suggesting that seasonal patterns may fluctuate across years. Supporting this, long-term
seasonal monitoring has shown that *P. murinus* prevalence was stable across years
(Timm *et al.*, 2025). Similar to haemosporidian infections in birds, *P. murinus* may persist
in bats as chronic infections, making seasonal peaks harder to detect and contributing to
the observed temporal stability (Valkiunas, 2004). In contrast, *P. murinus* intensity
exhibited clear seasonal variation. This finding is unexpected given that the abundance of
the bat fly remained temporally stable (Fig. 2B), and no significant association was found
between *P. murinus* intensity and bat fly numbers. Moreover, Witsenburg *et al*. (2015)
reported only a marginal effect of *P. murinus* parasitaemia on bat fly abundance under
natural conditions. These results may differ from methodological differences in *P.
murinus* detection. Such discrepancies may partly stem from methodological differences
since qPCR is more sensitive than microscopy for detecting infection intensity (Castex et
al., in prep (a), cf Chapter 2). The observed seasonal peak in *P. murinus* intensity may be
driven by changes in the vector behaviour rather than its abundance. Although bat fly
numbers remained constant, increased feeding activity during mid-summer could
enhance haemosporidian transmission. Such seasonal relapse patterns are well-
documented in other haemosporidian systems and may reflect concurrent dynamics
between parasite, vector and host (Cator *et al.*, 2012; Cornet *et al.*, 2014; Pigeault *et al.*,
2018).

The presence of multiple parasites within a host can significantly influence
infection dynamics (Telfer *et al.*, 2010). Parasites may interact either directly, through
physical or chemical interactions, or indirectly via host-mediated processes, such as
competition for resources or niches, or through immune-mediated effects (Pedersen and
Fenton, 2007). Our structural equation modelling analysis found a positive correlation
between wing mite and bat fly abundance, despite these ectoparasites being influenced
by distinct ecological and host-related factors. After controlling for other covariates, a
plausible explanation is the influence of an unmeasured cofactor affecting both parasite
abundances such as the host immunity or more intensive grooming. Indeed, both
parasites are more abundant on female bats, known to have heightened
immunosuppression during this period (Christe *et al.*, 2000) and their presence causes
increased grooming activity in bats (Giorgi *et al.*, 2001). Our result contrasted with a
previous study that reported a negative association between spinturnicid mites and streblid fly in various Brazilian bats, which was attributed by different colony formations and type of roost (Lourenço et al., 2020). Additionally, our results revealed a missing link with wing mite abundance positively influenced by *P. murinus* presence. Given the absence of any established biological interaction between *P. murinus* and wing mites, this relationship is likely mediated by indirect interactions such as host condition. Previous studies have shown that both wing mites and haemosporidian parasites infect bats with lower body condition (Lourenço and Palmeirim, 2007; Witsenburg et al., 2014), suggesting that host vulnerability may drive co-occurrence rather than direct parasite-parasite interactions.

**Conclusion**

Our study demonstrates that parasite dynamics in Daubenton's bats are shaped by a complex interaction of host traits, seasonal variation, and potential indirect interactions among co-infecting parasites. While wing mites and bat flies exhibit distinct ecological patterns, their co-occurrence suggests shared host-related drivers, particularly the compromised immunity of females. The temporal variation in *P. murinus* intensity, despite stable vector abundance, points to behavioural or physiological mechanisms, such as vector activity or host susceptibility, that require further investigation. Our findings highlight the value of examining both infection presence and intensity, as they respond to different ecological pressures. By including integrative approaches in parasitology such as the effect of time, space and host-life history traits, this study advances our understanding of coinfection ecology and highlights the need for longitudinal, multi-parasite approaches to better capture the complexity of host-parasite interactions in bat populations.

**Acknowledgements.** The authors would like to thank all people who participated in the sampling, especially Anouk Hoang and David Baumgartner for their effort in 2023. Thanks to Eddie Perochon and Kim Schalcher for their invaluable help in the analyses. Thanks to
Jérôme Wasseff for his help in developing the qPCR protocol and La Maison de la Rivière for giving access to their facilities.

