Unexpected bird–feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario

The high relevance of host‐switching for the diversification of highly host‐specific symbionts (i.e., those commonly inhabiting a single host species) demands a better understanding of host‐switching dynamics at an ecological scale. Here, we used DNA metabarcoding to study feather mites on passerine birds in Spain, sequencing mtDNA (COI) for 25,540 individual mites (representing 64 species) from 1,130 birds (representing 71 species). Surprisingly, 1,228 (4.8%) mites from 84 (7.4%) birds were found on host species that were not the expected to be a host according to a recent bird–feather mite associations catalog. Unexpected associations were widespread across studied mite (40.6%) and bird (43.7%) species and showed smaller average infrapopulation sizes than typical associations. Unexpected mite species colonized hosts being distantly related to the set of their usual hosts, but with similar body size. The network of bird–mite associations was modular (i.e., some groups of bird and mite species tended to be more associated with each other than with the others), with 75.9% of the unexpected associations appearing within the module of the typical hosts of the mite species. Lastly, 68.4% of mite species found on unexpected hosts showed signatures of genetic differentiation, and we found evidence for reproduction or the potential for it in many of the unexpected associations. Results show host colonization as a common phenomenon even for these putatively highly host‐specific symbionts. Thus, host‐switching by feather mites, rather than a rare phenomenon, appears as a relatively frequent phenomenon shaped by ecological filters such as host morphology and is revealed as a fundamental component for a dynamic coevolutionary and codiversification scenario.     

Feather mites play a role in cleaning host feathers: New insights from DNA metabarcoding and microscopy

Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane‐dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high‐throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long‐standing question of the nature of the relationship between birds and their vane‐dwelling feather mites, supporting previous evidence for a commensalistic–mutualistic role of feather mites, which are revealed as likely fungivore–microbivore–detritivore symbionts of bird feathers.     

Feather mites (Acari: Astigmata) and body condition of their avian hosts: a large correlative study

Feather mites are arthropods that live on or in the feathers of birds, and are among the commonest avian ectosymbionts. However, the nature of the ecological interaction between feather mites and birds remains unclear, some studies reporting negative effects of feather mites on their hosts and others reporting positive or no effects. Here we use a large dataset comprising 20 189 measurements taken from 83 species of birds collected during 22 yr in 151 localities from seven countries in Europe and North Africa to explore the correlation between feather mite abundance and body condition of their hosts. We predicted that, if wing‐dwelling feather mites are parasites, a negative correlation with host body condition should be found, while a mutualistic interaction should yield positive correlation. Although negative relationships between feather mite abundance and host body condition were found in a few species of birds, the sign of the correlation was positive in most bird species (69%). The overall effect size was only slightly positive (r =0.066). The effect of feather mite abundance explained <10% of variance in body condition in most species (87%). Results suggest that feather mites are not parasites of birds, but rather that they hold a commensalistic relationship where feather mites may benefit from feeding on uropygial gland secretions of their hosts and birds do not seem to obtain a great benefit from the presence of feather mites.     

Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds

Inferring cophylogeographic events requires matching the timing of these events on both host and symbiont (e.g., parasites) phylogenies because divergences of hosts and their symbionts may not temporally coincide, and host switches may occur. We investigate a large radiation of birds (Passeriformes) and their permanent symbionts, the proctophyllodid feather mites (117 species from 116 bird species; six genes, 11,468 nt aligned) using two time‐calibration strategies for mites: fossils only and host phylogeography only. Out of 10 putative cophylogeographic events 4 agree in timing for both symbiont and host events being synchronous co‐origins or codispersals; three were based on host shifts, but agree in timing being very close to the origin of modern hosts; two disagree; and one large basal mite split was seemingly independent from host phylogeography. Among these events was an ancient (21–25.3 Mya), synchronous codispersal from the Old World leading to the origin and diversifications of New World emberizoid passerids and their mites, the thraupis + quadratus species groups of Proctophyllodes. Our framework offers a more robust detection of host and symbiont cophylogeographic events (as compared to host‐symbiont reconciliation analysis and using host phylogeography for time‐calibration) and provides independent data for testing alternative hypotheses on timing of host diversification and dispersal.     

