Biology subjects

Upham, N. S.

Publications and source records attributed to Upham, N. S..

6 recordsLinked to original sources

bioRxiv2026

Conserved patterns of mammal-microbe codiversification and interspecific bacterial sharing

What determines whether a gut microbial lineage has fidelity to one host species or is shared freely across multiple species? Factors that predict microbial community composition, including host species, diet, and environmental variation, have been well documented in wild animals. However, the eco-evolutionary processes maintaining host species- or population-specific microbial lineages remain unresolved. Here, we analyze 519 gut microbiome samples collected from 15 species of wild rodents across two mountains in the Madrean Sky Islands of southeastern Arizona using full-length 16S rRNA sequencing. This montane system provides a natural experiment in which adjacent replicated elevational gradients bring different combinations of rodent species into sympatry, allowing host evolutionary history to be disentangled from shared environmental effects. We find that host phylogeny, rather than environment, is the primary driver of microbial strain sharing across host species. We recover replicated signatures of codiversification on both mountains, indicating shared evolutionary history between hosts and their microbes, despite ample opportunities for cross-species environmental transmission. This evolutionary coupling is associated with predicted differences in bacterial oxygen tolerance and optimal growth temperature: codiversifying lineages are predominantly obligate anaerobes with optimal growth near host body temperature, suggesting more limited out-of-host persistence than non-codiversifying taxa. This pattern mirrors findings from the human gut microbiome, suggesting conserved constraints on microbial dispersal across mammalian hosts. The cost-effectiveness of long-read amplicon sequencing for phylogenetic inference within bacterial species opens new opportunities for large-scale evolutionary and ecological studies of host-microbe interactions in wildlife.

ecology↗

bioRxiv2026

A holistic survey of small mammal diversity across an iconic Madrean Sky Island (Santa Catalina Mountains, Arizona, USA)

The Santa Catalina Mountains are an iconic member of the Madrean Sky Islands, rising above Tucson, Arizona, USA, where the Catalina Highway connects Sonoran desertscrub to stands of conifer forest nearly 2,800 meters in elevation. As one of the [~]54 forested mountain areas in this system, the Santa Catalinas host unique biotic communities relative to the surrounding lowlands. However, most of these sky islands lack the surveys of resident small mammals (either historical or recent) needed for studying biodiversity in the context of changing climate and habitat use. From 2021 to 2023, we surveyed 10 localities on the north and south slopes of the Santa Catalina Mountains using holistic sampling methods to document terrestrial small mammal diversity and preserve multiple tissue types. Here we summarize these new collections relative to previous voucher specimens and human observations, identifying gaps for future work to address. Our survey recorded the presence of 15 species, preserved 150 voucher specimens paired with a suite of flash-frozen tissues, and non-lethally sampled another 219 individuals (ear tissue, feces, ectoparasites, and measurements) to provide populational data from sites where vouchering occurred. Despite the road accessibility and long history of sampling in the Santa Catalina Mountains, our surveys extended the known elevational range for 8 species, including the first known specimen of Reithrodontomys fulvescens from the area. Our use of a transect-based survey design, which maximizes species diversity across biotic communities, paired with holistic specimen preservation techniques, provides a model for surveying patterns of population genetic and parasite sharing relationships across other Madrean Sky Islands, bridging a [~]40 year lull in specimen preservation while adding new data dimensions that promote integrative studies of small mammal biodiversity. With more complete sampling, other mountains will offer promising replicates for studying eco-evolutionary impacts of the regions episodic habitat connectivity. Teaser textSurveying the terrestrial small mammals of the Santa Catalina Mountains, part of the Madrean Sky Islands, we analyze modern occurrences relative to previous records and demonstrate the potential value of holistically surveying sky island small mammals.

zoology↗

bioRxiv2025

Uncovering historical small mammal biodiversity among the Madrean Sky Islands

The Madrean Sky Island Archipelago is a system of 54 mountains with isolated woodland habitat above 1,600 meters, primarily in the Sonoran Desert. These mountains harbor a wide variety of native small mammals spanning 11 families of bats, rodents, and shrews. Improved understanding of Madrean Sky Island biodiversity should advance studies of biogeography, phylogeny, host-symbiont interactions, and community assembly in this ecoregion. However, which species are found in each sky island and how their populations are genetically related remain open questions. To establish the current knowledge baseline, we used georeferenced voucher specimens to summarize the extent and timing of past collecting efforts for small mammals in woodland habitats across the Madrean Sky Islands. In total, at least 88 species (35 bats, 50 rodents, 3 shrews) from 9,540 specimens were collected from 1884-2023. Of these specimens, 79% come from 5 sky islands (Chiricahuas, Pinalenos, Huachucas, Animas, and Santa Catalinas) and at least 23 sky islands in the Madrean system have no recorded specimens. Mexicos 25 sky islands are mostly unsampled (only the San Luis, Sierra dos Ajos, and Sierra La Mariquita have any georeferenced specimens) and several of Arizonas larger sky islands have fewer than 40 specimens (Galiuros, Canelo Hills, Santa Teresas, Mules, and Dragoons). Most small mammal specimens (88%) were collected in 1980 or earlier without prioritizing frozen tissues for DNA/RNA preservation. Including 3,946 non-georeferenced specimens may add sampling for another 6 sky islands and 6 species, but georeferencing confirmation is needed and major patterns are unchanged. This distributional summary is the current basis for all derived biodiversity knowledge of Madrean Sky Island small mammals, illustrating clear gaps regarding most species of woodland-dwelling bats, rodents, and shrews. There is a critical need for future fieldwork and voucher specimen preservation (including of flash-frozen tissues) in this region, both to monitor changes compared to historical sampling and to test biodiversity assumptions on unsampled mountains.

ecology↗

bioRxiv2025

How many mammal species are there now? Updates and trends in taxonomic, nomenclatural, and geographic knowledge.

