussure, Pararrhynchium de Saussure, it is essential to delineate their relationships. A previous phylogenetic analysis based on mitochondrial genomes suggested the inconsistent relationships of these genera under traditional classification based on morphological characters. In this study, we first used single-copy orthologs [USCO] and ultraconserved elements [UCE] extracted from 10 newly sequenced low-coverage whole genomes to resolve the phylogenetic relationships of the above genera. The newly sequenced genomes are 152.99 Mb to 211.49 Mb in size with high completeness (BUSCO complete: 91.5-95.6%) and G + C content (36.31-38.76%). Based on extracted 5811 USCOs and 2312 UCEs, the phylogenetic relationships of Rhynchium and its related genera were: ((Allorhynchium + Lissodynerus) + (Pararrhynchium + (Anterhynchium + (Dirhynchium + Rhynchium)))), which was consistent with the mitochondrial genome results. The results supported the genus Rhynchium as monophyletic, whereas Anterhynchium was recovered as paraphyletic, with Anterhynchium (Dirhynchium) as a sister to Rhynchium and hence deserving generic status; In addition, in the genus Pararrhynchium, P. septemfasciatus feanus and P. venkataramani were separated, not clustered on a branch, just as P. septemfasciatus feanus was not together with P. striatum based on mitochondrial genomes. Since Lissodynerus septemfasciatus, the type species of the genus Lissodynerus, was transferred to Pararrhynchium, it is considered that the genus Lissodynerus should be restituted as a valid genus, not a synonym of Pararrhynchium.

Molecular Identification and Genetic Variation of Rattus Species From Oil Palm Plantations of Malaysia Based on Mitochondrial Cytochrome Oxidase Subunit I (COI) Gene Sequences

Rats (Rattus species) are the most notorious vertebrate pests in Malaysian oil palm plantations. Although many studies have been conducted on Asian rats, little attention has been paid to their species composition and phylogenetic relationships in oil palm plantations in Peninsular Malaysia. We determined the mitochondrial cytochrome oxidase subunit I (COI) gene sequence (708 bp) for 216 individual rats collected from five oil palm plantations in Peninsular Malaysia. Phylogenetic analysis in conjunction with comparison with sequences from the nucleotide sequence database revealed five distinct lineages in the Malaysian oil plantations: Rattus tiomanicus, Rattus argentiventer, Rattus exulans, Rattus tanezumi, and a taxon corresponding to the Malayan house rat, which was most frequently observed (∼50%). The last taxon has traditionally been classified as a synonym of Rattus rattus (Rattus rattus diardii) or Rattus tanezumi, but our phylogenetic analysis placed it as an independent lineage, which is not particularly closely related to R. rattus or R. tanezumi, and which we refer to as Rattus diardii. The construction of the network showed that there is considerable genetic variation within the lineages of R. diardii and R tiomanicus, suggesting that these two species are native to the Malay Peninsula.

Comparative phylogeography of two commensal rat species (Rattus tanezumi and Rattus norvegicus) in China: Insights from mitochondrial DNA, microsatellite, and 2b-RAD data

Rattus norvegicus and Rattus tanezumi are dominant species of Chinese house rats, but the colonization and demographic history of two species in China have not been thoroughly explored. Phylogenetic analyses with mitochondrial DNA including 486 individuals from 31 localities revealed that R. norvegicus is widely distributed in China, R. tanezumi is mainly distributed in southern China with currently invading northward; northeast China was the natal region of R. norvegicus, while the spread of R. tanezumi in China most likely started from the southeast coast. A total of 123 individuals from 18 localities were subjected to 2b-RAD analyses. In neighbor-joining tree, individuals of R. tanezumi grouped into geographic-specific branches, and populations from southeast coast were ancestral groups, which confirmed the colonization route from southeast coast to central and western China. However, individuals of R. norvegicus were generally grouped into two clusters instead of geographic-specific branches. One cluster comprised inland populations, and another cluster included both southeast coast and inland populations, which indicated that spread history of R. norvegicus in China was complex; in addition to on-land colonization, shipping transportation also have played great roles. ADMIXTURE and principal component analyses provided further supports for the colonization history. Demographic analyses revealed that climate changes at ~40,000 to 18,000 years ago and ~4000 years ago had led to population declines of both species; the R. norvegicus declined rapidly while the population of R. tanezumi continuously expanded since ~1500 years ago, indicating the importance of interspecies' competition in their population size changes. Our study provided a valuable framework for further investigation on phylogeography of two species in China.

