Distinguishing Cophylogenetic Signal from Phylogenetic Congruence Clarifies the Interplay Between Evolutionary History and Species Interactions.

Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: "Do closely related hosts interact with closely related symbionts?" and "Do host and symbiont phylogenies mirror one another?." These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other. However, in most situations, a positive answer to the first question, hereafter referred to as "cophylogenetic signal," does not imply a close match between the host and symbiont phylogenies. It suggests only that past evolutionary history has contributed to shaping present-day interactions, which can arise, for example, through present-day trait matching, or from a single ancient vicariance event that increases the probability that closely related species overlap geographically. A positive answer to the second, referred to as "phylogenetic congruence," is more restrictive as it suggests a close match between the two phylogenies, which may happen, for example, if symbiont diversification tracks host diversification or if the diversifications of the two clades were subject to the same succession of vicariance events. Here we apply a set of methods (ParaFit, PACo, and eMPRess), whose significance is often interpreted as evidence for phylogenetic congruence, to simulations under 3 biologically realistic scenarios of trait matching, a single ancient vicariance event, and phylogenetic tracking with frequent cospeciation events. The latter is the only scenario that generates phylogenetic congruence, whereas the first 2 generate a cophylogenetic signal in the absence of phylogenetic congruence. We find that tests of global-fit methods (ParaFit and PACo) are significant under the 3 scenarios, whereas tests of event-based methods (eMPRess) are only significant under the scenario of phylogenetic tracking. Therefore, significant results from global-fit methods should be interpreted in terms of cophylogenetic signal and not phylogenetic congruence; such significant results can arise under scenarios when hosts and symbionts had independent evolutionary histories. Conversely, significant results from event-based methods suggest a strong form of dependency between hosts and symbionts evolutionary histories. Clarifying the patterns detected by different cophylogenetic methods is key to understanding how interspecific interactions shape and are shaped by evolution.

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification.

The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation.

Phylogenetic tree reconciliation is extensively employed for the examination of coevolution between host and symbiont species. An important concern is the requirement for dependable cost values when selecting event-based parsimonious reconciliation. Although certain approaches deduce event probabilities unique to each pair of host and symbiont trees, which can subsequently be converted into cost values, a significant limitation lies in their inability to model the invasion of diverse host species by the same symbiont species (termed as a spread event), which is believed to occur in symbiotic relationships. Invasions lead to the observation of multiple associations between symbionts and their hosts (indicating that a symbiont is no longer exclusive to a single host), which are incompatible with the existing methods of coevolution. Here, we present a method called AmoCoala (an enhanced version of the tool Coala) that provides a more realistic estimation of cophylogeny event probabilities for a given pair of host and symbiont trees, even in the presence of spread events. We expand the classical 4-event coevolutionary model to include 2 additional outcomes, vertical and horizontal spreads, that lead to multiple associations. In the initial step, we estimate the probabilities of spread events using heuristic frequencies. Subsequently, in the second step, we employ an approximate Bayesian computation approach to infer the probabilities of the remaining 4 classical events (cospeciation, duplication, host switch, and loss) based on these values. By incorporating spread events, our reconciliation model enables a more accurate consideration of multiple associations. This improvement enhances the precision of estimated cost sets, paving the way to a more reliable reconciliation of host and symbiont trees. To validate our method, we conducted experiments on synthetic datasets and demonstrated its efficacy using real-world examples. Our results showcase that AmoCoala produces biologically plausible reconciliation scenarios, further emphasizing its effectiveness.

Co-phylogeographic structure in a disease-causing parasite and its oyster host.