**Data availability.** All scripts necessary to generate genomic data and perform analyses used in this study have been made available on https://github.com/clca98/PhD.

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**General discussion**

The central aim of my thesis was to identify the key factors driving parasite spread and persistence across host populations and species. I addressed these dynamics at multiple scales, using bats and their parasites as a model to disentangle the roles of host biology, parasite life history, and environmental context. To achieve this, I applied a multidisciplinary approach combining population genetics with epidemiological analyses. This framework allowed me to assess genetic connectivity among hosts and parasites and gain insights into the parasite behaviour and transmission. Overall, my findings show that parasite ecology is shaped by host traits, environmental conditions and also by interactions among co-occurring parasites. Together, these results provide a more integrative perspective on the processes governing host–parasite dynamics. Across all chapters, I consistently found that parasite spread was highly heterogeneous rather than uniform across hosts. This variability reflected the influence of host species (Chapter 1) and individual-level differences within host (Chapter 2, 3 and 4) and highlighted the critical role of host life-history traits, behaviour and population structure in shaping parasite dynamics (Fig. 1). The comparative perspective of four parasite species with distinct life histories reveals the complexity of host-parasite interactions and reinforces the importance of integrating ecological, genetic and epidemiological data to fully understand parasite evolution and transmission.

Host behaviour, dispersal patterns and population structure influenced parasite connectivity across sites, despite life-history strategies that differ markedly between ectoparasite species. Bat-associated bugs are roost-dwelling parasites that remain within the bat shelter and feed opportunistically (Usinger, 1966; Bartonička and Růžičková, 2012), whereas bat flies and wing mites are more intimately linked with their hosts, reproducing and feeding directly on bats (Marshall, 1970; Dowling, 2006). Notably, bat flies exhibit greater mobility due to their pupae deposition on the bat roost, allowing them to move between individuals more readily (Ching and Marshall, 1968; Marshall, 1970). In terms of host specificity, bat-associated bugs and bat flies are generalists, capable of parasitizing multiple bat species, while wing mites display a more specialized relationship, typically restricted to a single host species (Usinger, 1966; Bruyndonckx et
al., 2009a; Szentiványi et al., 2019). Despite their ecological differences and contrasting life-history strategies, all three ectoparasite species exhibited surprisingly high genetic connectivity across bat populations (Chapter 1 and 3). This shared pattern appears to be driven not by the parasites themselves, but by the movement ecology of their hosts.

<figure><img src="image_71.png" /><figcaption>**Fig. 1.** Factors influencing host-parasite associations in this study. Adapted from Kołodziej-Sobocińska 2019. Common factors influencing parasites are darker whereas parasite-specific factors are lighter. Unmeasured factors are mentioned in italic.</figcaption></figure>

Ectoparasite individuals were closer to individuals from other sites because of the shuffling of alleles during the mating of bats. Daubenton's bats displayed a strong interroost connectivity and frequent dispersal (Chapter 2), which contributed to the homogenization of parasite population across space (Chapter 3). More broadly, high movements between hosts are known to facilitate parasite transmission and dispersal among individuals from different colonies (Barrett et al., 2008; Archie et al., 2009; Biek and Real, 2010; Patterson and Ruckstuhl, 2013; Ezenwa et al., 2022; Sánchez et al., 2024). To better understand patterns of gene flow at a fine spatial scale, I focused my
sampling locally and applied Restriction site Associated DNA sequencing (RADseq).
However, within the spatial extent of our study, the ectoparasite genetic structure was
more shaped by bat mobility than by ectoparasite life-history constraints. Expanding our
sampling to include more geographically isolated populations or a broader spatial scale
may have revealed greater genetic differentiation among Daubenton's bat colonies and,
consequently, among their associated parasite populations. For instance, across
European populations of the common bent-wing bat (Miniopterus schreibersii), the
haemosporidian Polychromophilus melanipherus exhibited an intermediate genetic
pattern, reflecting both host and ectoparasite dynamics (Witsenburg et al., 2015b).
Genetic analyses of host-specific parasites can also serve as powerful tools for inferring
host movement patterns and reconstructing the evolutionary history of host populations,
particularly in systems where direct observation of host movement is challenging
(Nieberding and Olivieri, 2007; Bruyndonckx et al., 2010; Sromek et al., 2024).