Rats and the city: Implications of urbanization on zoonotic disease risk in Southeast Asia

Urbanization is rapidly transforming Southeast Asia, altering the landscape and the interactions between people, animals, and the environment. These changes have the potential to exacerbate many existing health challenges in the region, including those posed by zoonoses. Here, we used a novel, multidisciplinary, ecosystem-level approach to examine the influence of urbanization on zoonotic disease risk in a Southeast Asian city. We infer that urbanization alters the ecology of animal reservoirs, arthropod vectors, and pathogens in a manner that may increase transmission risk from multiple zoonotic diseases in urban areas. This effect was particularly strong for pathogens associated with environmental or tick-borne transmission, providing targets for the development of low-cost interventions to reduce zoonotic disease risk in tropical cities.

Urbanization is rapidly transforming much of Southeast Asia, altering the structure and function of the landscape, as well as the frequency and intensity of the interactions between people, animals, and the environment. In this study, we explored the impact of urbanization on zoonotic disease risk by simultaneously characterizing changes in the ecology of animal reservoirs (rodents), ectoparasite vectors (ticks), and pathogens across a gradient of urbanization in Kuching, a city in Malaysian Borneo. We sampled 863 rodents across rural, developing, and urban locations and found that rodent species diversity decreased with increasing urbanization—from 10 species in the rural location to 4 in the rural location. Notably, two species appeared to thrive in urban areas, as follows: the invasive urban exploiter Rattus rattus (n = 375) and the native urban adapter Sundamys muelleri (n = 331). R. rattus was strongly associated with built infrastructure across the gradient and carried a high diversity of pathogens, including multihost zoonoses capable of environmental transmission (e.g., Leptospira spp.). In contrast, S. muelleri was restricted to green patches where it was found at high densities and was strongly associated with the presence of ticks, including the medically important genera Amblyomma, Haemaphysalis, and Ixodes. Our analyses reveal that zoonotic disease risk is elevated and heterogeneously distributed in urban environments and highlight the potential for targeted risk reduction through pest management and public health messaging.

The contribution of incomplete lineage sorting and introgression to the evolutionary history of the fast-evolving genus Ctenomys (Rodentia, Ctenomyidae)

Incomplete lineage sorting and introgression have been increasingly recognized as important processes involved in biological differentiation. Both incomplete lineage sorting and introgression result in incongruences between gene trees and species trees, consequently causing difficulties in phylogenetic reconstruction. This is particularly the case for rapid radiations, as short internodal distances and incomplete reproductive isolation increase the likelihood of both ILS and introgression. Estimation of the relative frequency of these processes requires assessments across many genomic regions. We use transcriptomics to test for introgression and estimate the frequency of incomplete lineage sorting in a set of three closely related and geographically adjacent South American tuco-tucos species (Ctenomys), a genus comprising 64 species resulting from recent, rapid radiation. After cleaning and filtering, 5764 orthologous genes strongly support paraphyly of C. pearsoni relative to C. brasiliensis (putatively represented by the population of Villa Serrana). In line with earlier phylogenetic work, the C. pearsoni - C. brasiliensis pair is closely related to C. torquatus, whereas C. rionegrensis is more distantly related to these three nominal species. Classical Patterson's D-statistic shows significant signals of introgression from C. torquatus into C. brasiliensis. However, a 5-taxon test shows no significant results. Incomplete lineage sorting was estimated to have involved about 9% of the loci, suggesting it represents an important process in the incipient diversification of tuco-tucos.