With the increasing affordability of next-generation sequencing technologies, genotype-by-sequencing has become a cost-effective tool for ecologists and conservation biologists to describe a species' evolutionary history. For host­parasite interactions, genotype-by-sequencing can allow the simultaneous examination of host and parasite genomes and can yield insight into co-evolutionary processes. The eastern oyster, Crassostrea virginica, is among the most important aquacultured species in the United States. Natural and farmed oyster populations can be heavily impacted by 'dermo' disease caused by an alveolate protist, Perkinsus marinus. Here, we used restricted site-associated DNA sequencing (RADseq) to simultaneously examine spatial population genetic structure of host and parasite. We analysed 393 single-nucleotide polymorphisms (SNPs) for P. marinus and 52,100 SNPs for C. virginica from 36 individual oysters from the Gulf of Mexico (GOM) and mid-Atlantic coastline. All analyses revealed statistically significant genetic differentiation between the GOM and mid-Atlantic coast populations for both C. virginica and P. marinus, and genetic divergence between Chesapeake Bay and the outer coast of Virginia for C. virginica, but not for P. marinus. A co-phylogenetic analysis confirmed significant coupled evolutionary change between host and parasite across large spatial scales. The strong genetic divergence between marine basins raises the possibility that oysters from either basin would not be well adapted to parasite genotypes and phenotypes from the other, which would argue for caution with regard to both oyster and parasite transfers between the Atlantic and GOM regions. More broadly, our results demonstrate the potential of RADseq to describe spatial patterns of genetic divergence consistent with coupled evolution.

Evidence of cospeciation between termites and their gut bacteria on a geological time scale.

Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.

Symbionts in Hodgkinia-free cicadas and their implications for co-evolution between endosymbionts and host insects.

IMPORTANCE: Obligate symbionts in sap-sucking hemipterans are harbored in either the same or different organs, which provide a unique perspective for uncovering complicated insect-microbe symbiosis. Here, we investigated the distribution of symbionts in adults of 10 Hodgkinia-free cicada species of 2 tribes (Sonatini and Polyneurini) and the co-phylogeny between 65 cicada species and related symbionts (Sulcia and YLSs). We revealed that YLSs commonly colonize the bacteriome sheath besides the fat bodies in these two tribes, which is different with that in most other Hodgkinia-free cicadas. Co-phylogeny analyses between cicadas and symbionts suggest that genetic variation of Sulcia occurred in Sonatini and some other cicada lineages and more independent replacement events in the loss of Hodgkinia/acquisition of YLS in Cicadidae. Our results provide new information on the complex relationships between auchenorrhynchans and related symbionts.

Correlated evolution in an ectomycorrhizal host-symbiont system.

Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host-symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host-symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera (Lophozonia and Fuscospora), but also between more closely related hosts. Twenty-four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage diversification in ectomycorrhizal fungi.

Comparing different computational approaches for detecting long-term vertical transmission in host-associated microbiota.

Long-term vertical transmissions of gut bacteria are thought to be frequent and functionally important in mammals. Several phylogenetic-based approaches have been proposed to detect, among species-rich microbiota, the bacteria that have been vertically transmitted during a host clade radiation. Applied to mammal microbiota, these methods have sometimes led to conflicting results; in addition, how they cope with the slow evolution of markers typically used to characterize bacterial microbiota remains unclear. Here, we use simulations to test the statistical performances of two widely-used global-fit approaches (ParaFit and PACo) and two event-based approaches (ALE and HOME). We find that these approaches have different strengths and weaknesses depending on the amount of variation in the bacterial DNA sequences and are therefore complementary. In particular, we show that ALE performs better when there is a lot of variation in the bacterial DNA sequences, whereas HOME performs better when there is not. Global-fit approaches (ParaFit and PACo) have higher type I error rates (false positives) but have the advantage to be very fast to run. We apply these methods to the gut microbiota of primates and our results suggest that only a small fraction of their gut bacteria is vertically transmitted.

To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae.

Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.

Monogeneans and chubs: Ancient host-parasite system under the looking glass.

