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Background matching, a common form of camouflage, is a widespread anti-predator adaptation that hinders detection or recognition by increasing the resemblance of prey to its environment. However, the natural environment is complex and both spatially and temporally variable, which constrains effective background matching as an anti-predator strategy. Here, using remote sensing data (publicly available satellite imagery), we investigated how variation of habitat parameters predicts background matching in 16 Sahara–Sahel rodent species across spatial and temporal scales. All fur colour parameters (hue, saturation and brightness) strongly matched the respective habitats of the different species. Background matching in terms of hue was best at the microscale, whereas results for saturation and brightness showed more variation across spatial scales among species. Camouflage across the temporal scale (from 1 to 3 years before capture) was variable among species for all colour parameters. These complex interactions suggest that, in desert rodents, colour parameters are differentially sensitive to the respective scale of the habitat, plausibly reflecting the behaviour and life history of the species and the ecological properties determining their activity patterns. Consequently, the division between habitat (camouflage) generalists and specialists might become blurred in temporally changing and spatially variable environments.

1.Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. 2.Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. 3.The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of ingested fungi (e.g. edible macrofungi, polypores, lichens and ectomycorrhizae) and gut mycobiota (e.g. microfungi and yeasts), which mask the patterns of inter- and intraspecific variation in the authentic gut mycobiota. 4.Implying that ‘faecal samples are not an accurate indicator of gut composition’ creates an unnecessary controversy about faecal sampling because the comparison of samples from the caecum and faeces confounds many other possible drivers (including different animals from different locations, sampled in different years) of variation in gut microbiota. 5.It is relevant also that Antwis et al.'s (2021) data lack statistical power to detect an effect of exposure to radionuclides on the gut microbiota because (1) all of their samples of Apodemus mice had experienced a medium or high total absorbed dose rate and (2) they did not collect samples of bank voles (M. glareolus) from replicate contaminated and uncontaminated locations. 6.Discussion of Antwis et al.'s (2021) analysis, especially the claims presented in the Abstract, is important to prevent controversy about the outcome of research on the biological impacts of wildlife inhabiting the CEZ. peerReviewed

Identifying factors that drive infection dynamics in reservoir host populations is essential in understanding human risk from wildlife-originated zoonoses. We studied zoonotic Puumala orthohantavirus (PUUV) in the host, the bank vole ( Myodes glareolus ), populations in relation to the host population, rodent and predator community and environment-related factors and whether these processes are translated into human infection incidence. We used 5-year rodent trapping and bank vole PUUV serology data collected from 30 sites located in 24 municipalities in Finland. We found that PUUV seroprevalence in the host was negatively associated with the abundance of red foxes, but this process did not translate into human disease incidence, which showed no association with PUUV seroprevalence. The abundance of weasels, the proportion of juvenile bank voles in the host populations and rodent species diversity were negatively associated with the abundance index of PUUV positive bank voles, which, in turn, showed a positive association with human disease incidence. Our results suggest certain predators, a high proportion of young bank vole individuals, and a diverse rodent community, may reduce PUUV risk for humans through their negative impacts on the abundance of infected bank voles.

Most small rodent populations in the world have fascinating population dynamics. In the northern hemisphere, voles and lemmings tend to show population cycles with regular fluctuations in numbers. In the southern hemisphere, small rodents tend to have large amplitude outbreaks with less regular intervals. In the light of vast research and debate over almost a century, we here discuss the driving forces of these different rodent population dynamics. We highlight ten questions directly related to the various characteristics of relevant populations and ecosystems that still need to be answered. This overview is not intended as a complete list of questions but rather focuses on the most important issues that are essential for understanding the generality of small rodent population dynamics.

Prey animals can assess the risks predators present in different ways. For example, direct cues produced by predators can be used, but also signals produced by prey conspecifics that have engaged in non-lethal predator-prey interactions. These non-lethal interactions can thereby affect the physiology, behavior, and survival of prey individuals, and may affect offspring performance through maternal effects. We investigated how timing of exposure to predation-related cues during early development affects offspring behavior after weaning. Females in the laboratory were exposed during pregnancy or lactation to one of three odor treatments: (1) predator odor (PO) originating from their most common predator, the least weasel, (2) odor produced by predator-exposed conspecifics, which we call conspecific alarm cue (CAC), or (3) control odor (C). We monitored postnatal pup growth, and we quantified foraging and exploratory behaviors of 4-week-old pups following exposure of their mothers to each of the three odour treatments. Exposure to odors associated with predation risk during development affected the offspring behavior, but the timing of exposure, i.e., pre- vs. postnatally, had only a weak effect. The two non-control odors led to different behavioral changes: an attraction to CAC and an avoidance of PO. Additionally, pup growth was affected by an interaction between litter size and maternal treatment, again regardless of timing. Pups from the CAC maternal treatment grew faster in larger litters; pups from the PO maternal treatment tended to grow faster in smaller litters. Thus, in rodents, offspring growth and behavior are seemingly influenced differently by the type of predation risk perceived by their mothers. peerReviewed