Geographical structuring of feather mite assemblages from the Australian brush-turkey (Aves: Megapodiidae)

Populations of a host species may exhibit different assemblages of parasites and other symbionts. The loss of certain species of symbionts (lineage sorting, or "missing-the-boat") is a mechanism by which geographical variation in symbiont assemblages can arise. We studied feather mites and lice from Australian brush-turkeys (Aves: Megapodiidae: Alectura lathami) and expected to observe geographical structuring in arthropod assemblages for several reasons. First, because the brush-turkey is a sedentary ground-dwelling bird, we predicted that geographically close host populations should share more similar arthropod assemblages than distant ones. Second, because brush-turkeys do not brood their young, vertical transfer of arthropods is unlikely, and brush-turkeys probably acquire their mites and lice at social maturity through contact with other birds. Young birds could disperse and found new populations without carrying complete sets of symbionts. We predicted that young birds would have fewer species of arthropods than older birds; in addition, we expected that males (which are polygynous) would have more species than females. Birds were sampled from 12 sites (=populations) along the east coast of Queensland, Australia, that were separated by a distance of 12.5-2,005 km. In total, 5 species of mites from the Pterolichidae and 1 species from the Ascouracaridae were found. Two species of lice were collected but in numbers too low to be statistically useful. Differentiation of mite assemblages was evident; in particular, Leipobius sp. showed 100% prevalence in 3 host populations and 0% in the remaining 9. A dendrogram of brush-turkey populations based on mite assemblages showed 2 geographically correlated clusters of sites, plus 1 cluster that contained 2 sites near Brisbane and 1 approximately at a distance of 1,000 km. There was no strong effect of host age or sex on number of mite species carried. Horizontal transfer of feather mites by hippoboscid flies, in addition to physical contact between hosts, may play a role in homogenizing symbiont assemblages within populations.     

Feather mite loads influenced by salt exposure, age and reproductive stage in the Seychelles Warbler Acrocephalus sechellensis

Many factors may affect symbiont distributions within host populations. Intrinsic factors, such as genotype, body condition and age may account for variations in symbiont loads between individuals . However, abiotic factors may also contribute to variations. We investigated correlates of variation in the number of feather mites, Trouessartia sp. (Trouessartiidae), per individual in the Seychelles Warbler Acrocephalus sechellensis on Cousin Island. Warblers from territories exposed to high levels of salt spray had lower feather mite loads than warblers from territories unaffected by salt spray, and juveniles had higher mite loads than adults. When the effects of salt spray were controlled for statistically, incubating birds had lower mite loads than birds in other stages of reproduction. Thus, an extrinsic and two intrinsic factors contribute to predicting feather mite loads.     

The feather mite (Astigmata) fauna of some passerine birds (Passeriformes) in the south of Western Siberia

Feather mites (Astigmata) are specialized parasites living on the plumage and skin of birds. The paper presents data on infestation of some passerines (Passeriformes) by feather mites in the south of Western Siberia (Omsk and Tyumen Provinces). We found 24 species of feather mites belonging to the families Analgidae, Dermoglyphidae, Pteronyssidae, Trouessartiidae, and Proctophyllodidae on 16 bird species. Among them, 19 species are common parasites of the passerine birds examined; five species were detected on atypical hosts. Ten mite species were recorded for the first time on the passerine species examined. Analysis of the distribution of abundant and common mite species on their hosts has demonstrated that the majority of the bird parasites possess a specific distribution pattern in the host plumage with preference for certain feather types. We have also obtained new data on host associations of several mite species.     

Phylogeny and co-speciation in feather mites of the subfamily Avenzoariinae (Analgoidea: Avenzoariidae)

A cladistic analysis of phylogenetic relationships is carried out for the feather mite subfamily Avenzoariinae. The analysis is made at two different taxonomic levels, for 19 genera of the all family Avenzoariidae and for taxa of species rank for the Avenzoaria and Bychovskiata generic groups. A subsequent comparative analysis of phylogenetic hypotheseis for the subfamily Avenzoariinae and recently accepted phylogenetic hypotheses of the shorebirds Charadriiformes indicates co-speciation of feather mites with their hosts. As a result of the comparative analysis it is suggested, that the subfamily Avenzoariinae originated from an ancestor of the order Charadriiformes and co-speciated with this host order. The expected pattern of parallel evolution is disturbed by different evolutionary events, such as host shifts, extinction of mites and differential evolutionary rates of mite lineages in different phyletic branches of feather parasites.     

