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The genus Noctiliostrebla Wenzel (Diptera: Streblidae) stands out for its high degree of specificity exhibited in relation to bat species of the genus Noctilio Linnaeus and provides an exciting system for understanding the history behind host–parasite associations. Here, we present a phylogeny of Noctiliostrebla based on an analysis of DNA sequences and morphological characters, along with cophylogenetic and biogeographical analyses. Our results strongly support the monophyly of Noctiliostrebla, but with uncertainties within the genus. With a low frequency of cospeciation events explaining the associations between hosts and parasites, cophylogenetic analyses did not show an overall congruence between the host and parasite phylogenies. Indeed, two parallel histories were recovered in the host–parasite associations, which might indicate that niche segregation is determined evolutionarily, facilitating the coexistence of parasites and promoting diversification. Biogeographical analysis showed a strong spatial congruence between disjunct distributions of Noctiliostrebla and major river basins in South America and with areas of higher elevation, which might be associated with the glacial periods throughout the Pliocene and Pleistocene. Overall, our findings suggest an agreement with the expectations of the ‘Stockholm paradigm’ framework, in which biogeographical events and ecological factors act as important components to explain the associations, instead of cospeciation events.

Individual-based networks provide the building blocks for community-level networks. However, network studies of bats and their parasites have focused only on the species level. Intrapopulation variation may allow certain host individuals to play important roles in the dynamics of the parasites. Therefore, we evaluated how the variation in host sex, body size, ectoparasite abundance and co-occurrence configure individual-based networks of the lesser bulldog bat Noctilio albiventris and bat flies. We expected bat individuals with greater body mass and forearms acting as the core in the network. We also expected males to play a more important role in the network. We sampled a network of N. albiventris bat individuals and their bat flies to describe the structure of an antagonistic individual-based network. We aimed to identify the most relevant bat individuals in the network, focusing on the implications inherent to each of the following approaches: (i) core-periphery organization; (ii) modularity; (iii) species level metrics; and (iv) the main ecological driver of bat individual roles in the network, using niche-based predictors (body mass, forearm and sex). We showed that a network of N. albiventris individuals and their bat flies had low modularity containing a persistent nucleus of individuals and bat flies with well-established interactions. Male individuals with greater body mass played an important role in the network, while for females neither mass nor forearm length were important predictors of their role in the network. Finally, individuals with a high abundance of Paradyschiria parvula played a core role. These results provide an alternative perspective to understand the patterns and mechanisms of interspecific interactions between parasites on the host, as well as sex-biased parasitism.

The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.

Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250 bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.

The selection of roosts is considered a critical factor to the survival of Noctilio albiventris. Thus, we located and identified N. albiventris day roosts in the Pantanal, near the Miranda River. We identified four species of tree: Banara arguta, Inga vera, Ocotea diospyrifolia and Vitex cymosa. Additional studies are important to understand the impact of specific requirements in the selection of roosts for Noctilio albiventris and to compare the observed patterns in different environments.

The Neotropical genus Noctiliostrebla Wenzel (Diptera: Streblidae) is revised after examination of the types of all nominal species, and 11 species are recognized. Seven new species are described, and a lectotype is designated for Lipoptena dubia Rudow. Resulting information on species distributions and host records can be summarized as follows: Noctiliostrebla dubia (Rudow) is restricted to the Amazon region and is a parasite of Noctilio leporinus (Linnaeus) (Chiroptera: Noctilionidae); Noctiliostrebla traubi Wenzel is restricted to Central America and northern South America, being the only species of the genus parasitizing N. leporinus in Central America; the distribution ranges of N. maai Wenzel and N. traubi are similar, but the host of N. maai is N. albiventris Desmarest; Noctiliostrebla aitkeni Wenzel is restricted to northern South America and has only been recorded as parasitizing N. leporinus; Noctiliostrebla ecuadorensis sp. n. occurs only in Ecuador, on N. albiventris; Noctiliostrebla guerreroi sp. n. has only been recorded from the Amazon region on N. albiventris; Noctiliostrebla falsispina sp. n. is restricted to south-central South America and is a parasite of N. leporinus; the distributions of N. lamasi sp. n. and N. falsispina sp. n. are similar, and the two species usually co-occur on N. leporinus; Noctiliostrebla morena sp. n. has a similar distribution to those of N. falsispina sp. n. and N. lamasi sp. n., but parasitizes N. albiventris; Noctiliostrebla pantaneira sp. n. has a similar distribution to N. morena sp. n. and usually co-occurs with it on N. albiventris; Noctiliostrebla caissara sp. n. is restricted to the southeastern coast of South America and is a parasite of N. leporinus. All species are included in a key and illustrated.

Global loss of biodiversity is an ongoing process that concerns both local and global authorities. Studies of biodiversity mainly involve traditional methods using morphological characters and molecular protocols. However, conventional methods are a time consuming and resource demanding task. The development of high-throughput sequencing (HTS) techniques has reshaped the way we explore biodiversity and opened a path to new questions and novel empirical approaches. With the emergence of HTS, sequencing the complete mitochondrial genome became more accessible, and the number of genome sequences published has increased exponentially during the last decades. Despite the current state of knowledge about the potential of mitogenomics in phylogenetics, this is still a relatively under-explored area for a multitude of taxonomic groups, especially for those without commercial relevance, non-models organisms and with preserved DNA. Here we take the first step to assemble and annotate the genomes from HTS data using a new protocol of genome skimming which will offer an opportunity to extend the field of mitogenomics to under-studied organisms. We extracted genomic DNA from specimens preserved in ethanol. We used Nextera XT DNA to prepare indexed paired-end libraries since it is a powerful tool for working with diverse samples, requiring a low amount of input DNA. We sequenced the samples in two different Illumina platform (MiSeq or NextSeq 550). We trimmed raw reads, filtered and had their quality tested accordingly. We performed the assembly using a baiting and iterative mapping strategy, and the annotated the putative mitochondrion through a semi-automatic procedure. We applied the contiguity index to access the completeness of each new mitogenome. Our results reveal the efficiency of the proposed method to recover the whole mitogenomes of preserved DNA from non-model organisms even if there are gene rearrangement in the specimens. Our findings suggest the potential of combining the adequate platform and library to the genome skimming as an innovative approach, which opens a new range of possibilities of its use to obtain molecular data from organisms with different levels of preservation.