Host-parasite coevolution is one of the fundamentals of evolutionary biology. Due to the intertwined evolutionary history of two interacting species and reciprocal coadaptation processes of hosts and parasites, we can expect that studying parasites will shed more light onto the evolutionary processes of their hosts. Monogenea (ectoparasitic Platyhelminthes) and their cyprinoid fish hosts represent one of the best models for studying host-parasite evolutionary relationships using a cophylogenetic approach. These parasites have developed remarkably high host specificity, where each host species often serves as a potential host for its own host-specific monogenean species. Here, the cophylogenetic relationships in the Dactylogyrus-Squalius system was investigated, as Squalius is one of several cyprinoid genera with puzzling phylogeography and inhabits all four major peri-Mediterranean peninsulas. Of 29 endemic Squalius species examined for the presence of Dactylogyrus parasites, a total of 13 Dactylogyrus species were collected from the gills of 20 Squalius species across a wide range of distribution. Phylogenetic reconstruction revealed a polyphyletic origin for Dactylogyrus species parasitizing congeneric Squalius, with four major clades being recognized. On the basis of the delimitation of host specificity, strict specialists parasitizing single host species, geographic specialists parasitizing congeners in a limited geographical region, and true generalists parasitizing congeners in various geographical regions were recognized in Dactylogyrus species parasitizing Squalius. The phylogenetic reconstruction of Squalius hosts revealed two major clades, the first encompassing only peri-Mediterranean species and the second including species from other Euro-Asian regions. Distance-based cophylogenetic methods did not reveal a statistically significant global cophylogenetic structure in the studied system; however, several host-parasite links among Iberian endemic species contributed significantly to the overall structure. The widest host range and associated genetic variability were recorded for D. folkmanovae, parasitizing nine Squalius species, and D. vistulae, parasitizing 13 Squalius species. Two different dispersion mechanisms and morphological adaptations to Squalius hosts were clearly reflected in the contrasting cophylogenetic patterns for these two species with different levels of host specificity. While host-parasite cospeciation plays an important role in diversification within D. folkmanovae, diversification within D. vistulae is driven mainly by host switching.

Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids.

The study of congruency between phylogenies of interacting species can provide a powerful approach for understanding the evolutionary history of symbiotic associations. Orchid mycorrhizal fungi can survive independently of orchids making cospeciation unlikely, leading us to predict that any congruence would arise from host-switches to closely related fungal species. The Australasian orchid subtribe Drakaeinae is an iconic group of sexually deceptive orchids that consists of approximately 66 species. In this study, we investigated the evolutionary relationships between representatives of all six Drakaeinae orchid genera (39 species) and their mycorrhizal fungi. We used an exome capture dataset to generate the first well-resolved phylogeny of the Drakaeinae genera. A total of 10 closely related Tulasnella Operational Taxonomic Units (OTUs) and previously described species were associated with the Drakaeinae orchids. Three of them were shared among orchid genera, with each genus associating with 1-6 Tulasnella lineages. Cophylogenetic analyses show Drakaeinae orchids and their Tulasnella associates exhibit significant congruence (p < 0.001) in the topology of their phylogenetic trees. An event-based method also revealed significant congruence in Drakaeinae-Tulasnella relationships, with duplications (35), losses (25), and failure to diverge (9) the most frequent events, with minimal evidence for cospeciation (1) and host-switches (2). The high number of duplications suggests that the orchids speciate independently from the fungi, and the fungal species association of the ancestral orchid species is typically maintained in the daughter species. For the Drakaeinae-Tulasnella interaction, a pattern of phylogenetic niche conservatism rather than coevolution likely explains the observed phylogenetic congruency in orchid and fungal phylogenies. Given that many orchid genera are characterized by sharing of fungal species between closely related orchid species, we predict that these findings may apply to a wide range of orchid lineages.

Diversification processes between monogenoids (Dactylogyridae) and their marine catfish (Siluriformes: Ariidae) from the Atlantic coast of South America.

Due to their high specificity, monogenoids from fish provide an interesting model to study historical associations of hosts and parasites. High agreement between host and parasite phylogeny is often interpreted as evidence of cospeciation. However, cophylogenetic signal may also arise from other, either adaptive or non-adaptive, processes. We applied the recently developed Cophylospace Framework to better understand the evolutionary relationship between monogenoids and marine catfish from the Atlantic coast of South America. The associations between 12 marine catfish and 10 monogenoid species were assessed. Molecular data of host and parasite species were used for phylogenetic reconstruction. We used anchor morphology based on Procrustes coordinates to evaluate whether closely related hosts are associated with morphologically similar parasites. To assess the association between parasite phylogeny and host morphology, we produced a distance matrix based on morphological characters of catfishes. Agreement between phylogenies and between phylogeny and morphology was measured using Procrustes R2 computed with PACo. The parasite phylogeny obtained in this study represents the first complete phylogenetic hypothesis of monogenoids parasitizing ariids from South America. The Cophylospace analysis suggested that phylogenetic and morphological distance of monogenoids contributes similarly to explain the pattern of host­parasite associations, whereas parasite phylogeny is more strongly associated with the morphological traits of the hosts than with host phylogeny. This evidence suggests that cospeciation is not a major force accounting for diversification in the monogenoids studied. Rather host morphological traits seem to be a more important driver, which conforms with evidence from other host‒monogenoid systems.