Zoonotic diseases, caused by pathogens transmitted between other vertebrate animals and humans, pose a major risk to human health. Rodents are important reservoir hosts for many zoonotic pathogens, and rodent population dynamics affect the infection dynamics of rodent-borne diseases, such as diseases caused by hantaviruses. However, the role of rodent population dynamics in determining the infection dynamics of rodent-associated tick-borne diseases, such as Lyme borreliosis (LB), caused by Borrelia burgdorferi sensu lato bacteria, have gained limited attention in Northern Europe, despite the multiannual abundance fluctuations, the so-called vole cycles, that characterise rodent population dynamics in the region. Here, we quantify the associations between rodent abundance and LB human cases and Puumala Orthohantavirus (PUUV) infections by using two time series (25-year and 9-year) in Finland. Both bank vole (Myodes glareolus) abundance as well as LB and PUUV infection incidence in humans showed approximately 3-year cycles. Without vector transmitted PUUV infections followed the bank vole host abundance fluctuations with two-month time lag, whereas tick-transmitted LB was associated with bank vole abundance ca. 12 and 24 months earlier. However, the strength of association between LB incidence and bank vole abundance ca. 12 months before varied over the study years. This study highlights that the human risk to acquire rodent-borne pathogens, as well as rodent-associated tick-borne pathogens is associated with the vole cycles in Northern Fennoscandia, yet with complex time lags. peerReviewed

The generalist tick Ixodes ricinus is the most important vector for tick-borne pathogens (TBP), including Borrelia burgdorferi sensu lato, in Europe. However, the involvement of other sympatric Ixodes ticks, such as the specialist vole tick I. trianguliceps, in the enzootic circulations of TBP remains unclear. We studied the distribution of I. ricinus and I. trianguliceps in Central Finland and estimated the TBP infection likelihood in the most common rodent host in relation with the abundance of the two tick species. Ixodes trianguliceps was encountered in all 16 study sites whereas I. ricinus was frequently observed only at a quarter of the study sites. The abundance of I. ricinus was positively associated with open water coverage and human population density around the study sites. Borrelia burgdorferi s. l.-infected rodents were found only in sites where I. ricinus was abundant, whereas the occurrence of other TBP was independent of I. ricinus presence. These results suggest that I. trianguliceps is not sufficient, at least alone, in maintaining the circulation of B. burgdorferi s. l. in wild hosts. In addition, anthropogenic factors might affect the distribution of I. ricinus ticks and, hence, their pathogens, thus shaping the landscape of tick-borne disease risk for humans.