VKORC1 mutations in rodent populations of a tropical city-state as an indicator of anticoagulant rodenticide resistance

Anticoagulant rodenticides are commonly used in rodent control because they are economical and have great deployment versatility. However, rodents with Single Nucleotide Polymorphism (SNP) mutations within the Vkorc1 gene are resistant to the effects of anticoagulant rodenticide use and this influences the effectiveness of control strategies that rely on such rodenticides. This study examined the prevalence of rat SNP mutations in Singapore to inform the effectiveness of anticoagulant rodenticide use. A total of 130 rat tail samples, comprising 83 Rattus norvegicus (63.8%) and 47 Rattus rattus complex (36.2%) were conveniently sampled from November 2016 to December 2019 from urban settings and sequenced at exon 3 of Vkorc1. Sequencing analysis revealed 4 synonymous and 1 non-synonymous mutations in Rattus rattus complex samples. A novel synonymous mutation of L108L was identified and not previously reported in other studies. Non-synonymous SNPs were not detected in the notable codons of 120, 128 and 139 in R. norvegicus, where these regions are internationally recognised to be associated with resistance from prior studies. Our findings suggest that the prevalence of anticoagulant rodenticide resistance in Singapore is low. Continued monitoring of rodenticide resistance is important for informing rodent control strategies aimed at reducing rodent-borne disease transmission.

Prevalence and Molecular Characterization of Rickettsia spp. from Wild Small Mammals in Public Parks and Urban Areas of Bangkok Metropolitan, Thailand

Rural areas usually show a higher prevalence of rickettsial infection than urban areas. However, information on the rickettsial infection status in urban settings (e.g., built-up areas and city parks) is still limited, particularly in the Bangkok metropolitan area. In this study, we performed a molecular rickettsial survey of spleen samples of small mammals caught in public parks and built-up areas of Bangkok. Out of 198 samples, the Rattus rattus complex was found to be most prevalent. The amplification of rickettsial gltA fragment gene (338 bp) by nested PCR assay revealed positive results in four samples, yielding a low prevalence of infection of 2.02%. DNA sequencing results confirmed that three samples were matched with Rickettsia typhi, and one was identified as R. felis. It is noteworthy that this is the first report of the occurrence of R. felis DNA in rodents in Southeast Asia.

Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene

Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima’s D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.

Late Quaternary Environmental and Human Impacts on the Mitochondrial DNA Diversity of Four Commensal Rodents in Myanmar

We addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends.

A forest-specialist carnivore in the middle of the desert?Comments on https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5230

We present comments on an article recently published in Ecology and Evolution (“High‐resolution melting of the cytochrome B gene in fecal DNA: A powerful approach for fox species identification of the Lycalopex genus in Chile”) by Anabalon et al. that reported the presence of Darwin's fox (Lycalopex fulvipes), a temperate forest specialist, in the hyperarid Atacama Desert of northern Chile. We argue that this putative record lacks ecological support in light of ongoing research on this endangered species, and contains numerous methodological flaws and omissions related to the molecular identification of the species. Based on these issues, we suggest the scientific community and conservation decision‐makers disregard the alleged presence of the Darwin's fox in the Atacama Desert.

We present a Reply letter for a recent paper reporting the presence of Darwin´s fox, a forest‐specialist canid, in the Atacama Desert, 1,200 km north of its known distribution.

Whipworms of south-east Asian rodents are distinct from Trichuris muris

The whipworm Trichuris muris is known to be associated with various rodent species in the northern hemisphere, but the species identity of whipworm infecting rodents in the Oriental region remains largely unknown. We collected Trichuris of Muridae rodents in mainland and insular Southeast Asia between 2008 and 2015 and used molecular and morphological approaches to identify the systematic position of new specimens. We discovered two new species that were clearly distinct from T. muris, both in terms of molecular phylogenetic clustering and morphological features, with one species found in Thailand and another one in Borneo. We named the new species from Thailand as Trichuris cossoni and the species from Borneo as Trichuris arrizabalagai. Molecular phylogeny using internal transcribed spacer region (ITS1-5.8S-ITS2) showed a divergence between T. arrizabalagai n. sp., T. cossoni n. sp. and T. muris. Our findings of phylogeographically distinct Trichuris species despite some globally distributed host species requires further research into the distribution of different species, previously assumed to belong to T. muris, which has particular relevance for using these species as laboratory model organisms.