Does investment into ��expensive�� tissue compromise anti-parasitic defence? Testes size, brain size and parasite diversity in rodent hosts

Species richness of parasite assemblages varies among host species. Earlier studies that searched for host-related determinants of parasite diversity mainly considered host traits that affect the probability of host encounter with parasites, whereas host traits related to defensibility against parasites have rarely been investigated. From the latter perspective, evolutionary investment in ??expensive?? tissue or organs (like testes or brain) may trade off against energetically costly anti-parasitic defences. If so, richer parasite assemblages are expected in hosts with larger testes and brains. We studied the relationships between testes and brain size and diversity of parasites (fleas, gamasid mites and helminths) in 55 rodent species using a comparative approach and application of two methods, namely the method of independent contrasts and generalized least-squares (GLS) analysis. Both phylogenetically correct methods produced similar results for flea and helminth species richness. Testes size positively correlated with flea and helminth species richness but not gamasid mite species richness. No correlation between brain size and species richness of any parasite group was found by the method of independent contrasts. However, GLS analysis indicated negative correlation between brain size and mite species richness. Our results cast doubt on the validity of the expensive tissue hypothesis, but suggest instead that larger testes are associated with higher parasite diversity via their effect on mobility and/or testosterone-mediated immunosuppression.     

Divergent host phenotypes create opportunities and constraints on the distribution of two wing‐dwelling feather mites

The diversity of symbionts (commensals, mutualists or parasites) that share the same host species may depend on opportunities and constraints on host exploitation associated with host phenotype or environment. Various host traits may differently influence host accessibility and within‐host population growth of each symbiont species, or they may determine the outcome of within‐host interactions among coexisting species. In turn, phenotypic diversity of a host species may promote divergent exploitation strategies among its symbiotic organisms. We studied the distribution of two feather mite species, Proctophyllodes sylviae and Trouessartia bifurcata, among blackcaps Sylvia atricapilla wintering in southern Spain during six winters. The host population included migratory and sedentary individuals, which were unequally distributed between two habitat types (forests and shrublands). Visual mite counts showed that both mite species often coexisted on sedentary blackcaps, but were seldom found together on migratory blackcaps. Regardless of host habitat, Proctophyllodes were highly abundant and Trouessartia were scarce on migratory blackcaps, but the abundance of both mite species converged in intermediate levels on sedentary blackcaps. Coexistence may come at a cost for Proctophyllodes, whose load decreased when Trouessartia was present on the host (the opposite was not true). Proctophyllodes load was positively correlated with host wing length (wings were longer in migratory blackcaps), while Trouessartia load was positively correlated to uropygial gland size (sedentary blackcaps had bigger glands), which might render migratory and sedentary blackcaps better hosts for Proctophyllodes and Trouessartia, respectively. Our results draw a complex scenario for mite co‐existence in the same host species, where different mite species apparently take advantage of, or are constrained by, divergent host phenotypic traits. This expands our understanding of bird–mite interactions, which are usually viewed as less dynamic in relation to variation in host phenotype, and emphasizes the role of host phenotypic divergence in the diversification of symbiotic organisms.     

Cophylogenetic assessment of New World warblers (Parulidae) and their symbiotic feather mites (Proctophyllodidae)

