We examined global records of accessible natural history voucher collections (with publicly available data and reliable locality data) for terrestrial and freshwater vascular plants, fungi, freshwater fishes, birds, mammals, and herpetofauna (amphibians and reptiles) and highlight areas of the world that would be considered undersampled and sometimes called ‘unexplored’ (i.e., have relatively low, or no evidence of, past sampling efforts) under typical Western-scientific descriptions. We also question what ‘unexplored’ may mean in these contexts and explain how replacing the term in favor of more nuanced phrasing (e.g., ‘biodiversity blindspots,’ which emphasizes the lack of publicly available data about specimens) can mitigate future misunderstandings of natural history science. We also highlight geographic regions where there are relatively few or no publicly available natural history records to raise awareness about habitats that might be worthy of future natural history research and conservation. A major finding is that many of the areas that appear ‘unexplored’ may be in countries whose collections are not digitized (i.e., they don’t have metadata such as GPS coordinates about their voucher specimens publicly available). We call for museums to prioritize digitizing those collections from these ‘biodiversity blindspots’ and for increased funding for museums to aid in these efforts. We also argue for increased scientific infrastructure so that more reference collections with vouchers can be kept in the countries of origin (particularly those countries lacking such infrastructure currently).

Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.

The Trypanosoma cruzi clade represents one of the most complex and ecologically diverse assemblages of mammalian trypanosomes. Although the group’s human pathogenic member T. cruzi is best known as the etiological agent of Chagas disease, its evolutionary origins remain debated. Two main hypotheses attempt to explain the diversification of the T. cruzi clade: the supercontinent hypothesis, which proposes an ancient co-diversification with South American marsupials, and the bat-seeding hypothesis, which suggests a more recent origin through host-switching from bat trypanosomes. Here, we combined parasite and host phylogenies with global-fit cophylogenetic analyses to evaluate whether mammalian diversification has influenced the evolutionary history of the T. cruzi clade. Using PACo and ParaFit, we detected a weak but statistically significant global correspondence between mammal and trypanosome phylogenies. This correspondence was primarily associated with bat-trypanosome relationships, whereas associations involving non-bat mammals showed limited phylogenetic concordance. Together, these findings suggest that mammalian diversification may have influenced trypanosome evolution across multiple evolutionary contexts and timescales.

Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. How centromeres form in strongly host-adapted fungal pathogens has yet to be investigated. Here, we characterized the centromere structures in closely related species of mammalian-specific pathogens of the fungal phylum of Ascomycota. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-A ^Cnp1 of Schizosaccharomyces pombe . Using organisms from a short-term in vitro culture or infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. CENP-C, a scaffold protein that links the inner centromere to the kinetochore appears dispensable in one species, suggesting a kinetochore rewiring. Despite the loss of DNA methyltransferases, 5-methylcytosine DNA methylation occurs in these species, though not related to centromere function. These features suggest an epigenetic specification of centromere function. Short summary: Pneumocystis species offer a suitable genetic system to study centromere evolution in pathogens during host adaptation because of their unique specificity for mammals, and their phylogenetic proximity with the nonpathogenic yeast Schizosaccharomyces pombe , a popular model for cell biology. We used this system to explore how centromeres have evolved after divergence of the two clades ~460 million years ago. To address this question, we established a protocol combining short-term culture and ChIP-seq to characterize centromeres in multiple Pneumocystis species. We show that Pneumocystis have short epigenetic centromeres that function differently from those in S. pombe and exhibit similarities to centromeres in more distantly related host adapted fungal pathogens.

As emerging zoonoses represent a significant public health threat, understanding how pathogens' host ranges evolve is critical to protect human and wildlife health. Closely related hosts infected with host-specific pathogens provide valuable opportunities for clear inferences of host range evolution, as they allow for the examination of early diversification patterns in their resident pathogens. Pneumocystis, an obligate lung symbiont that is believed to be ubiquitous in mammals, exemplifies such a model. To explore the early stages of divergence in Pneumocystis, we collected geographically dispersed samples from two sister species of deer mice: Peromyscus leucopus (white-footed mice) and Peromyscus gossypinus (cotton mice). We sequenced two nuclear and two mitochondrial loci of Pneumocystis sampled from the lungs of these mice. These sequences revealed three distinct Pneumocystis taxa, two of which were found to cross-infect both host species and were often found coexisting within the same individual. Genetic diversity and phylogenetic analysis suggest that the three Pneumocystis taxa represent separate species. Further analysis of the mitochondrial large subunit rRNA gene from the most common taxon of these three revealed that host geographic origins influenced Pneumocystis genetic structure more than host species identity. Nevertheless, the results also suggest an overall interconnectedness of the symbiont metapopulation.