All animals host diverse microbial communities (bacteria, fungi, viruses, known as the microbiota) that inhabit external and internal surfaces of the host. Host-associated microbiota provide essential services to their hosts, such as provision of nutrients, protection against pathogens, and toxic compounds. As changes in the microbiota composition can impact delivery of these functions and thus host health, it is important to understand processes that shape host-associated microbiota. In this thesis, I assess the impacts of environmental contamination on the gut and skin microbiota (bacteria) of small mammals inhabiting areas affected by radionuclides derived from the Chernobyl (Ukraine) and Fukushima (Japan) nuclear accidents. I used marker gene sequencing and field studies to test (I) the effects of exposure to radionuclide contamination on the gut and (II) skin microbiota of the bank vole, Myodes glareolus. By conducting a capture-mark-recapture study, I tested (III) the effects of radiation exposure on the temporal dynamics of the bank vole gut microbiota. I also sampled two pairs of mouse species (Apodemus flavicollis, A. sylvaticus, A. speciosus, A. argenteus) that occur in sympatry in Chernobyl and Fukushima, to quantify (IV) the general influence of radiation exposure on the gut microbiota of rodents. These data indicate that chronic exposure to radionuclide contamination alters bank vole gut microbiota composition, yet has little notable impact on community composition of the skin microbiota: skin and gut microbiota thus respond to different environmental cues. Longitudinal data indicate that radiation exposure can constrain natural, temporal changes in the bank vole gut microbiota, which is potentially a sign of chronic stress. Also, I show that radiation exposure elicits comparable responses in the gut microbiota of different species of rodents, although host lifestyle can modulate the effects of exposure to radiation on gut microbiota composition. As such, exposure to environmental contaminants has clear potential to alter wildlife microbiota community composition. Given that the microbiota are pivotal to host health, it is important to quantify any microbiota changes in response to diverse anthropogenic disturbances if we are to understand the significance of host-environment interactions in a rapidly changing world. Tiivistelmä Eläinten mikrobiomi koostuu sen sisällä ja ulkopinnalla elävistä bakteeri-, sieni- ja virusyhteisöistä. Mikrobiomi tuottaa isäntäeliölle olennaisia ravinteita, sekä suojaa taudinaiheuttajia ja myrkyllisiä yhdisteitä vastaan. Koska muutokset mikrobiyhteisöissä voivat vaikuttaa isännän terveyteen, on tärkeää tutkia mikrobiomia muokkaavia tekijöitä. Väitöskirjassani tutkin saastuneen elinympäristön vaikutuksia suoliston ja ihon mikrobiomeihin (bakteerien yhteisöihin) pikkunisäkkäillä Tšernobylin (Ukraina) ja Fukushiman (Japani) ydinvoimalaonnettomuusalueilla. Laajoissa kenttätutkimuksissa selvitin ionisoivalle säteilylle altistumisen vaikutuksia metsämyyrän (Myodes glareolus) (I) suoliston ja (II) ihon mikrobiomeihin. Tutkin myös (III) säteilyaltistuksen vaikutusta ajallisiin muutoksiin metsämyyrän suolistomikrobiomissa pyynti-takaisinpyyntimenetelmällä. Lisäksi tutkin (IV) säteilyaltistuksen vaikutuksia laajemmin jyrsijöiden suolistomikrobiomiin käyttäen sympatrisia hiirilajeja Tšernobylissä (Apodemus flavicollis ja A. sylvaticus) sekä Fukushimassa (A. speciosus ja A. argenteus). Tulosteni mukaan pitkäaikainen altistuminen ympäristön säteilylle muokkaa metsämyyrien suolistomikrobiomin koostumusta, mutta ei vaikuta merkittävästi ihon mikrobiomiin, osoittaen että ihon ja suoliston mikrobiomeihin vaikuttavat erilaiset ympäristötekijät. Säteilyaltistus voi myös rajoittaa metsämyyräyksilöiden suolistomikrobiomissa tapahtuvia luonnollisia ajallisia muutoksia, mahdollisesti johtuen pitkäaikaisesta stressialtistuksesta. Lisäksi osoitan, että ympäristösäteilylle altistumisen vaikutukset suolistomikrobiomiin ovat samankaltaisia eri jyrsijälajeilla, mutta mikrobiomiin vaikuttavat myös lajien väliset erot elintavoissa. Tutkimukseni siis osoitti, että ympäristön saasteet voivat muokata luonnonvaraisten eläinten mikrobiomien koostumusta. Isäntäeliön ja sen ympäristön vuorovaikutus voi oleellisesti vaikuttaa eläinyksilöiden ja niiden populaatioiden terveyteen ja edelleen niiden kykyyn vastata ihmisen aiheuttamiin ympäristömuutoksiin.

1.Camouflage helps animals to hide from predators and is therefore key to survival. Although widespread convergence of animal phenotypes to their natural environment is well established, there is a lack of knowledge about how species compromise camouflage accuracy across different background types in their habitat. 2.Here we tested how background matching has responded to top‐down selection by avian and mammalian predators using Sahara‐Sahel desert rodents in North Africa. 3.We show that the fur coloration of several species has become an accurate match to different types of desert habitats. This is supported by a correlation analysis of colour and pattern metrics, investigation of animal‐to‐background similarities at different spatial scales, and is confirmed by modelling of two predator vision systems. 4.The background match was closest across large (or global) spatial scales, suggesting a generalist camouflage tactic for many background types. Some species, may have a better match to the background over small (or focal) spatial scales, which could be the result of habitat choices or differential predation. Nevertheless, predicted discrimination distances of fur coloration were virtually indistinguishable for mammalian and low for avian vision model, which implies effective camouflage. 5.Our study provides one of the best documented cases of multilevel camouflage accuracy in geographically widespread taxa. We conclude that background matching has become an effective and common adaptation against predatory threat in Sahara‐Sahelian desert rodents. peerReviewed