Host–symbiont relationships are ubiquitous in nature, yet evolutionary and ecological processes that shape these intricate associations are often poorly understood. All orders of birds engage in symbioses with feather mites, which are ectosymbiotic arthropods that spend their entire life on hosts. Due to their permanent obligatory association with hosts, limited dispersal and primarily vertical transmission, we hypothesized that the cospeciation between feather mites and hosts within one avian family (Parulidae) would be perfect (strict cospeciation). We assessed cophylogenetic patterns and tested for congruence between species in two confamiliar feather mite genera (Proctophyllodidae: Proctophyllodes, Amerodectes) found on 13 species of migratory warblers (and one other closely related migratory species) in the eastern United States. Based on COI sequence data, we found three Proctophyllodes lineages and six Amerodectes lineages. Distance‐ and event‐based cophylogenetic analyses suggested different cophylogenetic trajectories of the two mite genera, and although some associations were significant, there was little overall evidence supporting strict cospeciation. Host switching is likely responsible for incongruent phylogenies. In one case, we documented prairie warblers Setophaga discolor harboring two mite species of the same genus. Most interestingly, we found strong evidence that host ecology may influence the likelihood of host switching occurring. For example, we documented relatively distantly related ground‐nesting hosts (ovenbird Seiurus aurocapilla and Kentucky warbler Geothlypis formosa) sharing a single mite species, while other birds are shrub/canopy or cavity nesters. Overall, our results suggest that cospeciation is not the case for feather mites and parulid hosts at this fine phylogenetic scale, and raise the question if cospeciation applies for other symbiotic systems involving hosts that have complex life histories. We also provide preliminary evidence that incorporating host ecological traits into cophylogenetic analyses may be useful for understanding how symbiotic systems have evolved.     

Vertical transmission in feather mites: insights into its adaptive value

1. The consequences of symbiont transmission strategies are better understood than their adaptive causes. 2. Feather mites are permanent ectosymbionts of birds assumed to be transmitted mainly vertically from parents to offspring. The transmission of Proctophyllodes doleophyes Gaud (Astigmata, Proctophyllodidae) was studied in two European populations of pied flycatchers, Ficedula hypoleuca Pallas (Passeriformes, Muscicapidae). 3. The vertical transmission of this mite species is demonstrated here with an acaricide experiment. This study also compared (for two distant populations during 4 years) patterns in reductions in mite intensity in adult birds, from egg incubation to chick‐rearing periods, with the predictions of three hypotheses on how host survival prospects and mite intraspecific competition might drive feather mites' transmission strategy. 4. The results are in agreement with previous studies and show that feather mites transmit massively from parents to chicks. 5. The magnitude of the transmission was closer to that predicted by the hypothesis based on intraspecific competition, while a bet‐hedging strategy is also partially supported.     

Climate-Driven Variation in the Intensity of a Host-Symbiont Animal Interaction along a Broad Elevation Gradient

Gradients of environmental stress may affect biotic interactions in unpredictable ways responding to climate variation, depending on the abiotic stress tolerance of interacting partners. Here, we study the effect of local climate on the intensity of feather mites in six mountain passerines along a 1400 m elevational gradient characterized by shifting temperature and rainfall. Although obligatory symbionts of warm-blooded organisms are assumed to live in mild and homeothermic environments, those inhabiting external, non-blood-irrigated body portions of the host organism, such as feather mites, are expected to endure exposure to the direct influence of a fluctuating climate. As expected, feather mite intensity declined with elevation in all bird species, a pattern that was also found in cold-adapted passerines that have typical alpine habits. The elevation cline was mainly explained by a positive effect of the average temperature upon mite intensity in five of the six species studied. Precipitation explained less variance in mite intensity than average temperature, and showed a negative correlation in half of the studied species. We found no climate-driven migration of mites along the wings of birds, no replacement of mite species along elevation gradients and no association with available food resources for mites (estimated by the size of the uropygial gland). This study suggests that ectosymbionts of warm-blooded animals may be highly sensitive to climatic variation and become less abundant under stressful environmental conditions, providing empirical evidence of the decline of specialized biotic interactions among animal species at high elevations.     

Mite‐y bees: bumble bees (Bombus spp., Hymenoptera: Apidae) host a relatively homogeneous mite (Acari) community,shaped by bee species identity but not by geographic proximity