An overview of rickettsiae in Southeast Asia: Vector-animal-human interface

Rickettsioses are emerging, and re-emerging diseases caused by obligate intracellular arthropod-borne bacteria that infect humans and animals worldwide. Various rickettsiae such as Orientia, Rickettsia, Anaplasma and Ehrlichia have been circulated in companion, domesticated and wild animals through bites of infected ticks, fleas, lice or mites. This review summarizes the infections of rickettsiae, including the newly discovered regional species Rickettsia thailandii, Candidatus Rickettsia sepangensis, Candidatus Rickettsia johorensis, Candidatus Rickettsia laoensis, Candidatus Rickettsia mahosotii, Candidatus Rickettsia khammouanensis, Candidatus Anaplasma pangolinii, and other novel genotypes in vectors, humans and animals in Southeast Asia. Issues on some unidentified rickettsiae that elicit immune responses and production of antibodies that are cross-reactive with the antigens used are discussed. Knowledge gaps which required attention are also identified in this review.

High Prevalence of Rodent-Borne Bartonella spp. in Urbanizing Environments in Sarawak, Malaysian Borneo

Rodents are the most prominent animal host of Bartonella spp., which are associated with an increasing number of human diseases worldwide. Many rodent species thrive in urban environments and live in close contact with people, which can lead to an increased human risk of infection from rodent-borne pathogens. In this study, we explored the prevalence and distribution of Bartonella spp. in rodents in urban, developing, and rural environments surrounding a growing city in Sarawak, Malaysian Borneo. We found that although Bartonella spp. infection was pervasive in most rodent species sampled, prevalence was highest in urban areas and infection was most commonly detected in the predominant indigenous rodent species sampled (Sundamys muelleri). Within the urban environment, parks and remnant green patches were significantly associated with the presence of both S. muelleri and Bartonella spp., indicating higher localized risk of infection for people using these environments for farming, foraging, or recreation.

Boosting natural history research via metagenomic clean-up of crowdsourced feces

Biodiversity is in crisis due to habitat destruction and climate change. The conservation of many noncharismatic species is hampered by the lack of data. Yet, natural history research—a major source of information on noncharismatic species—is in decline. We here suggest a remedy for many mammal species, i.e., metagenomic clean-up of fecal samples that are “crowdsourced” during routine field surveys. Based on literature data, we estimate that this approach could yield natural history information for circa 1,000 species within a decade. Metagenomic analysis would simultaneously yield natural history data on diet and gut parasites while enhancing our understanding of host genetics, gut microbiome, and the functional interactions between traditional and new natural history data. We document the power of this approach by carrying out a “metagenomic clean-up” on fecal samples collected during a single night of small mammal trapping in one of Alfred Wallace’s favorite collecting sites.

Natural history research is in crisis and non-charismatic species are increasingly ignored; this Community Page article argues and demonstrates that shotgun sequencing of serendipitously obtained faecal samples could reverse this trend for 1000 mammal species within 10 years.

Advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs

DNA barcoding is now a common tool in parasitology and epidemiology, which require good methods for identification not only of parasites and pathogens but vectors and reservoirs. This special issue presents some advances and challenges in barcoding of microbes, parasites, and their vectors and reservoirs. DNA barcoding found new applications in disease ecology, conservation parasitology, environmental parasitology and in paleoparasitology. New technologies such as next-generation sequencing and matrix-assisted laser desorption-ionization time-of-flight have made it now possible to investigate large samples of specimens. By allowing the investigation of parasites at the interface between environment, biodiversity, animal and human health, barcoding and biobanking have important policy outcomes as well as ethics and legal implications. The special issue 'Advances and challenges in the barcoding of parasites, vectors and reservoirs' illustrates some recent advances and proposes new avenues for research in barcoding in parasitology.