Background: Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent during the Pliocene-Pleistocene interval, triggering the diversification of several species. Here, we investigated how these biogeographical and ecological events have shaped patterns of genetic diversity and divergence in African Jerboas, desert specialist rodents. We focused on two sister and cryptic species, Jaculus jaculus and J. hirtipes, where we (1) evaluated their genetic differentiation, (2) reconstructed their evolutionary and demographic history; (3) tested the level of gene flow between them, and (4) assessed their ecological niche divergence.Results: The analyses based on 231 individuals sampled throughout North Africa, 8 sequence fragments (one mitochondrial and seven single copy nuclear DNA, including two candidate genes for fur coloration: MC1R and Agouti), 6 microsatellite markers and ecological modelling revealed: (1) two distinct genetic lineages with overlapping distributions, in agreement with their classification as different species, J. jaculus and J. hirtipes, with (2) low levels of gene flow and strong species divergence, (3) high haplotypic diversity without evident geographic structure within species, and (4) a low level of large-scale ecological divergence between the two taxa, suggesting species micro-habitat specialization. Conclusions: Overall, our results suggest a speciation event that occurred during the Pliocene-Pleistocene transition. The contemporary distribution of genetic variation suggests ongoing population expansions. Despite the largely overlapping distributions at a macrogeographic scale, our genetic results suggest that the two species remain reproductively isolated, as only negligible levels of gene flow were observed. The overlapping ecological preferences at a macro-geographic scale and the ecological divergence at the micro-habitat scale suggest that local adaptation may have played a crucial role in the speciation process of these species.

Deserts and semi-deserts, such as the Sahara-Sahel region in North Africa, are exposed environments with restricted vegetation coverage. Due to limited physical surface structures, these open areas provide a promising ecosystem to understand selection for crypsis. Here, we review knowledge on camouflage adaptation in the Sahara-Sahel rodent community, which represents one of the best documented cases of phenotype-environment convergence comprising a marked taxonomic diversity. Through their evolutionary history, several rodent species from the Sahara-Sahel have repeatedly evolved an accurate background matching against visually-guided predators. Top-down selection by predators is therefore assumed to drive the evolution of a generalist, or compromise, camouflage strategy in these rodents. Spanning a large biogeographic extent and surviving repeated climatic shifts, the community faces extreme and heterogeneous selective pressures, allowing formulation of testable ecological hypotheses. Consequently, Sahara-Sahel rodents poses an exceptional system to investigate which adaptations facilitate species persistence in a mosaic of habitats undergoing climatic change. Studies of these widely distributed communities permits general conclusions about the processes driving adaptation and can give insights into how diversity evolves. peerReviewed

Infectious diseases are amongst the ten major causes of human mortality worldwide, 60% of them being animal-borne. Variations of abiotic and biotic conditions are likely to modify the transmission of parasites and pathogens within reservoir species, and, as a consequence, alter the zoonotic risk for human. My thesis aims at elucidating the dynamics and mechanisms of the maintenance of ticks, tick-borne pathogens (TBPs) and the Puumala hantavirus (PUUV) in the reservoir host, the bank vole (Myodes glareolus, BV). In Northern Europe, tick-borne diseases are growing in importance to human because of the latitudinal expansion of the tick Ixodes ricinus. Field monitoring revealed that I. ricinus was the only species found in the vegetation in Central Finland. The abundance of immature I. ricinus in nature was positively associated with the BV abundance. The highest risk periods for tick bites on humans were May– June and September. Ixodes ricinus was positively associated with open water coverage and human density, which might offer suitable moisture conditions and anthropogenic modifications favouring the species. The infection of BV with the zoonotic B. burgdorferi s.l. was associated with the abundance of I. ricinus at the site, indicating that this tick species was required for the transmission and persistence of this pathogen. An experiment revealed, for the first time, that B. afzelii can modify the behaviour and the breeding success of its host, and these effects are both sex- and size-specific and density-dependent. Space-state modelling of longitudinal field data revealed that PUUV infection likelihood was the lowest in BV previously infested with vectors in comparison to Anaplasma phagocytophilum infected BV, or individuals without any previous infections. Altogether, this study shows how seasonality, co-infecting pathogens and host population density influence the risk of tick-borne pathogens and the zoonotic risk in Central Finland.