1. Parasites can affect the communities of their hosts; and hosts, in turn, shape communities of parasites and other symbionts. This makes host–symbiont relationships a key but often overlooked aspect of community ecology. 2. Mites associated with bees have a range of lifestyles; however, little is known about mites associated with wild bees or about factors influencing the make‐up of bee‐associated mite communities. This study investigated how mite communities associated with bumble bees (Bombus spp.) are shaped by the Bombus community and geographic proximity. 3. Bees were collected from 15 sites in Ontario, Canada, and examined for mites. Mite abundance and species richness increased with local bee abundance. Several bee species also differed in mite abundance, species richness, prevalence, and diversity. Locally uncommon species tended to have more mites than other bees. Queen bees had the most mites, and males had more mites than workers. 4. Spatial proximity was not a predictor of mite community composition, despite a strong effect of proximity on bee community similarity. 5. On the 11 Bombus spp. examined, 33 mite species were found. Whereas nearly half of these mite species are obligate associates of bumble bees, none was restricted to particular Bombus species. 6. The best predictor of mite community composition was bee identity. Although many parasite communities show strong geographic patterns, the communities of primarily commensalistic bee‐mites in this study did not. These findings have implications for bumble bee conservation, given that pollen‐feeding commensals might become harmful at high densities or act as disease vectors.     

Feather mite abundance varies but symbiotic nature of mite‐host relationship does not differ between two ecologically dissimilar warblers

Feather mites are obligatory ectosymbionts of birds that primarily feed on the oily secretions from the uropygial gland. Feather mite abundance varies within and among host species and has various effects on host condition and fitness, but there is little consensus on factors that drive variation of this symbiotic system. We tested hypotheses regarding how within‐species and among‐species traits explain variation in both (1) mite abundance and (2) relationships between mite abundance and host body condition and components of host fitness (reproductive performance and apparent annual survival). We focused on two closely related (Parulidae), but ecologically distinct, species: Setophaga cerulea (Cerulean Warbler), a canopy dwelling open‐cup nester, and Protonotaria citrea (Prothonotary Warbler), an understory dwelling, cavity nester. We predicted that feather mites would be more abundant on and have a more parasitic relationship with P. citrea, and within P. citrea, females and older individuals would harbor greater mite abundances. We captured, took body measurements, quantified feather mite abundance on individuals’ primaries and rectrices, and monitored individuals and their nests to estimate fitness. Feather mite abundance differed by species, but in the opposite direction of our prediction. There was no relationship between mite abundance and any measure of body condition or fitness for either species or sex (also contrary to our predictions). Our results suggest that species biology and ecological context may influence mite abundance on hosts. However, this pattern does not extend to differential effects of mites on measures of host body condition or fitness.     

Feather mite abundance increases with uropygial gland size and plumage yellowness in Great Tits Parus major

Plumicolous feather mites are ectosymbiotic organisms that live on bird feathers. Despite their abundance and prevalence among birds, the ecology of the interaction between these organisms and their hosts is poorly known. As feather mites feed on oil that birds spread from their uropygial gland, it has been hypothesized, but never tested, that the number of feather mites increases with the size of the uropygial gland of their hosts. In this study the number of feather mites is considered with respect to uropygial gland size in a breeding population of Great Tits Parus major in order to test this hypothesis. As predicted, the number of feather mites correlated positively with the uropygial gland size of their hosts, showing for the first time that uropygial gland size can explain the variance in feather mite load among conspecifics. Previous studies relating feather mite load to plumage colour have suggested that feather mites may be parasitic or neutral. To confirm this, the yellowness of breast feathers was also assessed. However, the results ran in the opposite direction to that expected, showing a positive correlation between mite load and plumage yellowness, which suggests that further work is needed to give clear evidence for a specific nature of feather mites. However, Great Tits with higher mite loads had lower hatching and breeding success, which may support the idea that feather mites are parasites, although this effect must be taken with caution because it was only found in males. Age or sex effects were not found on the number of feather mites, and it is proposed that hormonal levels may not be sufficient to explain the variation in feather mite loads. Interestingly, a positive correlation was detected between uropygial gland size and plumage brightness, which could be a novel factor to take into account in studies of plumage colour.     

Origin and Evolution of Feather Mites (Astigmata)

Feather mites are highly specialized plumage and skin ectoparasites that are variously adapted for inhabiting certain microhabitats on a bird's body. Different feather mite taxa of higher (familial) rank adapted to the same microhabitats display similar main morphological adaptations even if they are rather distantly related to one another. Hypotheses on the evolution of general adaptations in morphology of feather mites during colonization and establishment in different microhabitats are presented. According to recent data, feather mites are a paraphyletic group consisting of three superfamilies: Analgoidea, Pterolichoidea and Freyanoidea. We present our view on the general feather mite phylogeny course at the familial rank for the Analgoidea by means of cladistic analysis. Co-speciation of parasites with their hosts is postulated as a main factor driving feather mite evolution. Examples are given of non-coevolutionary events, for example recolonization from one host species onto another, extinction and multiple speciation.     