Association of rodent-borne Leptospira spp. with urban environments in Malaysian Borneo

Although leptospirosis is traditionally considered a disease of rural, agricultural and flooded environments, Leptospira spp. are found in a range of habitats and infect numerous host species, with rodents among the most significant reservoirs and vectors. To explore the local ecology of Leptospira spp. in a city experiencing rapid urbanization, we assessed Leptospira prevalence in rodents from three locations in Malaysian Borneo with differing levels of anthropogenic influence: 1) high but stable influence (urban); 2) moderate yet increasing (developing); and 3) low (rural). A total of 116 urban, 122 developing and 78 rural rodents were sampled, with the majority of individuals assigned to either the Rattus rattus lineage R3 (n = 165) or Sundamys muelleri (n = 100). Leptospira spp. DNA was detected in 31.6% of all rodents, with more urban rodents positive (44.8%), than developing (32.0%) or rural rodents (28.1%), and these differences were statistically significant. The majority of positive samples were identified by sequence comparison to belong to known human pathogens L. interrogans (n = 57) and L. borgpetersenii (n = 38). Statistical analyses revealed that both Leptospira species occurred more commonly at sites with higher anthropogenic influence, particularly those with a combination of commercial and residential activity, while L. interrogans infection was also associated with low forest cover, and L. borgpetersenii was more likely to be identified at sites without natural bodies of water. This study suggests that some features associated with urbanization may promote the circulation of Leptospira spp., resulting in a potential public health risk in cities that may be substantially underestimated.

Leptospirosis is a significant zoonotic disease that is found in a range of environments worldwide, most notably tropical regions prone to flooding. The bacterial agents of this disease, Leptospira spp., are most often associated with rodents, including species frequently found in urban areas. In cities, rodent populations are often larger and denser than those found in natural environments, which can lead to higher rates of contact with people and impact human disease risk. To investigate the impacts of urbanization on Leptospira spp., we sampled rodents at locations with differing levels of human influence, from highly urbanized to rural, surrounding a city in Malaysian Borneo. We found that 31.6% of all rodents were positive for Leptospira spp. DNA, and that two primary species were present, L. interrogans and L. borgpetersenii, both of which are known human pathogens. Statistical analyses revealed that infected animals were more common in areas with higher levels of human influence, and were more likely to occur at sites with limited forest cover, and mixed commercial and residential activity. Our study adds to a growing body of evidence suggesting that there is a significant yet underappreciated risk of leptospirosis for people living in urban environments.

Exploring Rattus praetor (Rodentia, Muridae) as a possible species complex using geometric morphometrics on dental morphology

Taxonomic uncertainties in the Rattus genus persist due to among-species morphological conservatism coupled with within-species environmental variation in morphology. As a result, this genus contains a number of possible cryptic species. One important example can be found in R. praetor, where morphological studies indicate it is a possible species complex. Genetic studies of R. praetor (limited to analysis of mitochondrial DNA) have been inconclusive, but do indicate such subdivision. Here we use geometric morphometrics to explore this possible species complex by analysing the dental traits of 48 specimens from New Guinea and neighbouring regions. We find separate molar morphologies for Bougainsville Island, central New Guinea and west New Guinea which cannot be easily explained by different environmental factors (climate, precipitation and altitude), strongly suggesting the existence of a number of evolutionarily distinct taxa within what is currently called R. praetor thus supporting previous suggestions that R. praetor is a species complex. Our findings demonstrate the potential of advanced morphological analyses in identifying separate species, contrary to the claims of morphological conservatism. Future analyses should combine geometric morphometrics with genetic analyses over the species range and include sub-fossil specimens from the Bismarck archipelago and Solomon Islands to resolve the evolutionary history of R. praetor.

Heterogeneity of Orientia tsutsugamushi genotypes in field-collected trombiculid mites from wild-caught small mammals in Thailand