Viral spillover risk increases with climate change in High Arctic lake sediments.

The host spectrum of viruses is quite diverse, as they can sustainedly infect a few species to several phyla. When confronted with a new host, a virus may even infect it and transmit sustainably in this new host, a process called 'viral spillover'. However, the risk of such events is difficult to quantify. As climate change is rapidly transforming environments, it is becoming critical to quantify the potential for spillovers. To address this issue, we resorted to a metagenomics approach and focused on two environments, soil and lake sediments from Lake Hazen, the largest High Arctic freshwater lake in the world. We used DNA and RNA sequencing to reconstruct the lake's virosphere in both its sediments and soils, as well as its range of eukaryotic hosts. We then estimated the spillover risk by measuring the congruence between the viral and the eukaryotic host phylogenetic trees, and show that spillover risk increases with runoff from glacier melt, a proxy for climate change. Should climate change also shift species range of potential viral vectors and reservoirs northwards, the High Arctic could become fertile ground for emerging pandemics.

Large-herbivore nemabiomes: patterns of parasite diversity and sharing.

Amidst global shifts in the distribution and abundance of wildlife and livestock, we have only a rudimentary understanding of ungulate parasite communities and parasite-sharing patterns. We used qPCR and DNA metabarcoding of fecal samples to characterize gastrointestinal nematode (Strongylida) community composition and sharing among 17 sympatric species of wild and domestic large mammalian herbivore in central Kenya. We tested a suite of hypothesis-driven predictions about the role of host traits and phylogenetic relatedness in describing parasite infections. Host species identity explained 27-53% of individual variation in parasite prevalence, richness, community composition and phylogenetic diversity. Host and parasite phylogenies were congruent, host gut morphology predicted parasite community composition and prevalence, and hosts with low evolutionary distinctiveness were centrally positioned in the parasite-sharing network. We found no evidence that host body size, social-group size or feeding height were correlated with parasite composition. Our results highlight the interwoven evolutionary and ecological histories of large herbivores and their gastrointestinal nematodes and suggest that host identity, phylogeny and gut architecture-a phylogenetically conserved trait related to parasite habitat-are the overriding influences on parasite communities. These findings have implications for wildlife management and conservation as wild herbivores are increasingly replaced by livestock.

Cytoplasmic incompatibility in hybrid zones: infection dynamics and resistance evolution.

Cytoplasmic incompatibility is an endosymbiont-induced mating incompatibility common in arthropods. Unidirectional cytoplasmic incompatibility impairs crosses between infected males and uninfected females, whereas bidirectional cytoplasmic incompatibility occurs when two host lineages are infected with reciprocally incompatible endosymbionts. Bidirectional cytoplasmic incompatibility is unstable in unstructured populations, but may be stable in hybrid zones. Stable coexistence of incompatible host lineages should generate frequent incompatible crosses. Therefore, hosts are expected to be under selection to resist their endosymbionts. Here, we formulate a mathematical model of hybrid zones where two bidirectionally incompatible host lineages meet. We expand this model to consider the invasion of a hypothetical resistance allele. To corroborate our mathematical predictions, we test each prediction with stochastic, individual-based simulations. Our models suggest that hybrid zones may sustain stable coinfections of bidirectionally incompatible endosymbiont strains. Over a range of conditions, hosts are under selection for resistance against cytoplasmic incompatibility. Under asymmetric migration, a resistance allele can facilitate infection turnover and subsequently either persist or become lost. The predictions we present may inform our understanding of the cophylogenetic relationship between the endosymbiont Wolbachia and its hosts.

Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts.

Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.

Shared geographic histories and dispersal contribute to congruent phylogenies between amphipods and their microsporidian parasites at regional and global scales.