In host species exhibiting metapopulation structure, such as bats (Wiederholt et al., 2013; Johnson et al., 2015), genetic isolation is often expected to reduce genetic diversity and compromise resistance to infections (Frankham, 1995a; Spurgin and Richardson, 2010). However, my results suggest that parasite spread in Daubenton's bats is primarily driven by direct transmission through host movements and contacts rather than by genetic diversity (Chapter 2). Low levels of inbreeding were consistent with the high gene flow between colonies. Although increased connectivity can facilitate parasite spread, the benefits of gene flow appeared to outweigh the costs of elevated transmission risk (Collinge, 2009). The estimation of the effective population size further supported these findings, revealing that the population of Daubenton's bat in the Vaud canton is substantially larger than our sampling coverage (Chapter 2). Parasite persistence is known to be favoured in large host population (Anderson and May, 1979), where high densities increase transmission risk through frequent close contacts (Levin, 1996; Sugiura et al., 2018; Albery et al., 2025). These contact rates are amplified by host behaviour and sociality. In highly social species like bats, spatial overlap, shared roosts and communal habitat use create ideal conditions for parasite exchange and maintenance of infections (Patterson et al., 2007; Willoughby et al., 2017b; Fagundes et al., 2017; McKee et al., 2019; Lunn et al., 2021; Sándor et al., 2024b).
Infections were not uniform among Daubenton's bats and were not only governed by the host connectivity. Host life-history traits also emerged as strong predictors of parasite transmission, confirming their central role in shaping infection dynamics. Among these traits, sex consistently influenced the abundance of ectoparasites and the infection by *P. murinus* (**Chapter 2 and 4**). Sex-biased parasitism is well-documented in vertebrates, often skewed toward males due to behavioural, ecological and physiological factors (Folstad and Karter, 1992; Zuk and McKean, 1996; Poulin, 1996; Grear *et al.*, 2009; Kołodziej-Sobocińska, 2019; Wesołowska, 2022). In many species, males are more susceptible to infection due to immunosuppressive effect of testosterone (Klein, 2004; Grear *et al.*, 2009). However, this pattern is not universal. In host species where females form large social groups and males are solitary or in smaller groups, females experience higher parasite loads due to increased contact rates (Kołodziej-Sobocińska *et al.*, 2016). This pattern was reflected in this thesis with female Daubenton's bats exhibiting significantly higher parasitism than males (**Chapter 2 and 4**). The large aggregation of female Daubenton's bats at maternity roosts (Arthur and Lemaire, 2009) likely facilitated horizontal transmission of parasites through frequent contact and shared space. This pattern aligns with previous studies reporting female-biased parasitism in bats (Christe *et al.*, 2000, 2007; Lučan, 2006; Patterson *et al.*, 2008a; Encarnação *et al.*, 2012; Witsenburg *et al.*, 2014; van Schaik and Kerth, 2017; da Silva Reis *et al.*, 2021; Tai *et al.*, 2022). Host preferences in bat flies have been shown to be sex-specific, with female bat flies more strongly influenced by host sex and body condition than males (Szentiványi *et al.*, 2017). This suggests the importance of investigating sex-specific dynamics to determine if ecological or biological patterns affect male and female bat flies differently. Future studies applying similar approach on our samples could provide valuable insights, not only for bat flies but also for wing mites, potentially revealing overlooked patterns in parasite ecology and host exploitation.