New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies

The mutualistic symbioses between reef‐building corals and micro‐algae form the basis of coral reef ecosystems, yet recent environmental changes threaten their survival. Diversity in host‐symbiont pairings on the sub‐species level could be an unrecognized source of functional variation in response to stress. The Caribbean elkhorn coral, Acropora palmata, associates predominantly with one symbiont species (Symbiodinium ‘fitti’), facilitating investigations of individual‐level (genotype) interactions. Individual genotypes of both host and symbiont were resolved across the entire species’ range. Most colonies of a particular animal genotype were dominated by one symbiont genotype (or strain) that may persist in the host for decades or more. While Symbiodinium are primarily clonal, the occurrence of recombinant genotypes indicates sexual recombination is the source of this genetic variation, and some evidence suggests this happens within the host. When these data are examined at spatial scales spanning the entire distribution of A. palmata, gene flow among animal populations was an order of magnitude greater than among populations of the symbiont. This suggests that independent micro‐evolutionary processes created dissimilar population genetic structures between host and symbiont. The lower effective dispersal exhibited by the dinoflagellate raises questions regarding the extent to which populations of host and symbiont can co‐evolve during times of rapid and substantial climate change. However, these findings also support a growing body of evidence, suggesting that genotype‐by‐genotype interactions may provide significant physiological variation, influencing the adaptive potential of symbiotic reef corals to severe selection.     

Body size and coexistence in gamasid mites parasitic on small mammals: null model analyses at three hierarchical scales

We studied body size ratio in gamasid mites (Acari: Mesostigmata) parasitic on Palearctic small mammals at 3 hierarchical scales, namely infracommunities (an assemblage of mites harboured by an individual host), component communities (an assemblage of mites harboured by a host population), and compound communities (an assemblage of mites harboured by a host community). We used null models and asked a) whether body size distributions in these communities demonstrate non‐random patterns; b) whether these patterns indicate segregation or aggregation of body sizes of coexisting species; and c) whether patterns of body size distribution are scale‐dependent, that is, differ among infracommunities, component communities, and compound communities. In most mite assemblages, the observed pattern of body size distribution did not differ from that expected by chance. However, meta‐analyses demonstrated that component and compound communities of gamasid mites consistently demonstrated a tendency to reduced body size overlap, while we did not find any clear trend in mite body size distribution across infracommunities. We discuss reasons for scale‐dependence of body size distribution pattern in parasite communities and propose ecological and evolutionary mechanisms that allowed the reduced body size overlap in component and compound communities of ectoparasites to arise.     

Host and parasite life history interplay to yield divergent population genetic structures in two ectoparasites living on the same bat species

Host–parasite interactions are ubiquitous in nature. However, how parasite population genetic structure is shaped by the interaction between host and parasite life history remains understudied. Studies comparing multiple parasites infecting a single host can be used to investigate how different parasite life history traits interplay with host behaviour and life history. In this study, we used 10 newly developed microsatellite loci to investigate the genetic structure of a parasitic bat fly (Basilia nana). Its host, the Bechstein's bat (Myotis bechsteinii), has a social system and roosting behaviour that restrict opportunities for parasite transmission. We compared fly genetic structure to that of the host and another parasite, the wing‐mite, Spinturnix bechsteini. We found little spatial or temporal genetic structure in B. nana, suggesting a large, stable population with frequent genetic exchange between fly populations from different bat colonies. This contrasts sharply with the genetic structure of the wing‐mite, which is highly substructured between the same bat colonies as well as temporally unstable. Our results suggest that although host and parasite life history interact to yield similar transmission patterns in both parasite species, the level of gene flow and eventual spatiotemporal genetic stability is differentially affected. This can be explained by the differences in generation time and winter survival between the flies and wing‐mites. Our study thus exemplifies that the population genetic structure of parasites on a single host can vary strongly as a result of how their individual life history characteristics interact with host behaviour and life history traits.