In parasites that strongly rely on a host for dispersal, geographic barriers that act on the host will simultaneously influence parasite distribution as well. If their association persists over macroevolutionary time it may result in congruent phylogenetic and phylogeographic patterns due to shared geographic histories. Here, we investigated the level of congruent evolutionary history at a regional and global scale in a highly specialised parasite taxon infecting hosts with limited dispersal abilities: the microsporidians Dictyocoela spp. and their amphipod hosts. Dictyocoela can be transmitted both vertically and horizontally and is the most common microsporidian genus occurring in amphipods in Eurasia. However, little is known about its distribution elsewhere. We started by conducting molecular screening to detect microsporidian parasites in endemic amphipod species in New Zealand; based on phylogenetic analyses, we identified nine species-level microsporidian taxa including six belonging to Dictyocoela. With a distance-based cophylogenetic analysis at the regional scale, we identified overall congruent phylogenies between Paracalliope, the most common New Zealand freshwater amphipod taxon, and their Dictyocoela parasites. Also, hosts and parasites showed similar phylogeographic patterns suggesting shared biogeographic histories. Similarly, at a global scale, phylogenies of amphipod hosts and their Dictyocoela parasites showed broadly congruent phylogenies. The observed patterns may have resulted from covicariance and/or codispersal, suggesting that the intimate association between amphipods and Dictyocoela may have persisted over macroevolutionary time. We highlight that shared biogeographic histories could play a role in the codiversification of hosts and parasites at a macroevolutionary scale.

When are pathogen dynamics likely to reflect host population genetic structure?

Does the structure and connectivity of host populations influence the dynamics and evolution of their pathogens? This topical question is the essence of research investigating the ecology of a Pteropus fruit bat and its zoonotic Nipah virus (NiV) published by Olival et al. in this issue of Molecular Ecology. Questioned less overtly, but nonetheless implicit to the study, is "what are the mechanisms underpinning intraspecific host-pathogen congruence (IHPC) of genetic structure?". Olival et al. investigated the phylogeographical structure of Pteropus medius and NiV isolates across Bangladesh, from areas inside and outside of the Nipah belt-an area where most human spillover events occur. A high degree of host panmixia was discovered, with some population differentiation east of the Nipah belt. NiV genetic structure was congruent with the host. The authors attributed the panmixia and structuring, respectively, to (a) the highly vagile nature of P. medius, and (b) possible differences between bioregions within and outside the Nipah belt. Other potential explanatory mechanisms were acknowledged, including hybridization and transmission mode. This study makes a valuable contribution to a growing body of literature examining IHPC. This has implications not only for pathogen spillover to humans and domestic animals, but more generally for thinking about the mechanisms that underlie patterns of host and pathogen genetic associations.

Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community.

Most emerging pathogens can infect multiple species, underlining the importance of understanding the ecological and evolutionary factors that allow some hosts to harbour greater infection prevalence and share pathogens with other species. However, our understanding of pathogen jumps is based primarily around viruses, despite bacteria accounting for the greatest proportion of zoonoses. Because bacterial pathogens in bats (order Chiroptera) can have conservation and human health consequences, studies that examine the ecological and evolutionary drivers of bacterial prevalence and barriers to pathogen sharing are crucially needed. Here were studied haemotropic Mycoplasma spp. (i.e., haemoplasmas) across a species-rich bat community in Belize over two years. Across 469 bats spanning 33 species, half of individuals and two-thirds of species were haemoplasma positive. Infection prevalence was higher for males and for species with larger body mass and colony sizes. Haemoplasmas displayed high genetic diversity (21 novel genotypes) and strong host specificity. Evolutionary patterns supported codivergence of bats and bacterial genotypes alongside phylogenetically constrained host shifts. Bat species centrality to the network of shared haemoplasma genotypes was phylogenetically clustered and unrelated to prevalence, further suggesting rare-but detectable-bacterial sharing between species. Our study highlights the importance of using fine phylogenetic scales when assessing host specificity and suggests phylogenetic similarity may play a key role in host shifts not only for viruses but also for bacteria. Such work more broadly contributes to increasing efforts to understand cross-species transmission and the epidemiological consequences of bacterial pathogens.

Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae).

Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.