Elevated parasitism in females may also be linked to the increased physiological vulnerability during reproduction, as gravid and lactating females experience immunosuppression (Lloyd, 1983; Christe *et al.*, 2000; Plowright *et al.*, 2008), while males, who do not participate in nursing (McLean and Speakman, 1997), are less affected. Interestingly, parasites were influenced differently by the Daubenton's bat
reproductive status. Bat flies and the haemosporidian *P. murinus* were not impacted by reproductive status. Wing mites exhibited a marked seasonal variation in abundance, peaking in July during the lactation period and were more abundant on lactating females (**Chapter 4**). Host immunity varies seasonally in relation to stress, food availability or other factors (Martin *et al.*, 2007). This pattern reflects the physiological trade-off between reproduction and immunity in bats, where the energetic demands of lactation compromise immunocompetence (Racey and Entwistle, 2000; Otálora-Ardila *et al.*, 2022). Although similar trade-off have been observed in male Daubenton's bats (Ruoss *et al.*, 2019), my findings suggest that reproductive females bear a greater immunological cost, making them more susceptible to parasitism.

Surprisingly, the genetic diversity at the Major Histocompatibility Complex (MHC) region had no significant effect on the abundance of the parasites in this study (**Chapter 2**). This finding contrasts with previous research in vertebrates (Westerdahl *et al.*, 2005b; Šimková *et al.*, 2006; Ilmonen *et al.*, 2007; Loiseau *et al.*, 2008; Goüy De Bellocq *et al.*, 2008; Oliver *et al.*, 2009; Portanier *et al.*, 2019) and even in bats. For instance, Schad *et al.* (2012) demonstrated a correlation between MHC genotype, ectoparasite load and reproductive status in *Noctilio albiventris*, with non-reproductive males showing higher infestation and specific alleles associated with increased tick burden. These results suggest that individual immune gene constitution can shape ectoparasite susceptibility and contribute to fitness-related trade-offs. The absence of detectable MHC genetic diversity effect in **Chapter 2** may be partly attributed to the limited resolution of RADseq for capturing variation in specific immune-related loci. Targeted sequencing of immune region could provide deeper insights into the role of the bat immunity in parasite resistance. This result is particularly surprising given that wing mites, bat flies and the haemosporidian are known to influence host health either directly, by interacting with immune function (Christe *et al.*, 2000; Lilley *et al.*, 2014) or indirectly, through their impact on body condition (Lourenço and Palmeirim, 2007; Patterson *et al.*, 2008b; Witsenburg *et al.*, 2014; Szentiványi *et al.*, 2017; Tai *et al.*, 2022). Body condition is commonly used as a proxy for the physiological cost of infection (Sánchez *et al.*, 2018). External stressors such as reduced resource availability or immunodepression influence body condition, which in turn may alter susceptibility to parasitism. As a result, individuals in poor condition are
often more vulnerable to infection (Holmstad et al., 2005; Beldomenico et al., 2008) whereas those in better body condition may tolerate higher parasite loads (Beldomenico et al., 2008; Sánchez et al., 2018; Kołodziej-Sobocińska, 2019). In bats, both patterns have been observed. Bat flies tend to infest individuals in better body condition (Szentiványi et al., 2017; Tai et al., 2022), while wing mites and *P. murinus* are more prevalent on bats in poorer condition (Lučan, 2006; Lourenço and Palmeirim, 2007; Witsenburg et al., 2014; van Schaik and Kerth, 2017). Although body condition is widely recognized as a predictor of survival and reproductive success across taxa (Schulte-Hostedde et al., 2005), no experimental studies have yet assessed the direct impact of these three parasites on the fitness of the Daubenton's bat. Because insectivorous bats are notoriously challenging to maintain in captivity (Kunz and Parsons, 2009), such experiments remain scarce. Still, controlled manipulation of parasite infections, combined with measures of bat survival and reproductive success, would offer valuable insights into the fitness cost and the ecological significance of parasitism.