Trombiculid mites are the vectors of scrub typhus, with infected larval mites (chiggers) transmitting the causative agent, Orientia tsutsugamushi, during feeding. Co-existence of multiple O. tsutsugamushi strains within infected mites has previously been reported in naturally infected, laboratory-reared mite lines using molecular methods to characterize the 56-kDa type-specific antigen (TSA) gene. In the current study, more advanced next-generation sequencing technology was used to reveal the heterogeneity of O. tsutsugamushi genotypes in field-collected trombiculid mites from rodents and small mammals in scrub typhus-endemic areas of Thailand. Twenty-eight trombiculid mites collected from 10 small mammals were positive for O. tsutsugamushi, corresponding to a prevalence rate of 0.7% within the mite population. Twenty-four of the infected mites were Leptotrombidium spp., indicating that this genus is the main vector for O. tsutsugamushi transmission in Thailand. In addition, O. tsutsugamushi was detected in the mite genera Ascoschoengastia, Blankaartia, Gahrliepia, and Lorillatum. Of the 10 infested small animal hosts, six had 2-10 infected mites feeding at the time of collection. Deep sequencing was used to characterize mixed infections (two to three O. tsutsugamushi genotypes within an individual mite), and 5 of the 28 infected mites (17.9%) contained mixed infections. Additionally, 56-kDa TSA gene sequence analysis revealed identical bacterial genotypes among co-feeding mites with single or mixed infections. These results suggest that co-feeding transmission may occur during the feeding process, and could explain the occurrence of mixed infections in individual mites, as well as the recovery of multiple infected mites from the same host. This study also revealed highly diverse within-host O. tsutsugamushi genotypes. The occurrence of multiple O. tsutsugamushi genotypes within individual mites has important implications, and could provide a mechanism for pathogen evolution/diversification in the mite vector.

New record of the Oriental house rat, Rattus tanezumi, in Nepal inferred from mitochondrial Cytochrome B gene sequences

This study determines the presence of R. tanezumi from in Nepal using morphological and molecular analyses. Morphologically, it is indistinguishable with R. rattus owing to similar fur colour and morphometric data. However, molecular identification and phylogenetic analysis using sequences of the mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene revealed two different species R. rattus and R. tanezumi from collected specimens. The genetic distance between R. rattus and R. tanezumi was found 0.043. In phylogenetic tree, the clade of R. tanezumi is distinguished into two sub-clades, R. tanezumi found in Nepal, and East Asian countries, China, Laos, Thailand, Viet Nam, and South Korea have genetic distance 0.031, suggesting the different lineages of R. tanezumi. This study confirmed the R. tanezumi present in Nepal. Our findings suggest that morphological analysis and molecular study should be carried out simultaneously for accurate identification of small sized cryptic mammals like R. tanezumi and R. rattus.

Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea

The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America

We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.

Genetic diversity and evolution of Pneumocystis fungi infecting wild Southeast Asian murid rodents

Pneumocystis organisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity of Pneumocystis organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts. Pneumocystis DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the Pneumocystis lineages retrieved in our phylogenetic trees correspond to known Pneumocystis species, but some of the remaining lineages may correspond to new undescribed species. Most of these Pneumocystis species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of Pneumocystis species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among Pneumocystis and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of Pneumocystis and their hosts.

Population genetics, community of parasites, and resistance to rodenticides in an urban brown rat (Rattus norvegicus) population

Brown rats are one of the most widespread urban species worldwide. Despite the nuisances they induce and their potential role as a zoonotic reservoir, knowledge on urban rat populations remains scarce. The main purpose of this study was to characterize an urban brown rat population from Chanteraines park (Hauts-de-Seine, France), with regards to haematology, population genetics, immunogenic diversity, resistance to anticoagulant rodenticides, and community of parasites. Haematological parameters were measured. Population genetics was investigated using 13 unlinked microsatellite loci. Immunogenic diversity was assessed for Mhc-Drb. Frequency of the Y139F mutation (conferring resistance to rodenticides) and two linked microsatellites were studied, concurrently with the presence of anticoagulant residues in the liver. Combination of microscopy and molecular methods were used to investigate the occurrence of 25 parasites. Statistical approaches were used to explore multiple parasite relationships and model parasite occurrence. Eighty-six rats were caught. The first haematological data for a wild urban R. norvegicus population was reported. Genetic results suggested high genetic diversity and connectivity between Chanteraines rats and surrounding population(s). We found a high prevalence (55.8%) of the mutation Y139F and presence of rodenticide residues in 47.7% of the sampled individuals. The parasite species richness was high (16). Seven potential zoonotic pathogens were identified, together with a surprisingly high diversity of Leptospira species (4). Chanteraines rat population is not closed, allowing gene flow and making eradication programs challenging, particularly because rodenticide resistance is highly prevalent. Parasitological results showed that co-infection is more a rule than an exception. Furthermore, the presence of several potential zoonotic pathogens, of which four Leptospira species, in this urban rat population raised its role in the maintenance and spread of these pathogens. Our findings should stimulate future discussions about the development of a long-term rat-control management program in Chanteraines urban park.