The Mammal Diversity Database (MDD) is an open-access resource providing up-to-date taxonomic, nomenclatural, and geographic data for global mammal species. Since its launch in 2018, the MDD has transformed the traditionally static process of updating mammalian taxonomy into regular online releases reflecting the latest published research. To build on this foundation, we here present version 2.0 of the MDD (MDD2), which catalogues 6,759 living and recently extinct mammal species, representing net increases of 4.1% and 24.8% over MDD version 1.0 and Mammal Species of the World, 3rd edition (MSW3), respectively. Additionally, we identify a net increase of 68.8% (+2,754; 3,149 splits + de novo, 395 lumps) species since 1980 at a rate of [~]65 species/year based on past totals from 14 mammalian compendia, leading to projections of [~]7,084 species by 2030 and [~]8,382 by 2050 if these trends continue. Key updates in MDD2 include: (i) codings of US state, country, continent, and biogeographic realm geographic categories for each species; (ii) a comprehensive nomenclatural dataset for 50,230 valid and synonymous species-rank names, curated with type locality and specimen information for the first time; and (iii) integration between the MDD and the databases Hesperomys and Batnames for greater data accuracy and completeness. These updates bridge critical gaps in the taxonomic and nomenclatural information needed for ongoing revisions and assessments of mammalian species diversity. Using these data, we evaluate temporal and geographic trends over the past 267 years, identifying four major time periods of change in mammalian taxonomy and nomenclature: (i) the initial monographic description of traditionally charismatic species (1758-1880); (ii) the peak of descriptive taxonomy, describing subspecies, and publishing in journals (1881-1939); (iii) the shift toward revisionary taxonomy and polytypic species (1940- 1999); and (iv) the current technology-driven period of integrative revisionary taxonomy (2000- present). Geographically, new species recognition since MSW3 has been concentrated in equatorial, mountainous, and island regions, highlighting areas of high mammal endemism (e.g., Madagascar, Philippines, Andes, East Africa, Himalayas, Atlantic Forests). However, gaps in 21st century taxonomic activity are identified in West and Central Africa, India, and some parts of Indonesia. Currently lagging conservation assessments are alarming, with 25% of the MDD2-recognized mammal species allocated to the understudied conservation threat categories of Data Deficient (11%) or Not Evaluated (14%), underscoring the need for greater taxonomic integration with conservation organizations. Governance advancements in MDD2 include the establishment of external taxonomic subcommittees to guide data collection and curation, a rewritten website that improves access and scalability, a cross-platform application that provides offline access, and new partnerships to continue linking MDD data to global biodiversity infrastructure. By providing up-to-date mammalian taxonomic and nomenclatural data--including links to the text of original name descriptions, type localities, and type specimen collections--the MDD provides an integrative resource for mammalogists and conservationists to more easily track the status of their study organisms. Teaser Text: The Mammal Diversity Database 2.0, listing 6,759 mammal species and 50,230 species-level synonyms, unifies 267 years of taxonomic, nomenclatural, and geographic data to track global mammal biodiversity and provide a continually updated resource for the mammalogical community. Teaser Image: Figure 3. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/640393v1_fig3.gif" ALT="Figure 3"> View larger version (34K): org.highwire.dtl.DTLVardef@1012e67org.highwire.dtl.DTLVardef@8d99d7org.highwire.dtl.DTLVardef@6f21b9org.highwire.dtl.DTLVardef@f23fd_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Type locality locations for species-rank mammal taxa described from 1 January 2000 to 15 August 2024. Map gray-scale country coloration represents the total number of currently valid species type localities found per country described within this period. Colored dots represent the exact georeferenced type locality of all currently valid species (red circles) and names currently considered synonyms and subspecies (blue diamonds) in MDD2. Most coordinates were generated from the original description of each name when included directly in publication, while others were georeferenced using GeoLocate or WikiMedia GeoHack place coordinates when not included in the original description publication. The georeferenced localities were mapped and both programmatically and visually vetted for accuracy. Latitude and longitude in decimal degrees is included for each of the names mapped here in the MDD2 synonym list, Supplementary Data SD2. C_FIG

zoology↗

bioRxiv2020

The coevolution of mammae number and litter size

Mammals are unique in provisioning their offspring with milk, lactiferous nourishment produced in glandular organs called mammae. Mammae number is hypothesized to coevolve with litter size, acting as a constraint on offspring survival. However, predicted canonical relations between mammae number and litter size (i.e., the one-half and identity rules) are untested across Mammalia. Here we analyze data for 2,301 species and show how these characters coevolve. In Mammalia, mammae number approximates the maximum reported litter size of a species, and mammae number explains more variation in litter size than other species-level traits (mass, gestation length, diet, and seasonality of contemporary geographic distribution). Clades show differences in these patterns, indicating that certain life history strategies might break the rules of mammary evolution. Mammae number is an underappreciated constraint on fecundity that has influenced the radiation of mammals.

evolutionary biology↗

bioRxiv2020

Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals novel insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans.

evolutionary biology↗