Host age is another biological factor that impact the prevalence and intensity of
parasites. **Chapter 2 and 4** revealed a clear age-related gradient of infection with
juveniles being more heavily parasitized than subadults, who in turn showed higher
parasite abundance than adults. This pattern supports the hypothesis of gradually
acquired immunity through cumulative exposure to parasite over time (Woolhouse, 1998;
Cattadori et al., 2005; Bruns, 2019). Younger individuals are especially vulnerable due to
immunological immaturity (Christe et al., 2000; Kołodziej-Sobocińska, 2019; Friedrichs
et al., 2022; Roffler et al., 2024). Interestingly, *P. murinus* infection intensity peaked
markedly during the summer, coinciding with the birth of juveniles **(Chapter 4)**. This
seasonal pulse of immunologically naïve hosts likely facilitates parasite infection within
bat colonies, consistent with patterns described in other systems where synchronous
parturition increases transmission opportunities (Christe et al., 2000; Altizer et al., 2006;
Lučan, 2006; Reckardt and Kerth, 2009; Zhang et al., 2010; Encarnação et al., 2012).
Adults often benefit from acquired immunity and behavioural adaptations that reduce
exposure (Thomas et al., 1995). However, in some systems, older individuals may
become more susceptible due to immunosenescence (Ginaldi et al., 2001). Conversely
during early development, maternal antibodies may offer temporary protection,
particularly in breastfed individuals (Jackson and Nazar, 2006; Hurley and Theil, 2011). This mechanism has been well demonstrated in bat viruses (Breed et al., 2011; Peel et al., 2012; Amman et al., 2012; Epstein et al., 2013; Baker et al., 2014; Hayman et al., 2018; Brook et al., 2019).

Finally, host behaviour plays a crucial role in mediating parasite pressure, with numerous species exhibiting adaptations in response to parasitism (Sarabian et al., 2018). One example has been conceptualized as the “landscape of disgust” framework, which depicts how hosts can detect and alter their behaviour in response to differential exposure risks, leading to avoidance strategies (Weinstein et al., 2018; Hart and Hart, 2018). In bats, self-grooming is a key antiparasitic behavioural response to ectoparasite infection (Wilkinson, 1986; Giorgi et al., 2001; Kerth et al., 2003; Hofstede and Fenton, 2005). However, parasitism imposes a substantial cost with infected individuals increasing their grooming effort, which can be energetically demanding (Giorgi et al., 2001). In the endemic Malagasy fruit bat, *Rousettus madagascariensis*, this cost is partially offset as bat flies represent a substantial proportion of the bat protein intake (Ramanantsalama et al., 2022). The elevated grooming activity during infestation may partly account for the higher parasite abundance in reproductive females. Unlike females, males maintain consistent grooming effort during the reproductive period, potentially keeping ectoparasite loads at low levels (McLean and Speakman, 1997). Similarly, juveniles are particularly vulnerable due to their poorly developed anti-parasitic behaviours (Kołodziej-Sobocińska, 2019). Interestingly, social grooming also occurs in bat colonies, increasing close contact between individuals and potentially facilitating parasite transmission (Wilkinson, 1986). These dynamics highlight the dual role of grooming as both a defence mechanism and a contributor to parasite spread, shaped by host movements, age, sex, and reproductive status.