New record of Melomys burtoni (Mammalia, Rodentia, Murinae) from Halmahera (North Moluccas, Indonesia): a review of Moluccan Melomys

Mosaic-tailed rodents of the genus Melomys belong to the Australasian old endemic murine radiation and exhibit a rat-like morphology with arboreal or scansorial specializations. Here we report a new population of Melomys burtoni from the island of Halmahera (in the North Moluccas, Indonesia). Our molecular phylogenetic results highlight close relationships and recent evolutionary divergences among M. burtoni from Halmahera and the Australo-Papuan taxa M. burtoni and M. lutillus and other Moluccan taxa, including M. paveli. Multivariate as well as geometric morphometric analyses of cranial, and dental features support the recognition of M. burtoni from Halmahera as a slightly distinctive insular population, preventing us from elevating it as a new taxa. This population is recorded from lowland secondary forest and forest edge habitats in south-central Halmahera. As with other Moluccan endemic murines, colonization by an Australo-Papuan ancestor and subsequent isolation is the probable mode of diversification for M. burtoni in Halmahera. The discovery of Melomys in Halmahera fills a previously puzzling gap in knowledge of the murine fauna of the Moluccas and the biogeography of the Wallacean region.

The complex evolutionary history of big-eared horseshoe bats (Rhinolophus macrotis complex): insights from genetic, morphological and acoustic data

Palaeoclimatic oscillations and different landscapes frequently result in complex population-level structure or the evolution of cryptic species. Elucidating the potential mechanisms is vital to understanding speciation events. However, such complex evolutionary patterns have rarely been reported in bats. In China, the Rhinolophus macrotis complex contains a large form and a small form, suggesting the existence of a cryptic bat species. Our field surveys found these two sibling species have a continuous and widespread distribution with partial sympatry. However, their evolutionary history has received little attention. Here, we used extensive sampling, morphological and acoustic data, as well as different genetic markers to investigate their evolutionary history. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial data identified three reciprocally monophyletic lineages: one representing all small forms from Southwest China, and the other two containing all large forms from Central and Southeast China, respectively. The large form showed paraphyly with respect to the small form. However, clustering analyses of microsatellite and Chd1 gene sequences support two divergent clusters separating the large form and the small form. Moreover, morphological and acoustic analyses were consistent with nuclear data. This unusual pattern in the R. macrotis complex might be accounted for by palaeoclimatic oscillations, shared ancestral polymorphism and/or interspecific hybridization.

Global parasite and Rattus rodent invasions: The consequences for rodent-borne diseases

We summarize the current knowledge on parasitism-related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local epidemiology of rodent-borne diseases. Parasites play an important role in the invasion processes and successes of their hosts through multiple biological mechanisms such as "parasite release," "immunocompetence advantage," "biotic resistance" and "novel weapon." Parasites may also greatly increase the impact of invasions by spillover of parasites and other pathogens, introduced with invasive hosts, into new hosts, potentially leading to novel emerging diseases. Another potential impact is the ability of the invader to amplify local parasites by spillback. In both cases, local fauna and humans may be exposed to new health risks, which may decrease biodiversity and potentially cause increases in human morbidity and mortality. Here we review the current knowledge on these processes and propose some research priorities.