## Future directions

### Impact of the bat microbiota on parasitism

This thesis explored different factors influencing the susceptibility of bats to their parasites. Although innate or adaptive immunity were not directly measured during the
sampling, the composition of the gastrointestinal microbiome offers a promising proxy
for assessing bat defensive capacity against parasites. During the field sampling for this
thesis, faecal sampled were collected individually and preserved in absolute ethanol,
providing a valuable resource for future microbiome analyses. In vertebrates, microbiome
plays a role in modulating hosts immunity and inflammation (Schachtschneider et al.,
2013; Villarino et al., 2016; Rafaluk-Mohr et al., 2022; Omondi and Caner, 2022; Zhang
and Deitsch, 2022). However, its contribution to immune function in bats remains poorly
understood (Lutz et al., 2021; Jones et al., 2022). Interestingly, bat microbiomes are
unique among mammals as they more closely resemble those of flying birds (Song et al.,
2020). In birds, *Plasmodium* infection is associated with a change in the gut microbiome
composition (Palinauskas et al., 2022; Rohrer et al., 2023; Aželytė et al., 2023).
Characterizing the gut microbiome of the Daubenton's bats could help clarify its potential
role in shaping susceptibility to *Polychromophilus* infection. This is particularly relevant
given that bat gut microbiome composition varies seasonally following hibernation
(Maliničová et al., 2017; Xiao et al., 2019) and according to female reproductive status
(Dietrich et al., 2018; Gaona et al., 2019).

## Impact of the bat roost conditions on parasitism

While intrinsic characteristics of host and parasites, such as ecology and
behaviour, play a central role in shaping infection dynamics, environmental factors can
also exert significant influence (Sánchez et al., 2024). Yet, most studies tend to focus on
the bat as the habitat for its parasites, often overlooking the characteristics of the roosting
environment (Dick and Dittmar, 2014). Colony size, composition, occupancy and inter-
individual spacing are known to affect parasites but the physical structure of the roost
may be of particular importance (Hofstede and Fenton, 2005; Patterson et al., 2007). For
instance, in tree-roosting bats, higher densities of individuals within roost have been
linked to increased parasite transmission (Lunn et al., 2021). Environmental conditions
such as temperature are also known to affect key aspects of parasite biology, including
distribution, mating behaviour, adult emergence and reproduction, in various bat
parasites, such as bugs, bat flies and wing mites (Marshall, 1970; Bartonicka and Gaisler,
2007; Reinhardt et al., 2008; Lourenço and Palmeirim, 2008). Despite these insights, the
ecological determinants of bat parasite persistence and the specific environmental
conditions that favour parasite abundance remain poorly understood. Future research
could benefit from examining roost microclimate, particularly temperature and humidity
as proxies for environmental quality, assessing their impact on parasite abundance and
their role as vectors. In my thesis, sampling was primarily conducted in foraging areas.
However, five sites (sites 7, 8, 9, 18 and 20; see Fig. 1 from Chapter 4) corresponded to
known maternity colonies with different roost structures (respectively: building ceiling,
sewer manhole, two tree cavities and bridge crevice). Given that four of these sites were
located near the lake, substantial variation in temperature and humidity was unlikely.
Expanding future sampling to include broader range of roost entrances and microhabitats
could provide valuable insights into how roost conditions influence parasite ecology in
bats.

**General conclusion**

In this thesis, I explored how parasite spread is driven by a combination of host biology, parasite life history, and environmental context. Parasites play crucial roles in shaping ecosystems and driving evolutionary processes (Rózsa and Garay, 2023). Most existing studies rely on simplified host-parasite interactions, often overlooking the complexity of parasite communities and the interactions among coinfecting species (Petney and Andrews, 1998; Merrill et al., 2022). In contrast, my thesis offers an integrative view of these interactions. Through a multidisciplinary approach combining population genetics, infection dynamics, and molecular quantification techniques, I examined parasite abundance, transmission, and genetic structure across spatial and temporal scales. Each method provided a complementary perspective on parasite ecology, collectively revealing that parasite spread is the result of a complex and context-dependent interplay of biological and environmental factors. Bat dispersal, social behaviour, and reproductive ecology emerged as key drivers of parasite transmission, revealing the need to conserve host populations to support both biodiversity and disease management. Overall, this work highlights the value of integrative, high-resolution approaches in understanding the complexity of host-parasite systems, especially in non-model organisms. It contributes
to a growing recognition that advancing parasite ecology requires frameworks capable of capturing ecological complexity across species, scales, and transmission dynamics.

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