Hantavirus seropositivity in rodents in relation to habitat heterogeneity in human-shaped landscapes of Southeast Asia

To establish how the conversion of natural habitats for agricultural purposes may impact the distribution of hantaviruses in Southeast Asia, we tested how habitat structure affects hantavirus infection prevalence of common murine rodents that inhabit human-dominated landscapes in this region. For this, we used geo-referenced data of rodents analysed for hantavirus infection and land cover maps produced for the seven study sites in Thailand, Cambodia and Lao PDR where they were collected. Rodents were tested by serological methods that detect several hantaviruses, including pathogenic ones. Rodents with a seropositive status were more likely to be found near to agriculture on steep land, and also in environments with a high proportion of agriculture on steep land. These results suggest that in Southeast Asia, hantaviruses, which are often associated with generalist rodent species with a preference for agricultural land, may benefit from land conversion to agriculture.

Aboriginal and invasive rats of genus Rattus as hosts of infectious agents

From the perspective of ecology of zoonotic pathogens, the role of the Old World rats of the genus Rattus is exceptional. The review analyzes specific characteristics of rats that contribute to their important role in hosting pathogens, such as host-pathogen relations and rates of rat-borne infections, taxonomy, ecology, and essential factors. Specifically the review addresses recent taxonomic revisions within the genus Rattus that resulted from applications of new genetic tools in understanding relationships between the Old World rats and the infectious agents that they carry. Among the numerous species within the genus Rattus, only three species-the Norway rat (R. norvegicus), the black or roof rat (R. rattus), and the Asian black rat (R. tanezumi)-have colonized urban ecosystems globally for a historically long period of time. The fourth invasive species, R. exulans, is limited to tropical Asia-Pacific areas. One of the points highlighted in this review is the necessity to discriminate the roles played by rats as pathogen reservoirs within the land of their original diversification and in regions where only one or few rat species were introduced during the recent human history.

Evidence for high dispersal ability and mito-nuclear discordance in the small brown planthopper, Laodelphax striatellus

Understanding dispersal ability in pest species is critical for both theoretical aspects of evolutionary and population biology and from a practical standpoint, such as implementing effective forecasting systems. The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is an economically important pest, but few data exist on its dispersal ability. Here, we used mitochondrial and nuclear markers to elucidate the population genetic structure of SBPH and of the parasitic bacterium Wolbachia throughout temperate and subtropical China. Our results showed that the SBPH populations in China lack significant differences in genetic structure, suggesting extensive gene flow. Multilocus sequence typing revealed that Wolbachia infection was systematic and due to the same strain (wStri) within and across populations. However, the mtDNA haplogroups had a nonrandom distribution across the sampling localities, which correlated to latitudinal and climatic gradients. We explain this mito-nuclear discordance as a result of historical population recolonization or mitochondria adaptation to climate.

Progress on research on rodents and rodent-borne zoonoses in South-east Asia

This review aims to synthesise knowledge regarding the taxonomy of South-east Asian murine rodents and the challenges associated with the identification of habitat preferences and associated rodent-borne diseases. Recent studies concerning the Rattini tribe have identified unclear species boundaries that would benefit from further investigation. The development of barcoding may allow more accurate identification of rodents, specifically for complex species. However, knowledge on the distribution and habitat specialisations of many common murine rodents is still scarce, particularly regarding the specific habitat preferences of most synanthropic rodent species (Rattus tanezumi or Rattus exulans). Several studies have analysed the prevalence of major rodent-borne diseases in South-east Asia and it appears that the greatest risk of rodent zoonoses are in the lowland rain-fed and irrigated landscapes, generally in and around rice fields.

Trypanosoma from rodents as potential source of infection in human-shaped landscapes of South-East Asia

Reports of atypical human cases of Trypanosoma lewisi or T. lewisi-like and Trypanosoma evansi infections have increased in South-East Asia, urging to investigate the possible links between humans, animal reservoirs and habitats. We tested how habitat structure affects the infection by Trypanosoma species of common murine rodents, inhabiting human-dominated landscapes in South East Asia. For this, we used geo-referenced data of rodents investigated for Trypanosoma infection and land cover maps produced for seven study sites in Thailand, Cambodia and Lao PDR. High prevalence of infection by T. lewisi was observed in rodents living near human settlement and in areas with high cover of built-up habitat, while the infection of rodents by T. evansi was explained by increased landscape patchiness and high cover of rain-fed agriculture lands. These results suggest a likely role of wild rodents as reservoir and possible source of atypical human infection by animal trypanosomes.